Source: KANSAS STATE UNIV submitted to
PLANT BIOTECHNOLOGY CENTER
Sponsoring Institution
State Agricultural Experiment Station
Project Status
NEW
Funding Source
STATE
Reporting Frequency
Annual
Accession No.
0223633
Grant No.
(N/A)
Project No.
KS00-0116-ST
Proposal No.
(N/A)
Multistate No.
(N/A)
Program Code
(N/A)
Project Start Date
Oct 1, 2010
Project End Date
Sep 30, 2025
Grant Year
(N/A)
Project Director
Kennelly, ME, M.
Recipient Organization
KANSAS STATE UNIV
(N/A)
MANHATTAN,KS 66506
Performing Department
Plant Biotechnology Center
Non Technical Summary
Plant Biotechnology approaches to problems are used in numerous K-State departments including Agronomy, Biochemistry, Biology, Entomology, Horticulture, and Plant Pathology to address problems in plant growth, grain quality, and disease and pest resistance. The Plant Transformation Facility provides resources and expertise to produce transgenic plants, assists collaborators and clientele in answering fundamental questions pertaining to their research, and generates transgenic lines. The Integrated Genomics Facility provides access to and expertise in cutting edge genomics technologies. Typical projects partially supported by the Plant Biotechnology Center include a virology project that identifies proteins involved in movement of plant viruses within their insect vectors, and the identification of agronomically important genes in wheat and genes required for pathogenicity in fungal pathogens of wheat, maize, rice and turfgrass. The program also supports some highly qualified graduate students selected in an internal competition.
Animal Health Component
0%
Research Effort Categories
Basic
90%
Applied
10%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2012499106020%
2022499106020%
2021599110120%
2121599110115%
2122499106015%
2162499106010%
Knowledge Area
212 - Pathogens and Nematodes Affecting Plants; 216 - Integrated Pest Management Systems; 201 - Plant Genome, Genetics, and Genetic Mechanisms; 202 - Plant Genetic Resources;

Subject Of Investigation
1599 - Grain crops, general/other; 2499 - Plant research, general;

Field Of Science
1060 - Biology (whole systems); 1101 - Virology;
Goals / Objectives
Plant Transformation Center: Goals/Objectives: Provide KSRE scientists with the ability to produce transgenic plants. Expected outputs: Facility success will be measured by the number of scientists served, the number of transformed plant lines delivered, the number of publications resulting from the services provided, and the number of tours of the facility given to the general public. Integrated Genomics Facility (IGF): Goals/Objectives: Maintain and develop technological capacity of the Integrated Genomics Facility and support staff; Develop educational programs for workshops in genomics; and Develop strategies for expanding interactions between the IGF and KSU genomics initiatives, national genomics research programs, and industry. Expected outputs: Success will be measured as the number of extramural grants obtained by faculty that use IGF resources, and the number and impact of the resulting publications. Virology: Goals/Objectives: Identify viral and vector determinants of transmission and characterize the direct effect of virus infection on vectors; Develop genomics resources for arthropod vectors of plant viruses; Characterize insect proteomes and use proteomics tools to identify differentially expressed proteins in infected insects; and Identify unique molecules to combat virus diseases and develop novel strategies to prevent virus transmission. Expected outputs: Develop new viral disease control strategies for existing IPM programs, and Education of the Kansas public through the University Open House and an interactive display for the KSU Insect Zoo, and the development of K-12 educational. Wheat Genetic Resources and Molecular Genetics: Goals/Objectives: Develop resources for physical mapping of agronomic and resistance genes in wheat. Initially, the genes for red seed color, resistance to tan spot and preharvest sprouting will be targeted. Expected outputs: Progress success is measured by the number of agronomically important genes identified, the number of grant proposals developed, and the number and impact of the resulting publications. Fungal Genetics and Genomics: Goals/Objectives: Increase basic understanding of the evolution of fungal plant pathogens (Fusarium and Magnaporthe) and the genes they use to overcome disease resistance in their hosts; and Genetically map genes for pathogenicity, host specificity, and the production of mycotoxins and other secondary metabolites in a controlled inter-specific Fusarium cross. Expected outputs: Progress success is measured by the number of pathogenicity/mycotoxin/host specificity genes identified, the number of grant proposals developed, and the number and impact of the resulting publications. Graduate Student Rotation Program: Goals/Objectives: Train graduate students in all fields of plant biotechnology by offering research support to the best applicants that apply for graduate studies in this area at K-State. Expected outputs: Success can be measured by the number and quality of students funded, and whether project funds are matched by scholarships, grants, or departmental funds.
Project Methods
Plant Transformation Center (PTF): The crops studied are soybean, wheat, maize, rice, and tobacco. Clients provide a vector construct and phenotype description. The PTF grows plants, performs the genetic transformation, regenerates the transgenic plants, isolates DNA from the clones, and confirms transformation via PCR. The PTF provides clients with either primary transgenic plants or seed from these plants. The PTF also assists researchers with embryo rescue of wheat, trains researchers in plant tissue culture and transformation, and provides tours to the general public. Integrated Genomics Facility (IGF): The IGF provides access to genomics technologies for ultra high-throughput sequencing and gene expression analysis. Facility staff organize annual training workshops (some for graduate credit) and journal clubs on campus, and provide technical support for the Ecological Genomics Institute and the Arthropod Genomics Center. Virology: A G protein enables movement of virus particles within insect vectors. A soluble form of the G protein will be used as a surrogate to study protein-protein interactions under physiological conditions. EST libraries will be developed for two arthropod vectors, Peregrinus maidis and Frankliniella occidentalis, that include the defense-related transcripts. We will extend existing EST resources to include different life stages. The vector transcriptomes will be generated by the IGF and compared with transcriptomes of related species. Differentially expressed proteins will be identified via 2D gel electrophoresis and characterized by mass spectrometry. Wheat Genetic Resources and Molecular Genetics: Flow-sorted wheat chromosome 3A will be sequenced in the IGF. Minimum tiling paths generated from fingerprinted BAC clones containing genes of agronomic importance also will be sequenced. Candidate genes will be placed on the physical genomic map. A set of BAC clones representing the minimum tiling paths will be sequenced and assembled into contigs. Identified genes will be subjected to functional annotation by comparing with the NCBI non-redundant protein database. Fungal Genetics and Genomics: The genomes of two Fusarium species, F. fujikuroi and F. proliferatum, will be sequenced and assembled by the IGF. Progeny from an interspecific cross will be characterized by DNA sequence markers, their sexual fertility, and their pathogenicity on multiple host plant species to identify and localize pathogenicity genes. The Magnaporthe rice pathotype genome will be used as a scaffold to assemble genome sequences of isolates from wheat and turfgrass. Sequencing, genome assembly and preliminary bioinformatics analysis will be done by the IGF. Techniques developed in the Valent laboratory for analysis of rice-cultivar specificity will be used for cytological and functional analyses of host species specificity genes. Graduate Student Rotation Program: Funding will be provided for several students per year. Faculty nominate students and provide a project outline and the student's graduate application file. If funded, the faculty member develops a KAES project. Funding is for one year, with an option for renewal for a second.

Progress 10/01/19 to 09/30/20

Outputs
Target Audience:Wheat breeders, wheat geneticists, fungal geneticists, producers, other peer scientific researchers. Changes/Problems:The covid19 pandemic disrupted all university operations. In-person workshops, conferences, and trainings were canceled and/or moved online. Staffing in research labs was restricted to essential operations only. Regardless, the project accomplished many goals. What opportunities for training and professional development has the project provided?Unfortunately the covid19 pandemic disrupted research, teaching, service, extension, and other types of training. The Integrated Genomics Facility contributed to a KSU Zoom workshop on genomics technologies for microbiome research. The IGF continued training graduate students on an individual basis, but the typical workshops and seminars were canceled due to the pandemic. How have the results been disseminated to communities of interest?Results and outcomes were published in scientific journals as noted in the Publications section. Unfortunately the covid19 pandemic canceled or altered many conferences and workshops. However, faculty did present at the following events (in-person in early 2020, Zoom later on after the start of the pandemic): Redila C; Phipps S; Nouri S. Studying the genetic variation of wheat streak mosaic-associated viruses in Kansas fields through high-throughput sequencing. 2020. APS Annual Meeting. Redila C; Nouri S. Characterizing the wheat virome: Discovery of novel plant and fungal-associated viruses. 2020. APS Annual Meeting. D.H. Tran, A.M. Brokesh, C.C. Hunter, J.T. Steyer, D.J. Downes, M.A. Davis, R.B. Todd. The mechanism of nitrogen metabolite repression by the NmrA corepressor. 18th Annual K-INBRE Symposium, Hyatt Regency Wichita, Wichita, KS. January 18-19, 2020. C. Sehgal, A.M. Brokesh, C.C. Hunter, R.B. Todd. Genetics interactions between three transcription factors involved in NmrA-mediated repression in Aspergillus nidulans. 18th Annual K-INBRE Symposium, Hyatt Regency Wichita, Wichita, KS. January 18-19, 2020. C.A. Rabot, M.F. Grau, R., Entwistle, Y.-M. Chiang, M. Ahuja, C.E. Oakley, C.C.C. Wang, R.B. Todd, B.R. Oakley. Activation of silent gene clusters in Aspergillus nidulans using hybrid transcription factors. 17th International Aspergillus Meeting: Asperfest17. Sapienza University of Rome, Rome, Italy. February 16-17, 2020. C.A. Rabot, M.F. Grau, R., Entwistle, Y.-M. Chiang, M. Ahuja, C.E. Oakley, C.C.C. Wang, R.B. Todd, B.R. Oakley. Activation of silent gene clusters in Aspergillus nidulans using hybrid transcription factors. 15th European Conference on Fungal Genetics: ECFG15. Sapienza University of Rome, Rome, Italy. February 17-20, 2020. Stack, J. Diagnostics to Support Plant Health. University of Hawaii. 1 December 2020. (virtual/COVID) Stack, J. Surveillance as a Primary Plant Health Strategy. In, A Global Surveillance System for Crop Diseases and Pests. ASA, CSSA & SSSA Annual Meeting - 9 November 2020. (virtual - COVID-19) Stack, J. Plant Biosecurity in a World of Uncertainty: Wicked or what? Invited Seminar, University of Nebraska - 29 October 2020. (virtual - COVID-19) Stack, J. Novel Solutions Create Novel Problems: The case for an advanced diagnostics toolbox and point-of-care technologies. ServiTech Professional Development Conference, Kearney, Nebraska - 27-28 January 2020. Bin Tian, Hui Chen, Guihua Bai, and Harold N. Trick. Plant Transformation and Genome Editing Systems for Hexaploid Wheat. In Vitro Biology Meeting, Tampa, FL June 7th - 10th, 2020. Virtual only because of COVID-19 pandemic. Vijee Mohan, Syeda T. Alam, Elena Shulaev, Hyeonju Lee, Harold N. Trick and Jyoti Shah. Enhancing Wheat Resistance to Fusarium graminearum via Host-Induced Gene Silencing (HIGS) of the Fungal Virulence Gene FGL1. Proceedings of the 2020 National Fusarium Head Blight Forum. S. Canty, A. Hoffstetter, B. Wiermer and R. Dill-Macky, eds. ASAP Printing, Inc., Okemos, MI. Poster #35 (virtual) Akhunov E. Adaptive Introgression from Wild Emmer into Bread Wheat Revealed by Sequencing 1000 Wheat Exomes. Plant and Animal Genome XXVIII Conference, January 11-15, 2020. Akhunov E. Integrating Gene Expression Mapping, Epigenetics and GWAS to Understand the Genetic Control of Agronomic Traits in Hexaploid Wheat. Plant and Animal Genome XXVIII Conference, January 11-15, 2020. Dubcovsky J, Kuzay S, Zhang J, Xu Y, Liu Q, Paraiso F, Debernardi JM, Li C, Lin H, Akhunov E, Bai G. Map-Based Cloning of a QTL for Spikelet Number per Spike in Wheat. Plant and Animal Genome XXVIII Conference, January 11-15, 2020. Ward BP, Akhunova A, Jordan K, He F, Ren J, Brown-Guedira G, Akhunov E. High Density Genotyping and Diversity Analysis of a Historical Panel of Soft Winter Wheat Germplasm from the Eastern United States. Plant and Animal Genome XXVIII Conference, January 11-15, 2020. Gill BS, Jugulum M, Friebe B, Koo D-H. Fishing eccDNA elements that defy chromosome controlof mitosis and meiosis and drive rapid adaptive evolution. PAGXXVIII Jan 12, 2020, San Diego. Talk. Zhang W, Huang J, Cook DE, Epigenetic regulation of effector gene expression in a fungal plant pathogen. Plant Biology World Summit, conducted online July, 2020. (Oral) What do you plan to do during the next reporting period to accomplish the goals? Plant Transformation Center: Continue to evaluate new RNAi vectors for SCN control and focus on field tests and combining traits through conventional breeding. Evaluate gene-edited lines for wheat virus resistance. Establish collaborative research program with weed science researchers on reducing herbicide tolerance via gene editing. Continue research on heat tolerant starch synthase expression in wheat. Integrated Genomics Facility: Maintain technological and analytical capacities of the IGF at the modern level, thus ensuring the competitiveness of KSU faculty in genomics research and in obtaining extramural funding. Broaden the customer base of the IGFby outreaching to the KSU research community, through seminars at various KSU departments and personal interaction with individual faculty, and by developing new genomics applications for new biological systems. Collaborate with the wheat geneticists and breeders on the development of sequence-based genomic resources for Triticeaespecies and their pathogens. Fungal Genetics and Genomics: Continue sequence analysis of A. nidulans Continue genomic analysis of Fusarium populations Continue characterization of wheat and rice blast organisms Wheat Genetics Resources: Select homozygous newBdv2/Lr19recombinants with shortened alien segments and evaluate them for their resistance to barley yellow dwarf and leaf rust resistance. We will continue transferring the three wheat-barley recombinant stocks into advanced wheat cultivars and then combining all three into one genotype, which will be evaluated for beta glucan content. Continue to analyze the effect ofHpp-5Mgon homologous wheat-wheat recombination and analyzed its effect on meiotic recombination using immuno-fluorescence with synaptonemal complex and crossing over specific antibodies to further characterize the mechanism ofHpp-5Mgaction.

Impacts
What was accomplished under these goals? Publications and presentations arising from the work are listed in the products sections.

Publications

  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Koo D-H, Friebe B, Gill BS. 2020. Homoeologous recombination: A novel and efficient system for broadening the genetic variability in wheat. Agronomy 10, 1059; doi: 10.3390/agronomy10081059, 20-345-J.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Yan W, Jin X, Jiang B, Qi X, Chen Y, Li X, Liu X, Ren Y, Cui L, Song Q, Li H, Friebe B, Li J, Zhang Y. 2020. Development and molecular cytogenetic characterization of cold-hardy perennial wheatgrass adapted to northeastern China. Front. Plant Sci,?https://doi.org/10.3389/fpls.2020.00582.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Li H, Dong Z, Ma C, Xia Q, Tian X, Sehgal S, Koo D-H, Friebe B, Ma P, Liu W. 2020. A spontaneous wheat-Aegilops longissima translocation carrying Pm66 confers resistance to powdery mildew discovered by transcriptome analysis. Theor Appl Genet 133: 1149-1159.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Cook DE#, Kramer M, Torres D, Seidl MF, Thomma BPHJ#. 2020. A unique chromatin profile defines adaptive genomic regions in a fungal plant pathogen. eLife 2020; 9:e62208 DOI:?10.7554/eLife.62208
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: C Miao, Y Xu, S Liu, PS Schnable, JC Schnable. 2020 Increased power and accuracy of causal locus identification in time series genome-wide association in sorghum, Plant Physiology, 183:1898-1909
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Fumero, MV, W Yue, ML Chiotta, SN Chulze, JF Leslie & C Toomajian. Divergence and gene flow between Fusarium subglutinans and Fusarium temperatum isolated from maize in Argentina. Phytopathology. (published online 14 Dec 2020) (doi:10.1094/PHYTO-09-20-0434-FI).
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Fumero, MV, A Villani, A Susca, M Haidukowski, MT Cimmarusti, C Toomajian, JF Leslie, SN Chulze & A Moretti. Fumonisin and beauvericin chemotypes and genotypes of the sister species Fusarium subglutinans and Fusarium temperatum. Applied and Environmental Microbiology 86(13):e00133-20 (2020) (doi:10.1128/AEM.00133-20)
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: 13. John E. McLaughlin, Noura Al Darwish, Jeffrey Garcia-Sanchez, Neerja Tyagi, Harold N. Trick, Susan McCormick, Ruth Dill-Macky, Nilgun E. Tumer. 2020. Overexpression of a non-specific lipid transfer protein enhances resistance of wheat to Fusarium graminearum infection. Phytopathology. Published Online: 25 Aug 2020 https://doi.org/10.1094/PHYTO-04-20-0153-R
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Shubing Liu, Guihua Bai, Meng Lin, Mingcheng Luo, Dadong Zhang, Feng Jin, Bin Tian, Harold N. Trick and Liuling Yan. 2020. Identification of candidate chromosome region of?Sbwm1?for?Soil-borne wheat mosaic virus?resistance in wheat.?Sci Rep?10,?8119. https://doi.org/10.1038/s41598-020-64993-3
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Jordan Brungardt, Revathi Gonvind, and Harold N. Trick. 2020. A Simplified Method for Producing Laboratory Grade Recombinant TEV Protease from E. coli. Protein Expression and Purification. 174, October 2020, 105662 (available online May 5, 2020) https://doi.org/10.1016/j.pep.2020.105662
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: AL Perez-Quintero, M Ortiz-Castro, JM Lang, A Rieux, G Wu, S Liu, TA Chapman, C Chang, J Ziegle, Z Peng, FF White, MC Plazas, JE Leach, K Broders. 2020 Genomic Acquisitions in Emerging Populations of Xanthomonas vasicola pv. vasculorum Infecting Corn in the United States and Argentina, Phytopathology, 110:11611173
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: BA Pandian, A Varanasi, AR Vennapusa, R Sathishraj, G Lin, M Zhao, M Tunnell, T Tesso, S Liu, PV Prasad, J Mithila. 2020 Characterization, Genetic Analyses, and Identification of QTLs Conferring Metabolic Resistance to a 4-Hydroxyphenylpyruvate Dioxygenase Inhibitor in Sorghum (Sorghum bicolor),
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: A Gupta, L Hua, G Lin, I Molnar, J Dolezel, S Liu, W Li. 2020 Multiple origins of Indian dwarf wheat by mutations targeting the TREE domain of a GSK3-like kinase for drought tolerance, phosphate uptake, and grain quality, Theor Appl Genet. doi: 10.1007/s00122-020-03719-5
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: C Ji, Z Ji, B Liu, C He, H Liu, S Liu, B Yang, G Chen. 2020 Xa1 allelic R genes activate rice blight resistance suppressed by interfering TAL effectors, Plant communications, 1:100087
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Weiland JJ, Poudel RS, Flobinus A, Cook DE, Secor GA, and MD Bolton. 2020. RNAseq analysis of Rhizomania-infected sugar beet provides the first genome sequence of beet necrotic yellow vein virus from the USA and identified a novel alphanecrovirus and putative satellite viruses. Viruses 12, 626; doi:10.3390/v12060626
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Seidl MF, Kramer M, Cook DE, Fiorin G, van den Berg G, Faino L, and BPHJ Thomma. 2020. Repetitive elements contribute to the diversity and evolution of centromeres in the fungal genus Verticillium. mBio, 11?(5)?e01714-20;?DOI:?10.1128/mBio.01714-20


Progress 10/01/18 to 09/30/19

Outputs
Target Audience:Wheat breeders, wheat geneticists, fungal geneticists, producers, other peer scientific researchers. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Workshop on Genomic Technologies was held in summer 2019 with total of 21 participants, 18 of them students from multiple departments. 8 participating PIs trained at least one undergraduate researcher in their lab Tour of Integrated Genomics Facility for summer undergraduate research interns Tour of Biosecurity Research institute for summer undergraduate research interns How have the results been disseminated to communities of interest?Research was presented at multiple conferences/workshops and public events: Plant and Animal Genome Conference (San Diego, CA) American Phyopathological Society Conference (Cleveland, OH) Midwest Bioinformatics Conference (Kansas City, MO) Biennial Plant Breeding and Genetics Symposium (Manhattan KS) 30th Fungal Genetics Conference (Pacific Grove CA) 16th International Aspergillus Meeting (Pacific Grove, CA) 17th Annual K-INBRE Symposium (Overland Park, KS) K-State Open House (Manhattan KS) What do you plan to do during the next reporting period to accomplish the goals?Plant Transformation Center: Continue to provide wheat transformation and gene editing services to KSRE scientists Continue to evaluate new RNAi vectors for SCN control and focus on field tests and combining traits through conventional breeding. Evaluate gene-edited lines for wheat virus resistance. Continue research on heat tolerant starch synthase expression in wheat. Integrated Genomics Facility: Continue to provide high-quality services to KSU, national, and international clients Continue to conduct training workshops in emerging technologies Wheat Genetics Resource Center: We have identified novel Bdv2/Lr19 recombinants with shortened Thinopyrum segments and after obtaining homozygous recombinant stocks they will be evaluated for their leaf rust and BYD resistance under greenhouse and field conditions. Continue to evaluate the selected superior Fhb6/Everest, Fhb6/Lyman, and Fhb6/Overland recombinants for their FHB resistance and DON accumulation, select homozygous lines and distribute them to the breeding community. Continue transferring the three wheat-barley recombinant stocks into advanced wheat cultivars and then combining all three into one genotype, which will be evaluated for beta glucan content. Continue to evaluate the effectiveness of the Hpp-5Mg/ph1b super chromosomes to induce wheat-alien recombinants involving the WSMV resistance genes Wsm1 and Wsm3, analyzing their effect on wheat-wheat homologous recombination in proximal chromosome regions where recombination usually is suppressed, and analyzing the underlying molecular mechanism(s). Virology: Continue studies to identify and characterize emerging viruses in important crops including wheat Understand the mechanisms associated with plant tolerance to viruses Study ISVs (insect-specific viruses) Fungal Genetics and Genomics Further characterization of nitrogen metabolic gene expression in A. nidulans Further elucidation of population genetics/genomics in Fusarium Further characterization of Magnaporthe gene regulation, effectors

Impacts
What was accomplished under these goals? Plant Transformation Center: Continued to evaluate new RNAi vectors for SCN control (focus on methods to enhance expression levels such as amiRNAs, and alternate sequences of target genes). Continued research with the WSMV and TriMV resistance lines (combine current effective traits, screen other viruses). Produced a number of gene-edited lines for possible virus resistance. Continued to evaluate the potential of defensin-like proteins a resistance factor for various fungal and bacterial diseases in wheat and soybean. Integrated Genomics Facility: Continued support of more than 60 KSU faculy members and their graduate students and postdocs from across multiple KSU colleges, national clients, and international clients including training on planning and analysis of genomics experiments Wheat Genetics Resource Center: We have transferred Fhb6 into the moderate resistant winter wheat cultivars Everest, Lyman and Overland and select homozygous Fhb6 stocks by molecular marker and genomic in situ hybridization analyses. Continued further directed chromosome engineering combining the ph1b mutant stock with the homoeologous pairing promotor locus (Hpp-5Mg) to produce Bdv2/Lr19 recombinant stocks. ?Continued work combining Hpp-5Mg and ph1b into one super chromosome, which will make the crossing scheme much more efficient Virology: Sequencing and characterization of multiple KS viruses Studied virus-host interactions in wild wheat relatives Studied interactions of insect specific virus and Asian citrus psyllid Fungal Genetics/Genomics: Genotyping of hundreds of Fusarium graminearum isolates and characterization of variation Comparative population genomics and QTL mapping of F. fujikuroi Continued elucidation of molecular mechanisms regulating nitrogen metabolic gene expression in Aspergillus nidulans Characterization of mini-chromosomes in Magnaporthe

Publications

  • Type: Journal Articles Status: Published Year Published: 2019 Citation: J Zheng, E Zeng, Y Du, C He, Y Hu, Z Jiao, K Wang, W Li, M Ludens, J Fu, H Wang, FF White, G Wang, S Liu&, 2019 Temporal small RNA expression profiling under drought reveals a potential regulatory role of small nucleolar RNAs in the drought responses of Maize, Plant Genome, 12:180058.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: J Zheng, C He, Y Qin, G Lin, W Park, M Sun, J Li, X Lu, C Zhang, CT Yeh, C Gunasekara, E Zeng, H Wei, PS Schnable, G Wang, S Liu&, 2019 Co-expression analysis aids in the identification of genes in the cuticular wax pathway in maize, Plant J, 97:530-542.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Cook DE* (1), Valle-Inclan JE* (4), Pajoro A, Rovenich H, Thomma BPHJ, Faino L. 2019. Long-Read Annotation (LoReAn): automated eukaryotic genome annotation based on long-read cDNA sequencing. Plant Physiology 179: 38-54 DOI: https://doi.org/10.1104/pp.18.00848
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Zhang W (4), Corwin JA, Copeland D, Feusier J, Eshbaugh R, Cook DE (3), Atwell S, Kliebenstein D. 2019. Plant-Necrotroph co-transcriptome networks illuminate a metabolic battlefield. eLife 2019;8:e44279 DOI: 10.7554/eLife.44279
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Peng Z, Garcia-Oliveira E, Guifang L, Ying H, Dalby M, Migeon P, Tang Haibao, Farman M, Cook DE (3), White F, Valent B, Liu S. 2019. Effector gene reshuffling involves dispensable mini-chromosomes in the wheat blast fungus. PLoS Genetics 15(9):e1008272.https://doi.org/10.1371/ journal.pgen.1008272
  • Type: Book Chapters Status: Accepted Year Published: 2019 Citation: Sharma V (C), Zheng W (C), Huang J (B), and DE Cook #(1). CRISPR-Cas RNA targeting using transient Cas13a expression in Nicotiana benthamiana. Methods in Molecular Biology. Accepted for publication in 2019.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Nyine M, Wang S, Kiani K, Jordan K, Liu S, Byrne P, Haley S, Baenziger S, Chao S, Bowden R, Akhunov E. Genotype Imputation in Winter Wheat Using First-Generation Haplotype Map SNPs Improves Genome-Wide Association Mapping and Genomic Prediction of Traits. G3 (Bethesda). 2019 Jan 9;9(1):125-133.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Blake NK, Pumphrey M, Glover K, Chao S, Jordan K, Jannick JL, Akhunov ED, Dubcovsky J, Bockelman H, Talbert LE. Registration of the Triticeae-CAP Spring Wheat Nested Association Mapping Population. J. Plant. Reg. 13:294-297. doi:10.3198/jpr2018.07.0052crmp.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Gardiner LJ, Brabbs T, Akhunov A, Jordan K, Budak H, Richmond T, Singh S, Catchpole L, Akhunov E, Hall A. Integrating genomic resources to present full gene and putative promoter capture probe sets for bread wheat. GigaScience. 2019 Apr 1;8(4). pii: giz018. doi: 10.1093/gigascience/giz018.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Cordeiro EMG, Campbell JF, Phillips T, Akhunov E. Isolation by Distance, Source-Sink Population Dynamics and Dispersal Facilitation by Trade Routes: Impact on Population Genetic Structure of a Stored Grain Pest. G3 (Bethesda). 2019 May 7;9(5):1457-1468.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: He F, Pasam R, Shi F, Kant S, Keeble-Gagnere G, Kay P, Forrest K, Fritz A, Hucl P, Wiebe K, Knox R, Cuthbert R, Pozniak C, Akhunova A, Morrell PL, Davies JP, Webb SR, Spangenberg G, Hayes B, Daetwyler H, Tibbits J, Hayden M, Akhunov E. Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome. Nat Genet. 2019 May; 51(5):896-904.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Varella AC, Weaver DK, Blake NK, Hofland ML, Heo HY, Cook JP, Lamb PF, Jordan KW, Akhunov E, Chao S, Talbert LE. Analysis of recombinant inbred line populations derived from wheat landraces to identify new genes for wheat stem sawfly resistance. Theor Appl Genet. 2019 May 2. doi: 10.1007/s00122-019-03347-8.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Wang W, Pan Q, Tian B, He F, Chen Y, Bai G, Akhunova A, Trick HN, Akhunov E. Gene editing of the wheat homologs of TONNEAU1-recruiting motif encoding gene affects grain shape and weight in wheat. Plant J. 2019 Jun 20. doi: 10.1111/tpj.14440.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Kuzay S, Xu Y, Zhang J, Katz A, Pearce S, Su Z, Fraser M, Anderson JA, Brown-Guedira G, DeWitt N, Peters Haugrud A, Faris JD, Akhunov E, Bai G, Dubcovsky J. Identification of a candidate gene for a QTL for spikelet number per spike on wheat chromosome arm 7AL by high-resolution genetic mapping. Theor Appl Genet. 2019 doi: 10.1007/s00122-019-03382-5.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Yuye Wu, Tingting Guo, Qi Mu, Jinyu Wang, Xin Li, Yun Wu, Bin Tian, Ming Li Wang Guihua Bai, Ramasamy Perumal, Harold N. Trick, Scott R. Bean, Ismail M. Dweikat, Mitchell R. Tuinstra, Geoffrey Morris, Tesfaye T. Tesso, Jianming Yu, and Xianran Li. 2019. Allelochemicals targeted to balance competing selection forces in African agroecosystems. Nature Plants 5:12291236.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Jessica L. Shoup Rupp, Luisa Cruz, Harold N. Trick, and John P. Fellers. 2019. RNAi mediated silencing of endogenous wheat genes eIF(iso)4E-2 and eIF4G induce resistance to multiple RNA viruses in transgenic wheat. Crop Science (First look April 24, 2019). doi:10.2135/cropsci2018.08.0518.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Wei Wang, Quanli Pan, Bin Tian, Fei He, Yueying Chen, Alina Akhunova, Guihua Bai, Harold N. Trick, Eduard Akhunov. 2019. Gene editing of the wheat homologs of TONNEAU1-recruiting motif encoding gene affects grain shape and weight in wheat. Plant Journal 100: 251-264.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Tian B, Li J, Vodkin LO, Todd TC, Finer JJ, and Trick HN. 2019. Host-derived gene silencing of parasite fitness genes improves resistance to soybean cyst nematodes in transgenic soybean with deep sequencing analysis. Theoretical and Applied Genetics published online June 22, 2019 (https://doi.org/10.1007/s00122-019-03379-0)
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Jordan Brungardt, Timothy C. Todd, Thomas R. Oakley, and Harold N. Trick. 2019. Assessment of Soybean Cyst Nematode Bioassay Interference by Various Insecticides/miticides under Greenhouse Conditions Plant Health Progress 20 (2), 74-76.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Zhenqi Su, Amy Bernardo, Bin Tian, Shan Wang, Hongxiang Ma, Shibin Cai, Dongtao Liu, Dadong Zhang, Tao Li, Harold Trick, Paul St Amand, Jianming Yu, Guihua Bai. 2019. A deletion mutation in TaHRC confers Fhb1resistance to Fusarium head blight in wheat. Nature Genetics 51: 1099-1105
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Sujon Sarowar, Syeda Alam, Ragiba Makandar, Hyeonju Lee, Harold N. Trick, Yanhong Dong, and Jyoti Shah. 2019. Targeting the pattern-triggered immunity pathway for enhancing resistance to Fusarium graminearum Molecular Plant Pathology Molecular Plant Pathology 20(5) 626-640; (DOI: 10.1111/mpp.12781).
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: V Yadav, F Yang, MH Reza, S Liu, B Valent, K Sanyal, NI Naqvi, 2019, Cellular Dynamics and Genomic Identity of Centromeres in Cereal Blast Fungus, mBio, 10:e01581-19
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: L Li, Y Du, C He, CR Dietrich, J Li, X Ma, R Wang, Q Liu, S Liu, G Wang, PS Schnable, J Zheng, 2019 Maize glossy6 is involved in cuticular wax deposition and drought tolerance, J Exp Bot, 70:3089-3099.


Progress 10/01/17 to 09/30/18

Outputs
Target Audience:Wheat breeders, wheat geneticists, fungal geneticists, producers, other peer scientific researchers. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? We have organized the workshop for Wheat CAP graduate students (July 9-13) on the use of RNA-Seq/Bioinformatics to identify candidate genes controlling yield traits of interest. Twenty-two individuals from 15 US wheat breeding programs participated in this workshop. All lectures were recorded and are posted on the PBTN https://passel.unl.edu/communities/pbtn and WheatCAP website. We have organized the workshop for KSU graduate students on the Genomic Technologies (June 4-8). The workshop provided the lectures and laboratory on next and third generation sequencing, real-time PCR and bioinformatical approaches to study genes and genomes. Fifteen graduate students from multiple KSU departments participated in the event. We have organized the training workshop for KSU faculty, students and staff on the usage of Droplet Digital PCR in their research projects (May 16-17). The training was attended by 32 individuals. Carlos Pizolotto, Ph.D. student from University of Passo Fundo, Rio Grande do Sul, Brazil: March to September 2018. Completed internship in Jim Stack's lab to learn genome-enabled, molecular diagnostics for the wheat blast pathogen, Magnaporthe oryzae Triticum. Plant Biosecurity Workshop led by Dr. Stack: 28 participants from approximately 10 countries. Dr. Cook's lab hosted a visiting scientist, Prof. Velazhahan Rethinasamy, from the Department of Crop Sciences at Sultan Qaboos University in Muscat, Oman. He worked and was trained in the lab for 8 weeks on a project to develop CRISPR-RNA editing tools for use in fungal plant pathogens. Three undergraduate students have received year-long research training in fungal genetics in the Todd lab. The Toomajian lab has provided training for a collaborating postgraduate researcher from Argentina in the population genetic analysis of DNA sequence data. How have the results been disseminated to communities of interest?The results and outcomes of these studies have been published in many refereed journalpublications as noted in the products section. Further, project team members have attendedand presentedatseveral conferences: Genome-Informed Diagnostics for Early and Accurate Detection of Magnaporthe oryzae Triticum and Rathayibacter toxicus. Ag Biosecurity and Biodefense Consortium, Nebraska City, NE - 23 October 2018 Transnational Biological Threats and Global Security. Blue Ribbon Panel on Biodefense, Washington DC - 25 April 2018 Diagnostics, Biosecurity and IPM - Putting the Pieces Together. International IPM Symposium, Baltimore, MD - 21 March 2018 Todd, R.B. The 16th Annual K-INBRE Symposium. Overland Park Sheraton, Overland Park, KS. January 12-14, 2018. Todd, R.B. The 15th International Aspergillus Meeting: Asperfest15. Biology Auditorium, Main Campus, Technion, Haifa, Israel. February 25, 2018. Todd, R.B. 14th European Conference on Fungal Genetics ECFG14 - US-Israel BARD (Binational Agricultural Research and Development Fund) workshop: Nutritional factors modulating plant and fruit susceptibility to pathogens. [Joint session] Technion Israel Institute of Technology, Faculty of Medicine, Haifa, Israel. February 25-28, 2018. Todd, R.B. K-State GRAD forum. Regneir Hall, KSU. March 29, 2018. Todd, R.B. Borlaug Global Rust Initiative (BGRI) Technical Workshop - Delivering Genetic Gain in Wheat, Marrakech, Morocco. April 14-17, 2018. C. Toomajian, Population genomics of fungal maize pathogens from Argentina, Ecological Genomics Research Forum, Kansas State University, Manhattan KS, July 2018. Toomajian, C., W. Yue, and J. F. Leslie. 2017. Updating population structure and genetic differentiation of Fusarium graminearum populations from three major US regions using genotyping-by-sequrncing. In: S. Canty, B. Wiermer and D. Van Sanford (Eds.), Proceedings of the 2017 National Fusarium Head Blight Forum. (p. 72) East Lansing, MI/Lexington, KY: U.S. Wheat & Barley Scab Initiative. What do you plan to do during the next reporting period to accomplish the goals?Plant Transformation Center: Continue to provide wheat transformation and gene editing services to KSRE scientists Continue to evaluate new RNAi vectors for SCN control and focus on field tests as well as combining traits through conventional breeding. Evaluate gene-edited lines for wheat virus resistance. Continue research on heat tolerant starch synthase expression in wheat. Integrated Genomics Facility (IGF) and Wheat Genetics and Genomics: Collaborate with the wheat geneticists and breeders on the development of sequence-based genomic resources for Triticeae species. Maintain technological and analytical capacities of the IGF at the modern level, thus ensuring the competitiveness of KSU faculty in genomics research and in obtaining extramural funding. Establish novel cost-effective genomic tools for improved characterization of genomes and transcriptomes of diverse crop species and their pathogens. Fungal Genetics and Genomics: We will continue with our current efforts build genetic, genomic and epigenomic resources for Magnaporthe strains across the species complex. This will aid our goal to elucidate important genetic determinants of host-range, virulence and genome regulation. We plan to exploit our hybrid transcription factor engineering strategy for activating silent secondary metabolite gene clusters to elucidate the biosynthetic pathway for production of the antibiotic (+)-asperlin. We will determine important functional regions of a new factor required for repression of the nitrogen metabolism transcriptional regulator AreA. We will publish our work on leucine biosynthesis in A. nidulans. We will determine the site(s) of action for LeuR in the gdhA promoter and examine how LeuR and LeuB interact to regulate nitrogen assimilation and leucine biosynthesis. Continue work with collaborators to perform molecular genetic manipulation of F. fujikuroi and F. proliferatum parental strains to functionally verify our candidate genes controlling onion pathogenicity and gibberellic acid production levels. We also will identify through QTL mapping genes involved in determining the levels of fumonisins produced. We will write up our QTL results from the F. fujikuroi x F. proliferatum interspecific cross as well as our population genomic analyses of F. subglutinans and F. temperatum for peer-reviewed publication to disseminate broadly to the scientific community. Wheat Genetic Resources and Molecular Genetics: Develop gene edited wheat lines with modified genes affecting yield component, disease resistance and quality traits. Conduct functional validation of stem rust resistance genes identified in wheat landraces High resolution mapping and cloning of yield component genes in wheat Continue further directed chromosome engineering using our new strategy combining the ph1b mutant stock with the homoeologous pairing promotor locus (Hpp-5Mg) of Aegilops geniculata to produce compensating wheat-E. trachycaulus recombinants. Continue evaluation and selection of the Bdv2/Lr19 and Wsm3 recombinant stocks under field conditions and select homozygous Wsm3 recombinant stocks for evaluating their resistance to wheat streak mosaic and barley yellow dwarf virus. We will evaluate Fhb6 BC1F3 progenies under field condition for their resistance to FHB and DON accumulation and will select homozygous Fhb6 stocks by molecular marker and genomic in situ hybridization analyses, which then will be distributed to the wheat breeding community. We continue to search for novel sources of FHB resistance and once those have been identified will initiate directed chromosome engineering to produce compensating recombinants. We have identified three compensating wheat barley recombinant stocks (T7AS.7HL-7AL, T7BS.7HL-7BL, T7DS.7HL-7ADL) and will now select homozygous recombinant stocks and also combine all three recombinant chromosomes into one genotype of advanced wheat breeding cultivars, which will like result in a significant higher beta glucan content. We are presently combining Hpp-5Mg and ph1b into one super chromosome, which will make the crossing scheme much more efficient. We have identified several T5BS-5MgS.5MgL-5BL superchromosome recombinants that will be analyzed for their abilities to increase homoeologous and homologous recombination. We are also using this new strategy to produce novel wheat-alien recombinants with agronomically interesting traits according to industry requirements,

Impacts
What was accomplished under these goals? Plant Transformation Center: Transformation facility performed approximately 300 transformations experiments on wheat cultures, yielding over 350 transgenic T0 plants or T1 generation seeds, providing service to ten investigators (KSRE scientists and off campus collaborators). / Provided 5 laboratory tours to ~60 individuals from the public and students. / Field tested soybeans engineered with RNAi vectors for SCN control. / Identified and evaluated new effective traits to confer resistance to WSMV and TriMV. Looked into gene editing methodologies as a non GMO alternative./ Continued discovery research for potential defensin-like proteins and evaluated material for various fungal and bacterial disease resistance factors in wheat and soybean. / Continued research on heat tolerant starch synthase expression in wheat and in other crop species. / Received one patent relating to wheat virus research. Integrated Genomics Facility (IGF) / Wheat Genetics and Genomics: Designed and tested more than 200 diverse wheat accessions for the regulatory sequence capture assay for hexaploid bread wheat. The assay targets genomic regions including predicted miRNA binding sites and promoters of each gene model in the wheat genome. / Collaborated with IDT to develop low-cost genotyping assay based on rhAmpSeq. Nearly 7 million SNPs obtained for 800 exome-captured accessions representing global genetic and geographic diversity of wheat were used to select 2999 genome-wide distributed common SNPs. The assay will be used for cost-effective genomic selection in breeding programs. / Initiated the development of the Practical Haplotype Graph (PHG) tool for wheat, an effective SNP data storage and retrieval informatics tool that uses a representative set of wheat lines to predicting missing genotypes. Collaborated with USDA genotyping labs to re-sequence a panel 217 US wheat cultivars that represent genetic diversity of modern US breeding programs. / Developed a low-cost high-throughput method for detecting gene editing events in the wheat genome using next-generation sequencing of multiplexed amplicons and a bioinformatical analysis pipeline for quick assessment of frequency and types of editing events in the wheat genome. / With UM-TC partners, more than 200 barley accession genomes were sequenced to detect deleterious mutations to reduce the deleterious mutation load and accelerate the rate of genetic gain in breeding programs. / Optimized the MNase and ATAC-seq chromatin accessibility assays for wheat, to identify functionally active regions of the wheat genome, to identify regulatory regions of the wheat genome. Fungal Genetics and Genomics: Developed a wet lab and computational pipeline tode novoassemble genomes ofMagnaporthefungal strains to reference quality. Four rice infecting strains are completed to date and additional strains with diverse pathogenicity phenotypes are being identified. / Developed epigenome maps and genetic resources (i.e. gene deletions and tagged proteins) to understand gene regulation inMagnaportherice infecting strains. These resources will support further understanding of fungal pathogenesis. / Developed a novel strategy - hybrid transcription factor engineering - to activate normally silent secondary metabolite gene clusters, demonstrated inAspergillus nidulansand activated a gene cluster responsible for biosynthesis of an unknown product, which was identified as the antibiotic (+)-asperlin. / Begun to characterize a factor that represses the major fungal transcription activator of nitrogen metabolic genes AreA. / Increased our understanding of leucine amino acid biosynthesis in fungi, an important factor for virulence. / Identified a well-characterized secondary metabolite in one of our parental strains as the major genetic basis for onion pathogenicity - Determined that levels of the secondary metabolite gibberellic acid, produced by the progeny is genetically controlled by the known biosynthetic gene cluster for this metabolite and also by another regulatory locus on a separate chromosome. With Italian collaborators we are analyzing fumonisin production in these progeny so we can genetically map modifiers of the trait. / Undertaken a population genomic analysis of closely relatedF. subglutinansandF. temperatumstrains to investigate the evolution of pathogenicity and of speciation in fungal pathogens. Wheat Genetic Resources and Molecular Genetics:Re-sequenced worldwide collections of wheat and wild relatives, identifying wheat genome regions from wild relatives. These ancient lines shaped phenotypic diversity of modern wheat and expanded its environmental adaptation and range. The wild relatives are a valuable genomic resource to improve wheat./ Developed gene editing (GE) procedures for modifying wheat genome and edited several genes affecting grain size and weight. Showing GE to be an effective way to create novel gene variants positively affecting yield traits with potential to accelerate wheat variety development for improved yield potential. / Established effective pipeline for transferring gene edited traits to breeding lines. A gene affecting seed size and weight was successfully transferred to multiple wheat lines from national and international breeding programs. A new gene editing project was developed and targets multiple agronomic genes relevant for Kansas wheat production. / Two genes affecting number of spikelets per spike and number of productive tillers were mapped in wheat landraces and currently targeted for gene cloning. / Developed a genomic resource that includes diverse wheat landraces characterized by large scale re-sequencing, gene expression analysis and extensive disease resistance phenotyping. / Developed and genotyped the spring wheat NAM population was using 90K iSelect, GBS and exome capture assays to characterize the distribution of 102,000 recombination breakpoints across the wheat genome. The NAM population was used to identify QTL for the distribution of recombination along the chromosomes. The identified QTL increasing recombination in pericentromeric regions can be used to reduce linkage drag in these chromosomal regions making them accessible to selection. / Wheat leaf rust resistance gene Lr42 was identified and Lr42-bearing transformation lines were shown to be highly resistant to leaf rust - filed a provisional patent application("Cloning of a Leaf Rust Resistant Gene in Wheat"). / Identified a new source of BYDV resistance derived from E. trachycaulus. / Recombinant stocks from Dr. Adam Lukaszewski, purported to have a Thinopyrum intermedium-derived gene Bdv2 and the Th. elongatum-derived gene Lr19. The recombinant stocks involving wheat chromosomes 7A and 7D were confirmed by GISH analysis, presence of Lr19 was confirmed by artificial inoculation with leaf rust and the presence of Bdv2 was confirmed by ELISA. Our preliminary field evaluation suggests that Wsm3 transfer from Th. intermedium conferring resistance to wheat streak mosaic virus also may confer resistance to barley yellow dwarf virus. / Recently released the germplasm KS14WGRC61, has a new gene for resistance to Fusarium head blight, Fhb6.Fhb6 has been into the moderate resistant cultivars Everest, Overland, and Lyman. BC1F3 progenies will be evaluated for their FHB resistance and DON accumulation in the 2018/19 growing season. / Results show the long arm of chromosome 6R of rye to harbor Rf6, which gives good fertility restoration. / In Hpp-5Mg/ph1b, ph1b genotypes, crossing over tend to cluster close to each other, which allows the recovery of wheat-alien recombinants with very small alien chromatin and less linkage drag. This new strategy will improve wheat-alien gene transfer.?

Publications

  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Bandara YMAY, DK Weerasooriya, S Liu, CR Little, 2018 The necrotrophic fungus Macrophomina phaseolina promotes charcoal rot susceptibility in grain sorghum through induced host cell wall-degrading enzymes, Phytopathology, 108:948-956.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Cook DE, Valle-Inclan JE, Pajoro A, Rovenich H, Thomma BPHJ, Faino L. 2018. Long-Read Annotation (LoReAn): automated eukaryotic genome annotation based on long-read cDNA sequencing. Plant Physiology DOI: https://doi.org/10.1104/pp.18.00848
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Danilova TV, Friebe B, Gill BS, Poland J, Jackson E. 2018. Chromosomal rearrangements caused by double monosomy in wheat-barley group-7 substitution lines. Cytogenet Genome Res 154: 45-55, 18-200-J.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Deng W, K Zhang, S Liu, P Zhao, S Xu, H Wei, 2018 JRmGRN: Joint reconstruction of multiple gene regulatory networks with common hub genes using data from multiple tissues or conditions, Bioinformatics, 1-9.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Elbasyoni IS, Lorenz AJ, Guttieri M, Frels K, Baenziger PS, Poland J, Akhunov E. A comparison between genotyping-by-sequencing and array-based scoring of SNPs for genomic prediction accuracy in winter wheat. Plant Sci. 2018 270:123-130.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Gardiner LJ, Brabbs T, Akhunova A, Jordan K, Budak H, Richmond T, Singh S, Catchpole L, Akhunov E, Hall A. Integrating genomic resources to present full gene and promoter capture probe sets for bread wheat. bioRxiv 2018 July6th. https://doi.org/10.1101/363663.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Guo H, TM Nolan, G Song, S Liu, Z Xie, J Chen, PS Schnable, JW Walley, Y Yin, 2018 FERONIA receptor kinase contributes to plant immunity by suppressing jasmonic acid signaling in Arabidopsis thaliana, Curr Biol, 28:3316-3324.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Jordan K, Wang S, He F, Chao S, Lun Y, Paux E, Sourdille P, Sherman J, Akhunova A, Blake N, Pumphrey M, Glover K, Dubcovsky J, Talbert L, Akhunov E. The genetic architecture of genome-wide recombination rate variation in allopolyploid wheat revealed by nested association mapping. Plant J. 2018 95:1039-1054.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Koo D-H, Jugulum M, Putta K, Cuvaca IB, Peterson DE, Currie RS, Friebe B, Gill BS. 2018. Gene duplication and aneuploiudy trigger rapid evolution of herbicide resistance in common waterhemp. Plant Physiology 176: 1932-1938.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Koo D-H, Molin WT, Saski CA, Jiang J, Putta K, Jugulum M, Friebe B, Gill BS. 2018. Extrachromosomal circular DNA-based amplification and transmission of herbicide resistance in crop weed Amaranthus palmeri. Proc Nat Acad Sci USA 115: 3332-3337, 18-189-J*.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Liu S, JC Schnable, A Ott, CT Yeh, NM Springer,J Yu, G Muehlbauer, MCP Timmermans, MJ Scanlon, PS Schnable, 2018 Intragenic meiotic crossovers generate novel alleles with transgressive expression levels, Mol Bio Evol, msy174.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Lowe-Power TM, Hendrich CG, Roepenack-Lahaye E, Li B, Wu D, Mitra R, Dalsing B, Ricca P, Naidoo J, Cook DE, Jancewics, Masson P, Thomma B, Lahaye T, Michael AJ, Allen C. 2018. Metabolomics of tomato xylem sap during bacterial wilt reveals Ralstonia solanacearum produces abundant putrescine, a metabolite that accelerates wilt disease. Environmental Microbiology, 20 (4) 1330-1349. DOI: 10.1111/1462-2920.14020.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Neugebauer KA, Myron Bruce, Tim Todd, Harold N. Trick, and John P. Fellers. 2018. Wheat differential gene expression induced by different races of Puccinia triticina. PLOS One June 7 1-15. (https://doi.org/10.1371/journal.pone.0198350)
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Rawat N, A Schoen, L Singh, A Mahlandt, DL Wilson, S Liu, G Lin, BS Gill, VK Tiwari, 2018, TILL-D: An Aegilops tauschii TILLING resource for wheat improvement, Front Plant Sci, 9:1665
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Said M, Hribova E, Danilova TV, Karafiatova M, Cizkova J, Friebe B, Dolezel J, Gill BS, Vrana J. 2018. The Agropyron cristatum karyotype, chromosome structure an cross-genome homooeology as revealed by fluorescence in situ hybridization with tandem repeats and wheat single-gene probes. Theor Appl Genet, doi.org/10.1007/s00122-018-3148-9.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Tian B, Shyamal K. Talukder, Jianming Fu, Allan K. Fritz, and Harold N. Trick. 2018. Expression of a rice soluble starch synthase gene improved the grain yield in heat stress conditions in wheat. In Vitro Cell. Dev. Biol.-Plant. 54(3), 216-227.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Wang W, Pan Q, He F, Akhunova A, Chao S, Trick H, Akhunov E. Transgenerational CRISPR-Cas9 Activity Facilitates Multiplex Gene Editing in Allopolyploid Wheat. The CRISPR Journal 2018 1:65-74.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Yasuhara-Bell, J., Pedley, K.F., A.R., Farman, M.L., Valent, B., and Stack, J.P. 2018. Specific detection of the wheat blast pathogen (Magnaporthe oryzae Triticum) by loop-mediated isothermal amplification. Plant Dis. 102(12):2550-2559. 102:https://doi.org/10.1094/PDIS-03-18-0512-RE.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Zhang J, Gizaw SA, Bossolini E, Hegarty J, Howell T, Carter AH, Akhunov E, Dubcovsky J. Identification and validation of QTL for grain yield and plant water status under contrasting water treatments in fall-sown spring wheats. Theor Appl Genet. 2018 May 16. doi: 10.1007/s00122-018-3111-9.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Zheng J, E Zeng, Y Du, C He, Y Hu, Z Jiao, K Wang, W Li, M Ludens, J Fu, H Wang, F.F. White, G Wang, S Liu, 2018 Temporal small RNA expression profiling under drought reveals a potential regulatory role of snoRNAs in drought responses of maize, Plant Genome, doi:10.3835/plantgenome2018.08.0058.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Fellers, J.P., Trick, H.N., Cruz, L., Rupp, J. 2018. Plant Germplasm Resistant to RNA Viruses. Issued March 6, 2018. U.S. Patent #9,909,139 B2.


Progress 10/01/16 to 09/30/17

Outputs
Target Audience:Wheat breeders, wheat geneticists, producers, other peer sciencific researchers. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?We have trained two vistiing Scientists, 12post-docs, one visiting graduate student. Further, workshops have been a measurable part of our activity and more than100 attendees have been trained at the Furasium workshop and the Biosecurity workshop. How have the results been disseminated to communities of interest?The results and outcomes of these studies have been published in many refereed journal publications. Further, project team members have attendedand presentedatseveral conferences (2016 USWBSI "Scab" Forum, PAG XXV conference, 29th GSA Fungal Genetics Conference, 2016 APS annual meeting). What do you plan to do during the next reporting period to accomplish the goals?Simialr programs will continue and further advances in the resaerch described in the objectives will be completed.

Impacts
What was accomplished under these goals? Plant Transformation Center We have new RNAi vectors for SCN control have been identified and are under evaluation. New effective traits in conferring resistance to WSMV and TriMV have been identified and are under evaluation. Potential of defensin-like proteins have been identified and are being evaluated as resistance factors for various fungal and bacterial diseases in wheat and soybean. Continuing research on heat tolerant starch synthase expression in wheat and in other crop species. One patent was awarded and another was submitted to the Research Foundation. Integrated Genomics Facility (IGF) and Wheat Genetics and Genomics: Several new wheat genes were mapped or cloned. We have identified the AvrSr35 effector protein that is recognized by the Sr35 gene and triggers resistance response. The study was published inSciencewith the lead author being my graduate student. The story was highlighted broadly in public media including BBC News. We have sequenced the genome of wild wheat and identified targets of domestication selection harboring genes associated with agronomic traits selected by early humans. The study was published inScienceand broadly publicized in media. In addition, this study laid foundation for deploying the genetic diversity of wild emmer wheat in Kansas wheat breeding programs. We have developed a resource for predicting missing genotypes in association mapping projects using wheat haplotype map. We demonstrated the utility of the developed wheat diversity map as a platform for cross-linking multiple gene mapping projects. We have mapped and cloned genes controlling recombination rate variation in wheat. We have set up and validated gene editing technology for wheat, and showed the positive effect of gene editing on yield-component traits. We continue to work on maize/wheat disease studies and genomic structural variation. We have identified a wheat candidate resistant gene to leaf rust and have sequenced a wheat blast isolate and built the first wheat blast reference genome. We extended our program to develop an improved GBS, built tools to design CRISPR guide RNAs, and applied CRISPR to knockout maize genes. Fungal Genetics and Genomics: We have contributed to a community effort of comparative genome analysis of eighteen Aspergillus species, comprising plant and animal pathogens and industrial species. This study of key aspects of fungal biology, including primary and secondary metabolism, stress response, biomass degradation, and signal transduction, revealed both conservation and diversity among the species. This work was published in the high impact journal Genome Biology. We have increased the understanding of the regulation of nitrogen metabolic gene expression. This includes uncovering metabolic signaling to the transcription factor AreA, and discovery of a new factor required for repression of AreA action. We have increased our understanding of leucine amino acid biosynthesis in fungi, an important factor for virulence. We have identified and deleted the leucine biosynthesis genes in Aspergillus nidulans, and revealed redundancy of duplicated genes. We have made advances in characterizing regulation of leucine biosynthesis genes by the transcription factor LeuB. We have publicized the threat represented by wheat blast at several meetings including the Open Philanthropy Project meeting in Berkeley, CA, (January 24-25); the Supporters of Agricultural Research (SOAR) Foundation meeting with congressional staffers and reporters (March 1-2); and a meeting of The Board for International Food and Agricultural Development (BIFAD) in Washington DC (September 12). The Board of Regents Review for the Interdepartmental Genetics program has been completed under the guidance of faculty in this department. Virology: This program is on hiatus pending the arrival of a new hire.

Publications

  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Avni R, Nave M, Barad O, Baruch K, Twardziok SO, Gundlach H, Hale I, Mascher M, Spannagl M, Wiebe K, Jordan KW, Golan G, Deek J, Ben-Zvi B, Ben-Zvi G, Himmelbach A, MacLachlan RP, Sharpe AG, Fritz A, Ben-David R, Budak H, Fahima T, Korol A, Faris JD, Hernandez A, Mikel MA, Levy AA, Steffenson B, Maccaferri M, Tuberosa R, Cattivelli L, Faccioli P, Ceriotti A, Kashkush K, Pourkheirandish M, Komatsuda T, Eilam T, Sela H, Sharon A, Ohad N, Chamovitz DA, Mayer KFX, Stein N, Ronen G, Peleg Z, Pozniak CJ, Akhunov ED, Distelfeld A. Wild emmer genome architecture and diversity elucidate wheat evolution and domestication. Science. 2017 Jul 7;357(6346):93-97.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Balc�rkov� B, Frenkel Z, `kopov� M, Abrouk M, Kumar A, Chao S, Kianian SF, Akhunov E, Korol AB, Dole~el J, Val�rik M. A High Resolution Radiation Hybrid Map of Wheat Chromosome 4A. Front Plant Sci. 2017 10:2063.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Bin Tian, Shichen Wang, Timothy C. Todd, Charles D. Johnson, Guiliang Tang, Harold N Trick. 2017. Genome-wide identification of soybean microRNA responsive to soybean cyst nematodes infection by deep sequencing. BMC Genomics. 18:572 doi 10.1186/s12864-017-3963-4.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Cruz, C.D. and B. Valent. 2017. Wheat Blast Disease: Danger on the Move. Tropical Plant Pathology 42:210-222. doi:10.1007/s40858-017-0159-z.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Danilova TD, Akhunova AR, Akhunov ED, Friebe B, and Gill BS. 2017. Major structural genomic alterations can be associated with hybrid speciation in Aegilops markgrafii (Triticeae). The Plant J 92(2):317-330. doi: 10.1111/tpj.13657
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Del Ponte, Emerson M, Barbara Valent and Gary C. Bergstrom. 2017. A special issue on Fusarium head blight and wheat blast. Tropical Plant Pathology 42:143-145, doi:10.1007/s40858-017-0166-0.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: R.P. de Vries, R. Riley, A. Wiebenga, G. Aguilar-Osorio, S. Amillis, C. Akemi Uchima, G. Anderluh, M. Asadollahi, M. Askin, K. Barry, E. Battaglia, �. Bayram, T. Benocci, S.A. Braus-Stromeyer, C. Caldana, D. C�novas, G.C. Cerqueira, F. Chen, W. Chen, C. Choi, A. Clum, R. Augusto Corr�a dos Santos, A. Ricardo de Lima Dam�sio, G. Diallinas, T. Emri, E. Fekete, M. Flipphi, S. Freyberg, A. Gallo, C. Gournas, R. Habgood, M. Haimaut, L. Harispe, B. Henrissat, K.S. Hild�n, R. Hope, A. Hossain, E. Karabika, L. Karaffa, Z. Kar�nyi, N. Kraaevec, A. Kuo, H. Kusch, K. LaButti, E.L. Lagendijk, A. Lapidus, A. Levasseur, E. Lindquist, A. Lipzen, A.F. Logrieco, A. MacCabe, M.R. M�kel�, I. Malavazi, P. Melin, V. Meyer, N. Mielnichuk, M. Miskei, �.P. Moln�r, G. Mul�, C.Y. Ngan, M. Orejas, E. Orosz, J.P. Ouedraogo, K.M. Overkamp, H.-S. Park, G. Perrone, F. Piumi, P. Punt, A.F.J. Ram, A. Ram�n, S. Rauscher, E. Record, D. Mauricio Ria�o-Pach�n, V. Robert, J. R�hrig, R. Ruller, A. Salamov, N.S. Salih, R.A. Samson, E. S�ndor, M. Sanguinetti, T. Sch�tze, K. Sep?i?, E. Shelest, G. Sherlock, V. Sophianopoulou, F.M. Squina, H. Sun, A. Susca, R.B. Todd, A. Tsang, S.E. Unkles, N. van de Wiele, D. van Rossen-Uffink, J. Velasco de Castro Oliveira, T.C. Vesth, J. Visser, J.-H. Yu, M. Zhou, M.R. Andersen, D.B. Archer, S.E. Baker, I. Benoit, A.A. Brakhage, G.H. Braus, R. Fischer, J.C. Frisvad, G.H. Goldman, J. Houbraken, B. Oakley, I. P�csi, C. Scazzocchio, B. Seiboth, P.A. vanKuyk, J. Wortman, P.S. Dyer, I.V. Grigoriev. (2017) Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus. Genome Biology. 18: 28. doi: 10.1186/s13059-017-1151-0
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Farman, M., Gary Peterson, Li Chen, Barbara Valent, Paul Bachi, Lloyd Murdock, Don Hershman, Kerry Pedley, J. Mauricio Fernandes and Jorge Bavaresco. 2017. The Lolium pathotype of Magnaporthe oryzae recovered from a single blasted wheat plant in the United States. Plant Disease 101:684-692. doi: http://dx.doi.org/10.1094/PDIS-05-16-0700-RE.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Hu Y, Wu Q, Peng Z, Sprague SA, Wang W, Park J, Akhunov E, Jagadish KSV, Nakata PA, Cheng N, Hirschi KD, White FF, Park S. Silencing of OsGRXS17 in rice improves drought stress tolerance by modulating ROS accumulation and stomatal closure. Sci Rep. 2017 Nov 21;7(1):15950.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Charkhabi, NF, NJ Booher, Z Peng, L Wang, H Rahimian, M Shams-Bakhsh, Z Liu, S Liu, FF White, AJ Bogdanove, 2017 Complete genome sequencing and targeted mutagenesis reveal virulence contributions of Tal2 and Tal4b of Xanthomonas translucens pv. undulosa ICMP11055 in bacterial leaf streak of wheat, Front Microbiol, 8:1488.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Inoue, Yoshihiro, Trinh T. P. Vy, Kentaro Yoshida, Hokuto Asano, Chikako Mitsuoka, Soichiro Asuke, Vu L. Anh, Christian Joseph R. Cumagun, Izumi Chuma, Ryohei Terauchi, Kenji Kato, Thomas Mitchell, Barbara Valent, Mark Farman, Yukio Tosa. 2017. Evolution of the wheat blast fungus through functional losses in a host specificity determinant. Science 357:80-83.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Jugulum M, and Gill BS. 2017. Molecular cytogenetics to characterize mechanisms of gene duplication in pest resistance. Pest Management Science, DOI 10.1002/ps.4665
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Koo D-H, Liu W, Friebe B, and Gill BS. 2017. Homoeologous recombination in the presence of Ph1 gene in wheat. Chromosoma 126(4):531-540. doi:10.1007/s00412-016-0622-5
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Koo DH, Mithila Jugulam, Karthik Putta, Ivan B. Cuvaca, Dallas-E. Peterson, Randall S. Currie, Bernd Friebe, and Bikram S. Gill. 2017. Plant Physiology. Gene duplication and polyploidy trigger rapid evolution of herbicide resistance in waterhemp. Plant Physiology DOI:10.1104/pp.17.01668.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Lei, L, JG Steffen, EJ Osborne, C Toomajian. Plant organ evolution revealed by phylotranscriptomics in Arabidopsis thaliana. Scientific Reports 7:7567 (2017) (doi:10.1038/s41598-017-07866-6).
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Liu W, Koo D-H, Xia Q, Li C, Bai F, Song Y, Friebe B, and Gill BA. 2017. Homoeologous recombination-based transfer and molecular cytogenetic mapping of powdery mildew-resistant gene Pm57 from Aegilops searsii into wheat. Theor Appl Genet 130(4):841-848. DOI: 10.1007/s00122-017-2855-y
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Liu, S, J Zheng, P Migeon, J Ren, Y Hu, C He, H Liu, J Fu, FF White, C Toomajian, G Wang. Unbiased k-mer analysis reveals changes in copy number of highly repetitive sequences during maize domestication and improvement. Scientific Reports 7:42444 (2017) (doi:10.1038/srep42444).
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Liuzzi, V. C., V. Mirabelli, M. T. Cimmarusti, M. Haidukowski, J. F. Leslie, A. F. Logrieco, R. Caliandro, F. Fanelli, & G. Mul�. 2017. Enniatin and beauvericin biosynthesis in Fusarium species: Production profiles and structural determinant prediction. Toxins 9: 45, doi: 10.3390/toxins9020045.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Mei, W, S Liu, JC Schnable, CT Yeh, NM Springer, PS Schnable, WB Barbazuk, 2017 A Comprehensive analysis of alternative splicing in paleopolyploid maize, Front Plant Sci, 8:694.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Michelmore R, Coaker G, Bart R, Beattie G, Bent A, Bruce T, Cameron D, Dangl J, Dinesh-Kumar S, Edwards R, Eves-Van Den Akker S, Gassmann W, Greenberg JT, Hanley-Bowdoin L, Harrison RJ, Harvey J, He P, Huffaker A, Hulbert S, Innes R, Jones JDG, Kaloshian I, Kamoun S, Katagiri F, Leach J, Ma W, Mcdowell J, Medford J, Meyers B, Nelson R, Oliver R, Qi Y, Saunders D, Shaw M, Smart C, Subudhi P, Torrance L, Tyler B, Valent B, Walsh J. 2017. Foundational and translational research opportunities to improve plant health. Molecular Plant-Microbe Interactions 30:515-516.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Minaar-Ontong, A., L. Herselman, W.-M. Kriel, & J. F. Leslie. 2017. Morphological characterization and trichothecene genotype analysis of a Fusarium Head Blight population in South Africa. European Journal of Plant Pathology 148: 261-269. doi: 10.1007/s10658-016-1085-5.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Obasa, K, FF White, J Fellers, M Kennelly, S Liu, B Katz, J Tomich, D Moore, H Shinogle, K Kelley, 2017 A dimorphic and virulence-enhancing endosymbiont bacterium discovered in Rhizoctonia solani, Phytobiomes, 1: 14-23.
  • Type: Journal Articles Status: Accepted Year Published: 2017 Citation: Ott, A., S Liu*&, JC Schnable, CT Yeh, C Wang, PS Schnable. 2017 Tunable Genotyping-By-Sequencing enables reliable genotyping of heterozygous loci. Nucleic Acids Res,
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Pieck, Michael L., Amy Ruck, Mark L. Farman, Gary L. Peterson; James P. Stack, Barbara Valent and Kerry F. Pedley. 2017. Genomics-based marker discovery and diagnostic assay development for wheat blast. Plant Disease 101:103-109. doi: http://dx.doi.org/10.1094/PDIS-04-16-0500-RE.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Ronin YI, Mester DI, Minkov DG, Akhunov E, Korol AB. Building Ultra-High-Density Linkage Maps Based on Efficient Filtering of Trustable Markers. Genetics. 2017 Jul;206(3):1285-1295.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Rutter WB, Salcedo A, Akhunova A, He F, Wang S, Liang H, Bowden RL, Akhunov E. Divergent and convergent modes of interaction between wheat and Puccinia graminis f. sp. tritici isolates revealed by the comparative gene co-expression network and genome analyses. BMC Genomics. 2017. 18:291S.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Salcedo A, Rutter W, Wang S, Akhunova A, Bolus S, Chao S, Anderson N, De Soto MF, Rouse M, Szabo L, Bowden RL, Dubcovsky J, Akhunov E. Variation in the AvrSr35 gene determines Sr35 resistance against wheat stem rust race Ug99. Science. 2017. 358:1604-1606.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Sharpee, William, Yeonyee Oh, Mihwa Yi, Jongbum Jeon, William Franck, Alex Eyre, Laura Okagaki, Barbara Valent, Yong Hwan Lee and Ralph Dean. 2017. Identification and characterization of suppressors of plant cell death (SPD) genes from Magnaporthe oryzae. Molecular Plant Pathology 18: 850-863, doi: 10.1111/mpp.12449
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Shi F, Tibbits J, Pasam RK, Kay P, Wong D, Petkowski J, Forrest KL, Hayes BJ, Akhunova A, Davies J, Webb S, Spangenberg GC, Akhunov E, Hayden MJ, Daetwyler HD. Exome sequence genotype imputation in globally diverse hexaploid wheat accessions. Theor Appl Genet. 2017 Jul;130(7):1393-1404.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Wang, X., Jia, Y., Wamishe, Y., H. Jia, M.H., Valent, B. Dynamic Changes in the Rice Blast Population in the USA through Decades. 2017. Molecular Plant-Microbe Interactions, doi: 10.1094/MPMI-04-17-0101-R.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Wen, A, M Jayawardana, J Fiedler, S Sapkota, G Shi, Z Peng, S Liu, FF White, AJ Bogdanove, X Li, Z Liu, 2017 Genetic mapping of a major gene in triticale conferring resistance to bacterial leaf streak, Theor Appl Genet, doi.org/10.1007/s00122-017-3026-x
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Ye, H, S Liu, B Tang, J Chen, Z Xie, TM Nolan, H Jiang, H Guo, HY Lin, L Li, Y Wang, H Tong, M Zhang, C Chu, Z Li, M Aluru, S Aluru, PS Schnable, Y Yin, 2017 RD26 mediates crosstalk between drought and brassinosteroid signalling pathways, Nat Commun, 8:14573.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Zhao H, Zeng Z, Koo D-H, Gill BS, Birchler JA, and Jiang J. 2017. Recurrent establishment of de novo centromeres in the pericentromeric region of maize chromosome 3. Chromosome Res 25:299-311. DOI 10.1007/s10577-017-9564-x


Progress 10/01/15 to 09/30/16

Outputs
Target Audience:Wheat breeders, wheat geneticists, producers, other researchers. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?These projects facilitated the training for graduate students in plant pathology, plant breeding and genetics. Some Plant Biotechnology Center collaborators served as instructors in the 2016Fusarium Laboratory Workshop, presenting various lectures and lessons. How have the results been disseminated to communities of interest?The results of these experiments were disseminated to cooperators including wheat breeders and wheat geneticists in Kansas and throughout the Great Plains region. This information helps cooperators make decisions about which lines to keep and which to remove from the breeding programs. The results were incorporated into KSU extension publications that are widely used by wheat growers in the state. These publications help farmers evaluate the disease resistance of commercial cultivars and select the best available cultivars for their farm. Research manuscripts have been published, circulating the results to the scientific community.? What do you plan to do during the next reporting period to accomplish the goals?Plant Transformation Center/Virology: continue development of novel sources of resistance and novel traits. Wheat Genetics Resource Center: Multiple experiments will be planted during the 2016-2017 growing season. Various experiments will help us evaluate the disease reaction of current breeding lines and commercial cultivars in the Great Plains region. Ongoing greenhouse experiments will be performed to better elucidate the disease reaction of selected breeding lines. Additional laboratory studies will continue to seek an enhanced understanding of fungal physiology, wheat genetics, and mechanisms of resistance.

Impacts
What was accomplished under these goals? Plant Transformation Center - Performed wheat and soybean transformation/tissue culture services for 5-individual labs. Conducted 12 laboratory tours (~160-180 individuals) as outreach and general education. Continued to evaluate new RNAi vectors for soybean cyst nematode control including artificial micro-RNAs. Collaborated with ARS (J. Fellers) in developing WSMBV and TriMV resistant wheat plants. Produce transgenic corn plants to express putative thermostable starch synthase protein.A host-derived artificial microRNA was shown to improve the soybean resistance to soybean cyst nematode. Fungal Genetics and Genomics - Evaluate an interspecific cross of Fusarium to identify genes controlling pathogenicity and secondary metabolite (mycotoxin), especially genes outside the known gene clusters. Increased understanding of regulation nitrogen metabolic gene expression. Progress had been made on showing the role of TamA in regulation of amino acid biosynthesis precursor genes and secondary metabolism genes using RNA-seq linking regulation of primary and secondary metabolism. Progeny from 253 interspecific crosses were characterized using Genotyping By Sequencing (GBS) have generated thousands of sequence-based markers that can be placed on the genome assemblies. These genotyping results have been used to generate a high quality genetic map of the interspecific cross and this map was then used to improve the F. proliferatum genome assembly. Over 500 progeny were measured for pathogenicity on onion and rice and these offspring have been mapped using QTL approaches to genetically map and identify the pathogenicity loci. QTL mapping efforts by the Toomajian lab have identified a well-characterized secondary metabolite present in one but not the other of our parental strains for the interspecific cross as the major genetic basis for pathogenicity on onion. We have also identified that the levels of another secondary metabolite, gibberellic acid, produced by the progeny is genetically controlled not only by the known biosynthetic gene cluster for this metabolite, but also by another regulatory locus on a separate chromosome. We have performed a comparative genomic analysis between our parental species to highlight differences in the presence of secondary metabolite biosynthetic gene clusters as well as other genes. Expected publication in 2017. Virology - Identified wheat lines resistant to wheat curl mite and the wheat streak mosaic virus that it transmits. Improved the understanding of the acquisition and accumulation of Maize mosaic rhabdovirus in its vector, Peregrinus maidis. Wheat Genetics - Mapped a major gene conferring resistance to Hessian fly in bread wheat. Developed a consensus map of tetraploid wheat to help introgress genetic traits from diplois durum and bread wheat genomics and breeding. Phylogenetic relationships of wheats from Kazakhstan were analyzed. A better understanding of the environmental conditions favoring stripe rust in Kansas winter wheat were determined. The Wsm3 resistance genes associated with wheat streak mosaic virus and Triticum mosaic virus from Thinopyrum intermedium were mapped as was adult plant resistance to Puccinia triticina from a sub population of Aegilops tauschii.

Publications

  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Benoit, I., Zhao, M., Viva Duartes, A., Downes, D.J., Todd, R.B., Kloezen, W., Post, H., Heck, A.J.R., Altelaar, A.F.M., and de Vries, R.P. 2015. Spatial differentiation in Aspergillus niger colony grown for sugar beet pulp utilization. Scientific Reports. 5: 13592.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Cainong JC, Bockus WW, Feng Y, Chen PD, Qi LL, Sehgal SK, Danilova TV, Koo D-H, Friebe B, Gill BS. 2015. Chromosome engineering, mapping, and transferring of resistance to Fusarium head blight disease from Elymus tsukushiensis into wheat. Theor Appl Genet 128: 1019-1027.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Chiara, M., Fanelli, F., Mul�, G., Logrieco, A.F., Pesole, G., Leslie, J.F., Horner, D.S., and Toomajian, C. 2015. Genome sequencing of multiple isolates highlights subtelomeric genomic diversity within Fusarium fujikuroi. Genome Biol. Evol. 7(11):3062-3069.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Katz, M.E., Buckland, R., Hunter, C.C., and Todd, R.B. 2015. Distinct roles for the p53-like transcription factor XprG and autophagy genes in the response to starvation. Fungal Genetics and Biology. 83: 10-18. doi: http://dx.doi.org/10.1016/j.fgb.2015.08.006 [KAES contribution: 15-091-J.] JCR 5-year impact factor 2015: 3.231.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Chiara, M., Fanelli, F., Mul�, G., Logrieco, A.F., Pesole, G., Leslie, J.F., Horner, D.S., and Toomajian, C. 2015. Genome sequencing of multiple isolates highlights subtelomeric genomic diversity within Fusarium fujikuroi. Genome Biol. Evol. 7(11):3062-3069
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Kielsmeier-Cook J, Danilova TV, Friebe B, Rouse MN. 2015. Resistance to the Ug99 race group of Puccinia graminis f. sp. tritici in wheat-intra/intergeneric hybrid derivatives. Plant Disease 99:1317-1325 https://doi.org/10.1094/PDIS-09-14-0922-RE.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Kippes N, Debernardi JM, Vasquez-Grossa HA, Akpinarb BA, Budak H, Kato K, Chao S, Akhunov E, and Dubcovsky J. 2015. Identification of the VERNALIZATION 4 gene reveals the origin of spring growth habit in ancient wheats from South Asia. PNAS USA, 112, 39: E5401E5410.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Makandar, R. and Shah, J. 2015. Facilitation of Fusarium graminearum infection by 9- lipoxygenases in Arabidopsis and wheat. Mol. Plant-Microbe Interact. Jun 15. http://dx.doi.org/10.1094/MPMI-04-15-0096-R.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2015 Citation: Nalam, VJ, Alam, S, Keereetaweep, J, Venables, B, Burdan, D, Lee, H, Trick, HN, Sarowar, S, Narayanan S, Prasad PVV, Fritz AK, Boyle DL, and Gill BS. 2015. Impact of high night-time and high daytime temperature stress on winter wheat. J Agron Crop Sci 201:206-218. 376. Liu S, Sehgal SK, Lin M, Li J, Trick HN, Gill BS, and Bai G. 2015. Independent missplicing mutations in TaPHS1 causing loss of preharvest sprouting (PHS) resistance during wheat domestication. New Phytol (In press).
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Makandar, R, Nalam, VJ, Chowdhury, Z, Sarowar, S, Klossner, G, Lee, H, McAfee, D, Trick, HN, Gobbato, E, Parker, JE, and Shah, J. 2015. The combined action of ENHANCED DISEASE SUSCEPTIBILITY1 and PHYTOALEXIN DEFICIENT4 and SENESCENCEASSOCIATED101 promotes salicylic acid-mediated defenses to limit Fusarium graminearum infection in Arabidopsis thaliana. Mol. Plant-Microbe Interact. 28: 943-953. http://dx.doi.org/10.1094/MPMI-04-15-0079-R.
  • Type: Book Chapters Status: Published Year Published: 2015 Citation: Tiwari VK, Faris JD, Friebe B, Gill BS. 2015. Genome Mapping. Encyclopedia of food grains, Chapter 00220, Elsevier
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Tiwari VK, Wang S, Sehgal S, Vr�na J, Friebe B, Kubal�kov� M, Chhuneja P, Dole~el J, Akhunov E, Kalia B, Sabir J, and Gill, BS. 2015. SNP discovery for mapping alien introgressions in wheat. BMC Genomics 15:273.
  • Type: Book Chapters Status: Published Year Published: 2016 Citation: Todd RB . 2016. Chapter 11. Regulation of fungal nitrogen metabolism. pp. 281-303. In: The Mycota III: Biochemistry and Molecular Biology, Third Edition. (Hoffmeister, D. (Ed.). XVIII, 397p.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Li G, Wang Y, Chen MS, Edae E, Poland J, Akhunov E, Chao S, Bai G, Carver BF, Yan L. 2015. Precisely mapping a major gene conferring resistance to Hessian fly in bread wheat using genotyping-by-sequencing. BMC Genomics. 16:108.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Kalous JR, Martin JM, Sherman JD, Heo HY, Blake NK, Lanning SP, Eckhoff JL, Chao S, Akhunov E, Talbert LE. 2015. Impact of the D genome and quantitative trait loci on quantitative traits in a spring durum by spring bread wheat cross. Theor Appl Genet. 128:1799-1811.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Maccaferri M, Ricci A, Salvi S, Milner SG, Noli E, Martelli PL, Casadio R, Akhunov E, Scalabrin S, Vendramin V, Ammar K, Blanco A, Desiderio F, Distelfeld A, Dubcovsky J, Fahima T, Faris J, Korol A, Massi A, Mastrangelo AM, Morgante M, Pozniak C, N'Diaye A, Xu S, Tuberosa R. 2014. A high-density, SNP-based consensus map of tetraploid wheat as a bridge to integrate durum and bread wheat genomics and breeding. Plant Biotechnol J. 13:648-63. DOI: 10.1111/pbi.12288.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Bonman MJ, Babiker EM, Cuesta-Marcos A, Esvelt-Klos K, Brown-Guedira G, Chao S, See D, Chen M, Akhunov E, Zhang J, Bockelman HE, Gordon TC. 2015. Genetic Diversity among Wheat Accessions from the USDA National Small Grains Collection. Crop Science, 55:1243-1253.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Turuspekov Y, Plieske J, Ganal M, Akhunov E, Abugalieva S. 2015. Phylogenetic analysis of wheat cultivars in Kazakhstan based on the wheat 90 K single nucleotide polymorphism array. Plant Genet. Resources. 1:1-7, doi:10.1017/S1479262115000325.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Grabow, B.S. Shah, D. and De Wolf, E.D. 2016. Environmental conditions associated with stripe rust in Kansas winter wheat. Plant Disease (Plant Disease 100:2306-2312). (KAES 16-162-J).
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: 21. Bockus, W.W., De Wolf, E.D. and Todd, T.C. 2016. Management strategies for barley yellow dwarf on winter wheat in Kansas. Plant Health Progress (doi:10.1094/PHP-RS-15-0050).
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Danilova TV, Zhang G, Liu W, Friebe B, Gill BS. 2016. Homoeologous recombination-based transfer and molecular cytogenetic mapping of a wheat streak mosaic virus and Triticum mosaic virus resistance gene Wsm3 from Thinopyrum intermedium. Theor Appl Genet, DOI 10.1007/s00122-016-2834-8
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Koo D-H, Tiwari VK, H?ibov� E, Dole~el J, Friebe B, Gill BS. 2016. Molecular cytogenetic mapping of satellite DNA sequences in Aegilops geniculata and wheat. Cytogenet Genome Res148:314-321
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Kalia, B, Wilson, DL, Bowden, RL, Singh, RP and Gill, BS. 2016. Adult plant resistance to Puccinia triticina in a geographically diverse collection of Aegilops tauschii. Genet Resour Crop Evol doi:10.1007/s10722-016-0411-2.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Koo D-H, Liu W, Bernd Friebe B, Gill BS. Homoeologous recombination in the presence of Ph1 in wheat. Chromosoma, DOI 10.1007/s00412-016-0622-5.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Liu W, Koo D-H, Friebe B, Gill BS. 2016.A set of Triticum aestivum-Aegilops speltoides Robertsonian translocation lines. Theor Appl Genet 129: 2359-2368
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Rawat N, Pumphrey MO, Liu S Zhang X, Tiwari VK, Ando K, Trick HN, Bockus WW, Akhunov EA, Anderson JA, Gill BS. 2016. Wheat Fhb1 encodes a chimeric lectin with agglutinin domains and a pore-forming toxin-like domain conferring resistance to Fusarium head blight. Nature Genetics doi:10.1038/ng.3706
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Tiwari VK1, Heesacker A2, Riera-Lizarazu O3, Gunn H2, Wang S1, Wang Y4, Gu YQ4, Paux E5,6, Koo DH1, Kumar A7, Luo MC8, Lazo G4, Zemetra R2, Akhunov E1, Friebe B1, Poland J1, Gill BS1, Kianian S9, Leonard JM2. 2016. A whole-genome, radiation hybrid mapping resource of hexaploid wheat. Plant J. 2016 Apr;86(2):195-207. doi: 10.1111/tpj.13153
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Yi Wang, Tiwari VK, Rawat N, Gill BS, Coleman D and Gu YQ. 2016. GSP: a web-based platform for designing genome-specific primers in polyploid plants. Bioinformatics 32 (15): 2382-2383.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Bin Tian, Jiarui Li, Thomas R. Oakley, Timothy C. Todd, Harold N. Trick. 2016. Host-derived artificial microRNA as an alternative method to improve the soybean resistance to soybean cyst nematode. Genes 7(12), 122; doi:10.3390/genes7120122.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Gongjun Shi, Zengcui Zhang, Timothy L. Friesen, Dina Raats, Tzion Fahima, Robert S. Brueggeman, Shunwen Lu, Harold N. Trick, Zhaohui Liu, Wun Chao, Zeev Frenkel, Steven S. Xu, Jack B. Rasmussen, Justin D. Faris. 2016. The hijacking of a disease resistance pathway by a wheat fungal pathogen leads to disease. Science Advances 2(10): DOI: 10.1126/sciadv.1600822.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Jessica L. Shoup Rupp, Luisa F. Cruz, Harold N. Trick and John P. Fellers. 2016. RNAi mediated, stable resistance to Triticum mosaic virus in wheat. Crop Science. (56): 602-610 doi: 10.2135/cropsci2015.09.0577.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Segovia, V., Bruce, M., Shoup Rupp, J., Huang, L., Bakkeren, G., Trick, H.N., and Fellers, J.P. 2016. Two small secreted proteins from Puccinia triticina induce reduction of �-glucoronidase transient expression in wheat isolines containing Lr9, Lr24, and Lr26. Canadian Journal of Plant Pathology DOI: 10.1080/07060661.2016.1150884.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Arif, M., Busot, G.Y., Mann, R., Rodoni, B., Liu, S. and Stack, J.P. 2016. Emergence of a new population of the select agent Rathayibacter toxicus: an ecologically complex, geographically isolated bacterium. PLOS ONE doi.org/10.1371/journal.pone.0156182
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Moncrief, I., Garzon, C., Marek, S., Stack, J.P., Gamliel, A., Garrido, P., Proa?o, F., Gard, M., Dehne, H., and Fletcher, J. 2016. Development of simple sequence repeat (SSR) markers for discrimination among isolates of Fusarium proliferatum. Journal of Microbiological Methods 126:12-17
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Cruz, C.D., Magary, R.D., Christie, D.N., Fowler, G.A., Fernandes, J.M., Bockus, W.W., Valent, B., Stack, J.P. 2016. Climate suitability for Magnaporthe oryzae Triticum pathotype in the United States. Plant Disease 100:1979-1987
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Cruz, C.D., Bockus, W.W., Stack, J.P., Valent, B., Maciel, J.N., and Peterson, G.L. 2016. A Standardized Inoculation Protocol to Test Wheat Cultivars for Reaction to Head Blast caused by Magnaporthe oryzae (Triticum pathotype). Plant Health Progress 17:186-187.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: McRoberts, N., Thomas, C.S., Brown, J.K., Nutter, F.W., Stack, J.P. and Martin, R.D. 2016. The Evolution of a Process for Selecting and Prioritizing Diseases for Recovery Plans. Plant Disease 100:665-671. http://dx.doi.org/10.1094/PDIS-04-15-0457-FE
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Burrows, M.E., Thomas, C.S., McRoberts, N., Bostock, R.M., Coop, L., and Stack, J.P. 2016. Coordination of Diagnostic Efforts in the Great Plains: Wheat Virus Survey and Modeling of Disease Onset. Plant Disease 100:1037-1045. http://apsjournals.apsnet.org/doi/pdfplus/10.1094/PDIS-04-15-0467-FE.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Li, L, S Hey, S Liu, Q Liu, C McNinch, HC Hu, TJ Wen, C Marcon, A Paschold, W Bruce, PS Schnable, F Hochholdinger. 2016. Characterization of maize roothairless6 which encodes a D-type cellulose synthase and controls the switch from bulge formation to tip growth, Sci Rep 6:34395.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Chen, MS, S Liu, H Wang, X Cheng, M El Bouhssini, RJ Whitworth. 2016. Genes Expressed Differentially in Hessian Fly Larvae Feeding in Resistant and Susceptible Plants, Int J Mol Sci. 17(8):E1324.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Zhang, J, J Huguet, Y Hu, J Jones, N Wang, S Liu, FF White. 2016. Homologs of CsLOB1 in citrus function as disease susceptibility genes in citrus canker, Mol Plant Pathol., doi: 10.1111/mpp.12441.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Chen, MS, S Liu, H Wang, X Cheng, M El Bouhssini, RJ Whitworth, 2016 Massive Shift in Gene Expression during Transitions between Developmental Stages of the Gall Midge, Mayetiola Destructor, PLoS One, 11(5):e0155616.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Arif, M, GY Busot, R Mann, B Rodoni, S Liu, JP Stack. 2016. Emergence of a New Population of Rathayibacter toxicus: An Ecologically Complex, Geographically Isolated Bacterium, PLoS One, 11(5):e0156182.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Peng, Z, Ying H, J Xie, N Potnis, A Akhunova, J Jones, Z Liu, FF White, S Liu#, 2016. Long read and single molecule DNA sequencing simplifies genome assembly and TAL effector gene analysis of Xanthomonas translucens, BMC Genomics, 17:21
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: McCluskey, K., A. Alvarez, R. Bennett, D. Bokati, K. Boundy-Mills, D. Brown, C. T. Bull, M. Coffey, T. Dreaden, C. Duke, G. Dye, E. Ehmke, K. Eversole, K. Fenstermacher, D. Geiser, J. A. Glaeser, S. Greene, L. Gribble, M. P. Griffith, K. Hanser, R. Humber, B. W. Johnson, A. Kermode, M. Krichevsky, M. Laudon, J. Leach, J. F. Leslie, M. May, U. Melcher, D. Nobles, N. R. Fonseca, S. Robinson, M. Ryan, J. Scott, C. Silflow, A. Vidaver, K. M. Webb, J. E. Wertz, S. Yentsch & S. Zehr. 2016. The US culture collection network lays the foundation for progress in preservation of valuable microbial resources. Phytopathology 106: 532-540. doi: 10.1094/PHYTO-02-16-0074-RVW.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Oliver, J.E., and Whitfield, A.E. 2016. The Genus Tospovirus: Emerging Bunyaviruses that threaten food security. Annual Review of Virology 3: 101-124.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Afonso, C. L., Amarasinghe, G. K., B�nyai, K., B�o, Y., Basler, C.F., Bavari, S., Nicol�s Bejerman, N., Blasdell, K.R., Briand, F.X., Briese, T., Bukreyev, A., Calisher, C.H., Chandran, K., Ch�ng, J., Clawson, A.N., Collins, P.L., Dietzgen, R. G., Dolnik, O., Domier, L.L., D�rrwald, R., Dye, J.M., Easton, A.J., Ebihara, H., Farkas, S.L., Freitas-Ast�a, J., Formenty, P., Fouchier, R.A.M., F�, Y., Ghedin, E., Goodin, M.M., Hewson, R., Horie, M., Hyndman, T.H., Ji?ng, D., Kitajima, E.W., Kobinger, G.P., Kondo, H., Kurath, G., Lamb, R.A., Lenardon, S., Leroy, E.M., Li, C.X., Lin, X.D., L., Longdon, B., Marton, S., Maisner, A., M�hlberger, E., Netesov, S.V., Nowotny, N., Patterson, J.L., Payne, S.L. Paweska, J.T., Randall, R.E., Rima, B.K., Rota, P., Rubbenstroth, D., Schwemmle, M., Shi, M., Smither, S.J., Stenglein, M.D., Stone, D.M., Takada, A., Terregino, C., Tesh, R.B., Tian, J.H., Tomonaga, K., Tordo, N., Towner, J.S., Vasilakis, N., Verbeek, M., Volchkov, V.E., Wahl-Jensen, V., Walsh, J.A., Walker, P.J., Wang, D., Wang, L.F., Wetzel, T., Whitfield, A.E., Xi�, J., Yuen, K.Y., Zhang, Y.Z., Kuhn, J. H. 2016. Taxonomy of the order Mononegavirales: update 2016. Archives of Virology, 161:2351-2360.
  • Type: Other Status: Published Year Published: 2016 Citation: Barandoc-Alviar K., Ramirez, G.M., Rotenberg, D. and Whitfield, A.E. 2016. Analysis of acquisition and titer of Maize mosaic rhabdovirus in its vector, Peregrinus maidis (Hemiptera: Delphacidae). Journal of Insect Science 16:1-8.


Progress 10/01/14 to 09/30/15

Outputs
Target Audience:Wheat breeders, wheat geneticists, producers, other researchers. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?These projects facilitated the training for graduate students in plant pathology, plant breeding and genetics. Plant Biotechnology Center collaborators served as instructors in the 2015 Fusarium Laboratory Workshop, presenting various lectures and lessons. Training was provided for four PhD students in the production of Fusarium GBS libraries. Three undergraduates have also received training on the molecular genetic analysis of Fusarium isolates and the analysis of NGS (next-generation sequencing) data. How have the results been disseminated to communities of interest? The results of these experiments were disseminated to cooperators including wheat breeders and wheat geneticists in Kansas and throughout the Great Plains region. This information helps cooperators make decisions about which lines to keep and which to remove from the breeding programs. The results were incorporated into KSU extension publications that are widely used by wheat growers in the state. These publications help farmers evaluate the disease resistance of commercial cultivars and select the best available cultivars for their farm. Research manuscripts have been published, circulating the results to the scientific community. What do you plan to do during the next reporting period to accomplish the goals?Plant Transformation Center/Virology: continue development of novel sources of resistance and novel traits. Wheat Genetics Resource Center: Multiple experiments will be planted during the 2016-2017 growing season. These experiments will help us evaluate the disease reaction of current breeding lines and commercial cultivars in the Great Plains region. Greenhouse experiments will be established in the fall and winter to gather additional information about the disease reaction of selected breeding lines. Additionally, laboratory studies will continue to seek an enhanced understanding of fungal physiology, wheat genetics, and mechanisms of resistance. Fungal Genetics: Complete evaluating pathogenicity of these progeny on rice and perform QTL mapping of this pathogenicity trait with our genetic map. Work with collaborators to perform molecular genetic manipulation of parental strains to functionally verify our candidate genes controlling onion pathogenicity and gibberellic acid production levels.

Impacts
What was accomplished under these goals? Plant Transformation Center: Goals/Objectives: Provide KSRE scientists with the ability to produce transgenic plants. Expected outputs: Facility success will be measured by the number of scientists served, the number of transformed plant lines delivered, the number of publications resulting from the services provided, and the number of tours of the facility given to the general public. Integrated Genomics Facility (IGF): Goals/Objectives: Maintain and develop technological capacity of the Integrated Genomics Facility and support staff; develop educational programs for workshops in genomics; and develop strategies for expanding interactions between the IGF and KSU genomics initiatives, national genomics research programs, and industry. Expected outputs: Success will be measured as the number of extramural grants obtained by faculty that use IGF resources, and the number and impact of the resulting publications. Virology: Goals/Objectives: Identify viral and vector determinants of transmission and characterize the direct effect of virus infection on vectors; develop genomics resources for arthropod vectors of plant viruses; characterize insect proteomes and use proteomics tools to identify differentially expressed proteins in infected insects; and Identify unique molecules to combat virus diseases and develop novel strategies to prevent virus transmission. Expected outputs: Develop new viral disease control strategies for existing IPM programs, and Education of the Kansas public through the University Open House and an interactive display for the KSU Insect Zoo, and the development of K-12 educational. Wheat Genetic Resources and Molecular Genetics: Goals/Objectives: Develop resources for physical mapping of agronomic and resistance genes in wheat. Initially, the genes for red seed color, resistance to tan spot and pre-harvest sprouting will be targeted. Expected outputs: Progress is measured by the number of agronomically important genes identified, the number of grant proposals developed, and the number and impact of the resulting publications. Fungal Genetics Stock Center: Goals/Objectives: Provide basic genetic resources for filamentous fungi and the yeasts Candida and Cryptococcus to global user community. Expected outputs: Progress is measured by number of citations to strains originating from FGSC, number of strains and related resources distributed, and number of new resources incorporated into the collection. Fungal Genetics and Genomics: Goals/Objectives: Increase basic understanding of the evolution of fungal plant pathogens (Fusarium and Magnaporthe) and the genes they use to overcome disease resistance in their hosts; and genetically map genes for pathogenicity, host specificity, and the production of mycotoxins and other secondary metabolites in a controlled inter-specific Fusarium cross. Elucidate the molecular mechanisms controlling AreA transcription factor activity, its molecular interactions with the transcription factors TamA, and LeuB, and the regulation of nitrogen metabolic gene expression in response to nutrient availability, a critical determinant of infection of the host, in the important model for fungal plant pathogens Aspergillus. Expected outputs: Progress success is measured by the number of pathogenicity/mycotoxin/host specificity genes identified, the number of grant proposals developed, and the number and impact of the resulting publications. Plant Transformation Lab - Constructed and transformed soybeans for resistance to Soybean Cyst Nematode via RNAi methodology; improve heat-tolerant starch synthetase expression in wheat. Performed wheat and soybean transformation/tissue culture services for 6-individual labs. Conducted 15 laboratory tours (~160-180 individuals) as outreach and general education. Generated addition engineered wheat plants expressing thermostable starch synthesis genes. Identified additional SCN-resistance soybean events. Produced transgenic wheat and soybean expressing antimicrobial peptides. Virology - Identified wheat lines resistant to wheat curl mite and the wheat streak mosaic virus that it transmits. Wheat Genetics - Identified two putative additive slow-rusting (leaf rust) resistance genes. Tested select lines of Aegilops tauschii, a predecessor of bread wheat, for resistance to UG99 stem rust. Identify mechanisms for resistance to UG99 stem rust in bread wheat (Triticum aestivum). Fungal Genetics - Genomes of F. fujikuroi and F. proliferatum have been sequenced and assembled: IGF provided support and some of the genome sequencing services, but assembly and subsequent genome annotation has been led by Toomajian lab, including PhD student Wei Yue, with help from collaborator David Horner and Jingzhong Xie (Chinese Academy of Sciences, Beijing). Increased understanding of differential carbon and nitrogen metabolic gene expression within a fungal hyphal network during colony growth. Showed that the transcription factor XprG, which controls nutrient acquisition by the cannibalistic autolysis process, also regulates AreA subcellular localization in response to starvation. Adaptation to starvation is important during infection of nutrient poor hosts. Characterized the genome-wide effects of a mutagen to establish the feasibility of a whole genome resequencing approach for identification of causative mutations affecting gene function in fungal mutants arising from genetic screens. This work will allow streamlining of gene identification from genetic screens, and identification of new factors affecting regulation of metabolic genes. TamA was shown to act as a DNA binding transcription factor at some gene promoters but independently of its DNA binding domain at other promoters, revealing for the first time in fungi that the same transcription factor uses two distinct mechanisms to regulate its target genes. The disease reactions of many wheat breeding lines and commercial cultivars were determined with greenhouse and field experiments. These experiments focused on disease reactions for wheat head blast, barley yellow dwarf, tan spot and Fusarium head blight.

Publications

  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Baakeren, G, and Valent, B. 2014. Do pathogen effectors paly peek-a-boo? Front. Plant Sci., 18 December 2014. https://doi.org/10.3389/fpls.2014.00731.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Benoit, I., Zhao, M., Viva Duartes, A., Downes, D.J., Todd, R.B., Kloezen, W., Post, H., Heck, A.J.R., Altelaar, A.F.M., and de Vries, R.P. 2015. Spatial differentiation in Aspergillus niger colony grown for sugar beet pulp utilization. Scientific Reports. 5: 13592. [KAES contribution: 15-305-J] JCR 5-year impact factor 2015: 5.525.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Cainong JC, Bockus WW, Feng Y, Chen PD, Qi LL, Sehgal SK, Danilova TV, Koo D-H, Friebe B, Gill BS. 2015. Chromosome engineering, mapping, and transferring of resistance to Fusarium head blight disease from Elymus tsukushiensis into wheat. Theor Appl Genet 128: 1019-1027.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Chen S, Rouse MN, Zhang W, Jin Y, Akhunov E, Wei Y, Dubcovsky J. 2015. Fine mapping and haracterization of Sr21, a temperature-sensitive diploid wheat resistance gene effective against the Puccinia graminis f. sp. tritici Ug99 race group. Theor Appl Genet. 128:645-56.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Chiara, M., Fanelli, F., Mul�, G., Logrieco, A.F., Pesole, G., Leslie, J.F., Horner, D.S., and Toomajian, C. 2015. Genome sequencing of multiple isolates highlights subtelomeric genomic diversity within Fusarium fujikuroi. Genome Biol. Evol. 7(11):3062-3069.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Crespo-Herrera LA, Akhunov E, Garkava-Gustavsson L, Jordan KW, Smith CM, Singh RP, Ahman I. 2014. Mapping resistance to the bird cherry-oat aphid and the greenbug in wheat using sequence-based genotyping. Theoretical and Applied Genetics 2014 127:1963-73.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Cruz, L.F., Shoup Rupp, J.L., Trick, H.N. and Fellers, J.P. 2014. Stable Resistance to Wheat streak mosaic virus in Wheat Mediated by RNAi. In Vitro Cellular & Developmental Biology - Plant 50 (6): 665-67. https://doi.org/10.1007/s11627-014-9634-0
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Danilova TV, Friebe B, Gill BS. 2014. Development of a wheat single gene FISH map for analyzing homoeologous relationship and chromosomal rearrangements within the Triticeae. Theor Appl Genet 127:715730, DOI 10.1007/s00122-013- 2253-z
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Downes, DJ, Chonofsky, M, Tan, K, Pfannenstiel, BT, Reck-Peterson, SL, and Todd, RB. 2014. Characterization of the mutagenic spectrum of 4-nitroquinoline oxide (4-NQO) in Aspergillus nidulans by whole genome sequencing. G3: Genes, Genomes, Genetics. 4(12): 2483-2492. doi:10.1534/g3.114.014712 [KAES contribution: 15-090-J.]
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Downes DJ, Davis MA, Wong KH, Kreutzberger SD, Hynes MJ and Todd RB. 2014. Dual DNA binding and coactivator functions of Aspergillus nidulans TamA, a Zn(II)2Cys6 transcription factor. Molecular Microbiology 92: 1198-1211. KAES contribution: 14-065-J. JCR 5-year impact factor 2013: 5.026.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Gill BS, Raupp WJ, and Friebe B. 2014. Genomic perspective on the dual threats of imperiled native agro-ecosystems and climate change to world food security. J Crop Improv 28(1):88-98. 370.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Gill BS, Raupp WJ, Friebe B. 2014. Dual threats of imperiled native agroecosystems and climate change to world food security: Genomic perspectives. J Crop Improvement 28: 1-11.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Katz, M.E., Buckland, R., Hunter, C.C., and Todd, R.B. 2015. Distinct roles for the p53-like transcription factor XprG and autophagy genes in the response to starvation. Fungal Genetics and Biology. 83: 10-18. doi: http://dx.doi.org/10.1016/j.fgb.2015.08.006 [KAES contribution: 15-091-J.] JCR 5-year impact factor 2015: 3.231.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Gawroski P, Ariyadasa R, Himmelbach A, Poursarebani N, Kilian B, Stein N, Steuernagel B, Hensel G, Kumlehn J, Sehgal SK, Gill BS, Gould P, Hall A, and Schnurbusch T. 2014. A distorted Circadian clock causes early flowering and temperature-dependent variation in spike development in the Eps-3Am mutant of einkorn wheat. Genetics 196(4):1253-1261.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Guttieri MJ, Baenziger PS, Frels K, Carver B, Arnall B, Wang S, Akhunov E, Waters BM. 2015. Prospects for Selecting Wheat with Increased Zinc and Decreased Cadmium Concentration in Grain. Crop Science, 4:1712-1728. doi:10.2135/cropsci2014.08.0559.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Henry IM, Nagalakshmi U, Lieberman M. C., Ngo K. J, Krasileva KV, Vasquez-Gross H, Akhunova A, Akhunov E, Dubcovsky J, Tai H, Comai L. 2014. Efficient genome-wide detection and cataloging of EMS-induced mutations using exome capture and next-generation sequencing. Plant Cell, 2014, 26: 1382-1397.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: IWGSC (The International Wheat Genome Sequencing Consortium). 2014. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 18 July 2014. 345 (6194):286. DOI: 10.1126/science.1251788 (11 pp). 372.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Jordan KW, Wang S, Lun Y, Gardiner L, MacLachlan R, Hucl P, Wiebe K, Wong D, Forrest KL, Sharpe AG, Sidebottom CHD, Hall N, Toomajian C, Close T, Dubcovsky J, Akhunova A, Talbert L, Bansal UK, Bariana HS, Hayden MJ, Pozniak C, Jeddeloh JA, Hall A, Akhunov E. 2015. A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes. Genome Biology, 16:48. https://doi.org/10.1186/s13059-015-0606-4.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Kielsmeier-Cook J, Danilova TV, Friebe B, Rouse MN. 2015. Resistance to the Ug99 race group of Puccinia graminis f. sp. tritici in wheat-intra/intergeneric hybrid derivatives. Plant Disease.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Jugulam M, Niehues K, Godar AS, Koo D-H, Danilova T, Friebe B, Sehgal S, Varanasi V, Weirsma A, Westra P, Stahlman PW, Gill BS. 2014. Tandem amplification of chromosomal segment harboring EPSPS gene locus confers glyphosate resistance in (Kochia scoparia L.). Plant Physiol. 166:1200-1207.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Kumar S, Friebe B, Gill BS. 2014. Physical localization of rRNA genes by fluorescence in situ hybridization (FISH) and analysis of spacer length variants of 45S rRNA (slvs) genes in some species of genus Sesbania. Plant Systematics Evolution 300:1792-1802.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Middleton C, Kilian B, Akhunov E, Keller B, Wicker T. 2014. Sequencing of chloroplast genomes from wheat, barley, rye and their relatives provides a detailed insight into the evolution of the Triticeae tribe. PLoS One. 9(3):e85761.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Nalam, VJ, Alam, S, Keereetaweep, J, Venables, B, Burdan, D, Lee, H, Trick, HN, Sarowar, S, Makandar, R. and Shah, J. 2015. Facilitation of Fusarium graminearum infection by 9- lipoxygenases in Arabidopsis and wheat. Mol. Plant-Microbe Interact. Jun 15. http://dx.doi.org/10.1094/MPMI-04-15-0096-R.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Makandar, R, Nalam, VJ, Chowdhury, Z, Sarowar, S, Klossner, G, Lee, H, McAfee, D, Trick, HN, Gobbato, E, Parker, JE, and Shah, J. 2015. The combined action of ENHANCED DISEASE SUSCEPTIBILITY1 and PHYTOALEXIN DEFICIENT4 and SENESCENCEASSOCIATED101 promotes salicylic acid-mediated defenses to limit Fusarium graminearum infection in Arabidopsis thaliana. Mol. Plant-Microbe Interact. 28: 943-953. http://dx.doi.org/10.1094/MPMI-04-15-0079-R.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Sanchez PL, Costich DE, Friebe B, Coffelt TA, Jenks MA, Michael A. Gore MA. 2014. Genome size variation in guayule and mariola: fundamental descriptors for polyploid plant taxa. Industrial Crops and Products 54: 1 5.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Sela H, Ezrati S, Ben-Yehuda P, Manisterski J, Akhunov E, Dvorak J, Breiman A, Korol A. 2014. Linkage disequilibrium and association analysis of stripe rust resistance in wild emmer wheat (Triticum turgidum ssp. dicoccoides) population in Israel. Theoretical and Applied Genetics. 127: 2453-2463.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Liu, S, Sehgal, SK, Lin, M, Li, J, Trick, HN, Gill BS, and Bai, G. 2015. Independent mis-splicing mutations in TaPHS1 causing loss of pre-harvest sprouting (PHS) resistance during wheat domestication. New Phytologist Domestication contributed to reduce seed dormancy in wheat.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Suelter, T, Chumley, F, Rothe, N, Berard, R, Trick, HN. 2014. Enhanced methods for doubled haploid production in Triticum aestivum In Vitro Cell. Dev. Biol. Anim., 50 (2014), p. S14
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Tiwari VK, Faris JD, Friebe B, Gill BS. 2015. Genome Mapping. Encyclopedia of food grains, Chapter 00220, Elsevier
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Yang Z, Shen Z, Tetreault H, Johnson L, Friebe B, Frazier T, Huang L-k, Burklew C, Zhang X-Q, ingyu Zhao B. 2014. Production of autopolyploid lowland switchgrass lines through in vitro chromosome doubling. BioEnergy Research, DOI 15 10.1007/s12155-013-9364-x
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Zytnicki M, Akhunov E, Quesneville H. Tedna: a transposable element de novo assembler. Bioinformatics. 2014 30: 2656-2658.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Narayanan S, Prasad PVV, Fritz AK, Boyle DL, and Gill BS. 2015. Impact of high night-time and high daytime temperature stress on winter wheat. J Agron Crop Sci 201:206-218. 376. Liu S, Sehgal SK, Lin M, Li J, Trick HN, Gill BS, and Bai G. 2015. Independent missplicing mutations in TaPHS1 causing loss of preharvest sprouting (PHS) resistance during wheat domestication. New Phytol.


Progress 10/01/13 to 09/30/14

Outputs
Target Audience: Professional peers in industry and academia Changes/Problems: Staff for the Fungal Genetics Stock Center moved to Kansas State University in September 2014 from the University of Missouri-Kansas City. Purchased a Zeiss confocal microscope that was installed in January 2014. What opportunities for training and professional development has the project provided? 15th Annual Fusarium Laboratory Workshop Real time PCR Workshop Gene Expression Workshop How have the results been disseminated to communities of interest? Professional technical books and publications, presentations at professional meetings, patents. What do you plan to do during the next reporting period to accomplish the goals? Plant Transformation Lab - Characterize soybean constructs resistant to soybean cyst nematode; evaluate heat-tolerant starch synthetase in wheat. Virology - Develop WSMV and TriMV resistant lines of wheat through transgenic methods. Characterize transcriptomic and genome resources available for characterizing virus-insect vector interactions and develop high throughput proteomics screens to identify vector proteins that interact with viral glycoproteins. Wheat Genetics - Confirm presence of slow-rusting genes through tests at multiple locations and additional crosses. Develop nested association mapping panel to identify important quantitative agronomic traits in Aegilops tauschii, a progenitor of bread wheat. Fungal Genetics - Evaluate more than 500 progeny from an interspecific cross for pathogenicity towards potato, apple and rice. Complete genome sequences of both parents of the interspecific cross. Evaluate in Aspergillus nidulans nuclear import and export of transcription factors, DNA binding transcription factor action on the whole genome level and assess the role of interacting proteins as transcription corepressors. Generate data by using confocal microscope to test hypotheses of gene expression related to cell-to-cell movement and gene expression at this time in the Magnaporthe oryzae/rice interaction.

Impacts
What was accomplished under these goals? Plant Transformation Center: Goals/Objectives: Provide KSRE scientists with the ability to produce transgenic plants. Expected outputs: Facility success will be measured by the number of scientists served, the number of transformed plant lines delivered, the number of publications resulting from the services provided, and the number of tours of the facility given to the general public. Integrated Genomics Facility (IGF): Goals/Objectives: Maintain and develop technological capacity of the Integrated Genomics Facility and support staff; develop educational programs for workshops in genomics; and develop strategies for expanding interactions between the IGF and KSU genomics initiatives, national genomics research programs, and industry. Expected outputs: Success will be measured as the number of extramural grants obtained by faculty that use IGF resources, and the number and impact of the resulting publications. Virology: Goals/Objectives: Identify viral and vector determinants of transmission and characterize the direct effect of virus infection on vectors; develop genomics resources for arthropod vectors of plant viruses; characterize insect proteomes and use proteomics tools to identify differentially expressed proteins in infected insects; and Identify unique molecules to combat virus diseases and develop novel strategies to prevent virus transmission. Expected outputs: Develop new viral disease control strategies for existing IPM programs, and Education of the Kansas public through the University Open House and an interactive display for the KSU Insect Zoo, and the development of K-12 educational. Wheat Genetic Resources and Molecular Genetics: Goals/Objectives: Develop resources for physical mapping of agronomic and resistance genes in wheat. Initially, the genes for red seed color, resistance to tan spot and preharvest sprouting will be targeted. Expected outputs: Progress is measured by the number of agronomically important genes identified, the number of grant proposals developed, and the number and impact of the resulting publications. Fungal Genetics Stock Center: Goals/Objectives: Provide basic genetic resources for filamentous fungi and the yeasts Candida and Cryptococcus to global user community. Expected outputs: Progress is measured by number of citations to strains originating from FGSC, number of strains and related resources distributed, and number of new resources incorporated into the collection. Fungal Genetics and Genomics: Goals/Objectives: Increase basic understanding of the evolution of fungal plant pathogens (Fusarium and Magnaporthe) and the genes they use to overcome disease resistance in their hosts; and genetically map genes for pathogenicity, host specificity, and the production of mycotoxins and other secondary metabolites in a controlled inter-specific Fusarium cross. Expected outputs: Progress success is measured by the number of pathogenicity/mycotoxin/host specificity genes identified, the number of grant proposals developed, and the number and impact of the resulting publications. What was accomplished under these goals? Plant Transformation Lab - Constructed and transformed soybeans for resistance to Soybean Cyst Nematode via RNAi methodology; improve heat-tolerant starch synthetase expression in wheat. Virology - Identify wheat lines resistant to wheat curl mite and the wheat streak mosaic virus that it transmits. Wheat Genetics - Identified two putative additive slow-rusting (leaf rust) resistance genes. Tested select lines of Aegilops tauschii, a predecessor of bread wheat, for resistance to UG99 stem rust. Identify mechanisms for resistance to UG99 stem rust in bread wheat (Triticum aestivum). Fungal Genetics - Evaluate an interspecific cross of Fusarium to identify genes controlling pathogenicity and secondary metabolite (mycotoxin), especially genes outside the known gene clusters. Elucidate the molecular mechanisms controlling AreA transcription factor activity, its molecular interactions with TamA, AreA and LeuB proteins, and the regulation of nitrogen metabolic gene expression. Understand cell-to-cell movement and effectors involved in the colonization of rice tissue by the fungal pathogen Magnaporthe oryzae.

Publications

  • Type: Other Status: Published Year Published: 2014 Citation: 16. Hunter CC, Siebert KS, Downes DJ, Wong KH, Kreutzberger SD, Fraser JA, Clarke DF, Hynes MJ, Davis MA and Todd RB. (2014) Multiple nuclear localization signals mediate nuclear localization of the GATA transcription factor AreA. Eukaryotic Cell 13: 527-538. (KAES no. 14-064-J) 17. IWGSC (The International Wheat Genome Sequencing Consortium). 2014. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345: 286-296. (KAES no. 15-320-J) 18. Leslie, J. F. 2014. Mycotoxins in the sorghum grain chain. In: Mycotoxin Reduction in Grain Chains (J. F. Leslie & A. Logrieco, eds.), pp. 282-296. Wiley-Blackwell, Ames, Iowa. (KAES no. 13-021-B) 19. Leslie, J. F. 2014. Stabilizing research departments in a 10% world. In: Merrill Series on the Research Mission of Public Universities (Merrill Advanced Study Centers Report no. 118; M. L. Rice, ed.), pp. 78-85. University of Kansas, Lawrence, Kansas. (KAES no. 15-218-A) 20. Leslie, J. F., and A. Logrieco, eds. 2014. Mycotoxin Reduction in Grain Chains: A Practical Guide. John Wiley & Sons, Ames, Iowa. 352 pp. (KAES no. 14-068-B) 21. Liu, X.M, Khajuria, C., Li, J., Trick, H.N., Li, Huang, Gill, B.S., Reeck, G.R., Antony, G., White, F.F., Chen, M.S. 2013. Wheat Mds-1 encodes a heat-shock protein and governs susceptibility towards the Hessian fly gall midge. Nature Communications 4: 2070. (KAES no. 14-221-J) 22. Marcussen T, Sandve SR, Heier L, Spannagl M, Pfeifer M; International Wheat Genome Sequencing Consortium, Jakobsen KS, Wulff BB, Steuernagel B, Mayer KF, Olsen OA. Ancient hybridizations among the ancestral genomes of bread wheat. Science. 2014 345: 285-287 (KAES no. 15-053-J). 23. Middleton C, Kilian B, Akhunov E, Keller B, Wicker T. Sequencing of chloroplast genomes from wheat, barley, rye and their relatives provides a detailed insight into the evolution of the Triticeae tribe. PLoS One. 2014 9(3):e85761 (KAES no. 15-058-J). 24. Montero-Ast�a, M., Rotenberg, D., Leach, A., Schneweis, B., Park, K., Park, S.H., German, T.L., and Whitfield, A.E. 2014. Disruption of vector transmission by a plant-expressed viral glycoprotein. Molecular Plant-Microbe Interactions 27:296-304. (KAES no. 14-192-J) 25. Ostrander JC, Todd RB, and Kennelly MM. (2014) Characterization of resistance to thiophanate-methyl in Kansas isolates of Sclerotinia homoeocarpa. Plant Health Progress 15: 80-84. (KAES no. 14-063-J) 26. Perrone, G., M. Haidukowsky, G. Stea, F. Epifani, R. Bandyopadhyay, J. F. Leslie, and A. Logrieco. 2014. Population structure and aflatoxin production by Aspergillus Section Flavi from maize in Nigeria and Ghana. Food Microbiology 41: 52-59. (KAES no. 13-368-J) 27. Pfeifer M, Kugler KG, Sandve SR, Zhan B, Rudi H, Hvidsten TR; International Wheat Genome Sequencing Consortium, Mayer KF, Olsen OA. Genome interplay in the grain transcriptome of hexaploid bread wheat. Science. 2014 345: 285-287 (KAES no. 15-055-J). 28. Sela H, Ezrati S, Ben-Yehuda P, Manisterski J, Akhunov E, Dvorak J, Breiman A, Korol A. Linkage disequilibrium and association analysis of stripe rust resistance in wild emmer wheat (Triticum turgidum ssp. dicoccoides) population in Israel. Theoretical and Applied Genetics. 2014 127: 2453-2463. (KAES no. 15-242-J). 29. Stack, J.P., Bostock, R.M., Hammerschmidt, R., Jones, J.B. and Luke, E. 2014. The National Plant Diagnostic Network: Partnering to Protect Plant Systems. Plant Disease 98:708-715. 30. Stafford-Banks, C.A., Rotenberg, D.; Johnson, B.R., Whitfield, A.E., and Ullman, D.E. 2014. Analysis of the salivary gland transcriptome of Frankliniella occidentalis. PLoS ONE 9:e94447. (KAES no. 15-252-J)
  • Type: Other Status: Published Year Published: 2014 Citation: 31. Tiwari VK, Wang S, Sehgal S, Vr�na J, Friebe B, Kubal�kov� M, Chhuneja P, Dole~el J, Akhunov E, Kalia B, Sabir J, and Gill BS. 2014. SNP discovery for mapping alien introgressions in wheat. BMC Genomics 15: 273. (KAES no. 14-292-J) 32. Todd RB, Zhao M, Ohm RA, Leeggangers HACF, Visser L, and de Vries RP. (2014) Prevalence of transcription factors in ascomycete and basidiomycete fungi. BMC Genomics 15: 214. (KAES no. 14-055-J) 33. Wang S, Wong D, Forrest K, Allen A, Chao S, Huang B, Maccaferri M, Salvi S, Milner S, Cattivelli L , Mastrangelo A, Whan A, Stephen S, Barker G, Wieseke R, Plieske J, (IWGSC) Wheat Genome Sequencing Consortium, Lillemo M, Mather D, Appels R, Dolferus R, Brown-Guedira G, Korol A, Akhunova A, Feuillet C, SALSE J, Morgante M, Pozniak C, Luo MC, Dvorak J, Morell M, Dubcovsky J, Ganal M , Tuberosa R, Lawley C, Mikoulitch I, Cavanagh C, Edwards K, Hayden M, Akhunov E*. Characterization of polyploid wheat genomic diversity using a high-density 90,000 SNP array. Plant Biotechnology Journal. 2014 12: 287-296. (KAES no. 15-059-J). 34. Whitfield, A.E., Rotenberg, D., and German, T. L. 2014. Plant pest destruction goes viral. Nature Biotechnology 32:65-66. (KAES no. 14-193-J) 35. Zytnicki, M., Akhunov, E., and Quesneville, H. 2014. Tedna: a transposable element de novo assembler. Bioinformatics 30: 2656-2658.
  • Type: Other Status: Published Year Published: 2014 Citation: 11. Gill BS, Raupp WJ, and Friebe B. 2014. Genomic perspective on the dual threats of imperiled native agro-ecosystems and climate change to world food security. Journal of Crop Improvement 28: 88-98. (KAES no. 12-431-B) 12. Gornicki P, Zhu H, Wang J, Challa GS, Zhang Z, Gill BS, and Li W. 2014. The chloroplast view of the evolution of hexaploid wheat. New Phytologist 204:704-714. (14-339-J) 13. Gray MM, St Amand P, Bello NM, Galliart MB, Knapp M, Garrett KA, Morgan TJ, Baer SG, Maricle BR, Akhunov ED, Johnson LC. Ecotypes of an ecologically dominant prairie grass (Andropogon gerardii) exhibit genetic divergence across the U.S. Midwest grasslands' environmental gradient. Molecular Ecology 2014 23: 6011-6028. (KAES no. 15-243-J). 14. Grenier, B., A.-P. Loureiro-Bracarense, J. F. Leslie, and I. P. Oswald. 2014. Physical and chemical methods for mycotoxin decontamination in maize. In: Mycotoxins in Food Chains (J. F. Leslie & A. F. Logrieco, eds.), pp. 116-129. Wiley-Blackwell, Ames, Iowa. (KAES no. 13-363-B) 15. Henry IM, Nagalakshmi U, Lieberman M. C., Ngo K. J, Krasileva KV, Vasquez-Gross H, Akhunova A, Akhunov E, Dubcovsky J, Tai H, Comai L. Efficient genome-wide detection and cataloging of EMS-induced mutations using exome capture and next-generation sequencing. Plant Cell, 2014, 26: 1382-1397 (KAES# 15-060-J).
  • Type: Other Status: Published Year Published: 2014 Citation: Alexander, H. M., Mauck, K. E., Whitfield, A.E., Garrett K. A., and C. M. Malmstrom. 2014. Plant-virus interactions and the agro-ecological interface. 2014. European Journal of Plant Pathology 138:529-547. (KAES no. 13-325-J) 2. Bakkeren, G., and B. Valent. 2014. Do pathogen effectors play peek-a-boo? Frontiers in Plant Science 5:731. (KAES no. 15-228-J) 3. Bhatnagar, D., G. Payne, M. Klich, and J. F. Leslie. 2014. Identification of toxigenic Aspergillus and Fusarium species in the maize grain chain. In: Mycotoxins in Food Chains (J. F. Leslie & A. F. Logrieco, eds.), pp. 11-25. Wiley-Blackwell, Ames, Iowa. (KAES no. 10-333-B) 4. Bruce M, Neugebauer KA, Joly DL, Migeon P, Cuomo C, Wang S, Akhunov E, Bakkeren G, Kolmer JA, Fellers JP. Using transcription of six Puccinia triticina races to identify the effective secretome during infection of wheat, Frontiers in Plant-Microbe Interaction, Frontiers in Plant Sciences 2014 4:520 (KAES no. 14-227-J). 5. Crespo-Herrera LA, Akhunov E, Garkava-Gustavsson L, Jordan KW, Smith CM, Singh RP, Ahman I. Mapping resistance to the bird cherry-oat aphid and the greenbug in wheat using sequence-based genotyping. Theoretical and Applied Genetics 2014 127:1963-73 (KAES no. 15-062-J). 6. Danilova TV, Friebe B, and Gill BS. 2014. Development of a wheat single gene FISH map for analyzing homoeologous relationship and chromosomal rearrangements within the Triticeae. Theoretical and Applied Genetics 127: 715-730. (KAES no. 14-021-J) 7. Dietzgen, R.G., Kuhn, J.H., Clawson, A.N., Freitas-Ast�a, J., Goodin, M.M., Kitajima, E., Kondo, H., Wetzel, T., Whitfield, A.E. 2014. Dichorhavirus: a proposed new genus for Brevipalpus mite-transmitted, nuclear, bacilliform, bipartite, negative-strand RNA plant viruses. Archives of Virology 159:607-619. (KAES no. 15-253-J) 8. Downes, DJ, Chonofsky, M, Tan, K, Pfannenstiel, BT, Reck-Peterson, SL, and Todd, RB. Characterization of the mutagenic spectrum of 4-nitroquinoline oxide (4-NQO) in Aspergillus nidulans by whole genome sequencing. G3: Genes, Genomes, Genetics 4, 527-538. (KAES no. 15-090-J) 9. Downes DJ, Davis MA, Wong KH, Kreutzberger SD, Hynes MJ and Todd RB. (2014) Dual DNA binding and coactivator functions of Aspergillus nidulans TamA, a Zn(II)2Cys6 transcription factor. Molecular Microbiology 92: 1198-1211. (KAES no. 14-065-J) 10. Gawroski P, Ariyadasa R, Himmelbach A, Poursarebani N, Kilian B, Stein N, Steuernagel B, Hensel G, Kumlehn J, Sehgal SK, Gill BS, Gould P, Hall A, and Schnurbusch T. 2014. A distorted Circadian clock causes early flowering and temperature-dependent variation in spike development in the Eps-3Am mutant of einkorn wheat. Genetics 196: 1253-1261. (KAES no. 15-319-J)


Progress 01/01/13 to 09/30/13

Outputs
Target Audience: The primary target audience for this research is other scientists in universities, research institutes and commercial research laboratories. The goals include identifying genes used in pre-breeding programs for wheat, increased knowledge cell biology and population structure of plant pathogens Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Wheat Blast Symposium associated with the annual meeting of the North Central Division of the American Phytopathological Society (NC-APS); June 13-15 in Manhattan, Kansas. Fusarium Laboratory Workshop; 22-28 June at Kansas State University. How have the results been disseminated to communities of interest? Nothing Reported What do you plan to do during the next reporting period to accomplish the goals? Use RNAseq to determine expression profile in pathogen and susceptible and resistant wheat lines. Identify rust effectors by comparing effects of candidate genes identified in rust races that are virulent and avirulent to wheat lines carrying the Sr35 resistance gene. Compare the effectiveness of artificial micro RNAs to siRNA vectors on Soybean Cyst nematode egg and cyst production reductions. Screen transgenic soybean plants with resistance to soybean cyst nematodes for resistance to root knot nematodes. Establish new field sites in South America for testing wheat for resistance to wheat blast. Complete editing of and publish Mycotoxins in Grain Chains book for Wiley and Sons. Develop a week-long Wheat Production and Policy Workshop (Plant Biosecurity Research Experience) to be held in BSL-3 facilities at K-State. Identify the AreA nuclear export signal and intracellular locations for the AreA217 and KapA/SumO proteins in Aspergillus nidulans. Map genes segregating in inter-specific cross between Fusarium fujikuroi and Fusarium proliferatum responsible for pathogenicity to onions and rice. Complete F. occidentalis transcriptome assembly, and assemble genomes from two inbred lines of this thrip.

Impacts
What was accomplished under these goals? Wheat gene Sr35 is sufficient to confer resistance to Puccinia graminis f. sp. tritici race UG99. Identified 35 potential target genes for control of Soybean Cyst nematode fertility. Completed hairy root bioassays with thirty of these constructs. Eighteen of the target genes reduce nematode egg production by more than 50%. RNAi expression vectors of these genes have been identified as candidates for stable transformation. Analyzed inter-specific cross between Fusarium fujikuroi and Fusarium proliferatum for segregation of pathogenicity to apples, onions and rice. Evaluated the regulation of the gdhA gene by leucine as mediated by LeuB in the filamentous fungus Aspergillus nidulans. Identified an unexpected, novel DNA-binding site for LeuB. Collected >100 isolates of South American wheat strains (M. oryzae Triticum pathotype, Mot) and >150 strains from annual and perennial ryegrass (M. oryzae Lolium pathotype, Mol) and other grasses in the United States for testing of pathogenicity towards wheat under BL-3 containment and for developing molecular assays to differentiate strains pathogenic and non-pathogenic towards wheat. Produced more than 884 million RNAseq single-end reads from four biological replications and quantified global differential gene expression in F. occidentalis in response to Tomato Spotted Wilt Virus accumulation during development from larva to adult. dsRNA delivery methods to thrips were evaluated. Adult female thrips may be injected with 12 nL of a dsRNA solution. Membrane feeding is more difficult and delays insect development compared with feeding on plant tissue. Expression of potential target transcripts in the thrips may vary, and choosing a stable transcript is important.

Publications

  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Akhunov, E.D., S. Sehgal, H. Liang, S. Wang, A.R. Akhunova, G. Kaur, W. Li, K.L. Forrest, D. See, H. `imkov�, Y. Ma, M.J. Hayden, M. Luo, J.D. Faris, J. Dole~el & B.S. Gill. (2013) Comparative analysis of syntenic genes in grass genomes reveals accelerated rates of gene structure and coding sequence evolution in polyploid wheat. Plant Physiology 161:252-265.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Bruce, M., K.A. Neugebauer, D.L. Joly, P. Migeon, C. Cuomo, S. Wang, E.D. Akhunov, G. Bakkeren, J.A. Kolmer & J.P. Fellers. (2013) Using transcription of six Puccinia triticina races to identify the effective secretome during infection of wheat. Frontiers in Plant-Microbe Interactions, Frontiers in Plant Sciences 4:520.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Cavanagh, C.R., S. Chao, S. Wang, B.E. Huang, S. Stephen, S. Kiani, K. Forrest, C. Saintenac, G.L. Brown-Guedira, A. Akhunova, D. See, G. Bai, M.O. Pumphrey, L. Tomar, D. Wong, S. Kong, M. Reynolds, M.L. da Silva, H. Bockelman, L. Talbert, J.A. Anderson, S. Dreisigacker, S. Baenziger, A. Carter, V. Korzun, P.L. Morrell, J. Dubcovsky, M.K. Morell, M.E. Sorrells, M.J. Hayden, & E.A. Akhunov. (2013) Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars. Proceedings of the National Academy of Sciences (USA) 110:8057-8062.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Downes D.J., M.A. Davis, S.D. Kreutzberger, B.L. Taig & R.B. Todd. (2013) Regulation of the NADP-glutamate dehydrogenase gene gdhA in Aspergillus nidulans by the Zn(II)2Cys6 transcription factor LeuB. Microbiology 159:2467-2480.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Elbeaino, T., A.E. Whitfield, M. Sharma & M. Digiaro. (2013) Emaravirus-specific degenerate PCR primers allowed the identification of partial RNA-dependent RNA polymerase sequences of maize red stripe virus and pigeonpea sterility mosaic virus. Journal of Virological Methods 188: 37-40.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Geiser, D.M., T. Aoki, C.W. Bacon, S. Baker, M.K. Bhattacharyya, M.E. Brandt, D.W. Brown, L.W. Burgess, S.N. Chulze, J.J. Coleman, J.C. Correll, S.F. Covert, P.W. Crous, C.A. Cuomo, G.S. de Hoog, A. di Pietro, W.H. Elmer, L. Epstein, R.J.N. Frandsen, S. Freeman, A.E. Glenn, T.R. Gordon, K.E. Hammond-Kosack, L.E. Hanson, M. del Mar J�menez-Gasco, S. Kang, H.C. Kistler, G.A. Kuldau, J.F. Leslie, A. Logrieco, G. Lu, E. Lys�e, L.-J. Ma, S.P. McCormick, Q. Migheli, A. Moretti, F. Munaut, K. ODonnell, L. Pfenning, R.C. Ploetz, R.H. Proctor, S.A. Rehner, V.A.R.G. Robert, A.P. Rooney, B. bin Salleh, M.M. Scandiani, J. Scauflaire, E. Steenkamp, H. Suga, B.A. Summerell, D.A. Sutton, U. Thrane, F. Trail, A. van Diepeningen, H.D. VanEtten, A. Viljoen, C. Waalwijk, T.J. Ward, M.J. Wingfield, J.-R. Xu, X.-B. Yang, T. Yli-Mattila & N. Zhang. (2013) One fungus, one name: Defining the genus Fusarium in a scientifically robust way that preserves longstanding use. Phytopathology 103:400-408.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Gill, B.S. (2013) SNPing Aegilops tauschii genetic diversity and the birthplace of bread wheat. New Phytologist 98:641-642.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Giraldo, M.C., Y.F. Dagdas, Y.K. Gupta, T.A. Mentlak, M. Yi, A.L. Martinez-Rocha, H. Saitoh, R. Terauchi, N.J. Talbot & B. Valent. (2013) Two distinct secretion systems facilitate tissue invasion by the rice blast fungus Magnaporthe oryzae. Nature Communications 4:1996, doi:10.1038/ncomms2996.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Jacobson, A.L., S. Johnston, D. Rotenberg, A.E. Whitfield, W. Booth, E.L. Vargo & G.G. Kennedy. (2013) Genome size and ploidy of Thysanoptera. Insect Molecular Biology 22:12-17.
  • Type: Book Chapters Status: Published Year Published: 2013 Citation: Kiani S, A. Akhunova & E. Akhunov. (2013) Application of next-generation sequencing technologies for genetic diversity analysis in cereals. In: Cereal Genomics II, 2nd ed., (P.K. Gupta & R. K.Varshney), pp. 77-99. Springer, Berlin, Germany.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Krasileva, K.V., V. Buffalo, P. Bailey, S. Pearce, S. Ayling, F. Tabbita, M. Soria, S. Wang, I. Consortium, E.D. Akhunov, C. Uauy & J. Dubcovsky. (2013) Separating homeologs by phasing in the tetraploid wheat transcriptome. Genome Biology 14:R66.
  • Type: Book Chapters Status: Published Year Published: 2013 Citation: Leslie, J.F. & B.A. Summerell. (2013) An overview of Fusarium. In: Fusarium: Genomics, Molecular and Cellular Biology (D.W. Brown & R.H. Proctor, eds.), pp. 1-10. Horizon Scientific Press, Norwich, UK.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Liu, W., T.V. Danilova, M.N. Rouse, R.L. Bowden, B. Friebe, B.S. Gill & M.O. Pumphrey. (2013) Development and characterization of a compensating wheat-Thinopyrum intermedium Robertsonian translocation with Sr44 resistance to stem rust (Ug99). Theoretical and Applied Genetics 126:1167-1177.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Liu, X.M., C. Khajuria, J. Li, H.N. Trick, H. Li, B.S. Gill, G.R. Reeck, G. Antony, F.F. White & M.S. Chen. (2013) Wheat Mds-1 encodes a heat-shock protein and governs susceptibility towards the Hessian fly gall midge. Nature Communications 4: 2070. http://www.nature.com/ncomms/2013/130624/ncomms3070/full/ncomms3070.html.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Giraldo, M.C. & B. Valent. (2013) Filamentous plant pathogen effectors in action. Nature Reviews Microbiology 11:800-814.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Liu, S., S.K. Sehgal, J. Li, M. Lin, H.N. Trick, J. Yu, B.S. Gill & G. Bai. (2013) Cloning and characterization of a TaMFT-like gene for pre-harvest sprouting resistance in wheat. Genetics 195:263-273.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Luo, M.-C., Y.Q. Gub, F.M. You, K.R. Deal, Y. Ma, Y. Hua, N. Huo, Y. Wang, J. Wanga, S. Chena, C.M. Jorgensen, Y. Zhang, P.E. McGuire, S. Pasternak, J.C. Stein, D.Ware, M. Kramer, W.R. McCombie, S.F. Kianian, M.M. Martis, K.F.X. Mayer, S.K. Sehgal, W. Li, B.S. Gill, M.W. Bevan, H. Simkov�, J. Dolezel, S. Weining, G.R. Lazo, O.D. Anderson & J. Dvorak. (2013) A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor. Proceedings of the National Academy of Sciences (USA) 110:7940-7945.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Mascher, M., T.A. Richmond, D.J. Gerhardt, A. Himmelbach, L. Clissold, D. Sampath, S. Ayling, B. Steuernagel, M. Pfeifer, M. DAscenzo, E.D. Akhunov, P.E. Hedley, A.M. Gonzales, P.L. Morrell, B. Kilian, F.R. Blattner, U. Scholz, K.F. Mayer, A.J. Flavell, G.J. Muehlbauer, R. Waugh, J.A. Jeddeloh & N. Stein. (2013) Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond. Plant Journal 76:494-505.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Mohamed Nor, N.M.I., B. Salleh & J.F. Leslie. (2013) Fusarium species associated with mango malformation in peninsular Malaysia. Journal of Phytopathology 161:617-624.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Nachappa, P., D.C. Margolies, J.R. Nechols, A.E. Whitfield & D. Rotenberg. (2013) Tomato spotted wilt virus benefits a non-vector arthropod, Tetranychus urticae, by modulating different plant responses in tomato. PLoS ONE 8(9): e75909.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Olson, E.L., M.N. Rouse, M.O. Pumphrey, R.L. Bowden, B.S. Gill & J.A. Poland. (2013) Simultaneous transfer, introgression, and genomic localization of genes for resistance to stem rust race TTKSK (Ug99) from Aegilops tauschii to wheat. Theoretical and Applied Genetics 126:1179-1188.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Olson, E.L., M.N. Rouse, M.O. Pumphrey, R.L. Bowden, B.S. Gill & J.A. Poland. (2013) Introgression of stem rust resistance genes SrTA10187 and SrTA10171 from Aegilops tauschii to wheat. Theoretical and Applied Genetics 126:2477-2484.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Qi, L.L., J.J. Wu, B. Friebe, C. Qian, Y.Q. Gu, D.L. Fu & B.S. Gill. (2013) Sequence organization and evolutionary dynamics of Brachypodium-specific centromere retrotransposons. Chromosome Research 21:507-521.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: W�rschum, T., S.M. Langer, C.F. Longin, V. Korzun, E.A. Akhunov, E. Ebmeyer, R. Schachschneider, J. Schacht, E. Kazman & JC Reif. (2013) Population structure, genetic diversity and linkage disequilibrium in elite winter wheat assessed with SNP and SSR markers. Theoretical and Applied Genetics 126:1477-1486.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Yao, J., D. Rotenberg, A. Afsharifar, K. Barandoc-Alviar & A.E. Whitfield. (2013) Development of RNAi methods for Peregrinus maidis, the corn planthopper. PLoS ONE 8:e70243.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Saintenac, C., D. Jiang, S. Wang & E.A. Akhunov. (2013) Sequence-based mapping of the polyploid wheat genome. G3 3:1105-1114.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Saintenac, C., W. Zhang, A. Salcedo, M. Rouse, H.N. Trick, E. Akhunov & J. Dubcovsky. (2013) Map-based cloning of wheat stem rust resistance gene Sr35. Science 341:783-786.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Sehgal, B., B. Subramanyam, F.H. Arthur & B.S. Gill. (2013) Variation in susceptibility of field strains of three stored grain insect species to spinosad and chlorpyrifos-methyl plus deltamethrin on hard red winter wheat. Journal of Economic Entomology 106:1911-1919.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Yi, M. & B. Valent. (2013) Communication between filamentous pathogens and plants at the biotrophic interface. Annual Review of Phytopathology 51:587-611.


Progress 01/01/12 to 12/31/12

Outputs
OUTPUTS: A high-throughput Single Nucleotide Polymorphism (SNP) genotyping assay was developed for wheat and is being used to genotype a worldwide collections of cultivars. A component of the trait discovery pipeline now includes an association mapping panel of diverse wheat cultivars. This panel was genotyped with 9000 SNP markers and phenotyped for agronomic traits. Assays for the targeted enrichment of genic regions in the wheat genome and sequencing were developed. New markers for fine-scale mapping of GC2 were developed. Wheat structural genomics: The assembly of 3A physical map remains incomplete. We are constructing a SNP-based genetic map and anchoring the BAC-Contigs. Wheat functional genomics: We developed a TILLING population of >1200 M2 plants in Jagger wheat. We finished analysis of a diploid TILLING population but information on some mutant phenotypes is incomplete. Wheat phenomics: We increased seed of >40 wheat alien chromosome introgression (WACI) libraries. Part of the collection was screened for leaf rust, Hessian fly resistance, and mineral content. Wheat germplasm: Work on Fusarium Head Blight (FHB) resistance continues. Three germplasms resistant to the UG99 race of stem rust were released. We deployed methods for screening for WCM resistance and are screening advanced wheat germplasm for virus resistance. Wheat that is resistant to WCM also is resistant to WSMV. In a survey for wheat viruses across the state of Kansas, >30% of wheat plants were virus-infected. Continued work with the Wheat Streak Mosaic Virus (WSMV) and Triticum Mosaic Virus (TriMV) resistant transgenic wheat plants. Single resistant WSMV and TriMV resistance lines in the T5 generation are still resistant. A WSMV transgenic resistant line was crossed into an elite winter cultivar. Specific events were sent for an independent assessment of resistance. Big bluestem populations collected across the native precipitation gradient in the state were genotyped and phenotyped for drought adaptation traits. The patterns of genetic variation and transplant experiments suggest the existence of locally adapted genotypes. We developed additional genomic sequence resources for F. occidentalis and used them to identify proteins that were differentially abundant in virus-infected insects. For P. maidis, we established an RNAi system for use in functional analysis of gene function, and prepared samples for mRNA-seq analysis of insects responding to virus infection. We confirmed GN expression in plants (transient and transgenic) and expressed GN-Bt fusions in plants. Bioassays for measuring protein binding blocking virus transmission are being optimized. We localized the TSWV structural proteins in plants and are screening plants for resistance to TSWV. We continued evaluation of new RNAi vectors for Soybean Cyst Nematode (SCN) control in soybean, and identified 15 RNAi vectors targeting separate SCN genes each showing a 50% reduction of SCN eggs in hairy root bioassays. We developed new amiRNA vector constructs that were equally or more effective in shutting down endogenous genes as demonstrated by silencing of GFP expression in transgenic soybean lines. PARTICIPANTS: K-State Plant Pathology Department - A. Akhunova, A. Beyer, B. Friebe, J. Li, B. Ramundo, J. Raupp, D. Rotenberg, C. Saintenac, T.C. Todd, B. Valent, F.F. White, D. Wilson Other K-state Departments - Agronomy, Biology, Entomology, Hays Research Station Outside K-State - Montana State University, Royal Botanic Gardens-Sydney (Australia), University of California (Davis), University of Sydney (Australia), USDA-ARS units in Manhattan KS, St. Paul MN, and Fargo ND, Washington State University. TARGET AUDIENCES: The target audience is scientific peers, broadly across the field of biotechnology of plants and their associated microbes. The wheat germplasm releases and mapping techniques and information will be of use to wheat breeders, public and private. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
Development of a high-throughput wheat SNP genotyping assay. Wheat germplasm resistant to the UG99 race of stem rust has been released. Developed a new method to screen for resistance to Wheat Streak Mosaic Virus. Survey of wheat plants in Kansas found that > 30% were infected with one or more viruses.

Publications

  • No publications reported this period


Progress 01/01/11 to 12/31/11

Outputs
OUTPUTS: A high-throughput Single Nucleotide Polymorphism (SNP) genotyping assay was developed for wheat and is being used to genotype a worldwide collections of cultivars. A component of the trait discovery pipeline now includes an association mapping panel of diverse wheat cultivars. This panel was genotyped with 9000 SNP markers and phenotyped for agronomic traits. Assays for the targeted enrichment of genic regions in the wheat genome and sequencing were developed. New markers for fine-scale mapping of GC2 were developed. Wheat structural genomics: The assembly of 3A physical map remains incomplete. We are constructing a SNP-based genetic map and anchoring the BAC-Contigs. Wheat functional genomics: We developed a TILLING population of >1200 M2 plants in Jagger wheat. We finished analysis of a diploid TILLING population but information on some mutant phenotypes is incomplete. Wheat phenomics: We increased seed of >40 wheat alien chromosome introgression (WACI) libraries. Part of the collection was screened for leaf rust, Hessian fly resistance, and mineral content. Wheat germplasm: Work on Fusarium Head Blight (FHB) resistance continues. Three germplasms resistant to the UG99 race of stem rust were released. We deployed methods for screening for WCM resistance and are screening advanced wheat germplasm for virus resistance. Wheat that is resistant to WCM also is resistant to WSMV. In a survey for wheat viruses across the state of Kansas, >30% of wheat plants were virus-infected. Continued work with the Wheat Streak Mosaic Virus (WSMV) and Triticum Mosaic Virus (TriMV) resistant transgenic wheat plants. Single resistant WSMV and TriMV resistance lines in the T5 generation are still resistant. A WSMV transgenic resistant line was crossed into an elite winter cultivar. Specific events were sent for an independent assessment of resistance. Big bluestem populations collected across the native precipitation gradient in the state were genotyped and phenotyped for drought adaptation traits. The patterns of genetic variation and transplant experiments suggest the existence of locally adapted genotypes. We developed additional genomic sequence resources for F. occidentalis and used them to identify proteins that were differentially abundant in virus-infected insects. For P. maidis, we established an RNAi system for use in functional analysis of gene function, and prepared samples for mRNA-seq analysis of insects responding to virus infection. We confirmed GN expression in plants (transient and transgenic) and expressed GN-Bt fusions in plants. Bioassays for measuring protein binding blocking virus transmission are being optimized. We localized the TSWV structural proteins in plants and are screening plants for resistance to TSWV. We continued evaluation of new RNAi vectors for Soybean Cyst Nematode (SCN) control in soybean, and identified 15 RNAi vectors targeting separate SCN genes each showing a 50% reduction of SCN eggs in hairy root bioassays. We developed new amiRNA vector constructs that were equally or more effective in shutting down endogenous genes as demonstrated by silencing of GFP expression in transgenic soybean lines. PARTICIPANTS: K-State Plant Pathology Department - A. Akhunova, A. Beyer, B. Friebe, J. Li, B. Ramundo, J. Raupp, D. Rotenberg, C. Saintenac, T.C. Todd, B. Valent, F.F. White, D. Wilson Other K-state Departments - Agronomy, Biology, Entomology, Hays Research Station Outside K-State - Montana State University, Royal Botanic Gardens-Sydney (Australia), University of California (Davis), University of Sydney (Australia), USDA-ARS units in Manhattan KS, St. Paul MN, and Fargo ND, Washington State University. TARGET AUDIENCES: The target audience is scientific peers, broadly across the field of biotechnology of plants and their associated microbes. The wheat germplasm releases and mapping techniques and information will be of use to wheat breeders, public and private. PROJECT MODIFICATIONS: Cancelled a workshop on Mapping of Plant Genomes by HICF and FISH originally scheduled for summer 2011.

Impacts
Development of a high-throughput wheat SNP genotyping assay. Wheat germplasm resistant to the UG99 race of stem rust has been released. Developed a new method to screen for resistance to Wheat Streak Mosaic Virus. Survey of wheat plants in Kansas found that > 30% were infected with one or more viruses.

Publications

  • Qi LL, Pumphrey MO, Friebe B, Zhang P, Qian C, Bowden RL, Rouse MN, Jin Y, and Gill BS. 2011. A novel Robertsonian translocation event leads to transfer of a stem rust resistance gene (Sr52) effective against race Ug99 from Dasypyrum villosum into bread wheat. Theoretical and Applied Genetics 123:159-167.
  • Rawat N, Neelam K, Tiwari VK, Randhawa GS, Friebe B, Gill BS, and Dhaliwal HS. 2011. Development of molecular characterization of wheat Aegilops kotschyi addition and substitution lines with high grain protein, iron and zinc. Genome 54(11):943-953.
  • Saintenac C, Jiang D, Akhunov E (2011) Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome. Genome Biology 12:R88.
  • Summerell BA, and Leslie JF. 2011. Fifty years of Fusarium: How could nine species ever have been enough Fungal Diversity 50: 135-144.
  • Summerell BA, Leslie JF, Liew ECY, Laurence MH, Bullock S, Petrovic T, Bentley AR, Howard CG, Peterson SA, Walsh JL, and Burgess LW. 2011. Fusarium species associated with plants in Australia. Fungal Diversity 46: 1-27.
  • Whitfield AE, Rotenberg D, Aritua V, and Hogenhout SA. 2011. Analysis of expressed sequence tags from maize mosaic rhabdovirus-infected gut tissues of Peregrinus maidis reveals the presence of key components of insect innate immunity. Insect Molecular Biology 20:225-242.
  • Zhang Z, Belcram H, Gornicki P, Charles M, Just J, Huneau C, Magdelenat G, Couloux A, Samain S, Gill BS, Rasmussen JB, Barbe V, Faris JD, and Chalhoub B. 2011. Duplication and partitioning in evolution and function of homoeologous Q loci governing domestication characters in polyploid wheat. Proceedings of the National Academy of Sciences USA 108:18737-18742.
  • Zhang W, Friebe B, Gill BS, and Jiang J. 2011. Centromere inactivation and epigenetic modifications of a plant chromosome with three functional centromeres. Chromosoma 119:553-563.
  • Alo F, Furman BJ, Akhunov E, Dvorak J, Gepts P (2011) Leveraging genomic resources of model species for the assessment of diversity and phylogeny in wild and domesticated lentil. Journal of Heredity 102:315-29.
  • Bi C, Chen F, Jackson L, Gill BS and Li WL. 2011. Expression of lignin biosynthetic genes in wheat during development and upon infection by fungal pathogens. Plant Molecular Biology Reporter 29:149-161. Cantu D, Pearce SP, Distelfeld A, Christiansen MW, Uauy C, Akhunov E, Fahima F, Dubcovsky J (2011) Effect of the down-regulation of the high Grain Protein Content (GPC) gene on the wheat transcriptome during monocarpic senescence. BMC Genomics 12:492.
  • Dvorak J, Luo MC, Akhunov E. 2011. N.I. Vavilov's theory of centers of diversity in the light of current understanding of wheat domestication and evolution. Czech Journal of Genetics and Plant Breeding 47:S20.
  • Friebe B, Liu W, Qi LL, Wilson DL, Raupp WJ, Pumphrey MO, Poland J, Bowden RL, Fritz AK, and Gill BS. 2011. Notice of release of KS12WGGRC59 wheat streak mosaic virus- and Triticum mosaic virus-resistant wheat germplasm. Annual Wheat Newsletter 57:280.
  • Friebe B, Liu W, Wilson DL, Raupp WJ, Pumphrey MO, Poland J, Bowden RL, Fritz AK, and Gill BS. 2011. Notice of release of KS12WGGRC56 (TA5619, TA5620, TA5621) stem rust-resistant wheat germplasm. Annual Wheat Newsletter 57:278-279.
  • Friebe B, Liu W, Wilson DL, Raupp WJ, Pumphrey MO, Poland J, Bowden RL, Fritz AK, and Gill BS. 2011. Notice of release of KS12WGGRC58 (TA5630, TA5625, TA5643) stem rust-resistant wheat germplasm. Annual Wheat Newsletter 57:279-280.
  • Friebe B, Qi LL, Liu C, and Gill BS. 2011. Genetic compensation abilities of Aegilops speltoides chromosomes for homoeologous B-genome chromosomes of polyploid wheat in disomic S(B) chromosome substitution lines. Cytogenetics and Genome Research 134:144-150.
  • Friebe B, Qi LL, Liu C, Liu W, Wilson DL, Raupp WJ, and Gill BS. 2011. Notice of release of KS12WGGRC55 (TA5092) hard red winter wheat germplasm homozygous for the ph1b gene. Annual Wheat Newsletter 57:278.
  • Friebe B, Qi LL, Qian C, Zhang P, Wilson DL, Raupp WJ, Pumphrey MO, Poland J, Bowden RL, Fritz AK, and Gill BS. 2011. Notice of release of KS12WGGRC57 (TA5617) stem rust-resistant wheat germplasm. Annual Wheat Newsletter 57:279.
  • Gan X, Stegle O, J Behr J, Steffen JG, Drewe P, Hildebrand KL, Lyngsoe R, Schultheiss SJ, Osborne EJ, Sreedharan VT, Kahles A, Bohnert R, Jean G, Derwent P, Kersey P, Belfield EJ, Harberd NP, Kemen E, Toomajian C, Kover PX, Clark RM, Ratsch G, and Mott R. 2011. Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature 477: 419-423.
  • Gill BS, Friebe BR, and White F. 2011. Alien introgressions represent a rich source of genes for crop improvement. Proceedings of the National Academy of Sciences USA 108:7657-7658.
  • Gill BS, Sehgal SK, Friebe B, and Akhunov E. 2011. Wheat genome and gene analysis. In: Proceedings of the International Wheat Quality Conference IV (Chibbar RN and Dexter JE, Eds). Agrobios (International), Jodhpur, India. Pp. 483-491.
  • Hancock AM, Brachi B, Faure N, Horton MW, Jarymowycz LB, Sperone FG, Toomajian C, Roux F, and Bergelson J. 2011. Adaptation to climate across the Arabidopsis thaliana genome. Science 334: 83-86.
  • Krishnan HB, Jang S, Kim S, Kerley, Wonseok K, Oliver MS, and Trick HN. 2011. Biofortification of soybean meal: Immunological properties of the 27 kDa γ-zein. Journal of Agricultural and Food Chemistry 59: 1223-1228.
  • Lee J, Welti R, Schapaugh WT, and Trick HN. 2011. Phospholipid and triacylglycerol profiles modified by PLD suppression in soybean seed. Plant Biotechnology Journal 9: 359-372.
  • Leslie JF, and Summerell BA. 2011. In search of new Fusarium species. Plant Breeding and Seed Science 63: 93-101.
  • Liu W, Seifers DL, Qi LL, Pumphrey MO, Friebe B, and Gill BS. 2011. A compensating wheat Thinopyrum intermedium Robertsonian translocation conferring resistance to wheat streak mosaic virus and Triticum mosaic virus. Crop Science 51: 2382-2390.
  • Liu WX, Jin Y, Rouse M, Friebe B, Gill BS, and Pumphrey MO. 2011. Development and characterization of wheat Ae. searsii Robertsonian translocations and a recombinant chromosome conferring resistance to stem rust. Theoretical and Applied Genetics 122: 1537-1545.
  • Murugan M, Cardona L, Sotelo P, Duraimurugan P, Whitfield AE, Schneweis D, Starkey S, and Smith CM. 2011. Wheat curl mite resistance: Interactions of mite feeding with wheat streak mosaic virus infection. Journal of Economic Entomology 104: 1406-1414.