Progress 05/31/16 to 05/31/21
Outputs
Target Audience:The target audience includes research scientists in genomics and related disciplines, along with students obtaining degrees in these fields. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Training opportunities were provided on the following topics: A 3 credits Special Topics class in Next Generation Sequencing and RNAseq Analysis was provided for 11 graduate students. A manuscript with the data and analysis generated in the class is currently under preparation. Graduate students and postdocs: Rami Altameemi PhD student, trained in genome wide association analysis. Mustafa Aljadi PhD student, trained in genome assembly and annotation. Jefferey Bartel MSc student coadvised with Dr. Bucking, trained in DNA extraction and PCR Dr. Yeyan Qiu Post Doc, trained in all aspects of the sequencing facility Trevor VanDen Top Post Doc, trained in all aspects of the sequencing facility How have the results been disseminated to communities of interest?Results have been disseminated through presentations and publications in scientific journals. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Objective 1: Application of genomic tools for genomic selection in monocot crops such as wheat, oats in collaboration with SDSU breeding programs (100% Accomplished) Nothing to report Objective 2: Application of genetic and genomic tools to study plant microbe interactions, both pathogenic (e.g. fusarium and stem rust in wheat or crown rust in oats) in collaboration with SDSU plant pathologists and symbiotic such as mycorrhizal fungi and endophytes (in wheat, oats, and perennial grasses) in collaboration with SDSU soil microbiologists. (100% Accomplished) Working with Dr. Seghal we have identified some wild diploid and tetraploid wheat accessions capable of forming symbiotic relationships with nitrogen fixing bacteria. This year we have completed a transcriptomic analysis of these interactions allowing us to identify pathways expressed in response to the interaction with the nitrogen fixing bacteria. The two main groups of genes up and down regulated relate to nitrate and nitrogen metabolism and to thiamine biosynthesis and metabolism. Objective 3: Study the genetic mechanisms of adaptation to stress environments (e.g. saline soils). (100% Accomplished) In a transcriptome analysis comparing the response to weed stress in two teosinte lines we found common down-regulated sub-networks in weed-stressed plants were related to light, photosynthesis, and carbon cycles. Some unique response networks (e.g. aging, response to chitin) and gene sets were present in each line. Comparing these responses to maize's responses suggested three common gene ontologies up-regulated when weed-stressed: jasmonic acid response/signaling, UDP-glucosyl and glucuronyltransferases, and quercetin glucosyltransferase (3-O and 7-O). Overall, morphologic and transcriptomic differences suggest a greater varietal (rather than a conserved) response to weed stress, and implies multiple responses are possible. Objective 4: Manage the newly established sequencing facility and facilitate the application of next generation sequencing technologies in other research projects. (100% Accomplished) We have continued to process samples from a variety of clients: scientists at different departments at South Dakota State University (Plant Sciences, Natural Resources Management, Biology/Microbiology, Chemistry/Biochemistry, Pharmacy, Dairy and Food Science, and Animal Science); University of SD (Biology); Augustana University (Biology); SD School of Mines and Technology (Chemical and Biological Engineering); and Sanford Research. Amplicon sequencing (including 16S RNA metagenomics) has become very popular among our users, as well as RNAseq and genome sequencing.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Sekaran, U., Sandhu, S.S., Qiu, Y., Kumar, S., and Gonzalez Hernandez, J.L. 2019. Biochar and manure addition influenced soil microbial community structure and enzymatic activities at eroded and depositional landscape positions. Land Degradation and Development. https://doi.org/10.1002/ldr.3508
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Diing D., Agany, M., Potts, R., Gonzalez Hernandez, J.L., Gnimpieba, E.Z., and Pietri, J.E. 2020. Microbiome differences between human head and body lice ecotypes revealed by 16S rRNA gene amplicon sequencing. J. Parasitology. https://doi.org/10.1645/19-132
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Bruggeman, S.A., Horvath, D.P., Fennell, A.Y., Gonzalez Hernandez, J.L., and Clay. S.A. 2020. Teosinte (Zea mays ssp parviglumis) growth and transcriptomic response to weed stress identifies similarities and differences between varieties and with modern maize varieties. PLOS ONE. http://dx.doi.org/10.1371/journal.pone.0237715
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Aljutaily, T., Huarte, E., Martinez-Monteagudo, S., Gonzalez Hernandez, J.L., Rovai, M., and Sergeev, I.N. 2020. Probiotic-enriched milk and dairy products increase gut microbiota diversity: a comparative study. Nutrition Research. http://dx.doi.org/10.1016/j.nutres.2020.06.017
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Sekaran, U., Kumar, S., and Gonzalez Hernandez, J.L. 2020. Integration of crop and livestock enhanced soil biochemical properties and microbial community structure. Geoderma. https://doi.org/10.1016/j.geoderma.2020.114686
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Tameemi, R.A., Gill, H.S., Ali, S., Ayana, G., Halder, J., Sidhu, J.S., Gill, U.S., Turnipseed, B., Gonzalez Hernandez, J.L., and Sehgal, S.K. 2021. Genome-wide association analysis permits characterization of Stagonospora nodorum blotch (SNB) resistance in hard winter wheat. Scientific Reports. DOI: https://doi.org/10.1038/s41598-021-91515-6.
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Adachi, H., Sakai, T., Kourelis, J., Gonzalez Hernandez, J.L., Maqbool, A., and Kamoun, S. 2020. Jurassic NLR: conserved and dynamic evolutionary features of the atypically ancient immune receptor ZAR1. bioRxiv 2020.10.12.333484; doi: https://doi.org/10.1101/2020.10.12.333484
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Lai, L., Yilmaz, T., Kumar, S., Fennell, A., and Gonzalez Hernandez, J.L. 2022. Impacts of grasslands conversion to tilled croplands on select soil properties and greenhouse gas emissions. Soil Research. DOI https://doi.org/10.1071/SR21112
|
Progress 10/01/19 to 09/30/20
Outputs
Target Audience:The target audience includes research scientists in genomics and related disciplines, along with students obtaining degrees in these fields. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Training opportunities were provided on the following topics: A 3 credits Special Topics class in Next Generation Sequencing and RNAseq Analysis was provided for 11 graduate students. A manuscript with the data and analysis generated in the class is currently under preparation. Graduate students and postdocs: Rami Altameemi PhD student, trained in genome wide association analysis. Mustafa Aljadi PhD student, trained in genome assembly and annotation. Jefferey Bartel MSc student coadvised with Dr. Bucking, trained in DNA extraction and PCR Dr. Yeyan Qiu Post Doc, trained in all aspects of the sequencing facility How have the results been disseminated to communities of interest?Results have been disseminated through presentations and publications in scientific journals. What do you plan to do during the next reporting period to accomplish the goals?Objective 1. Application of genomic tools for genomic selection in monocot crops such as wheat, oats in collaboration with SDSU breeding programs. Formally release sets of hard red spring and winter wheat double haploid lines that combine multiple QTL providing resistance to FHB. Objective 2. Application of genetic and genomic tools to study plant-microbe interactions, both pathogenic (e.g. fusarium and stem rust in wheat or crown rust in oats) in collaboration with SDSU plant pathologists and symbiotic such as mycorrhizal fungi and endophytes (in wheat, oats, and perennial grasses) in collaboration with SDSU soil microbiologists. Continue study of the microbiome of prairie cordgrass and its effect on salinity tolerance. Work with soil scientists to incorporate soil microbiome analysis in their studies to identify agronomic practices that maximize divert of beneficial microorganisms. Objective 3. Study the genetic mechanisms of adaptation to stress environments (e.g. saline soils). Publish the prairie cordgrass annotated genome. Objective 4. Manage the newly established sequencing facility and facilitate the application of next generation sequencing technologies in other research projects. Continue the current level of service and support while looking at potential new sequencing applications.
Impacts
What was accomplished under these goals?
Objective 1: Application of genomic tools for genomic selection in monocot crops such as wheat, oats in collaboration with SDSU breeding programs (85% Accomplished) Nothing to report Objective 2: Application of genetic and genomic tools to study plant microbe interactions, both pathogenic (e.g. fusarium and stem rust in wheat or crown rust in oats) in collaboration with SDSU plant pathologists and symbiotic such as mycorrhizal fungi and endophytes (in wheat, oats, and perennial grasses) in collaboration with SDSU soil microbiologists. (95% Accomplished) Working with Dr. Seghal we have identified some wild diploid and tetraploid wheat accessions capable of forming symbiotic relationships with nitrogen fixing bacteria. This year we have completed a transcriptomic analysis of these interactions allowing us to identify pathways expressed in response to the interaction with the nitrogen fixing bacteria. The two main groups of genes up and down regulated relate to nitrate and nitrogen metabolism and to thiamine biosynthesis and metabolism. Objective 3: Study the genetic mechanisms of adaptation to stress environments (e.g. saline soils). (90% Accomplished) In a transcriptome analysis comparing the response to weed stress in two teosinte lines we found common down-regulated sub-networks in weed-stressed plants were related to light, photosynthesis, and carbon cycles. Some unique response networks (e.g. aging, response to chitin) and gene sets were present in each line. Comparing these responses to maize's responses suggested three common gene ontologies up-regulated when weed-stressed: jasmonic acid response/signaling, UDP-glucosyl and glucuronyltransferases, and quercetin glucosyltransferase (3-O and 7-O). Overall, morphologic and transcriptomic differences suggest a greater varietal (rather than a conserved) response to weed stress, and implies multiple responses are possible. Objective 4: Manage the newly established sequencing facility and facilitate the application of next generation sequencing technologies in other research projects. (75% Accomplished) We have continued to process samples from a variety of clients: scientists at different department in South Dakota State University (Plant Sciences, Natural Resources Management, Biology, Biochemistry, Pharmacy, Dairy Science, and Animal Science); University of SD (Biology); Augustana University (Biology); SD School of Mines and Technology (Chemical and Biological Engineering); and Sanford Research. Amplicon sequencing (including 16S RNA metagenomics) has become very popular among our users as well as RNAseq and genome sequencing.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Sekaran, U., Sandhu, S.S., Qiu, Y., Kumar, S., and Gonzalez Hernandez, J.L. 2019. Biochar and manure addition influenced soil microbial community structure and enzymatic activities at eroded and depositional landscape positions. Land Degradation and Development. https://doi.org/10.1002/ldr.3508
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Diing D., Agany, M., Potts, R., Gonzalez Hernandez, J.L., Gnimpieba, E.Z., Pietri, J.E. 2020. Microbiome differences between human head and body lice ecotypes revealed by 16S rRNA gene amplicon sequencing. J. Parasitology. https://doi.org/10.1645/19-132
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Bruggeman, S. A., Horvath, D.P., Fennell, A.Y., Gonzalez Hernandez, J.L., and Clay. S.A. 2020. Teosinte (Zea mays ssp parviglumis) growth and transcriptomic response to weed stress identifies similarities and differences between varieties and with modern maize varieties. PLOS ONE. http://dx.doi.org/10.1371/journal.pone.0237715
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Aljutaily, T., Huarte, E., Martinez-Monteagudo, S., Gonzalez Hernandez, J.L., Rovai, M., and Sergeev, I.N. 2020. Probiotic-enriched milk and dairy products increase gut microbiota diversity: a comparative study. Nutrition Research. http://dx.doi.org/10.1016/j.nutres.2020.06.017
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Sekaran, U., Kumar, S., and Gonzalez Hernandez, J.L . 2020. Integration of crop and livestock enhanced soil biochemical properties and microbial community structure. Geoderma. https://doi.org/10.1016/j.geoderma.2020.114686
|
Progress 10/01/18 to 09/30/19
Outputs
Target Audience:The target audience includes research scientists in genomics and related disciplines, along with students obtaining degrees in these fields. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Training opportunities were provided on the following topics: A 7 day Metagenomics Sequencing workshop was provided to 5 undergraduate students participating in the USDA funded REEU "Plant Microbiomes program." How have the results been disseminated to communities of interest?Results have been disseminated thru presentations and publications in scientific journals. What do you plan to do during the next reporting period to accomplish the goals?Objective 1. Application of genomic tools for genomic selection in monocot crops such as wheat, oats in collaboration with SDSU breeding programs. Formally release sets of hard red spring and winter wheat double haploid lines that combine multiple QTL providing resistance to FHB. Objective 2. Application of genetic and genomic tools to study plant-microbe interactions, both pathogenic (e.g. fusarium and stem rust in wheat or crown rust in oats) in collaboration with SDSU plant pathologists and symbiotic such as mycorrhizal fungi and endophytes (in wheat, oats, and perennial grasses) in collaboration with SDSU soil microbiologists. Continue study of the microbiome of prairie cordgrass and its effect on salinity tolerance. Work with soil scientists to incorporate soil microbiome analysis in their studies to identify agronomic practices that maximize divert of beneficial microorganisms. Objective 3. Study the genetic mechanisms of adaptation to stress environments (e.g. saline soils). Publish the prairie cordgrass annotated genome. Objective 4. Manage the newly established sequencing facility and facilitate the application of next generation sequencing technologies in other research projects. Continue the current level of service and support while looking at potential new sequencing applications.
Impacts
What was accomplished under these goals?
Objective 1: Application of genomic tools for genomic selection in monocot crops such as wheat, oats in collaboration with SDSU breeding programs (85% Accomplished) Nothing to report Objective 2: Application of genetic and genomic tools to study plant microbe interactions, both pathogenic (e.g. fusarium and stem rust in wheat or crown rust in oats) in collaboration with SDSU plant pathologists and symbiotic such as mycorrhizal fungi and endophytes (in wheat, oats, and perennial grasses) in collaboration with SDSU soil microbiologists. (90% Accomplished) Working with Dr. Bucking we have identified a number of endophytic bacteria in prairie cordgrass grown in saline soils. Some of these isolates have been used in greenhouse screenings to further study their effects. In initial testing, five of these isolates have shown the capacity to increase salt tolerance in prairie cordgrass. However we will need further experiments to attempt to accurately quantify their impact. Most the species were from the Bacillus genus. An invention disclosure has been filed with SDSU Tech Transfer Office. One isolate is a novel bacterial species; we have sequenced the genome, submitted the strain to two culture collections and a manuscript is ready for submission as soon as we get confirmation from the second culture collection. Objective 3: Study the genetic mechanisms of adaptation to stress environments (e.g. saline soils). (80% Accomplished) In a drought resistance study, we identified few Iranian wheat landraces with increased root length even after drought stress, suggesting that selection inside the landraces for long roots is possible even under drought pressure. Transcriptome profiling of one selected drought-resistant genotype "L-82" showed up-regulation of genes mostly involved in Oxidation-reduction processes, secondary metabolite biosynthesis, abiotic stress response, transferase activity and heat shock proteins. Objective 4: Manage the newly established sequencing facility and facilitate the application of next generation sequencing technologies in other research projects. (75 % Accomplished) We have continued to process samples from a variety of clients, scientists at different department in South Dakota State University (Plant sciences, Natural Resources Management, Biology, Biochemistry, Pharmacy, Dairy Sciences and Animal Science, University of SD (Biology), Augustana University (Biology), SD School of Mines and Technology (Chemical and Biological Engineering), and Sanford Research. Amplicon sequencing (including 16S RNA metagenomics) has become very popular among our users as well as RNAseq and genome sequencing.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
M Chaichi, F Sanjarian, K Razavi, JL Gonzalez-Hernandez. 2019. Analysis of transcriptional responses in root tissue of bread wheat landrace (Triticum aestivum L.) reveals drought avoidance mechanisms under water scarcity. PloS one 14 (3), e0212671
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
M Chaichi, F Sanjarian, K Razavi, JL Gonzalez-Hernandez. 2019. Phenotypic diversity among Iranian bread wheat landraces, as a screening tool for drought tolerance. Acta Physiologiae Plantarum 41 (6), 90
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Ma Q, B�cking H, Gonzalez Hernandez JL, Subramanian S. 2019. Single-cell RNA sequencing of plant-associated bacterial communities. Front Microbiol. 0:2452. Published Oct 29. doi:10.3389/fmicb.2019.02452
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Sekaran U, Abagandura GO, Singh S, Ibrahim MA, Owens VA, Subramanian S, Gonzalez-Hernandez J, Kumar S. 2019. Soil greenhouse gas fluxes from Prairie Cordgrass and Kura Clover mixture under different nitrogen fertilizer rates. ASA, CSSA and SSSA International Annual Meetings. San Antonio, TX. Nov 10-13.
|
Progress 10/01/17 to 09/30/18
Outputs
Target Audience:The target audience includes research scientists in genomics and related disciplines, along with students obtaining degrees in these fields.? Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Training opportunities were provided on the following topics: Next Generation Sequencing: These opportunities included training in diverse library preparation protocols, processing diverse samples, and sequencing. Dr. Yeyan Qiu (Research Associate) was trained in the preparation of multiple types of libraries and sequencing. Bioinformatics data analysis: One-on-one bioinformatics training was provided to 1 PhD student (Gitanjali NandaKafl). An 8 day Genome Sequencing workshop was provided to 10 graduate students (Gitanjali NandaKafl, Bikram Das, Katelyn Graber, Laura Jackson, Joshi Lok, Delayna Paulson, Alex Soupir, Trevor VanDenTop, Lingqi Kong and Jessica Noll). How have the results been disseminated to communities of interest?Results have been disseminated thru presentations and publications in scientific journals. What do you plan to do during the next reporting period to accomplish the goals?Objective 1. Application of genomic tools for genomic selection in monocot crops such as wheat, oats in collaboration with SDSU breeding programs. Formally release sets of hard red spring and winter wheat double haploid lines that combine multiple QTL providing resistance to FHB. Objective 2. Application of genetic and genomic tools to study plant-microbe interactions, both pathogenic (e.g. fusarium and stem rust in wheat or crown rust in oats) in collaboration with SDSU plant pathologists and symbiotic such as mycorrhizal fungi and endophytes (in wheat, oats, and perennial grasses) in collaboration with SDSU soil microbiologists. Continue the study of the microbiome of prairie cordgrass and its effect on salinity tolerance. Objective 3. Study the genetic mechanisms of adaptation to stress environments (e.g. saline soils). Complete the sequencing of the prairie cordgrass genome and annotate known genes associated with abiotic stresses tolerance. Objective 4. Manage the newly established sequencing facility and facilitate the application of next generation sequencing technologies in other research projects. Continue the current level of service and support while looking at potential new sequencing applications.
Impacts
What was accomplished under these goals?
Objective 1: Application of genomic tools for genomic selection in monocot crops such as wheat, oats in collaboration with SDSU breeding programs (85% Accomplished) Nothing to report Objective 2: Application of genetic and genomic tools to study plant microbe interactions, both pathogenic (e.g. fusarium and stem rust in wheat or crown rust in oats) in collaboration with SDSU plant pathologists and symbiotic such as mycorrhizal fungi and endophytes (in wheat, oats, and perennial grasses) in collaboration with SDSU soil microbiologists. (85% Accomplished) Working with Drs. Seghal and Ali we have completed an evaluation of a panel of winter wheat lines for spot blotch allowing us to identify a number of loci associated with resistance. This information was published in a journal article. The genetic information produced is being used in the SDSU winter wheat breeding program to facilitate selection of resistant lines. Working with Dr. Bucking we have identified a number of endophytic bacteria in prairie cordgrass grown in saline soils. Some of those isolates have been used in greenhouse screenings to further study their effect. In initial testing, five of these isolates have shown the capacity to increase salt tolerance in prairie cordgrass. We are conducting additional testing and preparing an invention disclosure. Working with Dr. Zhou we have isolated, from SD grassland soils, six microbial strains capable of photosynthesis and nitrogen fixation. Future research will focus on validation and developing these validated N2-fixing microbes as in situ, solar-powered living ammonia factories in crop fields. Objective 3: Study the genetic mechanisms of adaptation to stress environments (e.g. saline soils). (80% Accomplished) We have completed the sequencing and assembly of the prairie cordgrass genome. We obtained 10 chromosome level scaffolds, the same as the basic chromosome number of this species. We used RNAseq data to annotate several 1000s genes in the genome. Objective 4: Manage the newly established sequencing facility and facilitate the application of next generation sequencing technologies in other research projects. (60 % Accomplished) We have continued to process samples from a variety of clients. RNAseq, and metagenomic projects are the most common samples.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
KA Hern�ndez, VN Owens, A Boe, JL Gonz�lez-Hern�ndez, D Lee. 2018. Above-and Below-ground Prairie Cordgrass Response to Applied Nitrogen on Marginal Land. BioEnergy Research, 11: 440-448.
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
S Ayana, JS Ali, J Sidhu, JL Gonzalez-Hernandez, B Turnipseed, and S Sehgal. 2018. Genome-Wide Association Study for Spot Blotch Resistance in Hard Winter Wheat. Frontiers in Plant Science 9, 926.
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
N Wang, S Tian, L Gu, L Xu, Y Qiu, T Van Den Top, JL Gonzalez-Hernandez, M Hildreth, S Li and R Zhou. 2018. Isolation of potential photosynthetic N2-fixing microbes from topsoil of native grasslands in South Dakota. Proceedings of the South Dakota Academy of Science. Vol, 97: 1173-128
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
J. Gonzalez-Hernandez. 2018. RNAseq Capabilities at SDSU Genomics Sequencing Facility. Experimental Considerations. Sanford Research. Sioux Falls, SD. August 13.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
J. Gonzalez-Hernandez. 2018. SDSU Genomics Sequencing Facility: Capabilities and Applications. Center for Pediatrics Research 5th Annual Symposium. Sanford Research. Sioux Falls, SD. August 29.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
J. Gonzalez-Hernandez. 2018. The prairie cordgrass story. A story of ecology, development and genomics. New Mexico State University. October 19.
|
Progress 10/01/16 to 09/30/17
Outputs
Target Audience:Target audience was scientists in the field Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Training opportunities were provided on the following topics: Next Generations sequencing: These opportunities included training in diverse library preparation protocols, processing diverse samples, and sequencing. In addition to Micheallong Tran (Research Associate), Barb Villenga (Ph.D. student) started training in RNA extractions and libraries preparation. Bioinformatics data analysis: A one-day hands-on workshop on RNAseq data analysis was offered to 20 attendees. This workshop was sponsored by SD-ESPCOR and SD-BRIN. One-on-one bioinformatics training was provided to 3 graduate students (Mustafa Aljadim, Thamer Fahad Aljutaily, Yeyan Qiu), one visiting scientist (Fernando Aranda), one staff scientist (Liping Gu) and 2 faculty members (Eduardo Huarte, Ruanbao Zhao). Manuscript and presentations: Several graduate students participated in the preparation of manuscripts and scientific presentations (Y. Thurston, Barb Villenga, Rami Altemeemi). How have the results been disseminated to communities of interest?Results have been disseminated thru presentations and publications in scientific journals. What do you plan to do during the next reporting period to accomplish the goals?Objective 1) Application of genomic tools for genomic selection in monocot crops such as wheat, oats in collaboration with SDSU breeding programs. Formally release sets of hard red spring and winter wheat double haploid lines that combine multiple QTL providing resistance to FHB. Objective 2) Application of genetic and genomic tools to study plant-microbe interactions, both pathogenic (e.g. fusarium and stem rust in wheat or crown rust in oats) in collaboration with SDSU plant pathologistsand symbiotic such as mycorrhizal fungi and endophytes (in wheat, oats, and perennial grasses) in collaboration with SDSU soil microbiologists. Continue the study of the microbiome of prairie cordgrass and its effect on salinity tolerance. Objective 3) Study the genetic mechanisms of adaptation to stress environments (e.g. saline soils). Complete the sequencing of the prairie cordgrass genome and annotate known genes associated with abiotic stresses tolerance. Objective 4) Manage the newly established sequencing facility and facilitate the application of next generation sequencing technologies in other research projects. Continue the current level of service and support while looking at potential new sequencing applications.
Impacts
What was accomplished under these goals?
Objective 1) Application of genomic tools for genomic selection in monocot crops such as wheat, oats in collaboration with SDSU breeding programs. (~85% accomplished). We completed the evaluation of double haploid lines of spring and water wheat combining multiple FHB resistance sources. In spring and winter wheat, 4 and 6 lines, respectively showed better FHB resistance than the best resistant checks. Public release has not occurred yet but lines have been shared with collaborating breeding programs in SD, ND, MN, and NE. We also completed a study to identify DNA markers linked to different hybrid necrosis alleles in wheat. Hybrid necrosis occurs in certain crosses between adapted lines and synthetic wheat used to bring alleles from related tetraploid and diploid related species.This work has been is published in a journal article. Objective 2) Application of genetic and genomic tools to study plant-microbe interactions, both pathogenic (e.g. fusarium and stem rust in wheat or crown rust in oats) in collaboration with SDSU plant pathologistsand symbiotic such as mycorrhizal fungi and endophytes (in wheat, oats, and perennial grasses) in collaboration with SDSU soil microbiologists. (~70% accomplished). We are completing the transcriptome bioinformatic analyses of bracypodium, switchgrass and prarie cordgrass under different nutrient conditions and under mycorrhizal colonization. We also completed the analysis and publication of a study on aphid resistance in soybean. This study identified a putative novel locus for aphid resistance. Objective 3) Study the genetic mechanisms of adaptation to stress environments (e.g. saline soils). (~35% accomplished). We completed and plublished a study comparing the trasncriptome of prairecordgrass families of diverse salt tolerance. The phenotypes associated with salt tolerance were shown to be moderately heritable between parent and offspring. RNA-seq analysis revealed differential regulation in unique pathways including metabolism, signaling, photosynthesis, and the circadian rhythm. The results suggest that alternative regulation of the photosynthetic pathway could confer increased salt resistance in halophytes and can be monitored phenotypically or genetically in breeding programs. The improvement of salt tolerant traits in Prairie Cordgrass would increase its potential to be grown as a bioenergy crop on lands that are not suitable for the growth of food crops. Objective 4) Manage the newly established sequencing facility and facilitate the application of next generation sequencing technologies in other research projects. (~30% accomplished). During this year we expanded the capabilities from the original Illumina NextSeq500 intrument by adding Illumina Miseq and Oxford Nanopore sequencers. We also added new automated capabilities for nucleic acid extraction and library preparation. During this year we participatedin the sequecing of 3 bacterial and 5 plant genomes, as well as multiple RNAseq and metagenomic projects.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Arvid Boe, Paul J. Johnson, Vance Owens, D.K. Lee, J. Guo, and Jose L. Gonzalez-Hernandez*. 2017. Genetics and partitioning for biomass of prairie cordgrass compared to switchgrass on marginal cropland. Bioenergy Research. 10 (3), 864-875
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Figueir�, A. d. A., Gonzalez-Hernandez, J. L., Pacheco, M. T., Reese, R. N., de Morais, G. L., Guzman, F., Swaminathan, P. and Delatorre, C. A. 2017. RNAseq analysis reveals the role of secondary metabolism in the response of URS 21, a race-nonspecific resistant cultivar, to crown rust. Plant Pathology. (DOI:10.1111/ppa.12615)
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
DR Kandel, KD Glover, WA Berzonsky, JL Gonzalez-Hernandez, S Ali, S Chao, SJ Bhusal. 2017. Flanking SSR markers for alleles involved in the necrosis of hybrids between hexaploid bread wheat and synthetic hexaploid wheat. Journal of Crop Improvement 31 (6), 879-892
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Siddhi J Bhusal, Guo-Liang Jiang, Qijian Song, Perry B Cregan, David Wright, Jose L Gonzalez-Hernandez. 2017. Genome-wide detection of genetic loci associated with soybean aphid resistance in soybean germplasm PI 603712. Euphytica 213 (7), 144
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Michael Robben, Ethan Thibault, Michaellong Tran, Yajun Wu, Arvid Boe, Jose L. Gonzalez-Hernandez*. 2017. Transcriptome Analysis of the Heritable Salt Tolerance of Prairie Cordgrass (Spartina pectinata Link). Bioenergy Research. (https://doi.org/10.1007/s12155-017-9881-0)
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2017
Citation:
Qiu, Y. , Gu, L., Gibbons, J. L., Gonzalez Hernandez, J. L., Zhou, R. , "Developmentally Regulated Heterocyst Genome Editing in Anabaena cylindrica," The 2017 Gordon Research Conference on Nucleic Acids. Gordon Research Conference, Biddeford, ME, United States. (June 4, 2017).
|
Progress 05/31/16 to 09/30/16
Outputs
Target Audience:One target audience is the research community in general and plant geneticists, genomicists and breeders more specifically. We use peer-reviewed publications and presentations in conferences to target this group. A second target audience is the undergraduate student community. We use summer research internships to target this community. Our third target audience is the regional community at large through outreach activities. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Training opportunities were provided on the following topics: Next Generations sequencing: These opportunities included training in diverse library preparation protocols, processing diverse samples, and sequencing. In addition to Michaellong Tran (Research Associate I working in the Sequencing Facility), several other technicians and students participated. Bioinformatics data analysis: A two-day hands-on workshop on RNAseq data analysis was offered to 90 attendees. One-on-one training was provided to four graduate students (Devi Kandel, PhD; Stephanie Hansen Bruggeman, PhD, Lu Hang, PhD; Michael Robben, PhD) Wheat plants crossing: Training on how to grow wheat plants in the greenhouse and how to cross was provided to a graduate student (Rami Altemeemi, PhD). Manuscript and presentations: Several graduate students participated in the preparation of manuscripts and scientific presentations. (Devi Kandel, PhD; Michaellong Tran, MSc; Michael Robben, PhD, Yqoob Thurston, PhD; Siddi Bhusal, PhD). How have the results been disseminated to communities of interest?Dissemination of results was carried out thru peer-reviewed publications (3). What do you plan to do during the next reporting period to accomplish the goals? Initiate the sequencing of the prairie cordgrass genome and annotate known genes associated with abiotic stresses tolerance. Initiate the study of the microbiome of prairie cordgrass and its effect on salinity tolerance. Formally release sets of hard red spring and winter wheat double haploid lines that combine multiple QTL providing resistance to FHB.
Impacts
What was accomplished under these goals?
Objective 1: Application of genomic tools for genomic selection in monocot crops such as wheat, oats in collaboration with SDSU breeding programs. (80% accomplished). We have validated several resistance loci to Fusarium Head Blight (FHB) in double haploid lines of wheat. This is part of a funded project thru the US Wheat and Barley Scab Initiative. Double haploid lines combining multiple loci have been shared with breeders as pre-releases. A formal release of selected lines will take place in 2017. In collaboration with Dr. DK Lee at University of Illinois, we developed the first set of single nucleotide polymorphism (SNPs) assays in prairie cordgrass derived from specific transcript sequences; these molecular markers will be useful in breeding efforts. Objective 2:Application of genetic and genomic tools to study plant-microbe interactions, both pathogenic (e.g. fusarium and stem rust in wheat or crown rust in oats) in collaboration with SDSU plant pathologistsand symbiotic such as mycorrhizal fungi and endophytes (in wheat, oats, and perennial grasses) in collaboration with SDSU soil microbiologists. (~60% accomplished) We published our RNAseq study of the oat crown rust system identifying critical secondary metabolism pathways (avenanthramides and steroid saponins) related to the resistance to crown rust in a resistant line. We are also working on the interaction between mycorrhizal fungi and grasses also using RNAseq approaches. Several publications will be submitted in 2017. Objective 3: Study the genetic mechanisms of adaptation to stress environments (e.g. saline soils). (45% accomplished) We have completed studies ofsalt tolerance heritability and transcriptome analysis in prairie cordgrass showing the differential expression of photosynthesis and circadian rhythm regulation gene networks in the more salt tolerant genotypes. A manuscript has been completed and submitted for publication. We have also completed RNAseq analysis in spinach and rice in response to exposure to nanoparticles suggesting a similar response to that caused by pathogens; several publications are being prepared and expected to be submitted in 2017. Objective 4: Manage the newly established sequencing facility and facilitate the application of next generation sequencing technologies in other research projects. (Ongoing Effort) A next generation sequencing facility was established through funding from the National Science Foundation. All the equipment was purchased, installed and training has been completed.Installation is completed. I have provided consultation to over 15 PIs from different fields. Approximately 100 samples have been sequenced (to September 2016).
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Bimal Paudel, Michaellong Tran, Jose L. Gonzalez-Hernandez,, Arvid Boe, Gautam Sarath, and Jai S. Rohila. 2016. Proteomic Responses of Switchgrass and Prairie Cordgrass to Senescence. Frontiers in Plant Science (DOI: 10.3389/fpls.2016.00293)
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Hannah Graves, A.L. Rayburn, Jose L. Gonzalez-Hernandez, Gyoungju Nah, Do-Soon Kim and D.K. Lee. 2016. Validating DNA Polymorphisms Using KASP Assay in Prairie Cordgrass (Spartina pectinata Link) Populations in the U.S. Frontiers in Plant Science (DOI:10.3389/fpls.2015.01271)
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Figueir�, A. d. A., Gonzalez-Hernandez, J. L., Pacheco, M. T., Reese, R. N., de Morais, G. L., Guzman, F., Swaminathan, P. and Delatorre, C. A. (2016), RNAseq analysis reveals the role of secondary metabolism in the response of URS 21, a race-nonspecific resistant cultivar, to crown rust. Plant Pathology. ( doi:10.1111/ppa.12615)
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