Source: IOWA STATE UNIVERSITY submitted to NRP
GENETICS, GENOMICS AND BREEDING TO ALLEVIATE BIOTIC AND ABIOTIC STRESS IN SOYBEAN
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
HATCH
Reporting Frequency
Annual
Accession No.
0208526
Grant No.
(N/A)
Cumulative Award Amt.
(N/A)
Proposal No.
(N/A)
Multistate No.
(N/A)
Project Start Date
Aug 1, 2011
Project End Date
Jul 31, 2016
Grant Year
(N/A)
Program Code
[(N/A)]- (N/A)
Recipient Organization
IOWA STATE UNIVERSITY
2229 Lincoln Way
AMES,IA 50011
Performing Department
Agronomy
Non Technical Summary
The soybean crop is second only to corn in annual value in the US and was produced on approximately 76.8 million acres in 2009. Nearly half the world soybean crop is grown in the US. The US soybean crop is worth approximately twice that of wheat and 10 times that of rice. Soybean has numerous nutritional and industrial uses due to its unique seed chemical composition. With its high protein content (40%) and moderately high oil (20%), the soybean seed is the world's main source of vegetable protein and oil. It accounts for 55% of all oilseeds produced. Unfortunately soybean suffers from both biotic and abiotic stresses, and on an annual basis it suffers yield losses worth over 2 billion dollars just from biotic stresses. Therefore, improvement of soybean for disease resistance is a major priority to protect yield, growers' income and country's export and gross national product. Abiotic stress resulting in from iron deficiency chlorosis is a major problem in Iowa and much of the upper Midwest soybean producing states. In addition to improving soybean for resistance to both biotic and abiotic stresses, we will investigate the basis of insect attractants of flowers for improving cross pollination between male sterile and fertile lines for producing hybrid seeds. The project uses current molecular tools in understanding the genetic components involved in the expression of resistance or tolerance of soybean against the biotic and abiotic stresses. We will apply the new knowledge to be gained from these molecular studies and conventional breeding strategies in improving soybean for resistance/tolerance to biotic and abiotic stresses. Similarly, we will apply a genetic-molecular approach in order to decipher the genetic mechanism of pollen attraction for improving soybean for enhanced cross pollination; and thereby, higher yield from heterosis.
Animal Health Component
50%
Research Effort Categories
Basic
50%
Applied
50%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2011820104020%
2021820108020%
2031820112010%
2031820108110%
2061820104020%
2121820116010%
2121820108110%
Knowledge Area
212 - Pathogens and Nematodes Affecting Plants; 206 - Basic Plant Biology; 203 - Plant Biological Efficiency and Abiotic Stresses Affecting Plants; 202 - Plant Genetic Resources; 201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1820 - Soybean;

Field Of Science
1040 - Molecular biology; 1120 - Nematology; 1160 - Pathology; 1081 - Breeding; 1080 - Genetics;
Goals / Objectives
Goals: The goal of the project is to improve soybean for enhanced disease resistance, tolerance to iron chlorosis and increased seed yield. Objectives: A) Identify and develop markers for genes involved in iron homeostasis in soybean. B) Identify, characterize, and develop germplasm lines with novel resistance genes and gene families to Phytophthora root rot (PRR), brown stem rot (BSR), soybean cyst nematode (SCN), sudden death syndrome (SDS), iron deficiency chlorosis (IDC) and soybean rust (SR). C) Create broad-spectrum disease resistance in soybean by applying molecular genetic approaches. D) Identify genes and gene families potentially useful for hybrid soybean production via insect-mediated cross pollination. Expected Outputs: A) Molecular markers for selecting those genetic loci that are involved in efficient iron utilization in soybean germplasm will be generated. B) Novel genes conferring resistance to PRR, BSR, SCN, SDS and SR will be identified. Germplasm lines with resistance to PRR, BSR, SCN, SDS, IDC and SR will be developed and released to public. C) Transgenic soybean lines with broad-spectrum disease resistance to multiple pathogens will be developed. D) Genes involved in male fertility and female fertility will be isolated. Desirable soybean germplasm for generating hybrid seeds will be developed. Mechanisms of insect attraction by soybean flowers will be known. E) Graduate students, undergraduate students, and postdoctoral, assistant, associate and visiting scientists will be trained in the areas of plant genetics, plant breeding, plant molecular biology, plant physiology and plant pathology.
Project Methods
A) Identify and Develop Markers for Genes Involved in Iron Homeostasis in Soybean. For identifying molecular markers for candidate iron homeostasis loci, leaf and root tissues will be harvested from soybeans grown in iron replete and iron deplete conditions for a time course in three replications. Transcripts will be sequenced and counted. Data will be normalized and the Fisher Exact Test with a Bonferoni correction will be used to determine which genes are over or under expressed at each time point. Reverse transcriptase real time PCR will be conducted to confirm the expression levels of candidate genes for iron homeostasis. Single nucleotide polymorphisms (SNPs) of candidate genes among 248 lines will be used in determining the statistical association between the SNPs and iron efficiency scores. B) Identify, Characterize, and Develop Germplasm Lines with resistance to PRR, BSR, SCN, SDS, IDC and SR. Plant introduction lines will be screened for their resistance to different soybean diseases. Disease resistance genes will be mapped to identify molecular markers for selection of disease resistant genotypes. The work will be conducted in Iowa and Puerto Rico. In Iowa, field plantings will be conducted during the summer. Basic research will be conducted in growth chambers and greenhouse throughout the year. In Puerto Rico, soybeans will be planted year-round. Yield and agronomic evaluations are always conducted in Iowa. C) Genetic manipulation of soybean for disease resistance. Arabidopsis nonhost resistance genes essential for immunity against the soybean pathogen, P. sojae will be isolated by applying a map-based cloning approach. In addition to these Arabidopsis nonhost resistance genes, soybean disease resistance genes will be overexpressed in transgenic soybean lines for generating novel germplasms with durable and enhanced disease resistance. A plant antibody gene encoding an antibody against a toxin involved in SDS disease development will be expressed in transgenic soybean lines. Multiple transgenic lines per gene will be evaluated for possible enhanced disease resistance. D) Identify Genes and Gene Families to Enhance Insect Pollination. Attraction and subsequent floral reward to insects will be measured by decreased or increased seed-set on male-sterile, female-fertile plants. The Proboscis Extension Reflex (PER) test will be used to determine if floral volatiles attract (or repel) pollinators. The soybean genotypes that have very low and very high seed-set in the presence of pollinators will be used in the PER test. The PER response will be evaluated to determine if there is a correlation between presence of volatiles and insect-mediated cross-pollination, i.e. seed-set. Floral volatiles will be determined also by solid-phase microextraction and multidimensional gas chromatography-mass spectrometry. The data from the mass spectrometer will be compared to standards for compound identification.

Progress 08/01/11 to 07/31/16

Outputs
Target Audience:Target audiences include geneticists, physiologists, pathologists, soybean breeders, soybean growers in Iowa and the northern region of the U.S., crop consultants, and plant biologists. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?We have trained seven postdoctoral scientists, 15 graduate students, 11 undergraduate students for research in the areas of molecular plant pathology, plant breeding, plant genetics and bioinformatics. During their participation in the project, graduate students, postdoctoral and visiting scientists attend departmental seminars, lab meetings and supervise undergraduate students. Graduate students and postdoctoral scientists participated in training sessions to improve their programming skills, QTL analysis, GWAS analysis. They also attended annual scientific meetings as a part of their professional development. How have the results been disseminated to communities of interest?In January, Bhattacharyya spoke to the international research community composed of students, postdocs, and researchers from both private and public sectors at two workshops of the International Plant and Animal Genome Conference (i) on the application of soybean transposable element Tgm9 in inducing mutants for functional analyses of soybean genes and (ii) possible molecular basis of the phenotype of a soybean necrotic mutant induced by Tgm9. The meeting was held in the Town & Country Convention Center, San Diego, CA, during January 8-13,2016. Bhattacharyya spoke about the novel biotechnology approaches in fighting soybean sudden death syndrome at the 2016 Soybean Breeders' & Pathologists' Workshop held in St. Louis, MO, during 22-24 February 2016 attended by students, postdocs, and researchers from both private and public sectors. On March 1, he spoke to the students, postdocs, scientists and faculty about the novel transgenic approaches in enhancing SDS resistance in soybean in an seminar hosted by the Plant Pathology and Microbiology Department, Iowa State University. He also spoke about the role of folic acid in plant health to the students, scientists and faculty of ICAR-NRC Plant Biotechnology, IARI, on December 2, 2016. He then spoke about the same topic to the students, scientists and faculty of College of Veterinary Science, on December 6, 2016. On December 8, he spoke to students, postdocs, scientists, faculty and industry personnel about the progress towardsidentification ofadaptation genes for generating climate resilientcrop plants in the InternationalConference onClimateChange Adaptation and Biodiversity: Ecological Sustainability and Resource Management for Livelihood Security, Andaman Science Association, held in Port Blair, Andaman & Nicobar Islands, India. On December 10, he spoke to students, postdocs, scientists, faculty, and industry personnel about the identification and application of Arabidopsisnonhost immunity genes inenhancing disease resistance in soybean in an International Symposium hosted at the Central Plantation Crops Research Institute, Kerela, India. On December 14, Bhattacharyya spoke about a receptor-like protein that enhances resistance of soybean to pathogen and pests including soybean cyst nematodes in the Soybean Cyst Nematode Conference, hosted by APS at the Westin Colonnade, Coral Gables, Florida. The meeting was attended by students, postdocs, faculty, soybean growers, industry, and commodity board personnel. Cannon was a speaker at the Molecular and Cellular Biology of Soybean meeting, Columbus, OH, 2016 and spoke about the "Drivers of genome size change, and other insights from multi-species legume genome comparisons" in August, 2016 Cannon was a speaker at the annual meeting of ASPB (American Society of Plant Biologists) in July, 2016, where he spoke about "The Federated Plant Database Initiative for the legumes." Cianzio presented two invited talks. First she spoke at a symposium of the American Phytopathological Society on the relationship between phenotyping and genotyping to increase efficiency of breeding for disease resistance in soybean held in Tampa, FL on July 20, 2016. The symposium was attended by Plant Pathologists, breeders and personnel of the private seed industry. She was also an invited seminar on breeding for sudden death resistance in soybean, at the Univ. of Minnesota, Minneapolis on September 9, 2016. The seminar was attended by graduate students, and faculty members of the Crops and Soils and Plant Pathology department. Cianzio also presented results from her soybean cyst nematode research at the SCN research meeting - United Soybean Board, at Ames, IA, April 26, 2016 and presented a poster on soybean cyst nematode research evaluating the gene rhg1 at the Soybean Cyst Nematode Conference, Miami, Fl on December 14, 2016. Cianzio presented three talks about "Efforts to improve soybean yields and disease resistance for the benefit to the farmers" to stake holders,. The talks were presented at Extension meetings attended by farmers, crop consultants and seed dealers in Iowa at three different locations in Iowa. Graham was a keynote speaker at the International Symposium on Iron Nutrition and Interactions in Plants in Madrid, Spain, in May 2016. She spoke about "Using genomics to characterize soybean responses to iron deficiency" in that meeting. McCabe (Graham/Cianzio Labs) was speaker at the Baker Plant Breeding Symposium at Iowa State University. "Using RNA-seq to charaterize soybean responses to Brown Stem Rot". Singh spoke at workshops held at Iowa State University (Data Driven Science Initiative workshop on Jan 27/28, 2016; Phenotypic Prediction: Image Acquisition and Analysis on Feb 23-25, 2016) which included audience from the US and overseas particularly researchers including graduate students and post-doctoral fellows. These presentations were on data driven discovery for agricultural revolution and digital phenotyping for gene discoveries and genetic enhancement. On Mar 3, Singh spoke as an invited speaker at the R F Baker Symposium, which is organized by the graduate students in the Department of Agronomy, ISU, and include participants from public and private institutions working in plant breeding. In this presentation, Singh presented advances in machine learning and their applications in soybean breeding. Additionally, Singh presented a seminar at Monsanto (May 23), St. Louis, to a live audience as well as their global webinar. This presentation focused on breeding-engineering partnerships for the new way of crop improvement including Singh's program at ISU. Singh hosted a group of IA farmers on September 9 and talked about soybean breeding using engineering tools. In addition to IA farmers, graduate students and post-doctoral fellows from several program ware in the audience. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Soybean is an economically important crop. It is an important source of both oil and proteins for human nutrition and animal feed. It has become also a source of biodiesel. In this project we have applied multiple approaches primarily to protect yield losses of soybean from environmental stresses including both biotic and abiotic stresses. Outcomes of the project have positively impacted through advancing our knowledge and creating resources for the soybean research community, also by the development of novel soybean germplasm lines that will positively impact farm economy and the seed industry. The accomplishments are presented below under each objective. A) Molecular markers for selecting genetic loci that are involved in efficient iron utilization in soybean germplasm will be generated. Soybean producers lose millions of dollars to iron deficiency chlorosis (IDC). Our USDA-ARS collaborators measured the expression of all genes in the soybean genome in response 30, 60 and 120 minutes of iron stress in an IDC tolerant line. Previous research in model plants systems has demonstrated that the iron stress signal originates in the leaves but spreads to the roots to turn on iron uptake genes. Our analysis has revealed that the expression of DNA replication genes travels from shoot to root, while the expression of defense and iron uptake genes travels form root to shoot, suggesting a complex iron stress response in soybean. Further, iron stress responses that occur this early have not been reported in model species. This study identified thousands of candidate IDC tolerance genes that are being characterized using virus induced gene silencing. This research was partially funded by the Iowa Soybean Association, the North Central Soybean Research Program and the USDA-ARS. A field study was also conducted in 2014 and 2015 to determine the mechanism of IDC and identify molecular markers associated with IDC tolerance. Genome wide association (GWA) studies of IDC at multiple time-points and environments were conducted using more than 450 unique soybean germplasm accessions. A total of 61 and 91 SNPs were significantly associated with IDC under field conditions in 2014 and 2015, respectively. These SNPs were associated in response to Fe-stress. Putative candidate genes were identified on several chromosomes and will be tragets for marker development and usage. Additionally, we identified epistaticially interacting SNPs, particularly SNPs on GmChr03 that interact with multiple SNPs throughout the rest of the genome. B) Novel genes conferring resistance to PRR, BSR, SCN, SDS and ASR will be identified and germplasm lines with resistance to PRR, BSR, SCN, SDS, IDC and SR will be developed and released to the public. In order to characterize mechanisms of brown stem rot (BSR) (Rbs3) resistance, we have conducted genome-wide expression analyses in roots, stems and leaves, relative to a susceptible check. We identified more than 2,500 genes that responded to infection at seven days. Within the Rbs3 locus, we found that genes associated with toxin degradation and typical resistance genes were both differentially expressed in response to the BSR pathogen Phialophora gregata, but only in the resistant genotype. This suggests that BSR resistance could be regulated by two mechanisms. We have developed VIGS constructs that will be used to test this hypothesis. We are currently repeating this experiment using time points at 12, 24 and 36 hours after infection. These experiments will allow us to identify genes responding early to BSR infection that could be used for marker development and improved phenotyping in the future. Parallel to molecular studies on gene expression and functional analyses of soybean genes involved BSR resistance, we have bred and released three soybean germplasm lines resistant to soybean cyst nematodes (SCN) (AR16SCN, AR17SCN, AR18SCN). We have identified new molecular markers for quantitative trait loci (QTL) underlying sudden death syndrome (SDS) resistance in the cultivar MN1606. We have identified 16 new plant introduction (PI) lines with SDS resistance. To map the SDS resistance mechanisms in some of these lines, we have crossed some of these lines with an SDS susceptible line and developed several mapping populations. We have made progress in developing soybean lines that are resistant to Asian soybean rust (ASR). We plan to release a germplasm line that is resistant to ASR in 2017. We are evaluating new parameters to fine-tune the IDC screening protocol. Phytophthora sojae causes Phytophthors root rot (PRR) in soybean. We have mapped a new major PRR resistance gene, Rps12, and identified molecular markers linked to this gene. In a separate experiment, we have screened over 500 soybean PI lines for SDS and IDC. The PI lines were phenotyped under field and indoor screening (replicated and multiple field environments) conditions. We have selected several SDS resistant and IDC tolerant PI lines that have been used as parental sources in our soybean breeding programs. C) Transgenic soybean lines with broad-spectrum disease resistance to multiple pathogens will be developed. Earlier we have reported identification of four Arabidopsis nonhost resistance genes Pss1, 21, 25 and 30, that confer immunity of Arabidopsis against P. sojae and Fusarium virguliforme. F. virguliforme causes SDS in soybean. We have recently identified Pss6, which is also an Arabidopsis nonhost resistance gene that confers nonhost resistance against F. virguliforme and P. sojae. Transgenic soybean lines were developed for all five genes to test if any of these confer immunity against F. virguliforme under growth chamber and field conditions. Lines showing SDS resistance have been selected for crossing to soybean lines. Earlier we reported identification of four candidate soybean defense genes. Overexpression of three of these genes have shown to enhance SDS resistance under growth chamber and field conditions. D) Resource development for the soybean research community An Illumina Infinium BeadChip containing over 50,000 SNPs of soybean (Glycine max L. Merr.) has been developed (Song et al. 2013), and applied to characterize the USDA soybean germplasm collection of approximately 20,000 accessions. The genotyping information for these accessions has been made accessible to researchers at SoyBase, at http://soybase.org/snps/index.php. The markers are available in several forms at SoyBase interfaces: via a search form for particular named variants, via the genome browser, and via download - either as the complete set of accessions, or for indicated subsets, at http://soybase.org/snps/download.php. These markers and viewing tools are useable by researchers for identifying marker-trait associations across any collection of germplasm. This research was also funded by the USDA- ARS.

Publications

  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Bhattacharyya, M.K. (2016) The Tgm9-Induced Indexed Insertional Mutant Collection to Conduct Community-Based Reverse Genetic Studies in Soybean. Transposable Elements Workshop. Plant & Animal Genome XXIII, Town & Country Convention Center, San Diego, CA, January 8-13,�2016.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Bhattacharyya, M.K. (2016) Identification of Defense-related Proteins in the Root Necrotic Mutant rn1 in Soybean. Proteomics Workshop. Plant & Animal Genome �XXIII, Town & Country Convention Center, San Diego, CA, January 8-13,�2016.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Bhattacharyya, M.K. (2016) Novel biotech. approaches in fighting sudden death syndrome in soybean. 2016 Soybean Breeders & Pathologists Workshop. St. Louis, MO, 22-24 February 2016.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Bhattacharyya, M.K. (2016) Novel transgenic approaches in enhancing SDS resistance in soybean. Plant Pathology & Microbiology Department Seminar, March 1, 2016
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Bhattacharyya, M.K. (2016) Folic acid in plant health. ICAR-NRC Plant Biotechnology, IARI, December 2, 2016
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Bhattacharyya, M.K. (2016) Folic Acid in Plant Health. College of Veterinary Science, December 6, 2016.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Bhattacharyya, M.K. (2016) Towards�identification of�adaptation genes for generating climate resilient�crop plants. International�Conference on�Climate�Change Adaptation and Biodiversity: Ecological Sustainability and Resource Management for Livelihood Security, Andaman Science Association, Port Blair, Andaman & Nicobar Islands, India, 8-10, December, 2016.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Bhattacharyya, M.K. (2016) Identification and application of Arabidopsis�nonhost immunity genes in�enhancing disease resistance in soybean. International Symposium, Central Plantation Crops Research Institute, Kerela, 10-12, December, 2016.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Bhattacharyya (2016) Expression of a receptor-like protein enhances resistance of soybean to multiple pathogen and pests including soybean cyst nematodes. The Soybean Cyst Nematode Conference, APS Meeting, The Westin Colonnade, Coral Gables, Florida, December 14, 2016.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Cianzio, S.R. (2016) Relationship between phenotyping and genotyping to increase efficiency of breeding for disease resistance in soybean. APS Symposium, Tampa, FL, July 20, 2016.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Cianzio, S.R. (2016) Breeding for sudden death resistance in soybean. at the Crops and Soils and Plant Pathology Department, Univ. of Minnesota, Minneapolis, September 9, 2016.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Cianzio, S.R. (2016) Breeding for soybean cyst nematodes. SCN research meeting  United Soybean Board, Ames, IA, April 26, 2016.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Cianzio, S.R. (2016) Evaluation of the rhg1 gene. Soybean Cyst Nematode Conference, APS Meeting, Miami, Fl, December 14, 2016.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Lawrence-Dill C, AK Singh, B, Ganapathysubramanian. 2016. D3AI - Data Driven Discovery for Agricultural Innovation. Data Driven Science Initiative workshop. Jan 27-28, 2016, Ames, IA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Singh AK et al. 2016. Digital phenotyping for gene discoveries and genetic enhancement. Phenotypic Prediction: Image Acquisition and Analysis. Feb 23-25, 2016. ISU, Ames, IA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Singh AK (2016) Soybean Breeding. Seed Science Center, Feb 8, 2016. ISU, Ames, IA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Singh AK (2016) Application of Machine Learning in Soybean Breeding. R F Baker symposium, Mar 3, 2016. Ames, IA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Zhang J, A Singh, DS Mueller, AK Singh (2016) Genome-Wide Association and Epistasis Studies Unravel the Genetic Architecture of Sudden Death Syndrome Resistance in Soybean. Plant and Animal Genome conference. Jan 9-13, 2016. San Diego, CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Singh AK (2016) Advancing Soybean Breeding through Engineering partnerships. May 23, 2016. Monsanto, St. Louis.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Singh AK (2016) Soybean Breeding using engineering tools. Iowa Soybean Association. Sept 9, 2016, Boone, IA.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Cianzio, S.R., Lundeen, P. Bhattacharyya, M.K., Swaminathan, S., Gebhart, G., and Rivera-Velez, N. (2016) Registration of AR11SDS soybean germplasm resistant to sudden death syndrome, soybean cyst nematode and with adequate iron deficiency chlorosis. Journal of Plant Registrations 10:177188. Online 2015: doi:10.3198/jpr2015.02.0010crg.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Abeysekara, N.S., Desai, N., Guo, L., and Bhattacharyya, M.K. (2015) The Plant immunity inducer pipecolic acid accumulates in the xylem sap and leaves of soybean seedlings following Fusarium virguliforme infection. Plant Science 243:105114; doi:10.1016/j.plantsci.2015.11.008
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Abeysekara, N., Matthiesen, R.L., Cianzio, S., Bhattacharyya, M.K., and Robertson, A.E. (2016) Novel sources of partial resistance against Phytophthora sojae in PI 399036. Crop Sci. 56:114. doi: 10.2135/cropsci2015.09.0578
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Baumbach, J., Pudake R.N., Johnson, C.,�Ollhoff, A., Palmer, R.G., Bhattacharyya, M.K. and Sandhu, D. (2016) Transposon tagging of a male-sterility, female-sterility gene, St8, revealed that the meiotic MER3 DNA helicase activity is essential for fertility in soybean. PLoS One 11(3): e0150482. doi:10.1371
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Dash, S., Campbell, J.D., Cannon, E.K., Cleary, A.M., Huang, W., Kalberer, S.R., Karingula, V., Rice, A.G., Singh, J., Umale, P.E., Weeks, N.T., Wilkey, A.P., Farmer, A.D., Cannon, S.B. 2015. Legume information system (LegumeInfo.org): a key component of a set of federated data resources for the legume family. Nucleic Acids Research. doi: 10.1093/nar/gkv1159
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Huang, X., Das, A., Sahu, B.B., Srivastava, S.K., Leandro, L.F., ODonnell, K., and Bhattacharyya, M.K. (2016) Identification of hypervariable elements in an asexual pathogen. PLoS One 11(6): e0158183. doi:10.1371/journal.pone.0158183
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Liu, M., Li S., Swaminathan, S., Sahu, B.B., Leandro, L.F., Cardinal, A.J., Bhattacharyya, M.K., Song, Q., Walker, D.R., Cianzio, S.R. (2016) Identification of a soybean rust resistance gene in PI 567104B. Theor Appl Genet. 129: 863-877.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2017 Citation: Sahoo, D., Abeysekara, N., Cianzio, S., and Robertson, A.E., Bhattacharyya, M.K. (2017) A novel Phytophthora resistance gene, Rps12 mapped tightly to the Rps4/6 region in soybean. PLoS One, in press.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2017 Citation: Sahu, B.B., Baumbach, J., Singh, P., Srivastava, S.K., Yi, X., and Bhattacharyya, M.K. (2017) Investigation of the Fusarium virguliforme transcriptomes induced during infection of soybean roots suggests that enzymes with hydrolytic activities could play a major role in root necrosis. PLOS One, in press.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Samarah, N., Mullen, R., Cianzio, S.R., Gladon, R. and Goggi, S. 2016. Ethylene evolution from soybean seeds podded and depodded related to seed desiccation tolerance during maturation. Seed Science and Technology 44: 53-63
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Swaminathan, S., Abeysekara, N.S., Liu, M, Cianzio, C.R. and Bhattacharyya, M.K. (2015) Quantitative trait loci underlying host responses of soybean to Fusarium virguliforme toxins that cause foliar sudden death syndrome. Theor Appl Genet. 129:495-506. doi: 10.1007/s00122-015-2643-5. Epub 2015 Dec 17.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Xu, Z., Jiang, H., Sahu, B.B., Kambakam, S., Singh, P., Wang, X., Wang, Q., Bhattacharyya, M.K., and Dong, L (2016) Humidity assay for plant-pathogen interactions in miniature controlled discrete humidity environments with good throughput. Biomicrofluidics 10, 034108; http://dx.doi.org/10.1063/1.4950998


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

Outputs
Target Audience:Target audiences include geneticists, physiologists, pathologists, soybean breeders, soybean growers in Iowa and the northern region of the U.S., crop consultants, and plant biologists. Changes/Problems:Last year Dr. Reid Palmer passed away due to cancer-related illness. As a result, we will discontinue the Objective D as conducted by him. What opportunities for training and professional development has the project provided?We have trained seven postdoctoral scientists, 15 graduate students, 11 undergraduate students for research in the areas of molecular plant pathology, plant breeding, plant genetics and bioinformatics. During their participation in the project, graduate students, postdoctoral and visiting scientists attend departmental seminars, lab meetings and supervise undergraduate students. Gradaute students and PDFs participated in training sessions to improve their programming skills, QTL analysis, GWAS analysis. They also attended annual scientific meetings as a part of their professional development. How have the results been disseminated to communities of interest?Madan K. Bhattacharyya spoke at the Plant Interactions with Pests and Pathogens Workshop of the Plant & Animal Genome XXIII Conference, San Diego, CA, 10-14 January 2015 on "Arabidopsis Nonhost Resistance for Enhancing Disease Resistance in Soybean" to students and scientists of both public and private sectors. He also spoke at the 2nd International Conference on Frontiers in Biological Sciences (InCoFIBS-2015), Rourkela, Odisha, India, 22-24 January 2015 on "Transgenic Approaches in Managing Diseases in Soybean" to student and faculty community. He also spoke at the International Conference on Innate Immunity, Barcelona, Spain, 20-21 July 2015 on "Identification and Application of Nonhost iImmunity Mechanisms for Creating Broad-Spectrum Disease Resistance in Crop Plants" to students and scientists of both public and private sectors. Silvia Cianzio presented two posters at the Soybean Breeders Workshop, St. Louis, MO. 2015. Michele Graham spoke on "Using Genomics to Study Iron Deficiency Chlorosis in Soybean" at the Soybean Research Symposium: Linking Together Soybean Researchers, hosted by the Nebraska Soybean Board. Graham also presented two posters at the Plant and Animal Genome conference, San Diego CA, and one poster at the Soybean Breeders Workshop in St. Louis, MO and one poster at the American Society of Plant Biology meeting in Minneapolis, MN. Asheesh Singh presented a seminar on "The search for interacting loci: A tale of breeder-pathologists collaborations" at the University of Wisconsin, Madison. April 21, 2015. What do you plan to do during the next reporting period to accomplish the goals?A) Identify and develop markers for genes involved in iron homeostasis in soybean. For identifying molecular markers for candidate iron homeostasis loci, leaf and root tissues were investigated for differentially expressed genes by conducting transcriptomic assays and several candidate genes involved iron homeostasis were identified. We already have started to characterize these genes. We will continue to characterize these genes involved in iron deficiency chlorosis (IDC) tolerance using gene expression analyses and virus induced gene silencing. We have also earlier started to conduct genome wide association study (GWAS) for IDC. The GWAS for IDC will be completed and candidate genes for IDC tolerance will be identified based on single nucleotide polymorphisms (SNPs) of candidate genes among 500 diverse soybean lines. B) Identify, characterize, and develop germplasm lines with resistance to PRR, BSR, SCN, SDS, IDC and SR. Breeding work for developing disease resistant soybean lines led to identification of several disease resistant germplasm lines suitable for future breeding work. This work will be continued. Five of these lines with SDS and SCN resistance will be disclosed, and corresponding Material Transfer Agreements will be signed between ISURF and interested parties. GWAS will be continued to identify genes encoding SDS and Charcoal rot resistance. GWAS will be continued also for other agronomic traits. C) Genetic manipulation of soybean for disease resistance. We will continue to evaluate the Arabidopsis mutants that are susceptible to the SDS pathogen and isolate for additional Pss genes. The cloned Arabidopsis Pss genes conferring resistance to soybean pathogens will be used to generate transgenic soybean plants with durable and enhanced disease resistance. D) Resource development for the soybean research community. We will continue to maintain and extend the SoyBase genetics and genomics database, adding mapped traits from new publications, particularly for new features from GWAS studies.

Impacts
What was accomplished under these goals? Soybean is an economically important crops and a good source of both oil and proteins for human nutrition and animal feed. It has become also a good source of biodiesel. In this project we have applied multiple approaches primarily to protect soybean yield from losses due to environmental stresses including both biotic and abiotic stresses. Outcomes of the project include advancing our knowledge and creating resources for the soybean research community. New soybean germplasm lines will benefit farmers and consumers. The accomplishments are presented below under each objective. Obj. A) Molecular markers for selecting genetic loci that are involved in efficient iron utilization in soybean germplasm will be generated. Soybean producers lose millions of dollars to iron deficiency chlorosis (IDC). Our USDA-ARS collaborators measured the expression of all genes in the soybean genome in response to 1 and 6 hours of iron stress in an IDC tolerant line. This study identified hundreds of candidate IDC tolerance genes that are being characterized using virus induced gene silencing. This research suggests that IDC tolerant lines use sugar-signaling genes to signal iron stress to the roots, initiating uptake of iron from the soil. This research was also funded by the Iowa Soybean Association and the USDA-ARS. In addition to understanding the molecular basis of IDC, we have investigated approximately 450 diverse soybean plant introduction (PI) accessions from the USA gene bank (USDA; R. Nelson) to identify new sources PI accessions with tolerance to IDC. These PI accessions formed a genome wide association study (GWAS) panel and represent group maturities I, II and III. In 2014-15 and 2015, these diverse soybean accessions were phenotyped in specialized greenhouse system and IDC-affected field for response to IDC to unravel the genetic architecture of low-iron tolerance. For greenhouse screening, a unique high throughput screening system was developed, which allows for a rapid and high volume testing of soybean accessions, allowing for simultaneous testing of more than 500 accessions for IDC response. Genotypes in the GWAS panel varied in their response to IDC and are suitable for further studies to unravel the genetics of IDC tolerance. Since these accessions have already been genotyped using a 50K SNP chip, the data is being analyzed to find the associated SNP and genes. Results from this study are expected to help us identify new sources of IDC tolerance, understand the genetics, and help in breeding pipelines. Obj. B) Novel genes conferring resistance to PRR, BSR, SCN, SDS and SR will be identified and germplasm lines with resistance to PRR, BSR, SCN, SDS, IDC and SR will be developed and released to the public. We have bred soybean germplasm resistant to brown stem rot (BSR), and SDS. This year, IAR1902 SCN cultivar conferring SCN resistance and AR11SDS germplasm line conferring sudden death syndrome (SDS) resistance were registered and released. We have identified new plant introductions in maturity groups I, II, and III with SDS resistance, new plant introductions with BSR resistance, and a new resistant plant introduction with Asian soybean rust resistance. Numerous material transfer agreements were signed between ISU and interested parties for the genotypes released and are being used in breeding disease resistance and commercialization. In order to characterize mechanisms of BSR resistance, ISU and USDA-ARS collaborators have used microscopic studies to characterize BSR resistance governed by the Rbs1, Rbs2 and Rbs3 resistance genes. Our studies demonstrate that in Rbs1-infected plants, leaf symptoms are correlated with presence of the fungus in the leaves. In contrast, leaf symptoms are not correlated with fungal hyphae in the leaves and could be the result of a toxin. To further understand how resistance occurs in Rbs3 backgrounds, we have conducted genome-wide expression analyses in roots, stems and leaves, relative to a susceptible check. We identified more than 2,500 genes that responded to infection. These genes will be future targets for virus induced gene silencing. The same 450 diverse soybean PI accessions evaluated for tolerance to IDC were also phenotyped for Sclerotinia stem rot (white mold) reaction in a replicated field nursery and in the greenhouse, as well as for SDS and charcoal rot resistance in replicated field trials. Soybean genotypes with good white mold, SDS and charcoal rot resistance were identified. A full range of reaction for the three diseases in the genotype panel was observed, confirming this panel's utility for meaningful GWAS studies. Since these accessions have already been genotyped using a 50K SNP chip, analysis is now on-going to identify associated SNPs. Results from this study are expected to help identify new sources of resistance and understand the genetics, which will help in breeding for superior cultivars. Our work will lead to reduced input costs and improved sustainability. Similar projects on soybean cyst nematode and other diseases have been initiated. Obj. C) Transgenic soybean lines with broad-spectrum disease resistance to multiple pathogens will be developed.Earlier we identified Arabidopsis Pss1 as essential for the resistance of Arabidopsis against two soybean pathogens, Phytophthora sojae and Fusarium virguliforme, which cause root rot and SDS in soybean, respectively. We have cloned the Pss1 gene and by transferring this gene to transgenic soybean plants have demonstrated that it confers resistance to both P. sojae and F. virguliforme in soybean. We have identified Arabidopsis additional Pss genes, viz. Pss21, 25 and 30. We have also identified soybean genes that are involved in defense against the fungal pathogen F. virguliforme. Four of these candidate defense genes are transferred to soybean to enhance SDS resistance. Obj. D) Identify genes and gene families potentially useful for hybrid soybean production via insect-mediated cross pollination.This objective has been discontinued and replaced by a new objective described below. New Obj. D) Resource development for the soybean research community.Through USDA-ARS projects on campus, the SoyBase database continues to be actively extended, with addition of publications that describe the locations of traits, genes, and features of interest. A section of SoyBase was developed to present the SoyNAM Project, which is a multi-institution, multi-year nested association study designed to identify genomic regions of agronomic interest. Pedigrees for all of the entries in the Northern and Southern Uniform Testing Trials were collected and a database and web site developed to present them to the soybean breeding community. Two additional RNA-seq gene atlases were added to SoyBase. This along with the other data in SoyBase allows users to use tissue and developmental stage expression profiles to help identify genes conditioning important soybean traits. This work addresses the use of genomic and genetic data, information, and tools for germplasm improvement, thus empowering ARS scientists and partners to use a new generation of computational tools and resources. We have applied these bioinformatics tools and genomic resources to characterize a group of genes that help soybean and other plants respond to drought and salinity. Drought and salinity are major concerns for farmers throughout the world. Salinity often comes with irrigation, so occurs in many arid parts of the world. ARS researchers at ISU characterized a family of related genes in soybean, and identified several of these that are particularly active during soybean response to salt and desiccation stress. The corresponding genes in other species, including rice and the model plant Arabidopsis thaliana, have also been shown to help those plants respond to salt and drought. These genes are candidates for enhancement in soybean and other crops.

Publications

  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Liu, J., Graham, M.A., Pedley, K.F., Whitham, S.A. 2015. Gaining insight into soybean defense responses using functional genomics approaches. Briefings in Functional Genomics. DOI:10.1093/bfgp/elv009. Log 0000312505.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Abdelmajid, K.M., L. Ramos, D. Hyten, J. Bond, A. Bendahmane, P. Arelli, V.N. Njiti, S.R. Cianzio S.K. Kantartzi, and K. Meksem. 2014. Quantitative trait loci (QTL) that underlie SCN resistancde in soybean [Glycine max (L.) Merr.] PI438489B by 'Hamilton' recombinant inbred line (RIL) population. Atlas J. Plant Biol. 1:29-38.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Liu, M., C, Liepold, S. Swaminathan, and S.R. Cianzio. 2014. Advances of Asian Soybean Rust research. Chinese J. Oil Crop Sci. 36:676-684. Doi:10.7505/j.issn.1007-9084.2014.05.019.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Rincker, K., R. Nelson, J. Specht, D. Sleper, T. Cary, S.R. Cianzio, S. Casteel, S. Conley, P. Chen, V. Davis, C. Fox, G. Graef, C. Godsey, D. Holshouser, G. L. Jiang, S. Kantartzi, W. Kenworthy, C. Lee, R. Mian, L. McHale, S. Naeve, J. Orf, V. Poysa, W. Schapaugh, G. Shannon, R. Uniatowski, D. Wang and B. Diers. 2014. Genetic Improvement of U.S. Soybean in Maturity Groups II, III, and IV. Crop Science (1) 2014 0: 0: -doi:10.2135/cropsci2013.10.0665Rincker.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Bolon, Yung-Tsi, Stec, Adrian O. , Michno, Jean-Michel , Roessler, Jeffrey , Bhaskar, Pudota B. , Ries, Landon , Dobbels, Austin A. , Campbell, Benjamin W. , Anderson, Justin E., Grant, David M., Orf, James H., Naeve, Seth L., Muehlbauer, Gary J., Vance, Carroll P., Stupar, Robert M. (2014) Genome Resilience and Prevalence of Segmental Duplications Following Fast Neutron Irradiation of Soybean. Genetics genetics.114.170340; early online September 10, 2014, doi:10.1534/genetics.114.170340.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Sun, M., S.A. Goggi, K. Matson, R.G. Palmer, K. Moore, and S.R. Cianzio. 2015. Thin plate spline regression model used at early stages of soybean breeding to control field spatial variation. J. Crop Improv. (available on line at http://www.tandfonline.com/doi/full/10.1080/15427528.2015.1026623.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Arelli, P.R., A. Mengistu, R.L. Nelson, S.R. Cianzio and T. Vuong. 2015. New soybean accessions evaluated for reaction to Heterodera glycines populations. Crop Science 55:1236-1242. Doi:10.2135/cropsci2014.10.0696.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Belamkar, V., Weeks, N.T., Bharti, A.K., Farmer, A.D., Graham, M.A., Cannon, S.B. 2014. Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress. BMC Genomics 2014, 15:950 (3 November 2014).


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

Outputs
Target Audience: Target audiences include geneticists, physiologists, pathologists, soybean breeders, soybean growers in Iowa and the northern region of the U.S., crop consultants, plant biologists, and pollination biologists. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? We have trained three postdoctoral scientists, one assistant scientist, two graduate students, and three visiting scientists for research in the areas of molecular plant pathology and plant genetics. We have also trained two graduate students and two visiting scientists in plant breeding. A George Washington Carver intern worked on the project for 8 weeks this summer. In an ongoing collaboration, a student is learning to use bioinformatic analyses to identify genes involved in IDC tolerance. How have the results been disseminated to communities of interest? We have disseminated the results mainly through publications in peer-reviewed journals and released notes of new germplasm. We have also presented our results in scientific meetings or conferences including several agricultural and pollinator meetings. Some of the presentations were invited presentations. Thirty-five Material and Transfer Agreements were signed among ISU Research Foundation and public and private breeders for use of the lines released by this project. What do you plan to do during the next reporting period to accomplish the goals? A) Identify and Develop Markers for Genes Involved in Iron Homeostasis in Soybean. For identifying molecular markers for candidate iron homeostasis loci, leaf and root tissues will be harvested from soybeans grown in iron replete and iron deplete conditions for a time course in three replications. Transcripts will be sequenced and counted. Data will be normalized and the Fisher Exact Test with a Bonferoni correction will be used to determine which genes are over or under expressed at each time point. Reverse transcriptase real time PCR will be conducted to confirm the expression levels of candidate genes for iron homeostasis. Single nucleotide polymorphisms (SNPs) of candidate genes among 248 lines will be used in determining the statistical association between the SNPs and iron efficiency scores. Genome wide association study (GWAS) panel of close to 500 diverse soybean lines that will be phenotyped for IDC response in replicated field test. IDC response will be noted with visual and SPAD chlorophyll meter (Spectrum Technologies). This experiment will be repeated in field and in hydroponic condition indoors. B) Identify, Characterize, and Develop Germplasm Lines with resistance to PRR, BSR, SCN, SDS, IDC and SR. Plant introduction lines will be screened for their resistance to different soybean diseases. Disease resistance genes will be mapped to identify molecular markers for selection of disease resistant genotypes. The work will be conducted in Iowa and Puerto Rico. In Iowa, field plantings will be conducted during the summer. Basic research will be conducted in growth chambers and greenhouse throughout the year. In Puerto Rico, soybeans will be planted year-round. Yield and agronomic evaluations are always conducted in Iowa. C) Genetic manipulation of soybean for disease resistance. Arabidopsis nonhost resistance genes essential for immunity against the soybean pathogen, P. sojae will be isolated by applying a map-based cloning approach. In addition to these Arabidopsis nonhost resistance genes, soybean disease resistance genes will be overexpressed in transgenic soybean lines for generating novel germplasms with durable and enhanced disease resistance. D) Additional gene expression information will be added to SoyBase to help identify how various genes are regulated and when and where they are active in the plant.

Impacts
What was accomplished under these goals? Soybean suffers from several diseases, and annually 14% of the total yield valued at several billion dollars is compromised because of the incidence of diseases and pest attacks. Non-host resistance mechanisms have been considered to improve resistance of crop plants. We have identified Arabidopsis Pss21 and Pss25 genes that encode an ABC1-like protein 1 and a BEL family of homodeodomain protein (BLH2), respectively. Both genes confer resistance of Arabidopsis against two soybean pathogens, Phytophthora sojae and Fusarium virguliforme, causing root rot and sudden death syndrome (SDS) in soybean, respectively. We have identified four soybean genes, transcriptions of which are suppressed by F. virguliforme. Expression of the three of these genes encoding salicylic acid methyl transferases, ankyrin repeat-containing protein, and a novel unknown protein during infection enhanced resistance to both P. sojae and F. virguliforme. We have been characterizing soybean defense responses to Brown Stem Rot caused by the pathogen Phialophora gregata f. sp. sojae. P. gregata is a soil-borne pathogen that invades the main and lateral roots and progressively colonizes the xylem vessels of the root. It then spreads systemically colonizing the stem, petiole, and leaf tissues. Three independent P. gregata resistance genes, Rbs1, Rbs2, and Rbs3, have been identified and mapped to chromosome 16, Molecular Linkage Group (MLG) J. Each gene was identified from plant introductions from the National Soybean Germplasm Collection. In searches for new sources of BSR resistance, four potential plant introduction (PI) lines were identified: PI 594858B, PI 594637, PI 594638B and PI 594650A. By crossing each of the PI to lines containing Rbs1, Rbs2, or Rbs3 and evaluating the progeny for resistance to P. gregata, we can determine if the new PIs contain novel sources of resistance. PI 594638B, PI 594858B, and PI 594650A each segregated in a 15:1 ratio, with each of the known resistance genes, indicating the PIs contain at least one new resistance gene. Future tests will include characterization of segregating progenies of crosses among PIs to determine how many novel resistance genes exist. In addition, we are using microscopic analyses to characterize plant response to P. gregata. We have assembled a genome-wide association study (GWAS) panel of close to 500 diverse soybean accessions obtained from the USDA gene bank. These accessions were phenotyped for IDC response in replicated field test and also for Sclerotinia stem rot (white mold) reaction in a replicated field nursery. IDC response was noted with visual and SPAD ratings. Genotypes in our GWAS panel varied in their response to IDC and are suitable for GWAS studies to unravel the genetics of IDC tolerance. Since these accessions have already been genotyped using a 50K SNP chip, we are now analyzing our data. This IDC study will be repeated in 2015 under field as well as in hydroponic conditions. We have worked towards assessing and improving gene predictions for the soybean genome sequence. An updated version of the soybean genome assembly and new gene predictions are available at SoyBase, the USDA-ARS database. These gene models have been incorporated into the genome browser at SoyBase, along with detailed report pages for all gene predictions. A translation tool allows researchers to find and compare soybean gene predictions from older and newer research. This information will be used by breeders and other researchers to generate improved soybean varieties. Soybeans yields can be severely decreased by drought, heat stress, and, saline soil conditions. All of these stresses are likely to increase with climate change and intensification of agriculture: drought and heat stress due to higher temperatures, and saline soil conditions due to salts left in the soil during irrigation or by incursion of salty water in coastal areas. We have characterized a large group of related genes in soybean in soybean (the HD-Zip transcription factor gene family) that respond to salt and desiccation. The results of this work will be useful to plant breeders and researchers working to produce soybean varieties that are more tolerant to climate and environmental stresses.

Publications

  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Belamkar, V., Weeks, N.T., Bharti, A.K., Farmer, A.D., Graham, M.A., Cannon, S.B. 2014. Characterization and expression profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress. BMC Genomics 2014, 15:950
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Martin, Kathleen M., Hill, John H., Cannon Steven B. 2014. Occurrence and characterization of Bean common mosaic virus strain NL1 in Iowa. Plant Disease 98:11, 1593.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Anderson, J.E., Kantar, M.B., Kono, T.Y., Fu, F., Stec, A.O., Song, Q., Cregan, P.B., Specht, J.E., Diers, B.W., Cannon, S.B., McHale, L.H., Stupar, R.M. 2014. A roadmap for functional and structural variants in the soybean genome. Genes Genomes Genetics (G3), 10.1534/g3.114.011551
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Srivastava SK, Huang X, Brar HK, Fakhoury AM, Bluhm BH,Bhattacharyya MK. 2014. The genome sequence of the fungal pathogen Fusarium virguliforme that causes sudden death syndrome in soybean. PLoS One. 9(1):e81832. doi: 10.1371/journal.pone.0081832. eCollection 2014.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Abeysekara NS, Bhattacharyya MK. 2014. Analyses of the xylem sap proteomes identified candidate Fusarium virguliforme proteinacious toxins. PLoS One. 20;9(5):e93667. doi: 10.1371/journal.pone.0093667. eCollection 2014.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Hughes TJ, O'Donnell K, Sink S, Rooney AP, Scandiani MM, Luque A, Bhattacharyya MK, Huang X. 2014. Genetic architecture and evolution of the mating type locus in fusaria that cause soybean sudden death syndrome and bean root rot. Mycologia. 2014 Jul-Aug;106(4):686-97. doi: 10.3852/13-318. Epub 2014 Jun 2.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Atwood SE, O'Rourke JA, Peiffer GA, Yin T, Majumder M, Zhang C, Cianzio SR, Hill JH, Cook D, Whitham SA, Shoemaker RC, Graham MA. (2014) Replication protein A subunit 3 and the iron efficiency response in soybean. 2014. Plant Cell Environ. 37(1):213-34. doi: 10.1111/pce.12147.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Wang Y, Lu J, Chen S, Shu L, Palmer RG, Xing G, Li Y, Yang S, Yu D, Zhao T, Gai J. Exploration of presence/absence variation and corresponding polymorphic markers in soybean genome. J Integr Plant Biol. 56(10):1009-19. doi: 10.1111/jipb.12208.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Yang Y, Speth BD, Boonyoo N, Baumert E, Atkinson TR, Palmer RG, Sandhu D. 2014. Molecular mapping of three male-sterile, female-fertile mutants and generation of a comprehensive map of all known male sterility genes in soybean. Genome. 57(3):155-60. doi: 10.1139/gen-2014-0018.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Campbell BW, Mani D, Curtin SJ, Slattery RA, Michno JM, Ort DR, Schaus PJ, Palmer RG, Orf JH, Stupar RM. (2014) Identical Substitutions in Magnesium Chelatase ParalogsResult in Chlorophyll Deficient Soybean Mutants. G3 (Bethesda). pii: g3.114.015255. doi: 10.1534/g3.114.015255.


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

Outputs
Target Audience: Target audiences include geneticists, physiologists, pathologists, soybean breeders, soybean growers in Iowa and the northern region of the U.S., crop consultants, plant biologists, and pollination biologists. Changes/Problems: More funding is required to continue this level of production. What opportunities for training and professional development has the project provided? We have trained three postdoctoral scientists, one assistant scientist, two graduate students, and three visiting scientists for research in the areas of molecular plant pathology and plant genetics. We have also trained two graduate students and two visiting scientists in plant breeding. A George Washington Carver intern worked on the project for 8 weeks this summer. In an ongoing collaboration, a student is learning to use bioinformatic analyses to identify genes involved in IDC tolerance. Training has been taken for the use of the proboscis extension response system (PERS) using honey bees. In addition, undergraduates have been trained in pollination technique and implementation. How have the results been disseminated to communities of interest? We have disseminated the results mainly through publications in peer-reviewed journals and released notes of new germplasm. We have also presented our results in scientific meetings or conferences including several agricultural, and pollinator meetings. Some of the presentations were invited presentations. Thirty-five Material and Transfer Agreements were signed among ISU Research Foundation and public and private breeders for use of the lines released by this project. What do you plan to do during the next reporting period to accomplish the goals? Characterize the pss mutants and clone additional Pss genes to engineer enhanced disease resistance in transgenic soybean plants. Continue research on breeding for disease and pest resistance, release two cultivars and two germplasm lines; continue training graduate students. We will silence additional iron-responsive genes by conducting VIGS. We use hydroponics and soil conditions to evaluate the phenotypes of the silenced soybean plants for determining the role of selected genes in conferring tolerance to IDC. As we identify novel candidate genes involved in IDC responses, we will combine VIGS with RNAseq data to identify the gene networks regulate by the candidate genes. Determine the relationship between high and low seed-set soybean lines with flower morphology. The size and shape of soybean flowers from various high and low seed-set lines will be analyzed, and relationships between these data and seed-set data will be determined.

Impacts
What was accomplished under these goals? Soybean suffers from several diseases, and annually 14% of the total yield valued at several billion dollars is compromised because of the incidence of diseases and pest attacks. Nonhost resistance mechanisms have been considered to improve resistance of crop plants. We have identified Arabidopsis Pss1 as essential for the resistance of Arabidopsis against two soybean pathogens, Phytophthora sojae and Fusarium virguliforme, which cause root rot and sudden death syndrome (SDS) in soybean, respectively. We have cloned the Pss1 gene and showed that when the gene is transferred to soybean, it confers resistance to both P. sojae and F. virguliforme in soybean. We have bred soybean germplasms that are resistant to brown stem rot (BSR), and SDS diseases in soybean. This year, IAR1901 BSR cultivar conferring BSR resistance and AR10SDS germplasm line conferring SDS resistance were registered and released. We have identified new resistant QTL associated with SDS resistance, new resistance genes for BSR, and a new resistant gene conferring resistance to Asian soybean rust. This research was funded by the Iowa Soybean Association, the United Soybean Board and the North Central Soybean Research Program. Soybean producers lose millions of dollars in lost production to iron deficiency chlorosis (IDC). Using Virus Induced Gene Silencing (VIGS), we have identified GmRPA3, a DNA replication gene involved in tolerance to IDC. GmRPA3 was located within an IDC QTL. Lowering the expression of GmRPA3 in IDC susceptible lines inhibited growth and improved IDC tolerance. RNA-seq analyses demonstrated that silencing GmRPA3c resulted in the differential expression of thousands of genes involved in stress, defense and nutrient salvaging responses. We are now screening additional genes that could impart IDC tolerance by VIGS. This research was also partially funded by the Iowa Soybean Association, the United Soybean Board and the USDA-ARS. Research on volatiles from soybean flowers of insect-mediated low-seed-set genotypes was compared to volatiles of insect-mediated high seed-set genotypes. The Proboscis Extension Response (PER) test confirmed that certain volatiles are associated with high seed-set genotypes by using live honey bees. This information will result in faster and more efficient evaluation of potential parents for hybridization programs, which will result in lower hybrid seed costs for the farmer.

Publications

  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Geiser, D.M., Aoki, T., Bacon, C.W., Baker, S.E., Bhattacharyya, M.K., et al. 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: Kim, H., G. Xing, Y. Wang, T. Zhao, D. Yu, S. Yang, Y. Li, S. Chen, R.G. Palmer, and J. Gai. (2013) Constitution of resistance to common cutworm in terms of antibiosis and antixenosis in soybean RIL populations. Euphytica DOI 10.1007/s10681-013-1021-0.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: King, K.E., Peiffer, G.A., Reddy, M., Lauter, N., Lin, S.F., Cianzio, S., and Shoemaker, R.C. 2013. Mapping of iron and zinc quantitative trait loci in soybean for association to iron deficiency chlorosis resistance. Journal of Plant Nutrition 36:2132-2153.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Luckew, A.S., Leandro, L.F., Bhattacharyya, M.K., Nordman, D.J., Lightfoot, D.A., and Cianzio, S.R. 2013. Usefulness of 10 genomic regions in soybean associated with sudden death syndrome resistance. Theor Appl Genet 126:2391-2403.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Ott, A., Yang, Y., Bhattacharyya, M., Horner, H., Palmer, R., and Sandhu, D. 2013. Molecular mapping of D1, D2 and ms5 revealed linkage between the cotyledon color locus D2 and the male-sterile locus ms5 in soybean. Plants 2:441-454.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Pudake, R.N., Swaminathan, S., Sahu, B.B., Leandro, L.F., and Bhattacharyya, M.K. 2013. Investigation of the Fusarium virguliforme fvtox1 mutants revealed that the FvTox1 toxin is involved in foliar sudden death syndrome development in soybean. Curr Genet 59:107-117.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Raval, J., Baumbach, J., Ollhoff, A.R., Pudake, R.N., Palmer, R.G., Bhattacharyya, M.K., and Sandhu, D. 2013. A candidate male-fertility female-fertility gene tagged by the soybean endogenous transposon, Tgm9. Funct Integr Genomics 13:67-73.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2013 Citation: Bhattacharyya, M.K. 2013. Fvtox1 is a major virulence factor that causes foliar sudden death syndrome in soybean. BIT's 3rd Annual World Congress of Agriculture-2013. Hangzhou, China, September 23-25, 2013.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2013 Citation: Bhattacharyya, M.K. 2013. Arabidopsis nonhost disease resistance for improving disease resistance in soybean. Lilongwe University, Lilongwe, Malawi, Africa, July 1, 2013.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2013 Citation: Bhattacharyya, M.K. 2013. The role of a proteinacious toxin in developing the sudden death syndrome disease in soybean. Chitedze Research Station, Lilongwe, Malawi, Africa, June 28, 2013.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2013 Citation: Bhattacharyya, M.K. 2013. The Arabidopsis thaliana PSS1 gene confers nonhost resistance against two soybean pathogens, Phytophthora sojae and Fusarium viguliforme. The First International American Moroccan Agricultural Sciences Conference. Rabat, Morocco, Africa, March 18-19, 2013.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Bhattacharyya, M.K. 2013. Transgenic approaches in managing sudden death syndrome in soybean. USDA/NIFA Agriculture and Food Research Initiative Microbial Programs Awardee Meeting, Washington, DC, August 7-8, 2013.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2013 Citation: Bhattacharyya, M.K. 2013. Transgenic approaches in fighting sudden death syndrome in soybean. Plant Genomics & Biotechnology Workshop for 7th - 12th grade teachers and high school students, Tuskegee University, Tuskegee, AL, July 29, 2013.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2013 Citation: Bhattacharyya, M.K. 2013. Nonhost resistance for engineering disease resistance. CPBR Symposium, Washington, DC, March 5-6, 2013.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2013 Citation: Palmer, R.G. 2013. Study of soybean traits that contribute to insect pollinator attraction and reward. Chinese National Center for Soybean Improvement meeting. Nanjing Agricultural University, 3 September, 2013.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2013 Citation: Luckew, A.S., Leandro, L.F., Bhattacharyya, M.K., Nordman, D.J., Lightfoot, D.A., and Cianzio, S.R. 2013. Usefulness of 10 genomic regions in soybean associated with sudden death syndrome resistance. ASA meeting, Nov. 3-6, 2013, Tampa, FL.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2013 Citation: Liepold, C., M. Graham, and S.R. Cianzio. 2013. New sources of resistance to brown stem rot in soybeans. ASA meeting, Nov. 3-6, 2013, Tampa, FL.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2013 Citation: King, K.E., Peiffer, G.A., Reddy, M., Lauter, N., Lin, S.F., Cianzio, S., and Shoemaker, R.C. 2013. Mapping of iron and zinc quantitative trait loci in soybean for association to iron deficiency chlorosis resistance. International Iron Symposium, June 3-7, 2013 Amherst, MS.


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

Outputs
OUTPUTS: (1) Diseases and pests threaten soybean yields and deter farmers' income. The project continues to release germplasm lines and cultivars with improved disease resistance. During the period 2012, 15 soybean germplasm lines and cultivars were made available for public use. Discoveries on the functioning of the soybean cyst nematode resistance gene rhg1 were accomplished during 2012, in populations developed by the soybean breeding project of Iowa State with the specific purpose of conducting this research. A paper in Nature was published this past December. (2) To generate foliar sudden death syndrome (SDS) resistance in soybean, a synthetic gene encoding a plant antibody against the Fusarium virguliforme toxin FvTox1 was created. It conferred enhanced foliar SDS resistance in transgenic soybean lines. We have created several fvtox1 mutants lacking FvTox1. Investigation of fvtox1 mutants suggested that FvTox1 is involved in foliar SDS development. We have mapped a soybean locus encoding tolerance to F. virguliforme toxins. Arabidopsis thaliana nonhost resistance Pss1 and Pss30 genes have been mapped. Pss1 has have been cloned and transformed into a soybean line for enhancing disease resistance. (3) Phosphate uptake attribute determines the crop productivity. Quantitative trait loci (QTL) analysis of Total Phosphate (TP) was performed to identify candidate genes that are involved in P accumulation in soybean seed. One QTL region was identified on chromosome 12 in the combined data that contained a phosphate transporter gene. Two additional QTL were identified on chromosomes 7 and 17 with chromosome 7 having both a phosphate transport gene and a ZIP transporter gene in the region of the QTL. We identified 4,339 compositionally distinct genomic domains and 331 of these were identified as Long Homogeneous Genome Regions (LHGRs). We assigned these to four families based on GC content. We then characterized each family with respect to exon length, gene content, transposeable elements. The LHGR pattern of soybeans is unique in that while the majority of the genes within LHGRs are found within a single LHGR family with a narrow GC-range (Family B), that family is not the highest in GC content as seen in vertebrates and invertebrates. (4) Some plant volatile compounds play a major role as insect attarctants. Solids-phase microextraction and multidimensional gas chromatography-mass-spectrometry olfactometry were employed to sample and identify volatile compounds from soybean flowers. This technology is ideally suited to identify the various volatile compounds produced by soybean that contribute to insect pollinator discovery/attraction. The Proboscis Extension Response System (PERS) test was conducted with high and low seed-set lines developed from two different insect-mediated cross-pollinations. This technology broadened our previous finding that honeybees are quicker, and more easily conditioned to associate a sugar reward with the volatile organic compounds emitted by flowers of the high seed-set lines than the low seed-set lines. PARTICIPANTS: (1) In breeding soybean for disease and pests resistance project, Dr. Silvia R. Cianzio and her lab members, in addition to Dr. Leonor Leandro, Dr. Madan K. Bhattacharyya, Dr. Alison Robertson, Dr. Siva Swaminathan, Dr. Nilawa Abeysekera participated. (2) For molecular studies on FvTox1, synthetic plant anti-FvTox1 antibody and Pss genes, Dr. Madan Bhattacharyya collaborated with his graduate students, Rishi Sumit and Jordan Baumbach and postdoctoral scientists, Drs. Siva Swaminathan, Binod Sahu and Catherine Brooke, Nilwala Abeysekera and faculty, Drs. Leonor Leandro and Silvia Cianzio. (3) For the project on iron deficiency chlorosis Dr. Silvia Cianzio (ISU), Dr. Michelle Graham, USDA-ARS, Ames, and Dr. Carroll Vance, USDA-ARS, St. Paul, MN participated. Dr. Greg Peiffer, Dr. Keith King, and Dr. Jenna Woody conducted analyses as part of their PhD and M.S. programs in the iron chlorosis project and in studies of soybean genome organization. Partial funding was received from USDA-ARS and the North Central Soybean Research Program and the Iowa Soybean Association. (4) Dr. Jacek Koziel of the atmospheric Air Quality Laboratory provided the training, and facilities to characterize the soybean volatiles. Dr. Jerry Bromenshenk, (Bee Alert) provided the technical training and fabricated the two PERS units. TARGET AUDIENCES: Methods and results were disseminated through publication of peer-reviewed papers, abstracts and on-line industry reports, and presentations at scientific meetings and to individual stakeholders. (1) In breeding soybean for disease resistance, the target audiences are plant breeders (private and public), soybean growers in Iowa and the northern region of the U.S., and crop consultants. (2) The audiences for the foliar SDS pathogen, F. virguliforme anti-Fvtoxin1 antibody, Arabidopsis nonhost resistance gene, Phytophthora resistance projects include soybean pathologists as well as soybean breeders and molecular geneticists. (3) For the iron chlorosis project, the target audiences include geneticists, physiologists and plant breeders interested in plant nutrition and iron utilization. Studies on genome organization are targeted to evolutionary biologists. (4) The audiences for the soybean volatile research include scientists who want to identify volatiles from flowers, or other plant tissues. Additional audiences for the PERS test include scientists who study insect behavior. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
(1) Research on disease resistance and the release of resistant germplasm lines to diseases of economic importance in Iowa and the Midwest contributes to improve resistance of commercial cultivars. During 2012, 35 MTA agreements were signed between ISU and soybean breeders for use of new germplasm lines with resistance to soybean diseases in other soybean breeding programs. (2) Arabidopsis Pss1 essential for resistance of Arabidopsis against two soybean pathogens, P. sojae and F. virguliforme, has been cloned and incorporated into soybean for enhancing resistance against these two destructive pathogens. Pss30 conferring resistance of Arabidopsis against P. sojae could also confer immunity of soybean against this serious soybean pathogen. Expression of plant antibody against FvTox1 has shown to enhance resistance of soybean against F. virguliforme that causes SDS in soybean. (3) The identification of causative genic regions underlying iron efficiency in soybean provides inroads to the study of the mechanisms behind this complex trait. The identification of QTL affecting iron stress response has provided candidates from which molecular markers may be developed. The markers will facilitate the advancement of breeding programs for iron deficiency chlorosis. Identification of QTL affecting phosphorous content in soybean will lead to a better understanding of nutrient interactions in legumes. Studies of the organization of isochors in the genome will teach us much about how legume and other plant genomes have evolved. (4) Research on volatiles from soybean flowers of insect-mediated low-seed-set genotypes will be compared to volatiles of insect-mediated high seed-set genotypes. If certain unique compounds or differences in concentration of certain volatiles can be detected between these genotypes, chemical analyses can be used to identify potential insect-mediated high seed-set genotype without labor intensive field studies with insect pollinators. The PERS test confirms that volatiles that are associated with high seed-set by using live honeybees. Faster and more efficient evaluation of potential parents for hybridization programs will result in lower hybrid seed costs for the farmer.

Publications

  • Priester, J.H., Ge, Y., Mielke, R.E., Horst, A.M., Moritz, S.C., Espinosa, K., Gelb, J., Walker, S.L., Nisbet, R.M., An, Y.J., Schimel, J.P., Palmer, R.G., Hernandez-Viezcas, J.A., Zhao, L., Gardea-Torresdey, J.L., Holden, P.A. (2012) Soybean susceptibility to manufactured nanomaterials with evidence for food quality and soil fertility interruption. Proc Natl Acad Sci U S A. 109:E2451-6.
  • Perez-Sackett, P.T., Palmer, R.G. (2012) Effect of day and night temperature on the expression of male sterility of nuclear male-sterile (ms8ms8) soybean. Euphytica. 186:847-853.
  • Abdelmajid, K.M., L. Ramos, L. Leandro, G. Mbofung,D.L. Hyten, S.K. Kantartzi, R.L. Grier IV, V.N. Njiti, S.R. Cianzio, and K. Meksem. (2012) The PI 438489B by Hamilton SNP-based genetic linkage map of soybean [Glycine max (L.) Merr.] identified qunatitativd trait loci that underlie seedling SDS resistance. J. Plant Genome Sciences 1:18-30.
  • Pfeiffer, G. A., K. E. King, A. J. Severin, G. D. May, S. R. Cianzio, Shun Fu Lin, N. C. Lauter, and R. C. Shoemaker (2012) Identification of candidate genes underlying an iron efficiency QTL in soybean. Plant Phys. 158:1745-1754.
  • Liu, S., Kandoth, P.K., Warren, S.D., Yeckel, G., Heinz, R., Alden, J., Yang, C, Jamai, A., El-Mellouki, T., Juvale, P.S., Hill, J., Baum, T.J., Cianzio, S., Whitham, S.A., Korkin, D., Mitchum, M.G., Meksem, K. (2012) A soybean cyst nematode resistance gene points to a new mechanism of plant resistance to pathogens. Nature 492:256-260.
  • Baumbach, J., Slattery, R.A., Rogers J.P., Narayanan N.N., Xu, M., Palmer, R.G., Bhattacharyya, M.K., and Sandhu, D. (2012) Segregation distortion in a region containing a male-sterility, female-sterility locus in soybean. Plant Science, 195:151-156.
  • Brar H.K. and Bhattacharyya M.K. (2012) Expression of a single chain plant antibody against a phytotoxin enhanced tolerance to sudden death syndrome in soybean. Mol. Plant-Microbe Interact., 25:817-824.
  • Luckew, A.S., S. R. Cianzio and L.F. Leandro. (2012) Screening method for distinguishing soybean resistance to Fusarium virguliforme in resistant x resistant crosses. Crop Sci. 52:2215-2223.
  • Sahu, B.B., Sumit, R., and Bhattacharyya, M.K. (2012) Sequence based polymorphic (SBP) marker technology for targeted genomic regions: its application in generating a molecular map of the Arabidopsis thaliana genome. BMC Genomics, 13:20.
  • Sumit, R., Sahu, B.B., Xu, M., Sandhu, D., and Bhattacharyya, M.K. (2012) Arabidopsis nonhost resistance gene PSS1 confers immunity against an oomycete and a fungal pathogen but not a bacterial pathogen that cause diseases in soybean. BMC Plant Biology, 12:62.
  • Weibbeckke, C., M. Graham, S.R. Cianzio, and R.G. Palmer. (2012) Day temperature influences the male-sterile locus ms9 in soybean. Crop Sci. 52:1503-1510.


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

Outputs
OUTPUTS: In order to more precisely define the location of genes responsible for iron efficiency in soybean, QTL mapping studies were carried out with the same population used in an original mapping study, 16 years ago. Two near isogenic lines were genotyped to define a region introgressed from an iron inefficient genotype (T203) into iron efficient genotypes. The introgressed region was fine-mapped and a combination of phenotype analysis, gene expression analysis, and genetic mapping identified a transcription factor as the causative gene underlying a major iron QTL. One germplasm line with resistance to sudden death syndrome was released in 2011. Sudden death syndrome has become a serious pest to growers in Iowa, and in the northern soybean production region. The germplasm line is of an early maturity group adapted to the northern Midwest soybean production region. Material transfer agreements (MTA) have been signed between ISU and several commercial seed companies and public entities for the lines. For screening germplasm resistant to sudden death syndrome, a new protocol has been developed for the evaluation of progenies from resistant x resistant parents. The protocol is being used at ISU. Solids-phase microextraction and multidimensional gas chromatography-mass-spectrometry olfactometry were employed to sample and identify volatile compounds from soybean flowers. This technology is ideally suited to identify the various volatile compounds produced by soybean that contribute to insect pollinator discovery/attraction. In order to enhance SDS resistance in soybean, a synthetic gene encoding plant antibody against the Fusarium virguliforme toxin has been successfully created and expressed in transgenic soybean plants. To identify the pathogenicity mechanisms used by Fusarium virguliforme to cause SDS, a gene knock-out system based on homologous recombination has been developed. Using this system, several mutants for candidate pathogenicity genes have been created. To create broad-spectrum disease resistance in soybean against multiple pathogens, the Arabidopsis thaliana nonhost resistance Pss1 and Pss30 genes have been mapped. Candidate Pss1 and Pss30 genes have been identified. Methods and results were disseminated through publication of peer-reviewed papers, abstracts and on-line industry reports, and presentations at scientific meetings and to individual stakeholders. PARTICIPANTS: For the project on iron deficiency chlorosis Dr. Silvia Cianzio (ISU), Dr. Michelle Graham, USDA-ARS, Ames, and Dr. Carroll Vance, USDA-ARS, St. Paul, MN participated. Dr. Greg Peiffer, Dr. Keith King, and Ms. Sarah Atwood conducted analyses as part of their PhD and M.S. programs in the iron chlorosis project. Partial funding was received from USDA-ARS and the North Central Soybean Research Program and the Iowa Soybean Association. In breeding soybean for disease and pests resistance project, Dr. Silvia R. Cianzio and her lab members, in addition to Dr. Leonor Leandro, Dr. Madan K. Bhattacharyya, Dr. Alison Robertson, Dr. Siva Swaminathan, and Dr. Nilawa Abeysekera participated. Dr. Jacek Koziel of the atmospheric Air Quality Laboratory provided the training, and facilities to characterize the soybean volatiles. For molecular studies on FvTox1, synthetic plant anti-FvTox1 antibody and Pss genes, Dr. Madan Bhattacharyya collaborated with his graduate students, Rishi Sumit and Jordan Baumbach and postdoctoral scientists, Drs. Siva Swaminathan, Ramesh Pudake, Binod Sahu, Catherine Brooke, and Nilwala Abeysekera, and faculty, Dr. Leonor Leandro. TARGET AUDIENCES: In breeding soybean for disease resistance, the target audiences are plant breeders (private and public), soybean growers in Iowa and the northern region of the U.S., and crop consultants. The audiences for the soybean volatile research include scientists who want to identify volatiles from flowers, or other plant tissues. The audiences for the anti-Fvtoxin1 antibody, Arabidopsis nonhost resistance gene, Phytophthora resistance projects include soybean pathologists as well as soybean breeders and molecular geneticists. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
The identification of a causative gene underlying iron efficiency in soybean provides insight into the mechanisms behind this complex trait. This transcription factor and other iron stress differentially expressed genes have provided candidates from which molecular markers may be developed. The markers will facilitate the advancement of breeding programs for iron deficiency chlorosis. Identification of promoter motifs among similarly expressed genes will suggest about the regulation of iron homeostasis in soybean. Research on disease resistance and the release of resistant germplasm lines to diseases of economic importance in Iowa and the Midwest contributes to improve resistance of commercial cultivars. During 2011, 69 MTA agreements were signed between ISU and soybean breeders for use of new germplasm lines with resistance to soybean diseases in other soybean breeding programs. Research on volatiles from soybean flowers of insect-mediated low-seed-set genotypes will be compared to volatiles of insect-mediated high seed-set genotypes. If certain unique compounds or differences in concentration of certain volatiles can be detected between these genotypes, chemical analyses can be used to identify potential insect-mediated high seed-set genotype without labor intensive field studies with insect pollinators. Faster and more efficient evaluation of potential parents for hybridization programs will result in lower hybrid seed costs. Arabidopsis Pss1 is essential for resistance of Arabidopsis against two soybean pathogens, P. sojae and Fusarium virguliforme. Incorporation of this gene in soybean may confer resistance against these two destructive pathogens. Furthermore, Pss30 conferring resistance of Arabidopsis against P. sojae could also confer immunity of soybean against this serious soybean pathogen. Expression of plant antibody against FvTox1 may enhance resistance against F. virguliforme that causes SDS in soybean.

Publications

  • Woody, J., Severin, A., Bolon, Y-T., Bindu, J., Diers, B., Farmer, A., Weeks, N., Muehlbauer, G., Nelson, R., Grant, D., Specht, J., Graham, M., Cannon, S., May, G., Vance, C., and Shoemaker, R.. 2011. Gene expression patterns are correlated with genomic and genic structure in soybean. Genome 54:10-18.
  • Xu, M., Brar, H., Grosic, S., Palmer, R., and Bhattacharyya, M.K. (2010) Excision of an active CACTA-like transposable element from DFR2 led to variegated flowers in soybean. Genetics, 184:53-63.
  • Brar H.K., Swaminathan S., and Bhattacharyya M.K. (2011) The Fusarium virguliforme toxin FvTox1 causes foliar sudden death syndrome-like symptoms in soybean. Mol. Plant-Microbe Interact., 24:1179-1188.
  • Du, J., Tian, S., Hans, C., Jackson, S., Cannon, S.B., Shoemaker, R.C., and Ma, J. 2010. Evolutionary Conservation, Diversity and Specificity of LTR Retrotransposons in Flowering Plants: New Insights from Genome-Wide Analysis and Multi-Specific Comparison. Plant J., 63:584-598.
  • Findley, S.D., Pappas, A.L., Cui, Y., Birchler, J.A., Palmer, R.G. and Stacey. G. 2011 Fluorescence in situ hybridization-based karyotyping of soybean translocation lines. G3: Genes, Genomes, Genetics, 1:117-129.
  • Frasch, R.M., Weigand, C., Perez., P.T., Palmer, R.G., and Sandhu. D. 2011 Molecular mapping of two environmentally sensitive male-sterile mutants in soybean, Journal of Heredity, 102:11-16.
  • Jackson, S.A., Lee, Suk-Ha, Schmutz, J., and Shoemaker, R.C. 2011. Sequencing crop genomes: approaches and applications. New Phytologist, 191:915-925.
  • Mbofung, G.C.Y., Fessehaie, A., Bhattacharyya, M.K., and Leandro, L.F.S. (2011) A new Taqman real-time PCR assay for quantification of Fusarium virguliforme in soil. Plant Disease, 95:1420-1426.
  • Palmer, R.G., Gai, J., Dalvi, V.A., and Suso, M.J. 2011. Male sterility and hybrid production technology. pp. 193-20. In A. Pratapand and J. Knmar (eds.). Biology and Breeding of Food Legumes. CAB International, UK.
  • Palmer, R.G., Shoemaker, R.C. and Severin, A.J. 2011. Soybean Genetics. pp. 72-136. In J. Miladinovic, M. Hrustic and M. Vidic (eds. ). Soybean. Institute of Field and Vegetable Crops publisher, Novi Sad, Serbia.
  • Perez, P. T., Aviles, M.A., Cianzio, S. R., and Palmer. R. G. 2010. Molecular markers on the inheritance of white fly resistance. J. Crop Improvement 25:120-126.
  • Perez, P.T., Cianzio, S.R., Ortiz-Perez, E., and Palmer, R.G. 2009. Agronomic performance of soybean hybrids from single, 3-way, 4-way, and 5-way crosses, and backcross populations. J. Crop Improvement 23:95-118.
  • Perez, P.T., Cianzio, S.R., and Palmer, R.G. 2009. Evaluation of soybean [Glycine max (L.) Merr.] F1 hybrids. J. Crop Improvement, 23:1-18.
  • Perez, P.T., Diers, B., Tabor, G., Lundeen, P., and Cianzio, S.R. 2010. Genetic evaluation of new sources of brown stem rot resistance. Crop Sci. J., 50:20-25.
  • Perez-Sackett, P.T., Cianzio, S.R., Kara, P.C., Aviles, M., and R.G. Palmer. 2011 QTL mapping of whitefly resistance in soybean Journal of Crop Improvement, 25:134-150.
  • Severin, A., Cannon, S.B., Graham, M.A., Grant, D., and Shoemaker, R.C. 2011. Changes in twelve conserved soybean genomic regions following three rounds of polyploidy. The Plant Cell 23:3129-3136.
  • Severin, A., Peiffer, G. A., Xu, W. W., Hyten, D. L., Bucciarelli, B., O'Rourke, J. A., Bolon, Y-T., Grant, D., Farmer, A. D., May, G. D., Vance, C. P., Shoemaker R. C., and Stupar, R. M. 2010. An integrative approach to genomic introgression mapping. Plant Physiology, 154:3-12.
  • Slattery, R.A., Pritzl, S., Reinwans, K., Trautschold, B., and Palmer, R.G. 2011 Mapping eight male-sterile, female-sterile soybean mutants. Crop Science, 51:231-236.
  • Yang, H.,Qiao, X., Bhattacharyya, M.K., and Dong, L. (2011) Microfluidic droplet encapsulation of highly motile single zoospores for phenotypic screening of an antioomycete chemical. Biomicrofluidics, 5:044103.


Progress 01/01/10 to 12/31/10

Outputs
OUTPUTS: 1) The whole genome sequence of soybean was generated and assembled. Novel techniques using dinucleotide signatures were demonstrated to be of aid in the quality control of the assembly. RNASeq was used to create an atlas of the soybean transcriptome from 14 tissues and stages of development. RNASeq data was used to identify Single Nucleotide Polymorphisms (SNPs) between near-isogenic lines. The location of the SNPs delineated the introgressed region of the NIL. SNPs were genetically mapped to place and orient sequence-based contigs in the whole-genome assembly. 2) Two germplasm lines with resistance to soybean cyst nematode and sudden death syndrome were released in 2010. Both soybean cyst nematode and sudden death syndrome have become pests of great concerns to growers in Iowa, and commonly occur simultaneously in the same commercial fields. The germplasm lines are of early maturity groups adapted to the northern Midwest soybean production region. Material transfer agreements (MTA) have been signed between ISU and several commercial seed companies and public entities for these lines. Several advanced experimental lines with high yield and resistance to soybean cyst nematode have also been release for crossing by other soybean breeding programs. For screening germplasm resistant to sudden death syndrome, research was completed to modify evaluation protocols, adapted to the evaluation of progenies from resistant x resistant parents. The protocol is currently used at ISU. 3) A fungal toxin FvTox1 that causes SDS has been isolated and gene encoding the toxin has been cloned. In order to enhance SDS resistance in soybean, a synthetic gene encoding the plant antibody against this toxin has been successfully created. To create broad-spectrum disease resistance in soybean against multiple pathogens, the Arabidopsis thaliana Pss1 gene has been recently mapped. 4) A video 'Crossing Soybeans', by G Peiffer, R.C. Shoemaker, and R. G. Palmer has been posted to soybase. The direct link is: http://soybase.org/tutorials/index.php. 5) Results of soybean genome analyses and molecular studies on disease resistance were reported at the Molecular and Cellular Biology of the Soybean Conference, Durham, NC, August 8 - 11, 2010. Results on the fungal toxin and plant antibody against the fungal toxin were presented also in Plant & Animal Genome XVII Conference, San Diego, CA, January 9-13, 2010, Syngenta, Hauxley, Inc. on June 13, 2010; Syngenta, Inc., Minetonka on July 15, 2010; Syngenta, Research Triangle, NC, August 12, 2010; Institute of Plant Physiology and Ecology, Shanghai, December 1, 2010 and Sun Yat-Sen University at Guangzhou, December 3, 2010. Results of breeding work on disease resistance were presented at the Sudden Death Syndrome workshop, November 2010 at Arkansas, APHIS meeting June 2010, California, the ASA meeting, November 2010, California and at the annual Soybean Breeders Workshop in Missouri, February 2010. PARTICIPANTS: Dr. Carroll Vance, USDA-ARS, and Dr. Robert Stupar, St. Paul, MN participated in the identification of introgressed regions and the characterization of the soybean transcriptome. Drs. Perry Cregan and David Hyten, USDA-ARS, Beltsville, MD participated in the mapping of SNPs. Drs. Jeremy Schmutz and Scott Jackson, the Hudson Alpha Institute and Purdue University, respectively, participated in the assembly of the whole genome sequence. In breeding soybean for disease and pests resistance project, Dr. Silvia R. Cianzio and her lab members, in addition to Dr. Leonor Leandro, Dr. Madan K. Bhattacharyya, and Dr. Alison Robertson participated. For the soybean hybrid project, field participants included the USDA North Central Regional Plant Introduction Station, Ames, Iowa; Vende Seed Inc., Plainview, TX; Hoegemeyer Hybrids, Hooper, Nebraska, and visiting scientist Dr. Maria Jose Suso, from the Institute of Sustainable Agriculture, Cordoba, Spain. The Iowa Crop Improvement Association and the Iowa State University Seed Science Center participated in field studies. For molecular studies on FvTox1, synthetic plant anti-FvTox1 antibody and Pss1 gene mapping Dr. Madan Bhattacharyya his graduate students, Hargeet Brar and Rishi Sumit, and postdoctoral scientists, Dr. Siva Swaminathan and Dr. Ramesh Pudake participated. TARGET AUDIENCES: For soybean genome research, target audiences include geneticists, physiologists and plant breeders interested in plant nutrition and iron utilization. The target audience for the assembly of the whole genome sequence include all of the above, plus students and educators. For the breeding soybean for disease resistance, the target audiences include plant breeders (private and public), and soybean growers in Iowa and the northern region of the U.S. For hybrid soybean, audiences include commercial, public, and USDA groups interested in increasing soybean grain yield. The audience of hybrid seed production research includes soybean scientists who plan to make cross-pollination (sexual hybrids), also includes amateur hybridizers, and high school or college instructors who wish to understand/demonstrate cross-pollinations in soybean. The target audiences for the anti-Fvtox1 antibody and FvTox1 fungal toxin include soybean pathologists as well as soybean breeders, plant pathologists, soybean seed producers and molecular geneticists. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
A) The demonstration of novel methods to assist assembly of whole-genome sequence from soybean will assist in future assemblies of similarly complex genomes. The sequencing and assembly of the whole genome sequence of soybean represents a seminal advance in soybean genetics. This achievement will alter soybean genetic research and will greatly increase the potential for soybean improvement. The precise identification and delineation of introgressed regions of NILs will aid in the identification of genes responsible for many agronomically important traits. B) Research on disease resistance and the release of resistant germplasm lines to diseases of economic importance in Iowa and the Midwest will contribute to improve resistance of commercial cultivars. Public releases and MTAs allow access to other soybean breeding programs to the new genes identified in Plant Introductions of the National Soybean Germplasm Collection. C) To increase soybean grain yields, conventional and molecular approaches are being conducted to assess the potential for hybrid soybean. Phenotypic recurrent selection was used to increase insect-mediated cross-pollination on male-sterile soybean plants. The high seed-set and low seed-set lives will be compared anatomically, morphologically, and biochemically to determine which characteristics contribute to insect-pollinator preference. These characteristics will be identified and used to develop superior parents for hybrid seed production. The release of germplasm lines with these traits will be used by public and private soybean breeders in their own breeding programs. The ultimate goal is to commercial hybrid soybean. D) Expression of plant antibody against FvTox1 may enhance resistance against F. virguliforme that causes SDS in soybean.

Publications

  • Du, J., Tian, S., Hans, C., Jackson, S., Cannon, S.B., Shoemaker, R.C., Ma, J. 2010. Evolutionary Conservation, Diversity and Specificity of LTR Retrotransposons in Flowering Plants: New Insights from Genome-Wide Analysis and Multi-Specific Comparison. Plant Journal. 10. Available: http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2010.04263.
  • Grant, D., Nelson, R., Cannon, S., and Shoemaker, R. 2010. SoyBase, the USDA-ARS soybean genetics and genomics database. Nucleic Acids Research 2010 38(Database issue):D843-D846; doi:10.1093/nar/gkp798.
  • Healy, R.A., Palmer, R.G., and Horner. H.T. 2009. Multicellular secretory trichome development on soybean and related glycine gynoecia. International Journal of Plant Science 170 (4):444-456.
  • Hyten, D.L., Cannon, S.B., Song, Q., Weeks, N.T., Fickus, E.W., Shoemaker, R.C., Specht, J.E., May, G.D., Cregan, P.B. 2010. High-Throughput SNP Discovery through Deep Resequencing of a Reduced Representation Library to Anchor and Orient Scaffolds in the Soybean Whole Genome Sequence. BMC Genomics 11:38.
  • Nelson R.T., Avraham S., Shoemaker R.C., May G.D., Ware D. and Gessler D.D.G. (2010) Applications and methods utilizing the Simple Semantic Web Architecture and Protocol (SSWAP) for bioinformatics resource discovery and disparate data and service integration. BioData Mining 3:3 doi;10.1186/1756-038/3-3.
  • Peto, M.F., Grant, D.M., Shoemaker, R.C., Cannon, S.B. 2010. Applying Small-Scale DNA Signatures as an Aid in Assembling Soybean Chromosome Sequences. Adv Bioinformatics. doi:10.1155/2010/976792.
  • Schmutz, J., Cannon, S.B., Schlueter, J., Ma, J., Hyten, D.L., Song, Q., Mitros, T., Nelson, W., May, G.D., Gill, N., Peto, M.F., Shu, S., Goodstein, D., Thelen, J.J., Cheng, J., Sakurai, T., Umezawa, T., Shinozaki, K., Du, J., Bhattacharyya, M., Sandhu, D., Grant, D.M., Joshi, T., Libault, M., Zhang, X., Hguyen, H., Valliyodan, B., Xu, D., Futrell-Griggs, M., Abernathy, B., Hellsten, U., Berry, K., Grimwood, J., Yu, Y., Wing, R.A., Cregan, P.B., Stacey, G., Specht, J., Rokhsar, D., Shoemaker, R.C., and Jackson, S. 2010. Genome Sequence of the Paleopolyploid Soybean (Glycine max (L.) Merr.). Nature 463:178-183.
  • Severin, A., Peiffer, G. A., Xu, W. W., Hyten, D. L., Bucciarelli, B., O'Rourke, J. A., Bolon, Y-T., Grant, D., Farmer, A. D., May, G. D., Vance, C. P., Shoemaker R. C., and Stupar, R. M.. An integrative approach to genomic introgression mapping. Plant Phys. 2010.1104/pp.110.158949.
  • Severin, A.J., Woody, J.L., Bolon, Y.E., Joseph, B., Diers, B.W., Farmer, A.D., Muehlbauer, G.J., Nelson, R., Grant, D.M., Specht, J.E., Graham, M.A., Cannon, S.B., May, G.D., Vance, C.P., Shoemaker, R.C. 2010. RNA-Seq Atlas of Glycine max: A Guide to the Soybean Transcriptome. BMC Plant Biology. 10:610.
  • Xu, M., Brar, H.K., Grosic, S., Palmer, R.G., and Bhattacharyya, M.K. 2010. Excision of an active CACTA-like transposable element from DFR2 causes variegated flowers in soybean soybean [Gylcine max (L.) Merr.] Genetics 184:53-63.
  • Yang, K., Jeong, N., Moon, J., Lee, Y., Lee, Y., Kim H.M., Hwang, C.H., Back, K., Palmer, R.G., and Jeong, S. 2010. Genetic analysis of genes controlling natural variation of seed coat and flower colors in soybean. Journal of Heredity 101:757-768.


Progress 01/01/09 to 12/31/09

Outputs
OUTPUTS: Three cultivars with resistance to soybean cyst nematode and Phytophthora root rot (PRR) were released in 2009. One of the cultivars possesses a new gene for PRR resistance, discovered at the Ohio State University. This is one of the first releases in early maturity group possessing the new gene, which confers resistance to most of the races of Phytophthora sojae that causes PRR. To improve soybean for Asian rust resistance, a candidate resistant gene for Asian Soybean Rust, Rpp4, was identified. Viral induced gene silencing of the resistance gene added support to the identification of the gene. A fungal phytotoxin (FvTox1) gene of Fusarium virguliforme that causes sudden death syndrome (SDS) has been identified. Recombinant FvTox1 protein, expressed in an insect cell line with the aid of bacuolovirus causes foliar SDS symptoms in soybean. In order to enhance SDS resistance in soybean, a synthetic gene encoding plant antibody against this toxin has been successfully created. To create broad-spectrum disease resistance in soybean against multiple pathogens, the Arabidopsis thaliana Pss1 gene has been recently identified and mapped. Two soybean genes involved in systemic acquired resistance were isolated. In order to determine the mechanism of tolerance to iron toxicity, the whole genome expression analyses on soybeans under iron stress and iron sufficient conditions were carried out. The differentially expressed genes are clustered more tightly on the soybean genome sequence than expected by chance. Common promoter motifs were identified among the clustered genes. To improve soybean for high protein contents, a protein QTL region on chromosome 20 was identified. This region was saturated with SSR markers. To increase soybean grain yields, hybrid soybean breeding studies are conducted by conventional and molecular approaches. Phenotypic recurrent selection for increased insect-mediated cross-pollination was successful. A duplicated region on chromosome 10 was identified. The comparative analysis of the regions indicate that these regions were likely to be products of the recent genome duplication in soybean ~14 MYA. The duplicated genes of this region showed evidence of tissue specific expression. Both regions appeared to be hotspots for transposon accumulation. The active transposable elements are useful tools in isolating genes. The first soybean endogenous active transposable element has been isolated from a soybean line. Results of the Asian Rust study were reported at the 2009 National Soybean Rust Symposium in New Orleans, Louisiana, 9-11 December 2009. Results of the male sterility studies were presented at the University of Wisconsin-Stevens Point. Results of molecular studies on disease resistance and transposable element were presented at the International Plant & Animal Genome XVII Conference, San Diego, January 10-14, 2009 and VII World Soybean Conference, Beijing, China, August 5-10, 2009. Results of breeding work on disease resistance were presented at the VII World Soybean Conference, the ASA meeting, Pittsburgh, November 1-5, 2009 and the annual meeting of North Central Soybean Research Program, 20 November 2009. PARTICIPANTS: In breeding soybean for disease and pests resistance project, Dr. Silvia R. Cianzio and her lab members, in addition to Dr. Leonor Leandro, and Dr. Alison Robertson participated. For the project on iron deficiency chlorosis, Dr. Silvia Cianzio (ISU) and Dr. Carroll Vance (USDA-ARS, St. Paul, MN) participated. Dr. Jamie O'Rourke conducted analyses as part of her PhD program in the iron chlorosis project. Partial funding was received from USDA-ARS and the North Central Soybean Research Program. For the project on Asian Soybean Rust the primary participant was Dr. Michelle Graham, USDA-ARS, Iowa State University, and Dr. Steven Whitham, Department of Plant Pathology, Iowa State University. For pollination studies, Dr. Reid Palmer collaborated with E. Ortiz-Perez (DowAgro Sciences), F. Maalouf (ICARDA, Aleppo, Syria), and M. J. Suso (Instituto de Agricultura Sostenible, Cordoba, Spain), H. Wiley (Dairyland Seed Co.), H. T. Horner (ISU), and W. H. Davis (Verde Seed) and for molecular mapping studies with Dr. E. Ortiz-Perez (DowAgro Sciences), Dr. D. Sandhu (Univ. Wisconsin-Stevens Point), K. K. Katao (Obihiro Universitsy, Obihiro City, Japan), and Dr. H. T. Horner (ISU). For molecular studies on FvTox1, synthetic plant anti-FvTox1 antibody and Pss1 Dr. Madan Bhattacharyya collaborated with his graduate students, Hargeet Brar and Rishi Sumit and postdoctoral scientists, Dr. Siva Swaminathan and Dr. Ramesh Pudake, and Dr. D. Sandhu (Univ. Wisconsin-Stevens Point). For the transposable element project, Dr. Madan Bhattacharyya collaborated with Dr. Reid Palmer; Dr. Min Xu, Hargeet Brar, Sehiza Grosic conducted the experiments. TARGET AUDIENCES: For the breeding soybean for disease resistance, the target audiences include plant breeders (private and public), and soybean growers in Iowa and the northern region of the U.S. For the iron chlorosis project, the target audiences include geneticists, physiologists and plant breeders interested in plant nutrition and iron utilization. The target audience for the Asian Soybean Rust project includes pathologists, geneticists, and breeders. For hybrid soybean, audiences included university, commercial seed companies, and USDA researchers interested in insect-mediated cross-pollination. The audiences for the anti-Fvtoxin1 antibody, Arabidopsis nonhost resistance gene, Phytophthora resistance projects include soybean pathologists as well as soybean breeders and molecular geneticists. For the transposable element project, the audiences include soybean molecular geneticists and plant molecular geneticists. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
Research on Phytophthora sojae variability on infested soils indicated that the within field variation is important for this pathogen. The observation points out that planting field with soybean cultivars with single gene resistance may not be an effective production practice, if several different races are present at one individual field. The recently released soybean line with a new gene for PRR resistance should, however, be ideal because this new gene confers resistance to most P. sojae races. The identification of a candidate gene for Asian Soybean Rust provides a model by which the resistance mechanisms may be studied. Iron stress differentially expressed genes have provided candidates from which molecular markers may be developed. The markers will facilitate the advancement of breeding programs for iron deficiency chlorosis. Identification of promoter motifs among similarly expressed genes will suggest about the regulation of iron homeostasis in soybean. Agronomic performance data from hybrid soybean populations indicated that the use of high yielding exotic male parent did not consistently result in higher grain yields. The data obtained from insect pollinator studies suggest that attraction/rewards traits in soybean can be changed through phenotypic recurrent selection. This method should be used to improve hybrid soybean seed production. Arabidopsis Pss1 gene is essential for resistance of Arabidopsis against two soybean pathogens, P. sojae and F. virguliforme. Incorporation of this gene in soybean may confer resistance against these two destructive pathogens. Expression of plant antibody against FvTox1 may enhance resistance against F. virguliforme that causes SDS in soybean. Overexpression of soybean genes for systemic acquired resistance may induce broad-spectrum resistance against multiple pathogens. Isolated active transposable element is expected to facilitate molecular biological studies in soybean.

Publications

  • Bhattacharyya, M., Palmer, R.G., and Xu, M. 2009. Transposable elements in Glycine max and methods of use. Patent filed 31 July 2009.
  • Cervantes-Martinez, I.G., Sandhu, D., Min, X., Ortiz-Perez, E., Kato, K.K., Horner, H.T., and Palmer, R.G. 2009. The male-sterility locus ms3 is present in a fertility controlling gene cluster in soybean. J. Hered. 100:565-570.
  • Cianzio, S.R., Gebhart, G., Rivera-Velez, N., Lundeen, P., and Bhatthacharyya, M.K.. 2009. Soybean cultivar IAR3001 Phtyo/SCN. ISURF # 03712.
  • Cianzio, S.R., Gebhart, G., Rivera-Velez, N., and Lundeen, P. 2009. Soybean cultivar IAR1008BC SCN/Phtyo. ISURF # 03700.
  • Cianzio, S.R., Gebhart, G., Rivera-Velez, N., Lundeen, P., and Arelli, P. 2009. Soybean cultivar IAR2101 SCN. ISURF # 03711.
  • Joseph, B., Schlueter, J., Du, J., Graham, M., Ma, J., Shoemaker, R. 2009. Retrotransposons within the syntenic regions between soybean and Medicago truncatula and their contribution to local genome evolution. The Plant Genome 2:211-223.
  • Narayanan, N., Grosic, S, Tasma, I.M., Grant, D.M., Shoemaker, R.C., and Bhattacharyya, M.K. 2009. Identification of regulatory genes for active defense responses induced immediately following Phytophthora sojae infection in soybean. Theor Appl Genet. 118:399-412.
  • O'Rourke, J., Nelson, R., Grant, D., Schmutz, J., Grimwood, J., Cannon, S., Vance, C., Graham, M., Shoemaker, R. 2009. Integrating microarray analysis and the soybean genome to understand the soybeans iron deficiency response. BMC Genomics 10:376-393.
  • Ortiz-Perez, E., Wiley, H., Horner, H.T., Davis, W.H., and Palmer, R.G. 2008. Insect-mediated cross-pollination in soybean [Glycine max (L.) Merrill]: II. Phenotypic recurrent selection. Euphytica 162:269-280.
  • Palmer, R.G. and Doyle, J.J. 2009. Dedication: Anthony H.D. Brown: Conservation geneticist. Plant Breed. Rev. 31:1-20.
  • Palmer, R.G., Perez, P.T., Ortiz-Perez, E., Maalouf, F., and Suso, M.J. 2009. The role of crop-pollinator relationships in breeding for pollinator-friendly legume varieties. Euphytica 170:35-52.
  • Perez, P.T., Cianzio, S.R., and Palmer, R.G. 2009. Evaluation of soybean [Glycine max (L.) Merr.] F1 hybrids. J. Crop Improv. 23:1-18.
  • Perez, P.T., Cianzio, S.R., and Palmer, R.G. 2009. Heterotic patterns of soybean lines from single, 3-way, 4-way, and 5-way crosses, and backcross populations. J. Crop Improv. 23:95-118. Perez, P. T., Cianzio, S.R., and Palmer, R.G. 2009. Inheritance of white fly resistance. World Soybean Conference VIII, Beijing, China.
  • Perez, P. T., Cianzio, S.R., and Diers, B. 2009. Brown stem rot resistance sources in soybean. World Soybean Conference VIII, Beijing, China.
  • Perez, P. T., Cianzio, S.R., and Palmer, R.G. 2009. Molecular markers on the inheritance of white fly resistance. ASA, Pittsburgh, PA.
  • Perez, P. T., Cianzio, S.R., and Diers, B. 2009. PIs possess resistance genes to Brown stem rot in molecular linkage group L. ASA, Pittsburgh, PA.
  • Rotundo, J., Westgate, M., and Cianzio, S.R. 2009. Protein composition in soybean and inheritance effects. ASA, Pittsburgh, PA.
  • Sandhu, D., Tasma, M.I., Frasch, R., and Bhattacharyya, M.K. 2009. Systemic acquired resistance in soybean is regulated by two proteins, orthologous to Arabidopsis NPR1 BMC Plant Biol. 9:105.
  • Xu, M., Brar, H., Grosic, S., Palmer, R., and Bhattacharyya, M.K. 2009. Excision of an active CACTA-like transposable element from DFR2 led to variegated flowers in soybean. Genetics (http://www.genetics.org/aheadofprint.dtl).
  • Mathieu, M, Winters, E, Kong, F, Wan, J, Wang, S, Eckert, H, Luth, D, Paz, M, Donovan, C, Zhang, Z, Somers, D, Wang, K, Nguyen, H, Shoemaker, R, Stacey, G, and Clemente, T. 2009. Establishment of a soybean (Glycine max Merr.L) trasnsposon-based mutagenesisi repository. Planta 229:279-289.
  • Meyer, J.D.F., Silva, D.C.G., Yang, C., van de Mortel, M., Pedley, K., Hill, J., Shoemaker, R.C., Abdelnoor, R.V., Whitham, S.A. and Graham, M.A. 2009. Identification and analyses of candidate genes for Rpp4 mediated resistance to Asian Soybean Rust in soybean (Glycine max). Plant Physiology 150:295-307.


Progress 01/01/08 to 12/31/08

Outputs
OUTPUTS: The overall goal of the project is to improve soybean for yield and resistance to both biotic and abiotic stresses. To increase soybean yields and stabilize soybean production, breeding for disease and pests resistance is conducted by both conventional breeding and biotechnological approaches. A new soybean germplasm line possessing resistance to SDS (sudden death syndrome) was released. Several Material Transfer Agreements were signed between ISU and several commercial entities. This is one of the first germplasm lines with resistance to SDS, and adequate yield available for the northern U.S. Crosses have been made with new sources of soybean cyst nematode resistance, SDS, and with new brown stem rot resistant lines. Populations have been developed with these objectives. Affymetrix GeneChips were used to identify genes differentially expressed between iron sufficient and iron insufficient growth conditions. A detailed comparative analysis of the soybean genome structure to that of Arabidopsis and Medicago identified regions of fractionation that have occurred over millions of years of evolution. DNA sequence from homoeologous regions was mingled and assembled to demonstrate that a whole genome shotgun sequence assembly of soybean was possible. SSRs identified within BAC end sequences were identified and mapped, thus creating more molecular markers and anchoring the physical map to the genetic map. The identification of insect pollinators that are the most suitable for soybean and the soybean plant-insect pollinator interactions is necessary to improve insect-mediated cross-pollination to produce large quantities of F1 seed. The data generated from the pollinator studies help to define the direction to pursue for further increases in insect-mediated cross-pollination seed-set. In order to improve soybean for SDS resistance, a phytotoxin (FvTox1) produced by the fungal pathogen Fusarium virguliformae was isolated and gene encoding this proteinacious toxin was identified. To generate antibody against this toxin in transgenic soybean plants, two putative genes encoding the anti-FvTox1 antibody were isolated. The antibody genes, when expressed in Eschercia coli, made antibody that bound to FvTox1. Arabidopsis nonhost resistance genes for immunity against Phytophthora sojae were mutated, and several mutants carrying mutations in immunity genes have been identified. One mutant gene is mapped to chromosome 3. A soybean protein manipulated by P. sojae to cause root and stem rot disease has been isolated. This regulatory protein is expected to discover the mechanism used by the pathogen to attach soybean plants. The active transposable elements are useful tools in isolating genes based on their functions. The first soybean endogenous active transposable element has recently been isolated. Results of the iron deficiency chlorosis study were reported at the International Crop Legume Genetics and Genomics Conference in Puerto Vallarta, MX, 14 December 2008. Results of the anti-FvToxin1 antibody work was presented at the annual SDS meeting organized by North Central Soybean Research Program, 20 November 2008. PARTICIPANTS: For the project on iron deficiency chlorosis, Silvia Cianzio (ISU), Dr. Mike Grusak from the USDA-ARS Children's Hospital in Houston and Dr. Carroll Vance, USDA-ARS, St. Paul, MN participated. Jamie O'Rourke conducted analyses as part of her PhD program in the iron chlorosis project. Partial funding was received from USDA-ARS and the North Central Soybean Research Program. For the project on molecular marker development and genome analysis participants were Scott Jackson, Purdue University; Gary Stacey, University of Missouri; Perry Cregan, USDA-ARS, Beltsville, MD; and Rod Wing, University of Arizona. Jessica Schlueter performed data analyses as part of her Ph.D. dissertation research. Partial funding was received from USDA-ARS and the National Science Foundation. In breeding soybean for disease and pests resistance project, Dr. Silvia R. Cianzio and her lab members, in addition to Dr. Charlotte Bronson and Dr. Girma Tabor, participated. For the soybean sterility evaluation, Dr. Candice Gardner, USDA ARS, North Central Regional Plant Introduction Station, Ames, Iowa, provided insect cages, field space, and insect pollinators. Drs. R. L. Cooper, J. Tew, R.M.A. Mian, and T. Mendiola, at the Ohio Agricultural Research Development Center, Wooster, Ohio, provided insect pollinators and field space for our insect-pollinator comparison center. Evelyn Ortiz-Perez analyzed the data for the Iowa and Ohio study as part of her PhD program. In the anti-Fvtoxin1 antibody project, graduate student Hargeet Brar conducted all the experiments. In the nonhost resistance project, graduate student Rishi Sumit conducted most of the experiments. Shan Li identified the soybean protein that is presumably manipulated by a pathogen protein. Sehiza Grosic and Hargeet Brar conducted necessary experiments to complete the ongoing project on cloning a soybean transposable element. TARGET AUDIENCES: For the iron chlorosis project, the target audience includes geneticists, physiologists and plant breeders interested in plant nutrition and iron utilization. For the genome analysis and marker development project the target audience includes plant breeders, evolutionary biologists and genome assemblers. For hybrid soybeans, audience includes university, USDA, and commercial seed companies interested in hybrid soybean. For the breeding soybean for disease resistance, the target audience includes plant breeders (private and public), and soybean growers in Iowa and the northern region of the U.S. The audience for the anti-Fvtoxin1 antibody, Arabidopsis nonhost resistance gene, Phytophthora resistance projects includes soybean pathologists as well as soybean breeders and molecular geneticists. For the transposable element project, the audience includes soybean molecular geneticists and plant molecular geneticists. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
The release of germplasm lines and cultivar will contribute to improve soybean yields. The new germplasm lines will be used by public and private soybean breeders in their own breeding programs. Lines are advertised by the Iowa State University Research Foundation. Material Transfer Agreements are already in effect for private and public entities to utilize the new germplasm line in their programs. Seed treatments to control early infestations of Phytophthora sojae have not proven to be effective under all conditions. Particularly in Iowa, seed treatments have not shown any advantage to protect soybean plantings from seedling infections by the pathogen. On the basis of these results, seed treatments are not being recommended to soybean growers in Iowa. The additional planting cost of the application is not valuable. Physiological and genetic aspects of Fe nutrition and micronutrients were discussed and evaluated as a means to protect soybean yields of genotypes planted in deficient soils. The work is an ongoing objective of this project. The identification of genes differentially expressed between iron sufficient and iron stress conditions may help to identify key steps in iron homeostasis. This information will help scientists devise strategies that will facilitate breeding better iron efficiency in soybean. Differentially expressed genes have provided candidates from which molecular markers may be developed. The analysis of soybean genome structure and organization and the integration of the genetic markers with the physical map will aid in the assembly of the whole genome sequence. The identification of insect pollinators that are the most suitable for soybean and the soybean plant-insect pollinator interactions is necessary to improve insect-mediated cross-pollination to produce large quantities of F1 seed. The data generated from the pollinator studies help to define the direction to pursue for further increases in insect-mediated cross-pollination seed-set. It is expected that once an effective antiFvTox1 antibody is successfully expressed in transgenic soybean plants, tolerance of soybean to the F. virguliformae will be increased and enhanced SDS resistance can be expected. Isolated Arabidopsis nonhost resistance genes are expected to contribute significantly towards our understanding of nonhost resistance against the soybean pathogen P. sojae. A better understanding of the Arabidopsis nonhost resistance mechanism will lead to generation of transgenic soybean plants with enhanced Phytophthora resistance.

Publications

  • Cianzio, S.R., Gebhart, G., Rivera-Velez, N., Lundeen, P., Bhattacharyya, M.K., and Vander Molen, K. 2008. Soybean germplasm line IR10SDS ISURF (Docket # 03724).
  • Cianzio, S.R. and Shoemaker, R.C. 2008. Genetic correction of iron deficiency in soybean: Two improved germplasm lines from the lab to growers' production fields. Invited presentation. XIV International Symposium on Fe nutrition and interaction in plants, August 11, 2008, Beijing, People's Republic of China.
  • Cianzio, S.R., Shoemaker, R.C., and O'Rourke, J.A. 2008. Micronutrients in plants: physiological processes and genetic manipulation for breeding high-yielding genotypes. A review. Invited presentation and publication in process. International Plant Physiology Congress, August 28, 2008, Granada, Spain.
  • Gao, H. and Bhattacharyya, M.K. 2008. The soybean-Phytophthora resistance locus Rps1-k encompasses coiled coil-nucleotide binding-leucine rich repeat-like genes and repetitive sequences. BMC Plant Biol. 8:29.
  • Ortiz-Perez, E., Mian, R.M.A., Cooper, R.L., Mendiola, T., Tew, J., Horner, H.T., Hanlin, S.J., and Palmer, R.G. 2008. Seed-set evaluation of four male-sterile, female-fertile soybean lines using alfalfa leaf-cutter bees and honey bees as pollinators. J. Agric. Sci. (Cambridge) 146:461-469.
  • Palmer, R.G., Zhang, L., Huang, Z., and Min, X. 2008. Allelism and molecular mapping of soybean necrotic root mutants. Genome 51:243-250.
  • Palmer, R.G. and Min, X. 2008. Positioning three qualitative trait loci on soybean molecular linkage group E. J. Hered. 99:674-678.
  • Palmer, R.G. and Shoemaker, R.C. 2008. Soybean genetics p. 77-129. IN Miladinovic, J., Hrustic, M., Vidic, M. (ed.) Soybean Institute of Field and Vegetable Crops Publisher. Novi Sad, Serbia.
  • Palmer, R.G., Sandhu, D., Curran, D.K. and Bhattacharyya, M.K. 2008. Molecular mapping of 36 Soybean male-sterile, female-sterile mutants. Theor. Appl. Genet. 117:711-719.
  • Schlueter, J.A., Scheffler, B., Jackson, S. and R.C. Shoemaker. 2008. Fractionation of synteny in a genomic region containing tandemly duplicated genes across Glycine max, Medicago truncatula and Arabidopsis thaliana. J. Hered. 99:390-395.
  • Shoemaker, R., Grant, D., Olson, T., Warren, W.C., Wing, R., Yu, Y., Kim, H-R., Cregan, P., Joseph, B., Futrell-Griggs, M., Nelson, W., Davito, J., Walker, J., Wallis, J., Kremitski, C., Scheer, D., Clifton, S., Graves, T., Nguyen, H., Wu, X., Luo, M., Dvorak, J., Nelson, R., Cannon, S., Tomkins, J., Schmutz, J., Stacey, G. and S. Jackson. 2008. Microsatellite Discovery from BAC End Sequences and Genetic Mapping to Anchor the Soybean Physical and Genetic Maps. Genome 51:294-302.
  • Tasma, I.M., Brendel, V., Whitham, S.A., and Bhattacharyya, M.K. 2008. Expression and evolution of the phosphoinositide-specific phospholipase C gene family in Arabidopsis thaliana. Plant Physiol. Biochem. 46:627-637.


Progress 01/01/07 to 12/31/07

Outputs
OUTPUTS: The overall goal of the project is to improve soybean for yield and resistance to both biotic and abiotic stresses. cDNA arrays were used to identify genes that are differentially expressed between the two isolines. Using the same strategy genes were also identified that remain differentially expressed upon return to iron sufficient conditions. Twelve paralogous regions were sequenced and the regions were compared for sequence identity, gene composition and organization. A previously unknown FAD gene was identified. Results of the studies reported at an international conference on iron utilization in plants, at commodity board meetings, and published in refereed journals. To increase soybean grain yields, breeding hybrid soybean by conventional and molecular approaches is being conducted. Presentation was given to Pioneer Hi-Bred Intl. at Johnston, Iowa and discussions occurred with Verde Seed Inc., Plainview, Texas; Dairyland Seed Co. Inc., Otterbein, Indiana; Hoegemeyer Hybrids, Hooper, Nebraska; Monsanto, Chesterfield, Missouri; Midwest Oilseeds, Inc., Adel, Iowa. Three poster presentations were given at the Crop Science Society of America annual meetings in New Orleans. To increase soybean yields and stabilize soybean production, breeding for disease and pests resistance is conducted by both conventional breeding and biotechnological approaches. Five germplasm lines resistant to soybean cyst nematode (SCN), genetically diverse at the molecular level from other sources of SCN resistance, were released. A germplasm line with resistance to brown stem rot (BSR), proven by all available screening techniques (planting on infested soil at several locations and years, screened by the colonization method in greenhouse conditions, and by molecular markers) was released. A high-yielding cultivar with resistance to BSR was released and will be used by growers in commercial plantings. Crosses have been made with new sources of SCN resistance, sudden death syndrome, and with new BSR resistant lines. Populations have been developed with these objectives. In order to improve soybean for sudden death syndrome (SDS) resistance, a phytotoxin (FvTox1) produced by the fungal pathogen Fusarium virguliformae was isolated and gene encoding this proteinacious toxin was identified. To generate antibody against this toxin in transgenic soybean plants, a putative gene encoding the anti-FvTox1 antibody has been isolated. Currently, efficacy of this antibody gene to make plant antibody in soybean is being investigated. Genetic manipulation of genes involved in the expression of disease resistance can also lead to development of novel germplam that can confer broad-spectrum disease resistance against many pathogens. Arabidopsis nonhost resistance genes for immunity against Phytophthora sojae were mutated, and several mutants carrying mutations in immunity genes have been identified. Once these genes are cloned, their roles in enhancing Phytophthora resistance will be evaluated in stable transgenic soybean plants. PARTICIPANTS: Silvia Cianzio (ISU), Dr. Mike Grusak from the USDA-ARS Children's Hospital in Houston and Dr. Lila Vodkin, University of Illinois. Jamie O'Rourke conducted analyses as part of her PhD program in the iron chlorosis project. Partial funding was received from USDA-ARS and the North Central Soybean Research Program. For the investigation of the homoelogous sequences in the soybean genome, Dr. Brian Scheffler, USDA-ARS, Stoneville, Dr. Scott Jackson, Purdue, and Dr. Bruce Roe, University of Oklahoma. Jessica Schlueter conducted the majority of the sequence analyses as part of her PhD program. For the soybean hybrid seed production project, field participants included the USDA North Central Regional Plant Introduction Station, Ames, Iowa; Verde Seed Inc., Plainview, TX; Hoegemeyer Hybrids, Hooper, Nebraska. Graduate students and undergraduate hourly students participated in the project. In breeding soybean for disease and pests resistance project, Dr. Silvia R. Cianzio and her lab members, in addition to Dr. Charlotte Bronson and Dr. Girma Tabor participated. In the FvTox1 project, the graduate student Hargeet Brar conducted all the experiments. In the nonhost resistance project, graduate student Rishi Sumit conducted most of the experiments. Undergraduate students assisted him in conducting the research. TARGET AUDIENCES: For the iron chlorosis project, the target audience includes geneticists, physiologists and plant breeders interested in plant nutrition and iron utilization. For hybrid soybeans, audiences included university, USDA, and commercial seed companies interested in hybrid soybean. For the breeding soybean for disease resistance, the target audience and users will be plant breeders (private and public), and soybean growers. The audience for the toxin project was soybean pathologists as well as soybean breeders.

Impacts
The identification of genes which remain differentially expressed after the addition of iron may help scientists devise strategies that will compensate for the physiological damages done during early growth stages and iron stress. Differentially expressed genes have provided candidates from which molecular markers may be developed. The data generated from the sequence analysis of duplicated regions have determined that assembly of the duplicated regions, independently of each other, should not be an insurmountable problem. It was observed that generally alfalfa leaf cutting bees were equal to or superior to European honey bees to transport soybean pollen from male parents to female parents. Companies interested in hybrid soybean can use alfalfa leaf cutting bees to produce hybrid soybean seed. It was demonstrated that phenotypic recurrent selection for insect pollinator preference in soybean is an ideal breeding strategy to improve hybrid seed production. The release of germplasm lines and cultivar will contribute to improve soybean yields. The new cultivar will be planted commercially, and the germplasm lines will be used by public and private soybean breeders in their own breeding programs. The lines are advertised. It is expected that the soybean community will sign material transfer agreements (MTA) to utilize the lines in their programs. Isolated FvTox1 gene encoding a phytotoxin for SDS development will assist designing biotechnological approach for generating SDS resistant soybean germplasm.

Publications

  • Schlueter, J., Lin, J.-Y., Schlueter, S., Vasylenko-Sanders, I., Deshpandem, S., Yi, J., O'Bleness, M., Roe, B., Nelson R., Scheffler, B., Jackson, S. and Shoemaker, R. 2007. Gene duplication and paleopolypoloidy in soybean and the implications for whole genome sequencing. Biomed Central (BMC) Genomics 8:330.
  • Cervantes-Martinez, I.G., Min, X., Zhang, L., Huang, Z., Kato, K.K., Horner, H.T., and Palmer, R.G. 2007. Molecular mapping of the male-sterility loci ms2, and ms9 in soybean. Crop Sci. 47:374-379.
  • Cianzio, S.R., Gebhart, G., Rivera-Velez, N., and Lundeen, P. 2007. Soybean cultivar IAR2001 BSR. ISURF.
  • Cianzio, S.R., Tabor, G., Gebhart, G., Rivera-Velez, N., Lundeen, P., and Bronson, C. 2007. Soybean germplasm line AR9BSR. ISURF #03577.
  • Cianzio, S.R., Arelli, P., Diers, B., Knapp, H., Lundeen, P., Rivera-Velez, N., and Gebhart, G. 2007. Soybean germplasm lines AR4SCN, AR5SCN, AR6SCN, AR7SCN, and AR8SCN. ISURF #03578 to 03581.
  • Ortiz-Perez, E., Horner, H.T., Hanlin, S.J., and Palmer, R.G. 2006. Insect-mediated seed-set evaluation of 21 soybean lines segregating for male sterility at 10 different loci. Euphytica 152:351-360.
  • Ortiz-Perez, E., Cianzio, S.R., Wiley, H., Horner, H.T., Davis, W.H., and Palmer, R.G. 2007. Insect-mediated cross-pollination in soybean [Glycine max (L.) Merrill]: I. Agronomic evaluation. Field Crops Res. 101:259-268.
  • O'Rourke, J.A., Graham, M.A., Vodin, L., Gonzalez, D.O., Cianzio, S.R., and Shoemaker, R.C. 2007. Recovering from iron deficiency chlorosis in near-isogenic lines of soybeans: A microarray study. Plant Phys. And Biochemistry 45:287-292.
  • Palmer, R.G. 2007. Dedication: Theodore Hymowitz, scientist, plant explorer, soybean geneticist. Plant Breeding Reviews 29:1-18.


Progress 01/01/06 to 12/31/06

Outputs
The overall goal of the project is to improve soybean for yield and resistance to both biotic and abiotic stresses. In order to create and manage genetic variation, the soybean genome was investigated for homoelogous regions. A complex organization of soybean genome resulting from at least two rounds of large-scale genome duplication has been observed. Homeologous regions of the genome were isolated and sequenced. Analysis of the sequence indicated that high levels of homology are often observed with both gene content and order retained between regions. Levels of homology approached 100% in genic regions with homology levels remaining high in some intergenic regions. Regions often showed expansion or contraction as a result of tandem duplications and the expansion/contraction of gene families. In order to exploit hybrid vigor in soybean, male-sterile, female-fertile mutants ms2, ms3, and ms9 were mapped with molecular markers. These mutants were successfully applied in generating F1 hybrids with the aid of insect pollination. Iron Deficiency Chlorosis (IDC) is a complex quantitative trait that reduces yield in north central soybean producing states. Dicots and grasses respond to iron deficiency stress by two separate mechanisms. An extensive search of expressed sequence tag collections revealed that homologs of both mechanisms can be found in several species. This suggests that both mechanisms may have functioned in dicots and monocots at one time. Two soybean germplasm lines with improved resistance to IDC were developed and released. In order to stabilize the yield from pathogenic attacks, both conventional breeding and biotechnological approaches have been applied. A germplasm line with resistance to soybean cyst nematodes (SCN) and Phytophthora root rot (PRR) has been released. A cultivar with improved resistance to brown stem rot is also in advance stage of development. Crosses have been made with new sources of SCN and sudden death syndrome resistance in order to develop lines carrying resistance to both diseases. Populations have been also developed to identify soybean rust resistance genes. Genetic manipulation of genes involved in the expression of disease resistance can also lead to development of novel germplam that can confer broad-spectrum disease resistance against many pathogens. Arabidopsis nonhost resistance genes for immunity against P. sojae were mutated, and mutants carrying these mutations have been identified. Once these genes are cloned, their roles in enhancing Phytophthora resistance will be evaluated in stable transgenic soybean plants. Of the two nonhost resistance genes, Pen1 and NHO1, Pen1 is required for immunity against Phytophthora sojae that causes PRR. Both genes were overexpressed in stable transgenic soybean lines. Enhanced PRR resistance was observed in transgenic lines carrying Pen1 but not NHO1. Several of the disease resistance signal pathway Arabidopsis genes have been oveexpressed in soybean. One of these genes, EDS1, enhances Phytophthora resistance in transgenic soybean plants. However, overexpression of either Pen1 or EDS1 resulted in reduced seed germination and inhibited seedling growth.

Impacts
Knowledge of the organization and structure of the soybean genome is important when planning assembly and annotation strategies for dealing with the whole-genome shotgun sequence forthcoming from DOE. Analysis of duplicated regions will allow scientists to 'train' annotation and assembly software, thus resulting in a high quality sequence assembly. Knowledge that alternative mechanisms may have once functioned in soybean may provide clues as to how geneticists may engineer better IDC resistance. This would reduce yield loss due to IDC. Several soybean lines with improved disease resistance have been licensed for use in breeding programs both in the private and public sector. Six material transfer agreements (MTA) and licenses have been signed between ISU and the corresponding institutions. Two Arabidopsis genes, Pen1 and EDS1, are identified for creating novel disease resistance mechanism in soybean. Male-sterile, female-fertile mutants generated in this investigation allowed to produce large quantities of hybrid seeds. Yield of some of the hybrids was better than conventionally bred cultivars. Growing of hybrid soybeans is expected to be an alternative for yield improvement in future.

Publications

  • Carter, C., Shafir, S., Vaknin L., Palmer, R.G. and Thornburg, R.W. 2006. Proline accumulating in plant nectars is a determinant of preferential honeybee feeding. Naturwissenschaften 93:72-79.
  • Charlson, D. and Shoemaker, R. 2006. Evolution of iron acquisition in higher plants. J. Plant Nutrit. 29:1109-1125.
  • Cianzio, S.R., Lightfoot, D.A., Niblack, T.L., Rivera-Velez, N., Lundeen, P. and Gebhart, G. 2006. Soybean line AR1. ISURF #03376.
  • Cianzio, S.R., Shoemaker, R.C., Charlson, D., Gebhart, G., Lundeen, P. and Rivera-Velez, N. 2006. Soybean line AR2. ISURF #03381.
  • Cianzio, S.R., Shoemaker, R.C., Charlson, D., Gebhart, G., Lundeen, P. and Rivera-Velez, N. 2006. Soybean line AR3. ISURF #03380.
  • Hyten, D., Song, Q., Zhu, Y., Choi, I.Y., Nelson, R., Costa, J., Specht, J., Shoemaker, R.C. and Cregan, P. 2006. Impacts of genetic bottlenecks on soybean genome diversity. Proc. Natl. Acad. Sci. USA. 103:16666-16671.
  • Ji, J., Scott, M.P. and Bhattacharyya, M.K. 2006. Light is essential for degradation of ribulose-1,5-biphosphate carboxylase-oxygenase large subunit during sudden death syndrome development in soybean. Plant Biol. 8:597-605.
  • Lu, P., Shannon, J.G., Sleeper, D.A., Nguyen, H.T., Cianzio, S.R. and Arelli, P.R. 2006. Genetics of cyst nematode resistance in soybean PIs 467312 and 507354. Euphytica 149:259-265.
  • Ortiz-Perez, E., Horner, H.T., Hanlin, S.J. and Palmer, R.G. 2006. Evaluation of insect-mediated seed set among soybean lines segregating for male-sterility at the ms6 locus. Field Crops Res. 97:353-362.
  • Ortiz-Perez, E., Horner, H.T., Hanlin, S.J. and Palmer, R.G. 2006. Insect-mediated seed-set evaluation of 21 soybean lines segregating for male-sterility at 10 different loci. Euphytica 152:1573-1582.
  • Schlueter, J.A., Sanders, I.F., Deshpande, S., Yi, J., Siegfried, M., Roe, B.E., Schlueter, S.D., Scheffler, B.E. and Shoemaker, R.C. 2006. The FAD2 family of soybean: insights into the structural and functional divergence of a paleopolyploid genome. The Plant Genome 1:14-26.
  • Schlueter, J.A., Scheffler, B.E., Schlueter, S.D. and Shoemaker, R.C. 2006. Sequence conservation of homeologous BACs and expression of homeologous genes in soybean (Glycine max L. Merr). Genetics 174:1017-1028.
  • Shoemaker, R. and Doyle, J. 2006. Paleopolyploidy and gene duplication in soybean and other legumes. Current Opinions in Plant Biology 9:104-109.
  • Tabor, G.M., Cianzio, S.R., Tylka, G.L., Roorda, R. and Bronson, C.R. 2006. A new greenhouse method to assay soybean resistance to brown stem rot. Plant Disease 90:1186-1194.
  • Xu, M. and Palmer, R.G. 2006. Genetic analysis of four new mutants at the unstable k2Mdh1-ny20 chromosomal region in soybean. J. Hered. 97:423-427.