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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Soybean Genomics & Improvement Laboratory » Research » Research Project #425341

Research Project: Defining the Genetic Diversity and Structure of the Soybean Genome and Applications to Gene Discovery in Soybean, Wheat and Common Bean Germplasm

Location: Soybean Genomics & Improvement Laboratory

Project Number: 8042-21000-275-000-D
Project Type: In-House Appropriated

Start Date: May 14, 2013
End Date: May 13, 2018

The long-term objective is to develop a comprehensive understanding of the genetic variability and genome structure of soybean and wild soybean in order to develop the tools to discover and use genetic variability for the enhancement of soybean resistance to environmental stresses, product quality and productivity. In addition, one project objective also addresses the use of markers in wheat and common bean improvement through identifying loci impacting a range of traits including disease and environmental stress and product quality and developing additional markers for marker assisted selection. An additional objective is the whole genome sequence analysis of two perennial soybean species that can ultimately serve as sources of genetic variability for cultivated soybean. A final objective relates to determining the genetic influence of the soybean on the genotype of the nitrogen fixing bacteria that form root nodules on the soybean host plant. The specific objectives of the project are: Objective 1: Develop a Core Collection for wild soybean and provide whole genome sequence data of the Core Collection, as well as elite cultivars that will be used in crosses with selected wild soybean accessions, and analyze highly productive progeny as well as unselected progeny from the G. max x G. soja crosses to further define and delimit the genome regions associated with soybean domestication and agronomic performance. Objective 2: Discover QTL and genes controlling biotic and abiotic stress resistance, agronomic and quality traits in soybean, wheat, and common bean, and develop DNA markers that define haplotype variation across these and previously identified regions. Objective 3: Determine the DNA sequence and define sequence variation and linkage disequilibrium of at least one perennial Glycine species. Objective 4: Determine the nature of the host–regulated genetic control of the specific strain of Bradyrhizobium japonicum that occupy the nitrogen-fixing root nodules of soybean.

The genetic analysis of 1,150 wild soybean accessions in the USDA Germplasm Collection with 50,000 SNP DNA markers will provide the genetic data to select a Core Collection of 60 wild soybean accessions. Thirty of the accessions were used by collaborators in crosses with cultivated soybean followed by intense selection and yield evaluation. The whole genome sequence (WGS) of the Core Collection, the adapted parents used in the cultivated x wild crosses, as well as a set of the highest yielding progeny and a similar set of unselected progeny from each cross will be determined. These data will facilitate a comparative sequence analysis to identify genome regions containing genes associated with domestication and unique genomic regions/genes from the wild soybean. Genetic markers to introgress the wild soybean-derived genes into cultivated soybean will be identified. The available WGS of common bean and wheat will be analyzed to identify SSR DNA markers. Polymerase chain reaction (PCR) primer sets flanking the SSRs will be designed and used to establish SSR marker databases for common bean and wheat. To evaluate the utility of the databases, a set of SSRs will be selected to amplify DNA from a set of genotypes and the amplicons visualized for locus specificity and polymorphism. In the case of wheat, additional WGS analyses using the HiSeq 2000 DNA sequencer will be performed on a small set of hexaploid wheats to provide additional data for SSR identification. In the case of soybean, analysis of 50,000 SNP DNA markers on the USDA Germplasm Collection of more than 18,000 cultivated soybean accessions will be used to identify a set of 6,000 SNP markers that are highly informative and well distributed across the soybean chromosomes. The 6,000 SNPs will be used to create a new Illumina BeadChip for soybean genome analysis. This Beadchip, along with a previously designed 6,000 SNP BeadChip for common bean, will be used to discover genes/quantitative trait loci (QTL) controlling important traits including resistance to biotic and abiotic stresses and agronomic and seed quality. Genomic DNA libraries of perennial Glycine species G. tomentella and G. canescens will be prepared for DNA sequence analysis on the HiSeq 2000. Size-selected DNA libraries ranging from 500 bp to 10 kbp will be developed for paired-end sequence analysis. Construction of four DNA libraries with fragment sizes of 500bp, 2.5kb, 5kb, and 10kb will be produced. The resulting 150 bp sequence reads will be processed using SOAPdenovo software. The resulting sequence scaffolds will be anchored to the G. tomentella and G. canescens chromosomes using genetic maps created using genotyping by sequencing. Recombinant Inbred line (RIL) populations of progeny from crosses of Williams 82 soybean with nodulation-restricting genotypes PI377578 and PI417566 will be analyzed for nodulation phenotype. Bulked segregant analysis using 1536 SNP DNA markers will be used to identify the position of the gene in each population controlling restricted nodulation. Additional markers will be developed and used to verify the position of the genes controlling restricted nodulation.