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United States Department of Agriculture

Agricultural Research Service

Research Project: DEFINING THE GENETIC DIVERSITY AND STRUCTURE OF THE SOYBEAN GENOME AND APPLICATIONS TO GENE DISCOVERY IN SOYBEAN AND WHEAT GERMPLASM
2011 Annual Report


1a.Objectives (from AD-416)
The three objectives of the research are firstly, to define linkage disequilibrium and recombination rates across the soybean genome to facilitate efficient discovery of quantitative trait loci (QTL) through Association Analysis and efficient introgression of exotic germplasm, secondly, to define genome regions in cultivated soybean that are associated with domestication for the discovery of genetic variation lost through the domestication bottleneck that can be used to improve soybean and thirdly, to discover QTL and genes controlling biotic and abiotic stress resistance and quality traits in soybean and wheat, and develop DNA markers that define haplotype variation across these and previously identified regions.


1b.Approach (from AD-416)
Single nucleotide polymorphism (SNP) DNA markers will be discovered using high throughput genome sequence analysis in combination with the newly developed whole genome soybean sequence from the Department of Energy, Joint Genome Institute. A set of 50,000 SNPs, selected from across the genome, will be identified and genetically mapped in cultivated soybean as well as in a newly created cultivated x wild soybean population. The same SNPs will be used to characterize 16,795 soybean landraces as well as a set of 96 elite soybean cultivars and 1,116 wild soybean genotypes. This will allow an assessment of linkage disequilibrium and population structure across the genomes of the landraces, elite cultivars and wild soybeans. Association Analysis will be assessed as a new approach to detect genes/QTL underlying the important trait of seed protein concentration. The high resolution genetic maps in both cultivated x cultivated and cultivated x wild soybean populations combined with QTL analysis of traits related to soybean domestication will facilitate the identification of regions in cultivated soybean which, in comparison to wild soybean, have little or no genetic variation as a result of “selective sweeps” that occurred during soybean domestication. A universal set of 1536 soybean SNPs with high rates of polymorphism and even distribution across the genome will be developed and used to discover QTL underlying a number of disease resistance and quality traits in soybean. In addition, DNA marker development in hexaploid wheat will be continued and these markers and other SSR markers previously developed in our laboratory will be used in QTL analysis for a number of important traits in hexaploid wheat.


3.Progress Report
Progress was made in the genetic analysis of single nucleotide polymorphism (SNP) DNA markers in two extremely large soybean populations that consist of the progeny derived from hybridizing two soybeans. These SNP genetic markers are landmarks along the 20 soybean chromosomes and are interspersed with more than 45,000 genes in the soybean genome. The markers were mapped using the Genechip that we had previously developed. Both of the genetic populations had the soybean Williams 82 as one parent. Williams 82 was the soybean whose DNA sequence (nearly 1 billion DNA units) was completed in 2010. The first population consisted of 1098 soybean lines developed from crossing Williams 82 with a wild soybean PI 479752, and the second consisted of 961 lines from the cross of Williams 82 with the Essex soybean which was commonly grown and used as a parent in U.S. soybean breeding. A total of 23,814 of the SNP DNA markers were genetically analyzed in the Williams 82 x PI 479752 population and 14,933 in the Williams 82 x Essex population. The result is a very dense map of the soybean genome. These genetic maps will assist in improving the assembly of the Williams 82 soybean genome sequence. That is, the pieces or “scaffolds” of DNA sequence will be more accurately positioned onto the 20 soybean chromosomes.

Progress was made in the analysis of the USDA Soybean Germplasm Collection with 50,000 single nucleotide polymorphism (SNP) DNA markers. The USDA Soybean Germplasm Collection has over 19,000 cultivated and wild soybean accessions that have been collected over the past 90 years and which represent a wide diversity of genetic types. Over the past two years, DNA was isolated from each of these soybean accessions and was analyzed with the 50,000 SNP DNA markers. The 50,000 SNP DNA markers were selected to be positioned across each of the 20 soybean chromosomes. At this time the process of analyzing the resulting SNP genetic marker data is proceeding and requires the determination of the form of the SNP or “allele” that is present at each of the 50,000 SNP positions in each of the more than 19,000 soybean accessions. The initial determination of the alleles present in all accessions is nearly complete and it has been determined that DNA of about 2,000 accessions will have to be re-isolated and reanalyzed with the 50,000 SNP beadchip.


4.Accomplishments
1. Single Nucleotide Polymorphism (SNP) DNA marker discovery in common bean and the development of high throughput SNP DNA marker analysis. DNA markers are defined positions that are interspersed among the genes along the chromosomes of higher organisms. Because of their proximity to genes, DNA markers are used in plant and animal breeding to select individuals that carry the forms of particular genes that condition improved disease or stress resistance, improved quality traits or greater productivity. In the case of common bean only a relatively small set of genetic markers is available to plant breeders and geneticists. To expedite genetic marker discovery, ARS reseachers at Beltsville, MD, used a combination of two “next generation” DNA sequencers, the Roche 454-FLX and the Illumina Genome Analyzer II, to sequence specially constructed DNA libraries of two diverse common bean accessions. Careful analysis and comparison of the DNA sequence data derived from the two common bean accessions resulted in the discovery of 3,487 SNP DNA markers. A high throughput Illumina Inc. GoldenGate SNP assay was developed which contained 1050 of the 3,487 predicted SNP markers. A total of 827 of the 1050 SNP markers produced high quality data as demonstrated via the analysis of 48 cultivated and 48 wild common bean accessions. Genetic mapping defined the chromosome positions of 649 of the SNP markers. This initial SNP marker discovery in common bean will impact breeding and cultivar development by providing a set of markers that can be used in high throughput genetic analyses of common bean breeding populations to discover genes controlling traits of interest and for the selection of breeding lines that carry the forms of genes required for enhanced disease or stress resistance, improved quality traits or greater productivity.


Review Publications
Hyten, D.L., Song, Q., Fickus, E.W., Choi, I., Quigley, C.V., Hwang, E., Pastor Corrales, M.A., Cregan, P.B. 2010. High-throughput SNP discovery and assay development in Common Bean. Biomed Central (BMC) Genomics. 11:475.

Kendrick, M.D., Harris, D.K., Ha, B., Hyten, D.L., Cregan, P.B., Frederick, R.D., Boema, H.R., Pedley, K.F. 2011. Identification of a second Asian soybean rust resistance gene in Hyuuga soybean. Phytopathology. 101:535-543.

Haun, W.J., Hyten, D.L., Xu, W.W., Gerhardt, D.J., Albert, T.J., Richmond, T., Jeddeloh, J.A., Springer, N.M., Vance, C.P., Stupar, R. 2011. The composition and origins of intravarietal genomic heterogeneity in soybean. Plant Physiology. 155:645-655.

Kim, M., Hyten, D.L., Niblack, T.L., Diers, B.W. 2011. Stacking resistance alleles from wild and domestic soybean sources improves soybean cyst nematode resistance. Crop Science. 51:934-943.

Last Modified: 12/19/2014
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