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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
2013 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 completing the analysis of the USDA Soybean Germplasm Collection with 50,000 single nucleotide polymorphism (SNP) DNA markers. The USDA Soybean Germplasm Collection has approximately 18,480 cultivated and 1,165 wild soybean accessions that represent a wide diversity of genetic types. Over the past four years the DNA of each accession was isolated and analyzed with 52,041 SNP DNA markers. The analysis of the resulting data indicated that 42,509 SNP DNA markers produced high quality data. The entire dataset consisting of 19,652 cultivated and wild soybean accessions analyzed with the 42,509 SNP DNA markers was submitted to SoyBase, the USDA, ARS, Soybean Genome Database. In the near future, SoyBase will make all of the genetic marker data available to soybean researchers around the world at http://SoyBase.org. These data will provide information for a range of analyses of soybean genetic and genome variability and for the discovery of genes impacting important traits including resistance to biotic and abiotic pests, seed composition, growth habit and seed yield.

Accomplishments over the life of the project included the discovery of SNP DNA markers in soybean, common bean and wheat and the development of “genechips” for high throughput DNA marker analysis of soybean and common bean. In soybean these markers were used to create a genetic map with more than 5,800 DNA markers that was used to anchor the soybean whole genome DNA sequence to the 20 soybean chromosomes and resulted in the publication of the soybean whole genome sequence in 2010. A carefully selected set of 1536 SNP DNA markers in soybean was used to create the Universal Soy Linkage Panel 1.0 that was widely used to analyze soybean populations from breeders and geneticists around the U.S. These analyses resulted in the discovery of quantitative trait loci (QTL) i.e., genes, controlling numerous traits including resistance to biotic and abiotic stresses, seed composition, as well as traits related to plant growth and development and seed yield. One notable application of SNP marker technology in soybean was the use of Genome Wide Association Analysis (GWAS) for the detection of QTL/genes controlling seed protein and oil content. The GWAS was very successful in detecting 17 regions across the 20 soybean chromosomes containing QTL/genes controlling the level of seed protein. In the case of common bean, 3 genechips with more than 5,000 SNP markers each were used to analyze a set of more than 500 common bean accessions. A portion of these SNPs was also used to analyze a common bean genetic mapping population of 277 progeny to create a genetic map with 7,019 SNP DNA markers. In collaboration with the Dept. of Energy, Joint Genome Institute and North Dakota State Univ. the resulting genetic map has been used to anchor the common bean DNA sequence to the 11 common bean chromosomes and will soon result in the publication of the common bean whole genome sequence.


4.Accomplishments
1. Development of a “Core Collection” of cultivated soybean. Plant germplasm collections often contain many thousands of accessions that represent the total diversity of a plant species. Such is the case of the USDA Soybean Germplasm Collection that contains approximately 18,480 cultivated soybean accessions. Such large numbers of accessions would be difficult to evaluate in most research programs and thus the concept of Core Collections was developed. A Core Collection or Core Set is a selected subset of 10 – 20% of the entire collection that represents a large proportion of the diversity of the entire collection. Based upon the analysis of 18,489 cultivated soybean accessions from the USDA Soybean Germplasm Collection with 42,509 single nucleotide polymorphism (SNP) DNA markers, ARS researchers at Beltsville, MD eliminated 4305 accessions that were 99.9% genetically similar to another accession. Based upon a genetic analysis of the SNP DNA marker data of the 14,184 remaining accessions, a Core Collection of 1418 accessions that represented 79% of the genetic diversity of the entire collection was identified. The cultivated soybean Core Collection will allow soybean breeders and geneticists to analyze and search for useful genetic variation in a relatively small and manageable set of accessions that still is anticipated to contain most of the genetic variability of the entire USDA Soybean Germplasm Collection.

2. Design of a new “beadchip” for the genetic analysis and genetic improvement of Soybean. DNA markers are defined positions that are interspersed within and among the genes along the chromosomes of higher organisms. DNA markers can be used to create genetic maps in which the order and the distance between the positions of the DNA markers along each chromosome are defined. In plant genetic research such maps are used in a variety of ways to define the positions of genes on the chromosomes and to identify breeding lines that carry the form of a gene or genes that offer resistance to disease, abiotic stress or improved product quality. ARS researchers at Beltsville, MD selected an optimal set of 6,000 single nucleotide polymorphism (SNP) DNA markers from those they had previously developed and whose position on the soybean genetic map they had previously defined. These markers are evenly distributed across the 20 pairs of soybean chromosomes. The BARCSoySNP6K Illumina beadchip with 6,000 SNP DNA markers provides an extensive set of well positioned DNA markers that can be used by soybean geneticists and breeders to discover genes of interest and to rapidly incorporate such genes into new soybean varieties with enhanced stress resistance and nutritional quality.


Review Publications
Song, Q., Hyten, D., Jia, G., Quigley, C.V., Fickus, E.W., Nelson, R.L., Cregan, P.B. 2013. Development and evaluation of SoySNP50K, a high-density genotyping array for soybean. PLoS Genetics. 8(1):e54985.

Bales-Arcelo, C., Zhang, A., Liu, M., Mensah, C., Gu, C., Song, Q., Hyten, D., Cregan, P.B., Wang, D. 2013. Mapping soybean aphid resistance genes in PI 567598B. Theoretical and Applied Genetics. 126:2081-2091.

Last Modified: 10/21/2014
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