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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

Location: Soybean Genomics and Improvement

2012 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 assessing the application of Association Analysis for the determination of the position of genes that control seed protein content in 302 accessions from the USDA Soybean Germplasm Collection. Seed protein content in the accessions, determined in field trails, ranged from 35.5 to 50.5%. The 302 accessions were genetically analyzed with more than 32,000 SNP DNA markers. The Association Analysis using the seed protein and the DNA marker data detected 18 positions on the 20 pairs of soybean chromosomes that contained a gene or genes impacting seed protein concentration. The results based upon the Association Analysis appear to be very reliable because 11 of the 18 positions have been previously reported as containing genes that impact seed protein concentration.

Progress was made in the analysis of the USDA Soybean Germplasm Collection with the 50,000 single nucleotide polymorphism (SNP) DNA markers that are spread across the 20 pairs of soybean chromosomes. The USDA Soybean Germplasm Collection has over 18,680 cultivated, and 1,115 wild, soybean accessions that represent a wide diversity of genetic types. Over the past three years the DNA of each accession was isolated and analyzed with more than 51,000 SNP DNA markers. The initial analysis of the resulting data indicated that 42,509 SNP DNA markers produced high quality data. It was also determined that the data from more than 2,870 accessions were not completely reliable and these accessions have now been reanalyzed. Based upon the accessions with high quality data, the average genetic distance between any pair of cultivated soybean accessions was 0.29 as determined by the DNA marker analysis. This indicates that, on average, a different form or “allele” of the DNA marker is present at 29% of the DNA marker positions in a comparison of any two soybean germplasm accessions. The complete DNA marker dataset consisting of more than 19,700 accessions with data for 42,509 DNA markers is being further analyzed in preparation for submission to SoyBase, the USDA, ARS, Soybean Genome Database.


4.Accomplishments
1. Discovery of regions of the soybean genome likely to contain genes important in the domestication of soybean. The cultivated soybean that is grown on more than 70 million acres in the U.S. was domesticated about 5,000 years ago in China from the wild, viney, small black seeded wild soybean. In the process of the domestication of soybean and other crops a large proportion of the genetic variation present in the wild progenitor species is lost due to what is referred as a “genetic bottleneck”. This loss of genetic variability is desirable in that it may eliminate many of the undesirable traits present in the wild species, but it also may eliminate genetic variation that could be useful in modern crop improvement. Thus, it is important to define the regions of the soybean chromosomes and the specific genes in those regions that were responsible for the genetic improvement associated domestication. Using 42,000 DNA markers analyzed on 96 wild soybeans and 96 cultivated soybeans, ARS researchers at Beltsville, MD defined 18 regions across the 20 pairs of soybean chromosomes where there was significantly reduced genetic variation in the cultivated versus the wild soybean. These regions are putatively associated with soybean domestication. Little or no genetic variation is available in cultivated soybean in these regions. Thus, they provide targets to mine for genes that are currently not available in cultivated soybean germplasm that can be used in the genetic improvement of cultivated soybean.

2. Creation of a high density genetic map of the common bean. 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 developed and mapped more than 7,000 new single nucleotide polymorphism (SNP) DNA markers and created a genetic map of the 11 pairs of the common bean chromosomes. This map provides an extensive set of well positioned DNA markers that can be used by common bean geneticists and breeders to discover genes of interest and to rapidly incorporate such genes into new common bean varieties with enhanced stress resistance and nutritional quality. In addition, the DNA sequence associated with each of the SNP DNA markers is being used to “assemble” the DNA sequence of the whole common bean genome which is being completed by researchers at the Department of Energy, Joint Genome Institute.


Review Publications
Jiang, G., Wang, X., Green, M., Scott, R.A., Hyten, D., Cregan, P.B. 2012. QTL analysis of saturated fatty acids in a population of recombinant inbred lines of soybean. Molecular Breeding. 30:1163-1179.

De Souza, T., De Barros, E.G., Bellato, C.M., Fickus, E.W., Cregan, P.B., Pastor Corrales, M.A. 2011. Single nucleotide polymorphism (SNP) discovery in common bean. Molecular Breeding. 30:419-428.

Mamidi, S., Chikara, S., Goos, R.J., Hyten, D.L., Moghaddam, S.M., Cregan, P.B., Mcclean, P.E. 2012. Genome-wide association analysis identifies candidate genes associated with iron deficiency chlorosis in soybean. The Plant Genome. 11:154-164.

Du, J., Tian, Z., Sui, Y., Zhao, M., Song, Q., Cannon, S.B., Cregan, P.B., Ma, J. 2012. Pericentromeric effects shape the patterns of divergence, retention, and expression of duplicated genes in the Paleopolyploid Soybean. The Plant Cell. 24(1):21-32.

Last Modified: 9/22/2014
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