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
Project Number: 1245-21000-263-00
Start Date: May 14, 2008
End Date: May 13, 2013
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.
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.