Location: Soybean Genomics & Improvement Laboratory
Project Number: 8042-21000-304-003-R
Project Type: Reimbursable Cooperative Agreement
Start Date: Jul 1, 2022
End Date: Jun 30, 2025
Objective:
The project will conduct genetic characterization and genome-wide association study (GWAS) of seed nutritional compounds and seed filling in two highly diverse soybean populations, using the high throughput genotyping and the high throughput phenotyping technologies. The specific objectives are to: 1) Evaluate biological characteristics and seed nutritional composition (protein, oil, fiber and sucrose) in fresh vegetable and mature soybeans; 2) Conduct GWAS of seed composition and seed filling traits in soybeans; 3) Detect and explore the quantitative trait loci (QTL), genomic features and/or candidate genes underlying molecular mechanisms regulating seed composition and seed filling; and 4) Investigate the effects of domestication and artificial selection on the traits in modern soybeans.
Approach:
A total of 450 diverse germplasm of different origins and 343 breeding lines from multi-crosses will be grown in the field under different environments and evaluated for seed filling rate at different development stages. Seed composition including seed moisture, protein, lipid, sugars, fatty and amino acids in edamame and mature soybeans will be measured using NIR spectroscopy technology. The materials will be genotyped with SoySNP50K BeadChip containing >50,000 SNPs or high-throughput sequencing and a genome-wide association study (GWAS) will be performed based on the combined phenotypic and genotypic datasets in order to identify QTL controlling seed protein, oil, fiber, soluble sugars, amino and fatty acids, and seed filling rate. Candidate genes or causative variants will be further identified through whole genome sequencing analysis of approximately 400 accessions with contrast effects at the major QTL regions, analyses of haplotype block, gene function and gene expression. In order to observe the effects of domestication and artificial selection on the traits, sets of genotypes including wild soybean, landrace and modern cultivars from the Soybean Germplasm Collection will be phenotyped and genotyped and the QTL allele frequency as well as the allele effects among wild, landrace and elite germplasm will be compared.
