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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Soybean Genomics & Improvement Laboratory » Research » Research Project #445745

Research Project: Discover Genomic Loci Controlling Agronomic Traits & Develop Tools to Enable Rapid Characterization of Populations & Selection in Breeding Programs

Location: Soybean Genomics & Improvement Laboratory

Project Number: 8042-21000-304-005-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Mar 1, 2024
End Date: Aug 31, 2025

To cope with newly emerging diseases and pests, environmental extremes, and increasing demand for enhanced quality, breeders need to discover genes controlling the corresponding traits from new genetic resources and develop efficient selection methods to accelerate the breeding processes. Molecular characterization of populations or accessions is critical to determine the novelty of genes, map the positions of genes in the genome, and perform the genomic selection. This research is expected to meet these needs by genotyping populations created by the soybean collaborator with molecular tools and high-resolution genome-wide molecular markers. The objective of this collaboration is to discover genomic loci controlling nutritional quality, stress tolerance, seed yield and/or other economically important agronomic traits and for maker-assisted selection in soybean. Molecular markers and SNP assays developed at SGIL have resulted in collaborative research with researchers at Michigan State University in the past years. We will continue to analyze the mapping populations with high-quality molecular markers and assays (SoySNP50K, BARCSoySNP6K, and BARCSoySNP3K) developed in our laboratory to discover, map, and understand genes or QTLs/haplotypes controlling different traits, and perform a genomic selection of traits in collaboration with the researchers at Michigan State University.

A dataset containing 32 million genomic DNA variants from more than 1500 soybean varieties will be filtered based on variant quality and polymorphism. The sequences flanking each remaining variant will be retrieved to further screen for sequence specificity in the genome and will be used to design competitive allele-specific PCR genotyping (KASP) markers. Progeny populations from parents with contrasting performance differences in economically important traits will be used to discover QTL controlling these traits. Parental and recombinant inbred lines will be grown in the field and/or greenhouse and phenotyped for traits. DNA from breeding lines and parents will be genotyped using BARCSoySNP6K chips, and addition markers for each line will be imputed using SoySNP50K markers. Genome-wide association or linkage association analysis will be performed. To further refine the mapping of major QTL regions associated with traits, a population of remaining heterozygous lines will be developed from lines heterozygous for the identified major QTL regions and KASP markers will be used for genotyping these lines. In addition, the molecular markers will be used for genomic selection and prediction of the progeny trait performance.