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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Soybean Genomics & Improvement Laboratory » Research » Research Project #434471

Research Project: Characterization of Genetic Diversity in Soybean and Common Bean, and Its Application toward Improving Crop Traits and Sustainable Production

Location: Soybean Genomics & Improvement Laboratory

Project Number: 8042-21000-289-00-D
Project Type: In-House Appropriated

Start Date: May 14, 2018
End Date: May 13, 2023

Objective:
Objective 1: Discover QTL and genes controlling biotic and abiotic stress tolerance, and agronomic and quality traits in soybean and common bean and develop new DNA markers that define haplotype variation across new and previously identified genomic regions. [NP301, C1, PS1A; C3, PS3B] The aim of objective 1 is to develop community resources for efficient identification of genes/QTL impacting a range of traits and to facilitate marker assisted selection of alleles in soybean and common bean in collaboration with breeders. These include highly polymorphic markers, core germplasm collection and genotypic datasets of new exotic elite germplasm introduced to USDA Soybean Germplasm Collection. Objective 2: Evaluate diverse soybean populations developed from hybridization with wild soybean to discover unique QTL controlling seed protein and oil content, develop molecular markers, and make these available to breeders for improving soybean quality. [NP301, C1, PS1A; C3, PS3B] As many wild soybean germplasm may has different alleles controlling high protein and oil content than cultivated soybean, here we will explore wild soybean for the improvement of U.S. soybean seed protein and oil content with the markers developed from Objective 1 and genomic tools previously developed in our laboratory. Objective 3: Characterize genetic diversity of the Soybean Rhizobium Germplasm Collection using whole genome sequencing, evaluate nitrogen fixation efficiency of the core strains, and use the information to identify rhizobium genes associated with host-specific nodulation and nitrogen fixation in specific soybean genotype/rhizobium symbioses. [NP301, C1, PS1A; C3, PS3B] Genetic diversity of the rhizobia will be evaluated using genomic information and their influence on the nitrogen fixation efficiency in soybean will be analyzed. The research will result in the identification of efficient strains and genes for enhanced nitrogen fixation in soybean, resulting in better utilization of the diversity of rhizobium strains and soybean ancestors to improve biological nitrogen fixation in commercial soybean cultivars.

Approach:
Objective 1: Solexa short genomic DNA sequences from 16 diverse genotypes of different common bean market classes will be aligned to the common bean whole genome sequence (WGS) for SSR marker discovery. After filtering, primer sets will be designed to amplify the SSRs. A subset of 100 primer pairs will be randomly selected for testing polymorphism using genomic DNA from the 16 diverse common bean genotypes. A total of 12 pairs of diverse genotypes from different market classes of the Andean Diverse Panel of common bean will be sequenced. Called SNPs will be filtered based on a number of factors for beadchip assay. SNPs that are polymorphic within multi- market classes will be added to the Illumina Infinium BARCBean6K_3 BeadChip pool or used for KASP markers to fine map gene/QTL in targeted genomic regions. Based on the SNP data of the >18,000 cultivated soybean accessions assayed with SoySNP50K BeadChip, core sets of soybean accessions for each soybean maturity group will be created. The software Core Hunter 3 will be used to select the core collection with high allelic richness. Objective 2: a nested association mapping panel consisting of 150-300 F6 lines from each of 10 crosses of NC-Raleigh x wild soybean from the wild soybean core collection will be developed. The parents and the RILs will be grown in the field at two locations in two years. DNA isolated from the RILs and parents will be genotyped with Illumina BARCSoySNP6K BeadChips. Protein content and oil content of the parents and lines will be measured using a DA 7250 NIR Analyzer. The dataset will be used to identify QTL, genes and haplotypes controlling high seed protein and oil content in wild soybean that will be used for improving cultivated soybean and to predict accuracy of genomic selection. Objective 3: Genomic DNA of 760 soybean Bradyrhizobium strains will be isolated and sequenced at using NextSeq500 Sequencer. The resulting sequence will be aligned to the WGS of the B. japonicum strain USDA110 for variant discovery. Redundant or highly similar strains with 99.9% similarity among the soybean rhizobia will be identified. Within each cluster with 99.9% similarity, an accession from each cluster will be evaluated for nitrogen fixation efficiency using 8 ancestral cultivars which contribute more than 70% of the genetic diversity to the Southern and Northern American elite cultivars. Plant will be measured for chlorophyll content and biomass with or without inoculation of the stains, and scored for plant vegetative growth based on the growth of the plant inoculated with USDA110, a recommended soybean strain. The test in eight ancestors will be carried out in a greenhouse with replications.