Location: Soybean Genomics & Improvement Laboratory
Project Number: 8042-21000-304-000-D
Project Type: In-House Appropriated
Start Date: May 9, 2023
End Date: May 8, 2028
Objective:
Objective 1: Discover genomic loci controlling nutritional quality, stress tolerance, seed yield and other economically important agronomic traits in soybean and common bean and develop genomic tools to enable rapid characterization of populations and selection in breeding programs.
Sub-objective 1.A.: Develop efficient genome-wide KASP assays for soybean and common bean genetic and genomic research.
Sub-objective 1.B: Discover unique QTL and haplotypes associated with seed methionine content and cysteine content in populations derived from wild and cultivated soybean crosses and evaluate the efficiency of genomic selection for the traits. Discover genomic loci controlling other nutritional quality, stress tolerance, seed yield in soybean and common bean by collaborative research.
Objective 2: Identify novel genes controlling rhizobium nodulation in soybean accessions from the National Soybean Germplasm Collection and/or previously reported accessions and determine their underlying mechanism through mapping and gene-structure comparisons.
Objective 3: Distribute, acquire and maintain the safety, genetic integrity, and viability of rhizobium genetic resources and associated descriptive information.
Objective 4: Conduct research to develop genetic resource maintenance, evaluation, or characterization methods and then apply them to priority rhizobium genetic resources to avoid backlogs in microbial genetic resource and information management.
Sub-objective 4.A: Sequencing the rhizobium accessions isolated from the soybean, common bean, and other major legume crops.
Sub-objective 4.B: Application of sequencing information to develop core strain collections and high throughput genotyping assays for rhizobium strain identification.
Approach:
Objective 1: Sequence reads of common bean accessions will be aligned to the common bean whole genome sequence assembly. Called SNPs will be filtered based on SNP quality and polymorphism. Sequence flanking each of the remaining SNPs will be retrieved for further screening of their sequence specificity in the genome and will be used to design KASP markers. The dataset containing 32 million SNPs from >1500 soybean accessions will be used for soybean KASP assay design per the protocol described above. A total of 10 RIL families from cultivated x wild soybean cross will be used for the discovery of QTL controlling methionine and cysteine content. The parents and RILs were grown in the field at two locations. DNA of the RILs and parents were genotyped with BARCSoySNP6K Chips and the RILs will be imputed with SoySNP50K markers segregration between parents. Seeds will be ground for amino acid measurement. A genome-wide association analysis will be performed. To further fine-map the major QTL regions associated with the amino acid content, residual heterozygous line populations will be developed from the lines that are heterozygous in the identified major QTL regions. Objective 2: A cross between Williams 82 x VS12-0205 (non-nodulation) will be made to create a large F2 population. DNA from leaf tissues of the parent and progenies will be extracted and genotyped with SoySNP50K assay. When matured, each plant will be dug for nodulation observation. JoinMap 4.0 software will be used to map the locus. To further verify the gene that showed expression level difference, RNA from taproot and root hairs of the plants of each parent will be extracted separately at different days after inoculation. The relative expression levels of the candidate gene will be evaluated by the comparative threshold method. To validate the non-nodulation gene function, we will overexpress the candidate gene in VS12-0205 and knock out the candidate gene in the Williams 82 with the RNAi or CRISPR/Cas9-based genome-editing tools. Objective 3: Rhizobial cultures will be managed by their preservation, quality control and disbursement to ARS customers upon request. Technical information about rhizobia, culturing and symbiosis and advice will be given. Emphasis will be placed on preparing and sending cultures for long-term backup at the NCGRP, Fort Collins, CO. The information on old and new strains will be updated and deposited at the National Rhizobium Database for public access. Objective 4: DNA from rhizobium strains will be isolated from major legume crops and sequenced. The resulting sequence will be aligned to the WGS of B. japonicum strain USDA110, B. Elkanii USDA 61 as well as the Sinorhizobium meliloti strain USDA 1002 for SNPs and indels calls. Core sets of rhizobia will be created for common bean and soybean, respectively. A set of SNPs that can distinguish and classify accessions efficiently will be selected to be included in the high-throughput genotyping assay.
