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United States Department of Agriculture

Agricultural Research Service


Location: Soybean Genomics & Improvement Laboratory

2013 Annual Report

1a. Objectives (from AD-416):
The discovery of genes or quantitative trait loci (QTL) that control yield per se in elite soybean germplasm.

1b. Approach (from AD-416):
The high yield reference genotype, IA3023, was crossed to 25 diverse accessions to create 25 populations with 200 recombinant inbred lines (RILs) each. Thus, each population shares the reference genotype as one of the parents. The 5000 RILs will be phenotyped by collaborators and genotyped with SNPs as per a typical QTL population analysis. The 25 diverse accessions will be extensively genotyped or sequenced which allows for high marker density which can be extrapolated to all the RILs in the 25 populations, thus greatly increasing the power to detect and fine map QTL. Using this approach, essentially all SNPs present in all 5000 RILs can be determined and the most common QTL among the 25 diverse lines can be discovered.

3. Progress Report:
Funds were provided by the United Soybean Board, as part of Project #9241 entitled “Nested Association Mapping to Identify Yield QTL in Diverse High Yielding Elite Soybean Lines”. This project was undertaken for the purpose of identifying genetic factors that positively impact soybean yield. Soybean progeny were developed from matings of the high yielding soybean variety IA3023 with a broad spectrum of soybean lines from soybean breeders in Arkansas, Illinois, Indiana, Ohio, Tennessee, Missouri, and Nebraska. A total of 5,600 recombinant inbred soybean lines were developed from 40 crosses with IA3023. These lines are now being tested in replicated yield trials with the goal of applying Nested Association Mapping to discover genes that underlie soybean productivity. Progress was made in the discovery of single nucleotide polymorphism (SNP) DNA markers that are being used in the molecular genetic analysis of the 5,600 recombinant inbred lines and parents. DNA sequence data were obtained from the 41 Nested Association Mapping parents using the “next generation” Illumina HiSeq DNA sequencer at the USDA, Beltsville. The DNA sequence of each of the parents was aligned to the soybean Whole Genome Sequence in order to identify SNP DNA markers. The SNPs in this analysis were carefully screened to identify a set of 6,000 SNP markers that were well distributed across the 20 sets of soybean chromosomes and that distinguished the common parent IA3023 from as many as possible of the other 40 parental lines that were crossed with IA3023. These SNPs were used at the ARS, Beltsville, MD in the design of a custom Illumina Beadchip that contained the 6,000 SNPs and that will be used to analyze the 5,600 recombinant inbred lines and parents. Progress is monitored via quarterly written reports and by frequent phone conferences with the collaborators at the University of Illinois and the University of Nebraska and via e-mail correspondence concerning the progress of the project.

4. Accomplishments

Last Modified: 05/22/2017
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