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United States Department of Agriculture

Agricultural Research Service

Research Project: NESTED ASSOCIATION MAPPING TO IDENTIFY YIELD QTL IN DIVERSE HIGH YIELDING ELITE SOYBEAN LINES

Location: Soybean Genomics and Improvement

2011 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

This project is being undertaken for the purpose of identifying genetic factors that positively impact soybean yield. Soybean progeny are being 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. In the fall of 2010, seeds of 120 individual plants from each of 40 matings grown in Lincoln, NE and Urbana, IL were harvested. A leaflet had previously been collected from each of the 140 plants for the purpose of DNA isolation. The harvested seeds were sent to Argentina for seed increase in preparation for yield testing of 70 progeny lines from each mating in Lincoln, NE and Urbana, IL in the summer of 2011. The yield trails with 70 progeny lines from each of 39 matings (one mating was lost) were successfully planted at Clay Center, NE and at a site near Urbana, IL. In order to develop a set of 6,000 single nucleotide polymorphism (SNP) DNA markers to analyze the 70 lines from each of the 39 matings, DNA was extracted from the seed of the IA3023 parental line as well as the other 39 soybean parental lines. These DNAs are being sequenced on the Illumina HiSeq “Next Generation” DNA sequencer at the USDA, Beltsville, MD.


Last Modified: 9/22/2014
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