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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Soybean Genomics & Improvement Laboratory » Research » Research Project #422188


Location: Soybean Genomics & Improvement Laboratory

2013 Annual Report

1a. Objectives (from AD-416):
Identification of genes or Quantitative Trait Loci (QTLs) that positively impact soybean seed composition and yield, and 2) identification of DNA markers that soybean breeders can use to combine these genes or QTLs into new varieties more rapidly than is now possible.

1b. Approach (from AD-416):
ARS will complete the genetic analysis of the 5,600 Nested Association Mapping recombinant inbred lines (RILs) and parents that have been developed earlier as part of this project. Single Nucleotide Polymorphism (SNP) DNA markers developed at the USDA, Beltsville will be used in this genetic analysis. The Cooperators at the Univ. of Illinois and the Univ. of Nebraska will evaluate the yield of the 5,600 RILs and parents in the field and the Collaborator at the Univ. of Nebraska will also evaluate seed composition (protein and oil) and seed size. The combined genotypic and phenotypic data will be used to identify genes/QTL that control soybean yield and seed composition.

3. Progress Report:
Funds are provided by the United Soybean Board, as part of Project #2241 entitled “Nested Association Mapping to Identify Yield QTL in Diverse High Yielding Elite Soybean Lines – Continued Evaluation”. 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. 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 DNA markers and in the design of a custom Illumina beadchip containing 5,305 single nucleotide polymorphism (SNP) DNA markers. The Illumina beadchip is being used in the molecular genetic analysis of the 5,600 recombinant inbred lines and parents. DNA was extracted from leaf tissue of F5 plants from which the recombinant inbred lines of 18 different crosses were derived. For each cross, DNA was extracted from 140 leaf tissue samples. The complete set of 2520 DNA samples (18 crosses x 140 lines) and parents were analyzed with the 5,305 SNP DNA markers on the Illumina beadchip. High quality SNP DNA marker data were obtained for the 140 lines and parents for 15 of the 18 sets of 140 lines. In three of the crosses there was some missing data. The DNA of lines for which data were not obtained will be reanalyzed in the near future. DNA of the 140 lines from the remaining 22 crosses is now in the process of being extracted. Leaf tissue from approximately 20 F7 plants from each of the F5-derived lines (22 crosses x 140 lines) is being collected at the University of Nebraska. The tissue is lyophilized for 24 hours and then frozen and shipped to the USDA, Beltsville, MD where DNA is being extracted. The DNA of 140 F5-derived lines and the parents of the remaining 22 crosses will then be analyzed with the Illumina Beadchip containing 5,305 SNP DNA markers.

4. Accomplishments