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United States Department of Agriculture

Agricultural Research Service

Research Project: GENOME-WIDE DISCOVERY OF THE GENES/LOCUS DETERMINING THE OIL COMPOSITION AND OIL "FUNCTIONAL" MARKERS BY EXPLORING SOYBEAN GENETIC DIVERSITY

Location: Plant Genetics Research

2011 Annual Report


1a.Objectives (from AD-416)
1. Determine DNA sequences and expression levels of genes expressed in soybean seeds from fourteen genotypes. 2. Discover variations of gene sequences and expression levels in soybean seeds of the fourteen genotypes. 3. Discover a set of soybean oil "functional" markers for the fourteen genotypes.


1b.Approach (from AD-416)
Overall objective of the collaborative research proposal is to identify oil and meal traits and genes that influence those traits to improve the quality and value of US Soybean in the target area of composition. The proposed research will use genomics and bioinformatics approaches to predict the gene important for oil storage composition and identify gene markers to facilitate oil gene discovery. The proposed research will select fourteen genotypes containing diverse levels of oleic acid, linolenic acid and stearic acid levels, and determine their seed storage lipid profiles. In addition, deep sequencing technology will be used to determine sequences and accumulation levels of genes expressed in seeds from the fourteen genotypes and to identify their sequence and/or accumulation level variations among the genotypes. Association and a variety of data mining approaches will be used to predict the genes potentially regulating and participating in seed storage oil production. The sequence and expression variations that occur in those oil related genes will be further developed as a set of oil "functional" markers.


3.Progress Report

The project is designed to apply next generation sequence technologies to determine DNA sequences and expressions of soybean seed genes in major soybean germplasm in U.S. soybean breeding programs, and to further identify their variations that lead to seed oil composition and content changes. The project aims to discover genes important to soybean oil quality traits and generate a novel set of functional markers for soybean biotechnologists and breeders to develop new soybean germplasm with superior seed quality traits using marker assisted breeding and transgenic approaches. This is a three-year plan starting on April 1, 2011. To date, we have selected a total of 14 genotypes, and planted six germplasm to generate biological materials for library construction. In addition, Bowtie Software and Sequence Alignment/Map (SAM) tools were tested to align a set of testing sequence reads to soybean reference genome sequence of Williams 82 to determine gene sequence variation across different germplasm. Integrative Genomics Viewer (IGV) was also tested to view the sequence alignments and the sequence variations such as single nucleotide polymorphisms (SNPs). This project directly relates to objective 1 of the parent project "Analyze mRNA and storage oil profiles of cotyledons over the course of seed maturation to infer biological networks underlying soybean seed oil composition and content, and to predict their key gene candidates."


Last Modified: 7/14/2014
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