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United States Department of Agriculture

Agricultural Research Service

Research Project: Functional Genomics for Evaluating Genes and Gene Regulatory Networks of Soybean Quality Traits

Location: Plant Genetics Research

Title: Identification of transcript polymorphisms for seed quality improvement by exploring soybean genetic diversity

Authors
item An, Yong-Qiang
item Goettel, Herbert
item Upchurch, Robert
item Wang, Ming
item Xia, Eric -
item Liu, Zongrang
item Chen, Pengyin -

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: December 11, 2013
Publication Date: January 10, 2014
Repository URL: http://https://pag.confex.com/pag/xxii/webprogram/Paper12951.html
Citation: An, Y., Goettel, H.W., Upchurch, R.G., Wang, M.L., Xia, E., Liu, Z., Chen, P. 2014. Identification of transcript polymorphisms for seed quality improvement by exploring soybean genetic diversity (abstract). Plant & Animal Genome. Paper No. 036.

Technical Abstract: The difference in seed oil composition and content among soybean genotypes could be mostly attributed to transcript sequence and/or expression variations of oil-related genes that that lead to changes in the functions of the proteins that they encode and/or their accumulation in seeds. We sequenced transcriptomes of soybean seeds from nine genotypes varying in oil composition and content. Having applied a wide range of bioinformatics algorithms, we identified a large collection of transcript polymorphisms including variations in transcript sequence (SNPs and indels), transcript accumulation and transcript splicing among the genotypes, and further predicted the transcript polymorphisms that potentially cause oil quality variation based on their biological effects. We successful rediscovered that the deletion of FAD2-1A gene and a non-synonymous SNP in FAB2C caused elevated oleic acid and stearic acid levels in soybean lines M23 and FAM94-41 respectively. An effective algorithm was also developed to successfully predict several large DNA deletions. We sequenced the genome and seed transcriptome of Jack, and compared their efficiency in discovering SNPs at various sequencing depth. Polymorphisms identified by this project could be used to further develop into a set of functional markers for breeders to design effective crossing and marker assisted selection strategies for oil quality improvement.

Last Modified: 11/1/2014
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