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ARS Home » Plains Area » Lubbock, Texas » Cropping Systems Research Laboratory » Plant Stress and Germplasm Development Research » Research » Publications at this Location » Publication #324185

Title: Integrated and translational genomics for analysis of complex traits in crops

item Chopra, Ratan
item BUROW, MARK - Texas A&M Agrilife
item CHAGOYA, JENNIFER - Texas A&M Agrilife
item SIMPSON, CHARLES - Texas A&M Agrilife
item Burow, Gloria
item Burke, John
item Xin, Zhanguo

Submitted to: Annual International Plant & Animal Genome Conference
Publication Type: Proceedings
Publication Acceptance Date: 12/8/2015
Publication Date: 1/8/2016
Citation: Chopra, R., Burow, M., Chagoya, J., Simpson, C., Burow, G.B., Burke, J.J., Xin, Z. 2016. Integrated and translational genomics for analysis of complex traits in crops. In: Proceedings of the International Plant & Animal Genome Conference. January 8-13, 2016, San Diego, California. Paper No. 21251.

Interpretive Summary:

Technical Abstract: We report here on integration of sequencing and genotype data from natural variation (by whole genome resequencing [wgs] or genotype by sequencing [gbs]), transcriptome (RNA-seq) and mutant analysis (also by wgs) with the goal of translating gems from these resources into useable DNA markers in the form of single nucleotide polymorphic (SNP) markers for crop improvement in peanut and sorghum. In peanut (Arachis sp), RNA-Seq was utilized to identify polymorphic SNPs in a cross between A. duranensis x A. cardenasii. Polymorphic SNPs were further used to develop a genetic map to identify QTLs for plant architectural traits including leaf measurements, main stem height, presence of main stem flowers, and seed weight. Validation of peanut architecture associated SNPs from this diploid population will be tested in populations of tetraploid peanuts. Meanwhile in sorghum, a genome wide association study for sorghum seedling stress was performed using GBS data and QTLs were identified for absorbance of flavonoids, shoot/root lengths, and shoot/root weights. SNPs associated with these traits in sorghum were screened in mutant germplasm and validated in a recombinant inbred population. To date there is an exponentially increasing amount of sequence and genotype data for major crops including peanut and sorghum, and integrated studies through a translational genomics approach and pipeline for identification of valuable SNP markers are vital for marker assisted breeding to become an integral part of germplasm enhancement.