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United States Department of Agriculture

Agricultural Research Service

Research Project: Discovery of Drought Stress Biomarker-genes for Assisting Breeding

Location: Plant Stress and Germplasm Development Research

Project Number: 3096-21000-019-11-R
Project Type: Reimbursable Cooperative Agreement

Start Date: Jan 1, 2014
End Date: Dec 31, 2014

1. To discover biomarker-genes associated with physiological and morphological traits that improve drought stress tolerance. 2. To validate biomarker associations with stress resistance traits.

Selected germplasm with diverse level of drought response and plant-architecture or root-morphology will be subjected to the next-generation sequencing (NGS)technology. Research will be carried out at the USDA-ARS Cropping Systems Research Laboratory (CSRL), Plant Stress and Germplasm Development Research, and Texas Tech University Center for Biotechnology and Genomics (CBG). Germplasm and parents of RIL populations subjected to NGS using Illumina MiSeq sequencing will be used for differentially expressed gene expression analyses and Single Nucleotide Polymorphism (SNP)-biomaker discovery. The RIL populations and germplasm will be evaluated for drought stress responses. The genomic data generated by NGS will be aligned to the assembled D cotton (G. raimondii, D5) genome reference sequence ( and to the A2 cotton genome (G. arboreum, if available). The generated SNPs will discover functional alleles for these important traits. In addition, the A2 and D5 genome reference will provide chromosomal map position and additional flanking DNA sequences. Since all samples used for pooling in the NGS analyses will be subjected to drought stress evaluations, the alleles (SNPs) of the phenotype contributing parent can be used to develop primer-biomarkers for genetic and QTL mapping approaches.

Last Modified: 10/16/2017
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