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ARS Home » Plains Area » Lubbock, Texas » Cropping Systems Research Laboratory » Plant Stress and Germplasm Development Research » Research » Research Project #423437


Location: Plant Stress and Germplasm Development Research

2013 Annual Report

1a. Objectives (from AD-416):
To pursue breeding for enhanced abiotic stress tolerance in sorghum, which will encompass (but not be limited to) activities such as next generation sequencing and bioinformatic analysis of transcriptomes of four parental sorghum lines and genome wide re-analysis of QTL maps of mapping populations.

1b. Approach (from AD-416):
1. Perform high-density Illumina genotyping of PI610727, Shan Qui Red, PI567946, Tx430, and SRN39 (parents of RIL populations) and bioinformatics for single nucleotide polymorphism analysis. 2. Pursue re-analysis of cold-tolerance QTL data from these 4 RIL populations in a single, joint genome-wide association analysis using the high-density genotypes from part (1). 3. Perform pilot expression study: collect RNA from the cold-grown inbred parents (same 5 lines as in part 1) and their hybrids during germination, perform RNAseq, and look for cis-regulatory differences (differences in abundance between parental alleles) in the hybrids. 4. Perform statistical analysis and documentation (in form of graphs, photos, etc.) of results and provide the ARS coordinator with data, documentation, and reports from the endeavors of the agreement for use in submission of reports to funding agency.

3. Progress Report:
This is an ongoing study that involves application of gbs (genotype by sequencing) methodologies to analyze genotype of 3 cold-tolerant populations of sorghums for single nucleotide polymorphisms (SNP). Preliminary analyses gave an output of 2931 and 1817 single nucleotide polymorphism genotype data for RTx430 x PI610727 and BTx623 x PI567946 populations, respectively. These information are significant towards fine mapping of QTL regions for early season cold tolerance in sorghum.

4. Accomplishments