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ARS Home » Plains Area » Lubbock, Texas » Cropping Systems Research Laboratory » Plant Stress and Germplasm Development Research » Research » Research Project #437837

Research Project: Drought Stress Germplasm and Biomarker-gene Discovery for Assisting Breeding

Location: Plant Stress and Germplasm Development Research

Project Number: 3096-21000-022-029-R
Project Type: Reimbursable Cooperative Agreement

Start Date: Jan 1, 2020
End Date: Dec 31, 2020

To identify germplasm resilient to drought stress and discover biomarkers associated with physiological and morphological stress-traits by differently expressed and mapping genes

The current levels of cotton production are under threat by the fact that reservoirs and aquifers, such as the Ogallala, are being depleted faster than they can be replenished. Therefore, there is a need for a more resilient drought stress upland cotton germplasm to sustain yield and fiber quality losses. In addition, molecular markers or biomarkers associated with stress resistance traits can increase the efficiency of breeding by facilitating marker-assisted selection (MAS) resulting in significant decreases in cost, time, and the risk associated with subjective phenotypic assays when selecting resistant lines. The proposed project aims to identify more resilient drought stress upland cotton germplasm that can sustain economic yield and fiber quality losses under stress/drought or limited irrigation conditions. Selected germplasm with diverse levels of stress or drought response and plant-architecture or root-morphology will be subjected to different evaluations of water/irrigation regimes to induce plant stress responses. In addition, some of these selected entries will be subjected to genetic and quantitative trait loci (QTL) mapping, differently expressed gene, and biomarker trait association analyses. This research will be carried out at the USDA-ARS, Plant Stress and Germplasm Development Research (PSGD) unit, Lubbock, TX and the next-generation sequencing (NGS) at Texas Tech University Center for Biotechnology and Genomics (CBG). In addition, DNA will be processed from these progeny and entries and will be genotyped using the CottonSNP63k Illumina Infinium array or chip. The alleles SNP biomarkers of the phenotype contributing parent can be used for genetic/genomic studies and assisting breeding germplasm with improved stress or drought response. Generated NGS data will be aligned to the assembled two ancestral diploid parents (D5 and A2), and tetraploid Upland and Pima cotton genome reference-sequences. The alignment of selected sequences to the genome references will provide chromosomal map position and the genotyping of SNPs will provide additional information for marker-assisted selection or MAS during the breeding process. Information generated by genetic and QTL mapping, differently expressed gene, and biomarker trait association analyses together with cultivar-pedigree information will help us to establish correlations between resistance stress-responses and progeny or germplasm lines having a wide spectrum of stress resistance.