Location: Plant Stress and Germplasm Development Research
Project Number: 3096-21000-022-007-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Nov 15, 2020
End Date: May 30, 2022
Objective:
1. Characterize genetic and molecular mechanisms contributing to contrasting stress tolerance responses and disease resistance.
2. Identify and characterize candidate genes based on transcript abundance or differentially expressed gene analysis associated with tolerance and susceptibility responses to abiotic stresses such as water deficit and nutrient starvation and biotic-disease resistance such as Fusarium wilt in cotton.
3. Development of tools such as molecular markers (from next-generation sequencing) and mutant populations to be used for the development of stress-tolerant (abiotic and biotic) cotton genotypes.
Approach:
Producing more with lower water resources, facing poor soil fertility and emerging threat-crop diseases is an especially daunting endeavor. This research will be carried out at the USDA-ARS Plant Stress and Germplasm Development Research Unit (PSGDRU) and Texas Tech University, Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST). At the PSGDRU through diverse collaborative projects using next generation sequencing (NGS) technology, genomic information from expressed genes has been generated. Extracted total RNA or small RNA was used to develop cDNA libraries from selected germplasm with diverse levels of drought response and plant-architecture or root morphology and disease resistance. Research using diverse set of cotton lines and mapping populations with different response to drought and disease resistance at the PSGDRU, Lubbock indicated that it is possible to maintain high fiber quality under limited water conditions or reduce the impact on fiber quality. In addition, RNA-Seq was performed on breeding material or cotton entries identified/developed with resistance to Fusarium wilt (FOV) such as race 4 (FOV4) and root-knot nematode (RKN) by USDA-ARS and University cooperators. Transcriptome sequencing was conducted on double stranded cDNA by paired-end sequencing on Illumina MiSeq and HiSeq sequencers. Comparative gene expression profiling of sequencing data will be done to identify molecular and regulatory responses between contrasting stress-susceptible or tolerant and disease-resistant phenotypes. Differential cDNA sequences revealing significantly highly abundance transcripts or differentially expressed genes will be assigned with identifiers for annotation and display of differentially expressed transcripts and for mapping into pathways and expression validation, using MapMan software (ver. 3.50) and qRT-PCR. In addition, development of tools such as molecular markers (from next-generation sequencing) and two mutant populations (employing chemical and fast neutron mutagenesis) to be used for the development of stress-tolerant (abiotic and biotic) cotton genotypes will be accomplished through this collaborative research. Single nucleotide polymorphism (SNP) biomarkers from selected cotton genotypes will be identified and eventually use for marker-assisted breeding. Mutant populations together with massive phenotype and genotype by sequencing approaches will facilitates gene discovery for any trait of interest (i.e. fiber quality, drought tolerance, nutrient use efficiency, etc.). This research aims to create invaluable resources to address diverse research purposes.
