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ARS Home » Plains Area » Lubbock, Texas » Cropping Systems Research Laboratory » Plant Stress and Germplasm Development Research » Research » Research Project #434976

Research Project: Development a SNP Isogenic Research/breeding Platform of Cotton Substitution Lines with Alien Introgression of Monitoring Fusrium Wilt

Location: Plant Stress and Germplasm Development Research

Project Number: 3096-21000-022-20-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Mar 8, 2019
End Date: May 30, 2021

Objective:
1. Create a novel isogenic research/breeding platform comprising CS_RILs for 3 species donors, and (CS*CS) RILs for 3 combinations, where the genomic composition of each RIL is well-characterized by high-density genotyping using the CottonSNP63K Infinium II array or KASP technologies. 2. To assist in fingerprinting, genetic and association mapping analyses to identify markers and chromosome segment-associations with FOV race 4 (FOV4) resistance.

Approach:
Cotton (Gossypium spp.) one of the most important cash crops in the US and the primary economic source in Uzbekistan. Fusarium wilt caused by the fungus Fusarium oxysporum f. sp. vasinfectum (FOV) disease of cotton causes significant economic losses to cotton farmers in the USA, Uzbekistan and many other countries. Host-plant resistance is the only cost-effective long-term solution to address the problem of FOV, but its use is seriously impeded by the narrow genetic base of Upland cotton. This project proposes to create a novel isogenic research/breeding platform comprising chromosome substitution (CS)_ recombinant inbred lines (RILs) for 3 species donors, and (CS*CS)_RILs for 3 combinations, where the genomic composition of each RIL is well-characterized by high-density genotyping. Using seed from the USDA-ARS_MS cooperators, we aim to high-density genotype, validate substitutions and characterize background genomic constitutions, and seed-increase individual plants of around 300 chromosome-specific cotton (G. hirsutum L.) RILs (CS_RILs), including conventional CS_RILs specific to chromosome-04 (these are RILs formed by intermitting the interspecific chromosome substitution lines (CS-B04, -T04 and -M04) with the isogenic parent TM-1, and other RILs formed by creating recombinant inbred lines after intercrossing the same substitution lines involving chromosome-04 from different species, i.e., (CS*CS)_RILs, for CS-B04 x CS-T04, etc. The CottonSNP63K Infinium II array or KASP technologies will be used to genotype selected Uzbek germplasm and CS-RILs with alien introgression. This isogenic platform will serve needs for introgression, genetic research, mapping, marker-trait association and breeding. Lines and thus the platform will be immortalized via seed increases of each true-breeding line that has been high-density genotyped. The platform will afford unparalleled dissection of single-gene effects of the alien chromosome-04 representatives of 4 species (G. hirsutum and three other AD-genome Gossypium species). The anticipated products of this research will be potential DNA markers for assisting breeding of FOV resistance gene(s) that can expedite the selection process in cotton breeding programs and genetic diversification and targeted introgression of useful traits from wild species