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ARS Home » Plains Area » Lubbock, Texas » Cropping Systems Research Laboratory » Plant Stress and Germplasm Development Research » Research » Research Project #439226

Research Project: Genetic Analysis and RNA Marker Development for FOV4 Resistance Breeding in Cotton.

Location: Plant Stress and Germplasm Development Research

Project Number: 3096-21000-022-033-R
Project Type: Reimbursable Cooperative Agreement

Start Date: Aug 15, 2019
End Date: Feb 1, 2021

To determine cotton resistance mechanisms to FOV by identifying genetic polymorphisms and gene expression characteristics relating to defence and develop molecular tools to expand breeding for FOV4 resistance in Upland cotton from a diversity of Gossypium sources.

Fusarium wilt caused by the fungus Fusarium oxysporum f. sp. vasinfectum (FOV) is a serious economic disease of cotton (Gossypium hirsutum L.) in the U.S. and many other countries. FOV is a soil and seed borne pathogen surviving in soil for long periods without a host. It cannot be eradicated once established. In 2003 FOV race 4 (FOV4) was identified in California soils. Since then, FOV4 has spread throughout California’s San Joaquin Valley. In 2017 FOV4 was found around El Paso, Texas now threatening Upland cotton production. Greenhouse pathogenicity tests show FOV4 severity increases in the presence of root knot nematode (RKN) (Meloidogyne incognita) and FOV race 1 (FOV1) pathogens. Host-plant resistance is the only cost-effective solution, seriously impeded by Upland cotton’s narrow genetic base. The proposed research will used eight cotton genotypes selected based on their known FOV4, FOV1 and RKN resistance/tolerance profiles, their current use as whole genome reference sequence genotypes, and as parents of recombinant inbred line (RIL) genetic mapping populations: Barbren-713-32-38 (FOV4 susceptible) and a backcrossed-derived isoline (BC5S2, FOV4 resistant introgressed from G. arboreum), both FOV1 and RKN resistant; Pima S-7 and Pima 379 (Pima types highly susceptible to FOV4, tolerant to FOV1); Acala NemX and TM1 (mid-tolerant/resistant to FOV4, susceptible to FOV1 and for NemX RKN resistant) and Upland UH001 (tolerant/resistant to FOV4); Pima S-6 (tolerant to FOV4). Several pathogen combinations of soil artificial inoculations will be performed using the above genotypes: These inoculations will be non-infected control, inoculation with FOV1, FOV4, RKN, FOV1+RKN, and FOV4+RKN. RNA will be isolated from control and inoculated roots. RNA-seq analysis will be conducted using an in-house pipeline in response to soil-infestation of series of inoculations. After RNA-seq analyses identified differently expressed genes or defense genes will be validated at Mississippi State University using in-house-developed transgenic procedures: overexpression, RNA interference (RNAi), virus induced gene silencing (VIGS), and CRISPR/Cas9. Conventional breeding has introgressed genes for tolerance/resistance to FOV4, providing a diagnostic basis to understand the genetic and genomic basis for FOV4 tolerance/resistance mechanisms in cotton. In conjunction with SNP map data, key defense genes (including susceptibility genes) will be identified and subjected to functional validation as stated. The validated defense genes will be used to develop RNA based markers to aid FOV4 resistance breeding and making tools available to the scientific community.