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ARS Home » Plains Area » College Station, Texas » Southern Plains Agricultural Research Center » Insect Control and Cotton Disease Research » Research » Research Project #440487

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

Location: Insect Control and Cotton Disease Research

Project Number: 3091-22000-040-003-R
Project Type: Reimbursable Cooperative Agreement

Start Date: Feb 15, 2021
End Date: Aug 14, 2022

FOV is a soil and seed borne pathogen surviving in soil for long periods without a host. It cannot be eradicated once established. In the last decade and a half, new isolates of Fusarium that are extraordinarily pathogenic on cotton have appeared in the U.S. 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 has been found around El Paso, Texas now threatening Upland cotton production in Texas, the largest cotton-producing state, and across the contiguous U.S. belt. 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 develops molecular tools expediting breeding for FOV4 resistance in Upland cotton from a diversity of Gossypium sources.

Eight cotton genotypes are used, 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 and UH001 (tolerant/resistant to FOV4, susceptible to FOV1 and for NemX RKN resistant); Pima S-6 (tolerant to FOV4, susceptible to FOV1 and RKN). Pima S-7, Pima 379, TM1 and NemX are RIL population parents; TM1 is the primary G. hirsutum whole genome reference sequence. RNA samples are sequenced (RNA seq) and single nucleotide polymorphisms (SNPs), various other genetic elements, and gene expression data are utilized to identify candidate defense genes which are validated with transgenic methods: 1. Conduct RNA-seq analysis using an in-house pipeline in response to soil-infestation of series of inoculations: (a). identified tolerance/resistance genotypes under greenhouse and infested FOV4 fields: Upland G. hirsutum genotypes: NemX, TM-1, UH001; and Pima G. barbadense genotypes: Pima 379, PS6 and PS7. (b). new genotype-sources identified under greenhouse inoculation in backcross progeny from diploid G. arboreum via initial triple species hybrid into Barbren-713-32-x lines (G. hirsutum background) that are homozygous for Ren2,3 and Mi1,2 and are highly resistant to both root-knot and reniform nematodes and FOV1, but susceptible to FOV4. (c). pathogen combinations of soil artificial inoculations with None, FOV1, FOV4, RKN, FOV1+RKN, FOV4+RKN. 2. Validation of defense genes using in-house-developed transgenic procedures (a). overexpression. (b). RNA interference (RNAi). (c). virus induced gene silencing (VIGS). (d). CRISPR/Cas9. 3. Tools are made available to scientists.