Comprehensive assessment of host–plant interaction and genomic identification of multi‐genic resistance to Fusarium wilt race 4 (FOV4) in cotton

Abstract

Existing and emerging disease threats create the need to continuously identify and develop cultivars that can more efficiently defend against devastating pathogens. For two decades Fusarium oxysporum f. sp. vasinfectum (FOV) race 4 (FOV4), the fungus that causes the Fusarium wilt disease, has threatened cotton ( Gossypium spp.) production in the San Joaquin Valley of California and more recently in New Mexico and in the El Paso, TX region. In this study, a comprehensive genetic quantitative trait locus (QTL) mapping and genomic host–plant interaction research approach was conducted to identify simple sequence repeat and single nucleotide polymorphism markers and a set of biomarker‐candidate genes involved in Fusarium wilt resistance. Results from this research revealed resistant transgressive segregants—ancestral reciprocal rearrangements—duplication between gene‐ancestral forms in the A and D subgenomes, especially chromosomes A02 and A03 and translocation between A03 and D02, and the complexity of FOV4 resistance. In addition, QTL analyses revealed that the largest contribution (29%–61% of vascular root staining variation) to the FOV4 resistance resided in A02 ( qtlA02‐Fov4 ₁ ) and D03 ( qtlD03Fov4 ₁ ). Genes linked to enhanced phenylpropanoid metabolism and identified expressed genes are research targets to dissect polygenic forms of disease resistance, providing an opportunity for new strategies for marker and/or genomic selection. A final set of putative QTL markers and quantitative trait differentially expressed genes loci (QTDEL) associated with FOV4 resistance in cotton is proposed for identifying and selecting resistant phenotypes under naturally infested FOV4 field and artificial FOV4 inoculations in the greenhouse. This novel approach could also be applied to other pathogen–host systems.