InDel variations and gene expression analysis related to Fusarium wilt resistance in Gossypium barbadense

Fusarium wilt resistance of Gossypium barbadense is very important to maintain its yield and quality, and to disease resistance breeding. Although many individual genes, which are quantitative trait loci associated with wilt resistance have been identified, knowledge of genes controlling wilt resistance in G. barbadense is still limited. In order to screen the InDel fragment related to Fusarium wilt resistance in G. barbadense, a genome‐wide association study was conducted using 110 recombinant inbred lines of Xinhai 14 (susceptible cotton) and 06–146 (resistant cotton). In this study, 207,040 high‐quality InDel loci were identified, of which 595 and 632 InDels were significantly associated (p < 1 × 10−3) with wilt resistance in G. barbadense in the additive and dominant effect module analyses, respectively. Combined transcriptome expression analysis within the FOV7 stably inherited qFOV7‐D03‐1 interval identified three ≥2 bp InDels for two differentially expressed genes. qPCR analysis was used to further validate that the expression of GB_D03G0204 and GB_D03G0238 was significantly different in the parental, resistant, and high susceptibility varieties. The GB_D03G0238 gene InDel was significant in both additive and dominant effect models, and the GB_D03G0204 gene InDel was significantly associated with wilt resistance in G. barbadense in the dominant effect model. The InDel fragments related to wilt resistance in G. barbadense discovered in this study can help gain insights into the genetic basis of wilt resistance and improve cotton breeding with excellent wilt resistance and high fiber quality traits.