Evaluation of resistance to Verticillium wilt in Gossypium hirsutum-Gossypium arboreum introgression lines and identification of putative resistance genes using RNA-seq.

Verticillium wilt (VW), a fungal disease caused by Verticillium dahliae (Vd), is one of the most destructive threats to cotton production. Moreover, widely cultivated upland cotton (Gossypium hirsutum, 2n = 4x = AADD = 52) often demonstrates low resistance to Vd. In contrast, G. arboreum (2n = 2x = AA = 26) shows high resistant to VW, making it a valuable source for breeding, despite the challenges posed by hybridization incompatibility between the two species. Here, a population of introgression lines derived from G. hirsutum and G. arboreum was evaluated for resistance to VW through both glasshouse and field tests. Among these lines, DM11039 demonstrated high resistance to VW. Both DM11039 and the recipient TM-1 underwent transcriptome sequencing during Vd infection at 0, 4, 12, 24, 48, and 96 h post inoculation. The analysis identified differentially expressed genes (DEGs), which were predominantly associated with resistance mechanisms. Based on the results from transcriptome sequencing and weighted correlation network analysis, three DEGs from each parent-G. arboreum and G. hirsutum- in DM11039 were subjected to virus-induced gene silencing in cotton seedlings. The findings revealed that silencing of GaPP2A1, GaPDH-E1, or GaLRK10L-1.2, which are located within the introgression segments from G. arboreum, significantly impaired disease resistance in cotton. This suggests that these genes are potentially linked to the disease phenotype. In contrast, silencing of GHA13G1263, GhZIP1 or GHA10G2498 from G. hirsutum did not result in any changes in disease resistance in DM11039. The results indicate G. arboreum harbors resistance genes to VW. Furthermore, the introgression population presents a valuable resource for future cotton breeding.