Transcriptome Analysis of a Cotton Cultivar Provides Insights into the Differentially Expressed Genes Underlying Heightened Resistance to the Devastating Verticillium Wilt

Abstract

Cotton is an important economic crop worldwide. Verticillium wilt (VW) caused by Verticillium dahliae (V. dahliae) is a serious disease in cotton, resulting in massive yield losses and decline of fiber quality. Breeding resistant cotton cultivars is an efficient but elaborate method to improve the resistance of cotton against V. dahliae infection. However, the functional mechanism of several excellent VW resistant cotton cultivars is poorly understood at present. In our current study, we carried out RNA-seq to discover the differentially expressed genes (DEGs) in the roots of susceptible cotton Gossypium hirsutum cultivar Junmian 1 (J1) and resistant cotton G.hirsutum cultivar Liaomian 38 (L38) upon Vd991 inoculation at two time points compared with the mock inoculated control plants. The potential function of DEGs uniquely expressed in J1 and L38 was also analyzed by GO enrichment and KEGG pathway associations. Most DEGs were assigned to resistance-related functions. In addition, resistance gene analogues (RGAs) were identified and analyzed for their role in the heightened resistance of the L38 cultivar against the devastating Vd991. In summary, we analyzed the regulatory network of genes in the resistant cotton cultivar L38 during V. dahliae infection, providing a novel and comprehensive insight into VW resistance in cotton.

Genome-wide analysis of serine carboxypeptidase-like protein (SCPL) family and functional validation of Gh_SCPL42 unchromosome conferring cotton Verticillium der Verticillium wilt stress in Gossypium hirsutum

“…We found a similar situation via qRT-PCR regarding the expression after G. hirsutum. The RNA transcription levels of 6 genes (GhSCPL13, 15,34,42,59 and 84) were significantly increased in both materials at different times, but only Gh_SCPL42 changed most significantly in the roots. In contrast, the change in Gh_SCPL13 was most obvious in the stem tissue.…”

“…6). Compared with 0 h, the RNA transcription levels of 6 genes (GhSCPL- 13,15,34,42,59 and 84) in both materials were significantly induced at different periods under Verticillium wilt stress, and the expression levels were significantly increased, these genes might be involved in the process of response to Verticillium wilt stress in cotton. And in the same period, the expression of these genes in the resistant material was significantly higher than that in the susceptible material.…”

“…5B). The results showed that the expression of 16 genes (Gh_SCPL13, 15,22,34,40,42,57,59,66,70,73,74,83,84, 94 and 95) changed significantly within 0 ~ 24 h, 19 genes expressions(Gh_SCPL-71, 72, 75,76,77,79,80,81,82,85,86,87,88,89,90,91,92, 93 and 96) significantly higher than other genes, while the expression levels did not change significantly in each period. In order to further explore the candidate genes of resistance to Verticillium wilt in G. hirsutum, based on the resequencing results of 5-resistance and 5-susceptible extreme materials(Table S4).…”

“…We typed 16 genes whose expression changed significantly before and after inoculation (Fig. 5C), and it was found that 11 of them (Gh_SCPL- 13,15,22,34,40,42,57,59,83,84 and 95) had differential SNPs in the upstream, downstream, exonic or intronic regions.…”

“…Through the previous expression analysis combined with the gene typing results, we speculated that 11 genes (GhSCPL- 13,15,22,34,40,42,57,59, 83, 84 and 95) from SCPL gene might be involved in the defense of Verticillium wilt stress in G. hirsutum. qRT-PCR was used to detect the transcript levels of these 11 genes in resistant material (Zhongzhimian 2) and susceptible material (Junmian 1) (Fig.…”