Analysis of Different Resistant Gossypium hirsutum Inoculated with Verticillium dahliae Infection by Small RNA and Degradome Sequencing

This study aims to identify miRNAs and their potential targets involved in regulating the defense response of cotton verticillium wilt in different resistant Gossypium hirsutum varieties. RNA libraries and degradome libraries from control samples and infected roots of G. hirsutum (resistant cotton variety ‘Zhongmian-49’ and susceptible cotton variety ‘Junmian-1’) were constructed. High-throughput small RNA sequencing was used to identify and analyze miRNAs from two different resistant G. hirsutum varieties under different stress modes. Degradome sequencing was used to detect cleaved target genes. The real-time reverse transcription-PCR (qRT-PCR) was used to verify the miRNAs and detect target genes related to growth, development and resistance. A total of 69 known miRNAs and 330 novel miRNAs were identified in all libraries. By comparing the expression levels of miRNAs in control samples and V. dahliae stress libraries, we found that there are 23 differentially expressed miRNAs in ‘Zhongmian-49’, and 62 differentially expressed miRNAs in ‘Junmian-1’. In addition, 615 degradation sites were identified in 615 target genes by degradome analysis. Bioinformatics analysis further showed that genes might be involved in the regulation of many cellular and molecular processes in the growth, development and resistance process of cotton. Finally, qRT-PCR further confirmed 8 target genes with potential roles in cotton growth and resistance regulation. This study shows that the resistant and susceptible varieties of G. hirsutum have different responses to V. dahliae inoculation at the miRNA level, and that miRNA may contribute to the successful defence of the resistant cultivars.