Resequencing and Transcriptome Analyses Reveal Variations and Expression Patterns of the RR Gene Family in Cucumber

Cucumber (Cucumis sativus L.) is an important economic crop worldwide. Response regulators (RRs) play crucial roles in plant growth, development, and responses to both biotic and abiotic stresses.

Combined analysis of 182 re-sequencing and transcriptome datasets was conducted to investigate CsRR variations, with subsequent RT-qPCR experiments confirming its functional significance.

In this study, 18 CsRR genes were identified and classified into three groups according to their protein structures: A-ARRs (3), B-ARRs (8), and PRRs (7). Resequencing uncovered critical mutations (non-synonymous SNPs, frameshift, and stop-gain variants) in CsRR genes. Transcriptome data revealed that five genes responded to abiotic stress and four responded to biotic stress. CsPRR1 was upregulated in both resistant and susceptible lines at five dpi, downregulated in resistant plants at nine dpi, and showed no significant difference at 11 dpi. CsPRR2 was consistently upregulated in both lines at 5, 9, and 11 dpi. CsPRR3 was upregulated in resistant lines at nine dpi but downregulated at 11 dpi. CsARR8 was significantly downregulated in both lines at 9 and 11 dpi. Notably, CsPRR2 demonstrated dual functionality related to (i) the regulation of immature fruit skin color via a stop-gain InDel and (ii) resistance to Foc, as the gene was upregulated in both resistant and susceptible lines after inoculation with the pathogen.

This study integrated resequencing and transcriptomic data to comprehensively characterize CsRR genes, establishing a foundation for further exploration of their functional mechanisms in cucumber.