Understanding the role of GhRCC1.61 in flowering time in upland cotton through integrated analyses of gene family, RNA-seq, VIGS and allelic variation.

key messageThe flowering time of the GhRCC1.61 response was preliminarily decrypted, and a molecular marker was developed based on the allelic variation in the exons. The regulator of chromosome condensation 1 (RCC1) superfamily is closely related to plant growth and development; however, in-depth studies on the role of GhRCC1s in the flowering time of upland cotton are lacking. In this study, 62 members of the RCC1 superfamily were identified from the upland cotton genome using a bioinformatics approach, and these members were comprehensively and systematically characterized. RNA-seq and qRT-PCR analyses revealed that a gene, GhRCC1.61, was significantly differentially expressed between early- and late-maturing varieties. When the expression of GhRCC1.61 was reduced via virus-induced gene silencing, the plants presented significantly delayed budding and flowering. By integrating existing genome-wide association studies we identified a single-nucleotide polymorphism locus (A/G; D13:1,391,542) within the exonic region of GhRCC1.61 that was significantly associated with flowering time. By calculating fixation index and nucleotide diversity, we found that the genomic region of GhRCC1.61 differed between early- and late-maturing varieties. An investigation of the frequency distribution of GhRCC1.61 allelic variants across the four cotton ecological zones in China was conducted. The frequency of the G allele was relatively high in the Northwest Inland Region and Northern Special Early-Maturity Region. These findings suggest that this gene might be affected by natural or artificial selection during the variety enhancement process. Furthermore, a kompetitive allele-specific PCR marker was developed based on its allelic variation. These findings not only deepen the understanding of GhRCC1s but also offer valuable genetic resources for the molecular breeding of early-maturing upland cotton.