Interaction of the cyclin-dependent kinase inhibitor GhKRP6 with RING-Type E3 ligase influences the fiber length in Upland cotton

Upland cotton ( Gossypium hirsutum L.) is the major crop producing renewable fiber for textiles. Cotton fiber length is an economically important trait that affects the quality of the yarn. The Upland cotton multi-parent advanced generation intercross (MAGIC) population was developed for genetics research to understand how fiber traits can be improved without reducing fiber yield. A genome-wide association study of the MAGIC population identified a significant fiber length QTL on Chromosome D11 ( qFL-D11–1 ). To understand how the qFL-D11–1 regulates fiber length, we developed F 5 lines by crossing the longest and the shortest fiber recombinant inbred lines (RILs) of the MAGIC population to establish lines with parental haplotypes at the qFL-D11–1 but segregating for other loci. The F 5 lines and parental RILs were sequenced to detect exchanges from parents' genomic regions in the progeny. One segregating genomic region in the F 5 lines coincided with qFL-D12–1 , which additively affected fiber length. Correlation analysis of the expression patterns of genes from the two QTLs with the fiber lengths in the MAGIC population showed the highest correlation of the RING-type ubiquitin E3 ligase ( GhUbE3 ) from qFL-D12–1 . Kip-related protein-6 (KRP6) is the candidate gene from the qFL-D11–1 . A yeast two-hybrid and bimolecular fluorescence complementation assays demonstrated a physical interaction between GhKRP6 ( Ghir_D11G020340 ) and GhUbE3 ( Ghir_D12G006080 ). RNAseq showed that the GhUbE3 expression is reciprocal to the interacting GhKRP6 during fiber development. Virus-induced gene silencing (VIGS) of GhKRP6 increased fiber length. The data indicates that GhUbE3 controls the dose of GhKRP6's inhibitory activity and, therefore, the duration of fiber elongation. • Cyclin-dependent kinase inhibitor GhKRP6 from the qFL-D11–1 regulates the fiber cell cycle. • High expression of GhKRP6 during fiber elongation prevents cells from mitosis and endoreduplication. • The qFL-D12–1 contributes additively to the fiber length trait. • The RING-Type E3 Ligase GhUbE3 from qFL-D12–1 interacts with GhKRP6. • GhUbE3 expresses reciprocally with GhKRP6 during fiber cell development.