Genetic mapping and transcriptome profiling revealed leaf lobe formation and leaf size are regulated by GhRl4 in Gossypium hirsutum L.

Leaf shape determines canopy structure and cotton productivity. Except for the L-D₁ locus, which determine the okra-leaf shape, the genetic control of other leaf shapes remains unknown in cotton. In the current study, using BSA-seq, RNA-seq, and molecular methods, GhRl₄ was mapped to chromosome A01, and it was identified as a key regulator of round-leaf shape in the cotton accession (M113116). Transcriptional suppression of GhRl₄ by virus-induced gene silencing (VIGS) led to the formation of leaf lobes and enlarged leaf size. Compared to the wild-type, the coding sequence of round-leaf alleles of GhRl₄ had a 21 bp deletion at the potential target site of miR319c. GhRl₄ belongs to the TCP (TEOSINTE BRANCHED1, CYCLODEA, and PROLIFERATING CELL FACTOR) 4 subfamily, previously implicated in the regulation of leaf shape in model plants. Further, transcriptome analysis indicated that PILS (PIN-LIKES), GIF (GRF-INTERACTING FACTOR), WIP (WIP DOMAIN PROTEIN), CUC (CUP-SHAPED COTYLEDON), and TCP family genes might be involved in the development of the round-leaf. Identifying the genetic and biochemical basis of phenotypic variation for leaf shape diversity would enable the use of genetic diversity and genomic tools for development of climate resilient high yielding cotton cultivars.