Fine mapping and characterization of the Crinkled Dwarf gene in cotton

Cotton (Gossypium) is an important natural fiber crop worldwide. Plant height, which is an important commercial cotton breeding trait, is also useful for plant architecture research. Crinkled Dwarf (cr), a natural mutant of Sea Island cotton (Gossypium barbadense L.), simultaneously displays crinkled leaves and dwarfing. However, the genes controlling cr have not been characterized, and the molecular mechanism of the trait remains unknown. In this study, genetic analysis indicated that cr was likely controlled by a major recessive gene, although the cr phenotype was sensitive to environmental factors, including light intensity. Using bulked-segregant analysis and recombinant methods, the cr gene was mapped to a 35.8-kbp genomic interval on chromosome D03 that contained three annotated protein-coding genes. Comparative transcriptome analysis showed that cr enhanced stress/disease resistance and repressed plant development/growth. Endogenous phytohormone measurements showed that most auxin compounds were decreased in the cr mutant. Although the cr mutation was insensitive to exogenous auxin, gibberellin and cytokinin treatments promoted and repressed main stem elongation, respectively. However, no hormone treatment could fully rescue the crinkled leaf phenotype. These findings will contribute to the breeding of cotton lines with improved plant architecture or yield, and aid in the dissection of the genetic basis of cr.