Map-based cloning of qLPA01.1, a favorable allele from the Gossypium tomentosum chromosome segment line

Cotton is an important natural fiber crop worldwide which plays a vital role in our daily life. High yield is a constant goal of cotton breeding, and lint percentage (LP) is one of the important components of cotton fiber yield. A stable QTL controlling LP, qLPA01.1, was identified on chromosome A01 from Gossypium hirsutum introgressed lines with G. tomentosum chromosome segments in a previous study. To fine-map qLPA01.1, an F2 population with 986 individuals was established by crossing G. hirsutum cultivar CCRI35 with the chromosome segment substitution line HT_390. A high-resolution genetic map including 47 loci and spanning 56.98 cM was constructed in the QTL region, and qLPA01.1 was ultimately mapped into an interval corresponding to an ~80 kb genome region of chromosome A01 in the reference genome, which contained six annotated genes. Transcriptome data and sequence analysis revealed that S-acyltransferase protein 24 (GoPAT24) might be the target gene of qLPA01.1. This result provides the basis for cotton fiber yield improvement via marker-assisted selection (MAS) and further studies on the mechanism of cotton fiber development.