EMS-induced short cotton fiber mutant Ligon lintless-y (liy) and its genomic location

A short fiber mutant Ligon-lintless-y was created through seed treatment with ethyl methanesulfonate (EMS). Genetic analysis indicated that the mutation is controlled by a single recessive locus designated liy. Besides causing short seed fibers, the mutation also affects other traits including plant height. From an F2 mapping population, we selected 100 short fiber progeny (liy/liy), and bulked their DNAs. We sequenced this DNA bulk along with the two parents of the mapping population. The liy locus was mapped on chromosome A07. Flanking SNP/InDel markers were developed. We also evaluated global transcriptional changes during cotton fiber development at 3, 8 and 16 days post anthesis triggered by liy mutation. Gene set enrichment analysis revealed that many metabolic pathways, including carbohydrate, cell wall, hormone metabolism and transport were substantially altered in liy developing fibers. We discuss perturbed expression of genes involved in signal transduction and biosynthesis of phytohormones, such as auxin, abscisic acid, gibberellin and ethylene.