An EMS-Induced Mutation in a Tetratricopeptide Repeat-like Superfamily Protein Gene (Ghir_A12G008870) on Chromosome A12 Is Responsible for the Liy Short Fiber Phenotype in Cotton

A short fiber mutant Ligon-lintless-y was created through treating the seeds of the cotton line MD15 with ethyl methanesulfonate (EMS). Genetic analysis indicated that the short fiber phenotype is controlled by a single recessive locus designated li_y. From F₂ populations derived from crosses between the mutant and its wild type (WT), we selected 132 short fiber progeny (li_y/li_y), and made two DNA bulks. We sequenced these DNA bulks along with the two parents of the population. The li_y locus was located on chromosome A12. Using multiple F₂ populations and F₃ progeny plants, we mapped the li_y locus within a genomic region of 1.18 Mb. In this region, there is only one gene, i.e., Ghir_A12G008870 encoding a tetratricopeptide repeat (TPR)-like superfamily protein, that has a non-synonymous mutation between the li_y mutant and its WT. Analysis of a SNP marker representing this gene in the F₂ and F₃ progeny plants demonstrated its complete linkage with the li_y short fiber phenotype. We further analyzed this SNP marker in a panel of 384 cotton varieties. The mutant allele is absent in all varieties analyzed. RNAseq and RT-qPCR analysis of the gene Ghir_A12G008870 during fiber development showed a significant expression difference between the li_y mutant and its WT in developing fiber cells beginning at 12 days post anthesis. Virus-induced gene silencing of the gene Ghir_A12G008870 significantly reduced the fiber length of the WT cotton line MD15. Taken together, our results suggest that the gene Ghir_A12G008870 is involved in the cotton fiber cell elongation process and is a promising candidate gene responsible for the li_y short fiber phenotype.