An EMS-induced mutation in a tetratricopeptide repeat-like superfamily protein gene ( Ghir_A12G008870 ) on chromosome A12 is responsible for the li y short fiber phenotype in cotton

Key message The EMS-induced threonine/isoleucine substitution in a tetratricopeptide repeat-like superfamily protein encoded by gene Ghir_A12G008870 is responsible for the Ligon-lintless-y ( li y ) short fiber phenotype in cotton. Abstract A short fiber mutant Ligon-lintless-y was created through treating the seeds of the cotton line MD15 with ethyl methanesulfonate. Genetic analysis indicated that the short fiber phenotype is controlled by a single recessive locus designated li y . From F 2 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 F 2 populations and F 3 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-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 F 2 and F 3 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.