Genetic fine mapping and candidate gene analysis of the Gossypium hirsutum Ligon lintless-1 ( Li1 ) mutant on chromosome 22(D)

Ligon lintless-1 ( Li1 ) is a Gossypium hirsutum mutant that is controlled by a dominant gene that arrests the development of cotton fiber after anthesis. Two F 2 mapping populations were developed from mutant ( Li1 × H7124) F 1 plants in 2012 and 2013; each was composed of 142 and 1024 plants, respectively. Using these populations, Li1 was mapped to a 0.3-cM region in which nine single-strand conformation polymorphism markers co-segregated with the Li1 locus. In the published G. raimondii genome, these markers were mapped to a region of about 1.2 Mb (the Li1 region) and were separated by markers that flanked the Li1 locus in the genetic map, dividing the Li1 region into three segments. Thirty-six genes were annotated by the gene prediction software FGENESH (Softberry) in the Li1 region. Twelve genes were candidates of Li1 , while the remaining 24 genes were identified as transposable elements, DNA/RNA polymerase superfamily or unknown function genes. Among the 12 candidate genes, those encoding ribosomal protein s10, actin protein, ATP synthase, and beta-tubulin 5 were the most-promising candidates of the Li1 mutant because the function of these genes is closely related to fiber development. High-throughput RNA sequencing and quantitative PCR revealed that these candidate genes had obvious differential gene expression between mutant and wild-type plants at the fiber elongation stage, strengthening the inference that they could be the most likely candidate gene of the Li1 mutant phenotype.