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

Abstract

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 F2 mapping populations were developed from mutant (Li1 × H7124) F1 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.

A Gly65Val substitution in an actin, GhACT_LI1, disrupts cell polarity and F‐actin organization resulting in dwarf, lintless cotton plants

“…The phenotype is characterized by dwarf plants with crinkled leaves and cotton fiber cells that cease elongation at an early stage, resulting in mature fibers that are dramatically shorter than wild‐type fibers (Figure a–h) (Gilbert et al ., ; Thyssen et al ., ). The mutation has been characterized as a single dominant gene located on Chr.22(d), also called D04 in the reference G. hirsutum genome (Karaca et al ., ; Rong et al ., ; Gilbert et al ., ; Jiang et al ., ; Thyssen et al ., ). The most recent report of candidate genes was based on correspondence of genetic markers to genome sequences of the related diploid Gossypium raimondii , and an actin gene was among a handful of candidates at the Li 1 locus (Jiang et al ., ).…”

Peer Review #1 of "TransPrise: a novel machine learning approach for eukaryotic promoter prediction (v0.2)"

“…We used Fgenesh mRNAbased gene prediction models, since Fgenesh-annotated promoters have a more pronounced nucleotide consensus as compared to the promoters annotated by MSU (Triska et al 2017b). Fgenesh was successfully used to annotate several plant genomes (Chan et al 2017a;Chan et al 2017b;Davis et al 2010;Ito et al 2005;Jiang et al 2015;Nasiri et al 2013;Sanusi et al 2018;Sheshadri et al 2018;Yao et al 2005). Therefore, we selected the Fgenesh annotation as the gold standard for our analysis.…”

Unraveling Cotton Fiber Development Using Fiber Mutants in the Post‐Genomic Era

“…The mutation was characterized as a single dominant gene located on chromosome D04 (chromosome 22) (Rong et al, 2005;Gilbert et al, 2013;Thyssen et al, 2015). Complementary DNA microarray and candidate gene analysis based on the genome sequences of the diploid G. raimondii identified a handful of candidates including an actin near the Li 1 locus (Gilbert et al, 2014;Jiang et al, 2015). Using high-resolution genetic mapping, Thyssen et al (2017) reported that the causative gene of the Li 1 mutation is a substitution of glycine to valine at position 65 in the protein sequence of an actin gene, GhACT_LI1 (Gh_D04G0865).…”