title: RNA-Seq-Mediated Transcriptome Analysis of a Fiberless Mutant Cotton and Its Possible Origin Based on SNP Markers.
abstract: As the longest known single-celled trichomes, cotton (Gossypium L.) fibers constitute a classic model system to investigate cell initiation and elongation. In this study, we used a high-throughput transcriptome sequencing technology to identify fiber-initiation-related single nucleotide polymorphism (SNP) markers and differentially expressed genes (DEGs) between the wild-type (WT) Upland cotton (G. hirsutum) Xuzhou 142 and its natural fuzzless-lintless mutant Xuzhou 142 fl. Approximately 700 million high-quality cDNA reads representing over 58 Gb of sequences were obtained, resulting in the identification of 28,610 SNPs--of which 17,479 were novel--from 13,960 expressed genes. Of these SNPs, 50% of SNPs in fl were identical to those of G. barbadense, which suggests the likely origin of the fl mutant from an interspecific hybridization between Xuzhou 142 and an unknown G. barbadense genotype. Of all detected SNPs, 15,555, 12,750, and 305 were classified as non-synonymous, synonymous, and pre-terminated ones, respectively. Moreover, 1,352 insertion/deletion polymorphisms (InDels) were also detected. A total of 865 DEGs were identified between the WT and fl in ovules at -3 and 0 days post-anthesis, with 302 candidate SNPs selected from these DEGs for validation by a high-resolution melting analysis and Sanger sequencing in seven cotton genotypes. The number of genotypic pairwise polymorphisms varied from 43 to 302, indicating that the identified SNPs are reliable. These SNPs should serve as good resources for breeding and genetic studies in cotton.
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
authors.forename: Qifeng
authors.initials: Q
authors.lastname: Ma
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
authors.forename: Man
authors.initials: M
authors.lastname: Wu
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
authors.forename: Wenfeng
authors.initials: W
authors.lastname: Pei
authors.affiliation: College of Biology and Food Technology, Anyang Institute of Technology, Anyang, China.
authors.forename: Xiaoyan
authors.initials: X
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
authors.forename: Honghong
authors.initials: H
authors.lastname: Zhai
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
authors.forename: Wenkui
authors.initials: W
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
authors.forename: Xingli
authors.initials: X
authors.lastname: Li
authors.affiliation: Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, New Mexico, United States of America.
authors.forename: Jinfa
authors.initials: J
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
authors.forename: Jiwen
authors.initials: J
authors.lastname: Yu
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
authors.forename: Shuxun
authors.initials: S
authors.lastname: Yu
mesh_terms: D020869:Gene Expression Profiling; D005819:Genetic Markers; D003368:Gossypium / Q000235:genetics* / Q000502:physiology; D009154:Mutation; D020641:Polymorphism, Single Nucleotide; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D005819:Genetic Markers