title: Characterization of the global transcriptome for cotton (Gossypium hirsutum L.) anther and development of SSR marker.
abstract: Cotton is an important fiber plant, and it's attractive to elucidate the molecular mechanism of anther development due to the close relationship between the anther fertility and boll-setting, and also fiber yield. In the present paper, 47.2 million paired-end reads with average length of 82.87 bp from the anthers of TM-1 (Gossypium hirsutum L.), a genetic standard line, were generated through transcriptome sequencing, and 210,965 unigenes of more than 100 bp were obtained. BLAST, KEGG, COG, and GO analyses showed that the genes were enriched in the processes of transcription, translation, and post-translation as well as hormone signal transduction, the transcription factor families, and cell wall-related genes mainly participating in cell expansion and carbohydrate metabolism. Further analysis identified 11,153 potential SSRs. A suit of 5122 primer pair sequences were designed, and 82 of 300 randomly selected primer pairs produced reproducible amplicons that were polymorphic among 22 cotton accessions from G. hirsutum, Gossypium barbadense and Gossypium arboreum. The UPGMA clustering analysis further confirmed high quality and effectiveness of these novel SSR markers. The present study provided insights into the transcriptome profile of the cotton and established a public information platform for functional genomics and molecular breeding.
authors.affiliation: College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China.
authors.forename: Xianwen
authors.initials: X
authors.lastname: Zhang
authors.affiliation: College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China.
authors.forename: Zhenwei
authors.initials: Z
authors.lastname: Ye
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, The Chinese Academy of Agricultural Sciences, Anyang 455004, China.
authors.forename: Tiankang
authors.initials: T
authors.lastname: Wang
authors.affiliation: Key Laboratory for Crop Germplasm Innovation and Utilization of Hunan Province, Hunan Agricultural University, Changsha 410128, China.
authors.forename: Hairong
authors.initials: H
authors.lastname: Xiong
authors.affiliation: College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China.
authors.forename: Xiaoling
authors.initials: X
authors.lastname: Yuan
authors.affiliation: Cotton Sciences Research Institute of Hunan Province, Changde 415101, China.
authors.forename: Zhigang
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, The Chinese Academy of Agricultural Sciences, Anyang 455004, China. Electronic address: yylcri@126.com.
authors.forename: Youlu
authors.initials: Y
authors.lastname: Yuan
authors.affiliation: College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China. Electronic address: tigerzhiliu@gmail.com.
authors.forename: Zhi
authors.initials: Z
authors.lastname: Liu
mesh_terms: D001483:Base Sequence; D016000:Cluster Analysis; D020224:Expressed Sequence Tags; D035264:Flowers / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D017343:Genes, Plant / Q000235:genetics; D003368:Gossypium / Q000235:genetics*; D018895:Microsatellite Repeats / Q000235:genetics*; D008969:Molecular Sequence Data; D010940:Plant Proteins / Q000145:classification / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics / Q000302:isolation & purification; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000235:genetics*
chemical_list: D010940:Plant Proteins; D018749:RNA, Plant
keywords: Cotton; Polymorphism; SSR; Transcription factor; Transcriptome