title: The Li2 mutation results in reduced subgenome expression bias in elongating fibers of allotetraploid cotton (Gossypium hirsutum L.).
abstract: Next generation sequencing (RNA-seq) technology was used to evaluate the effects of the Ligon lintless-2 (Li2) short fiber mutation on transcriptomes of both subgenomes of allotetraploid cotton (Gossypium hirsutum L.) as compared to its near-isogenic wild type. Sequencing was performed on 4 libraries from developing fibers of Li2 mutant and wild type near-isogenic lines at the peak of elongation followed by mapping and PolyCat categorization of RNA-seq data to the reference D5 genome (G. raimondii) for homeologous gene expression analysis. The majority of homeologous genes, 83.6% according to the reference genome, were expressed during fiber elongation. Our results revealed: 1) approximately two times more genes were induced in the AT subgenome comparing to the DT subgenome in wild type and mutant fiber; 2) the subgenome expression bias was significantly reduced in the Li2 fiber transcriptome; 3) Li2 had a significantly greater effect on the DT than on the AT subgenome. Transcriptional regulators and cell wall homeologous genes significantly affected by the Li2 mutation were reviewed in detail. This is the first report to explore the effects of a single mutation on homeologous gene expression in allotetraploid cotton. These results provide deeper insights into the evolution of allotetraploid cotton gene expression and cotton fiber development.
authors.affiliation: Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, Louisiana, United States of America.
authors.forename: Marina
authors.initials: M
authors.lastname: Naoumkina
authors.affiliation: Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, Louisiana, United States of America.
authors.forename: Gregory
authors.initials: G
authors.lastname: Thyssen
authors.affiliation: Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, Louisiana, United States of America.
authors.forename: David D
authors.initials: DD
authors.lastname: Fang
authors.affiliation: Cotton Chemistry & Utilization Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, Louisiana, United States of America.
authors.forename: Doug J
authors.initials: DJ
authors.lastname: Hinchliffe
authors.affiliation: Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, Louisiana, United States of America.
authors.forename: Christopher
authors.initials: C
authors.lastname: Florane
authors.affiliation: USDA-ARS-Southern Plains Area, College Station, Texas, United States of America.
authors.forename: Kathleen M
authors.initials: KM
authors.lastname: Yeater
authors.affiliation: Plant and Wildlife Science Department, Brigham Young University, Provo, Utah, United States of America.
authors.forename: Justin T
authors.initials: JT
authors.lastname: Page
authors.affiliation: Plant and Wildlife Science Department, Brigham Young University, Provo, Utah, United States of America.
authors.forename: Joshua A
authors.initials: JA
authors.lastname: Udall
mesh_terms: D002473:Cell Wall / Q000235:genetics; D002874:Chromosome Mapping; D032561:Cotton Fiber; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant / Q000235:genetics*; D003368:Gossypium / Q000166:cytology / Q000235:genetics*; D009154:Mutation / Q000235:genetics*; D010940:Plant Proteins / Q000378:metabolism; D011123:Polyploidy; D060888:Real-Time Polymerase Chain Reaction; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA; D012689:Sequence Homology, Nucleic Acid; D014157:Transcription Factors / Q000378:metabolism; D059467:Transcriptome
chemical_list: D010940:Plant Proteins; D014157:Transcription Factors