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United States Department of Agriculture

Agricultural Research Service

Research Project: Molecular Approaches for More Efficient Breeding to Improve Cotton Fiber Quality Traits

Location: Cotton Fiber Bioscience Research Unit

Title: The Li2 mutation results in reduced subgenome expression bias in elongating fibers of allotetraploid cotton (Gossypium hirsutum L.)

Authors
item Naoumkina, Marina
item Thyssen, Gregory
item Fang, David
item Hinchliffe, Doug
item Florane, Christopher
item Yeater, Kathleen
item Page, Justin -
item Udall, Joshua -

Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: February 5, 2014
Publication Date: February 4, 2014
Citation: Naoumkina, M.A., Thyssen, G.N., Fang, D.D., Hinchliffe, D.J., Florane, C.B., Yeater, K.M., Page, J.J., Udall, J.A. 2014. The Li2 mutation results in reduced subgenome expression bias in elongating fibers of allotetraploid cotton (Gossypium hirsutum L.). PLoS One. 9(3):e90830.

Interpretive Summary: The major cultivated cotton species are allotetraploids that contain two largely redundant genomes of their diploid progenitors. Cotton fiber quality characteristics were significantly improved after polyploidization. Ligon lintless-2 (Li2) is a monogenic dominant mutant in cotton that results in extremely shortened lint fibers on mature seeds. In this study we used next generation sequencing technology to evaluate the effects of fiber mutation on transcriptome of both subgenomes of allotetraploid cotton. We sequenced 4 libraries from developing fibers of Li2 mutant and wild type near-isogenic lines at peak of elongation and used a cotton Single Nucleotide Polymorphism index generated between DD genome G. raimondii and the AA genome G. arboreum to categorize reads of allotetraploid G. hirsutum as belonging to the AT or DT subgenomes. Our results revealed: 1) approximately two times more genes were induced in AT subgenome comparing to DT subgenome in wild type and mutant fiber; 2) the subgenome expression bias was significantly reduced in Li2 fiber transcriptome; 3) Li2 has a significantly greater effect on DT than AT subgenome. This is the first report exploring the effects of a single dominant mutation on the homeologous gene expression in allotetraploid cotton. This work will lead to an understanding of how gene regulation between homeologs AT and DT subgenomes contributes to enhanced fiber morphology in cultivated cotton allopolyploids.

Technical 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 PolyCat mapping 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 AT subgenome comparing to DT subgenome in wild type and mutant fiber; 2) the subgenome expression bias was significantly reduced in Li2 fiber transcriptome; 3) Li2 has a significantly greater effect on DT than AT subgenome. Transcriptional regulators and cell wall homeologous genes that were significantly affected by Li2 mutation were reviewed in details. This is the first report exploring the effects of a single dominant mutation on the homeologous gene expression in allotetraploid cotton. These results provide deeper insights into expression evolution of allotetraploid cotton.

Last Modified: 9/21/2014
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