Integrated metabolomics and genomics analysis provides new insights into the fiber elongation process in Ligon lintless-2 (Li2) mutant cotton (Gossypium hirsutum L.)

Authors: Naoumkina, Marina; Hinchliffe, Doug; Turley, Rickie; Bland, John; Fang, David

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/1/2013
Publication Date: 3/7/2013
Citation: Naoumkina, M.A., Hinchliffe, D.J., Turley, R.B., Bland, J.M., Fang, D.D. 2013. Integrated metabolomics and genomics analysis provides new insights into the fiber elongation process in Ligon lintless-2 (Li2) mutant cotton (Gossypium hirsutum L.). Biomed Central (BMC) Genomics. 14:155,_DOI:10.1186/1471-2164-14-155.

Interpretive Summary: Cotton fiber is the most prevalent natural raw material used in the textile industry. Increased competition with synthetic fibers is forcing breeders to improve cotton fiber characteristics such as yield, length, strength and fineness. However, one of the major limitations in genetic improvement of fiber is the lack of information at the molecular level regarding genes and regulatory elements that control fiber development. The length of the fiber is one of the most important characteristics and affects spinning efficiency and the quality of the resulting yarn. Ligon lintless-2, a cotton mutant line, produces significantly shorter fiber than normal cotton. To understand molecular mechanisms controlling fiber length we analyzed metabolic compounds and gene expression levels in the fibers of mutant comparing to wild type. Comprehensive analyses revealed that amount of sugars were significantly reduced in mutant fibers. Gene expression levels in major biological processes associated with fiber elongation were decreased in mutant fibers. Levels of other compounds, known as signaling factors in many organisms, gamma-aminobutyric acid (non protein amino acid) and serotonin (neurotransmitter) were increased in mutant fibers. A number of factors associated with cell elongation found in this study will facilitate further research in understanding metabolic processes of cotton fiber elongation.

Technical Abstract: The length of cotton fiber is an important agronomic trait characteristic that directly affects the quality of yarn and fabric. The cotton (Gossypium hirsutum L.) fiber mutation, Ligon lintless-2, is controlled by a single dominant gene (Li2) and results in extremely shortened lint fibers on mature seeds with no visible pleiotropic effects on vegetative growth and development. The Li2 mutant phenotype provides an ideal model system to study fiber elongation. To understand metabolic processes involved in cotton fiber elongation, changes in metabolites and transcripts in the Li2 mutant fibers were compared to wild-type fibers during development. Principal component analysis of GC-MS data determined no separation of mutant samples at elongation stage indicating that the Li2 mutation eliminated elongation effect on the metabolome of mutant fibers. A significant reduction of all detected free sugars, sugar alcohols, sugar acids, and sugar phosphates were observed in mutant fibers. Biological processes associated with carbohydrate biosynthesis, cell wall loosening, and cytoskeleton were down-regulated in Li2 fibers. Gamma-aminobutyric acid, known as a signaling factor in many organisms, was significantly elevated in mutant fibers. Higher accumulation of 2-ketoglutarate, succinate, and malate suggested higher nitrate assimilation in the Li2 line. Levels of nitrogen transport amino acids along with transcriptional activation of genes involved in nitrogen compound metabolism, including biosynthesis glutamine family amino acids and nucleic acids, suggest re-direction of carbon flow into nitrogen metabolism in Li2 mutant fibers.