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

Marina Naoumkina1*, Doug J Hinchliffe2, Rickie B Turley3, John M Bland4 and David D Fang1

Author Affiliations

1 Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA 70124, USA

2 Cotton Chemistry & Utilization Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA, 70124, USA

3 Crop Genetics Research Unit, USDA-ARS, Mid South Area, Stoneville, MS, 38772, USA

4 Food Processing and Sensory Quality Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA, 70124, USA

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BMC Genomics 2013, 14:155  doi:10.1186/1471-2164-14-155

Published: 7 March 2013



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 metabolites from GC-MS data separated Li2 mutant fiber samples from WT fiber samples at the WT elongation stage, indicating that the Li2 mutation altered the metabolome of the mutant fibers. The observed alterations in the Li2 metabolome included significant reductions in the levels of detected free sugars, sugar alcohols, sugar acids, and sugar phosphates. Biological processes associated with carbohydrate biosynthesis, cell wall loosening, and cytoskeleton were also 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. Transcriptional activation of genes involved in nitrogen compound metabolism along with changes in the levels of nitrogen transport amino acids suggested re-direction of carbon flow into nitrogen metabolism in Li2 mutant fibers.


This report provides the first comprehensive analysis of metabolite and transcript changes in response to the Li2 mutation in elongating 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.

Cotton; Li2 mutation; Fiber; Elongation; Metabolomics; Gamma-aminobutyric acid (GABA)