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

Abstract

BackgroundThe 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.ResultsPrincipal 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.ConclusionsThis 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.

RNA-seq analysis of short fiber mutants Ligon-lintless-1 (Li1) and – 2 (Li2) revealed important role of aquaporins in cotton (Gossypium hirsutum L.) fiber elongation

“…We examined genome-wide gene expression in elongating cotton fiber cells at 8 DPA in Li 1 , Li 2 mutants and WT under different growing conditions, in the field and greenhouse. The time point 8 DPA was selected because our earlier research revealed significant transcript and metabolite changes between the Li 2 and WT NILs during this time of fiber development [ 5 , 6 ]. Approximately 1.06 billion 100 bp reads from 13 libraries, including 9 libraries from field grown plants (this work) and 4 libraries from greenhouse grown plants (previously reported [ 9 ]), were trimmed with Sickle [ 19 ] and mapped to transcripts from the G. raimondii genome reference sequence [ 18 , 20 ].…”

“…Therefore, the transport of sugars is unlikely altered in short fiber mutants. In our previous report we observed significant reductions in the levels of detected free sugars, sugar alcohols, sugar acids, and sugar phosphates in the Li 2 metabolome; also biological processes associated with carbohydrate biosynthesis were significant down-regulated in the Li 2 transcriptome [ 6 ]. Consequently, detection of low amount of sugars in sap of Li 1 – Li 2 fibers might be the result of reduced de novo synthesis of sugars in mutants.…”

Comparative Evolutionary and Developmental Dynamics of the Cotton (Gossypium hirsutum) Fiber Transcriptome

“…Notably, phenylpropanoids, particularly flavonoids, are known to inhibit fiber elongation [64], but protect cells from abiotic and biotic stresses [72]. The involvement of flavonoids in fiber processes has been shown in many studies at the transcript, protein, and metabolic levels [12], [13], [20], [64], [73]. Tan et al [64], in particular, showed that the flavonoid naringenin negatively regulates fiber development and that higher levels of naringenin accumulate in short, brown fibers.…”

Transcript profiling by microarray and marker analysis of the short cotton (Gossypium hirsutum L.) fiber mutant Ligon lintless-1 (Li 1 )

“…Previously, our laboratory conducted extensive analysis of the Li 2 mutant using microarray technology, molecular mapping and metabolomic analysis [25,26]. We developed microsatellite markers associated with the Li 2 genetic locus, and identified transcripts or genes and metabolites that were affected by the Li 2 mutation.…”