Cotton fiber elongation network revealed by expression profiling of longer fiber lines introgressed with different Gossypium barbadense chromosome segments.

Ruiping Tian,Peng Wang,Tianzhen Zhang,Jiedan Chen,Lei Fang,Sen Wang,Xinghe Li

doi:10.1186/1471-2164-15-838

Abstract

BackgroundCotton fiber, a highly elongated, thickened single cell of the seed epidermis, is a powerful cell wall research model. Fiber length, largely determined during the elongation stage, is a key property of fiber quality. Several studies using expressed sequence tags and microarray analysis have identified transcripts that accumulate preferentially during fiber elongation. To further show the mechanism of fiber elongation, we used Digital Gene Expression Tag Profiling to compare transcriptome data from longer fiber chromosome introgressed lines (CSILs) containing segments of various Gossypium barbadense chromosomes with data from its recurrent parent TM-1 during fiber elongation (from 5 DPA to 20 DPA).ResultsA large number of differentially expressed genes (DEGs) involved in carbohydrate, fatty acid and secondary metabolism, particularly cell wall biosynthesis, were highly upregulated during the fiber elongation stage, as determined by functional enrichment and pathway analysis. Furthermore, DEGs related to hormone responses and transcription factors showed upregulated expression levels in the CSILs. Moreover, metabolic and regulatory network analysis indicated that the same pathways were differentially altered, and distinct pathways exhibited altered gene expression, in the CSILs. Interestingly, mining of upregulated DEGs in the introgressed segments of these CSILs based on D-genome sequence data showed that these lines were enriched in glucuronosyltransferase, inositol-1, 4, 5-trisphosphate 3-kinase and desulfoglucosinolate sulfotransferase activity. These results were similar to the results of transcriptome analysis.ConclusionsThis report provides an integrative network about the molecular mechanisms controlling fiber length, which are mainly tied to carbohydrate metabolism, cell wall biosynthesis, fatty acid metabolism, secondary metabolism, hormone responses and Transcription factors. The results of this study provide new insights into the critical factors associated with cell elongation and will facilitate further research aimed at understanding the mechanisms underlying cotton fiber elongation.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-838) contains supplementary material, which is available to authorized users.

Highlights

Cotton fiber, a highly elongated, thickened single cell of the seed epidermis, is a powerful cell wall research model
The fiber quality of these Chromosome segment introgression line (CSIL) showed significant difference compared to the recurrent parent TM-1 and these CSILs provide good materials for the study of fiber elongation and the functional genetic study of cotton fiber trait
Gene expression patterns during cotton fiber elongation To obtain a global view of transcriptome profiles relevant to cotton fiber elongation, we sequenced 24 libraries of elongating fibers from CSILs and their recurrent parent TM-1

Summary

Introduction

A highly elongated, thickened single cell of the seed epidermis, is a powerful cell wall research model. Mutant analysis in combination with microarray or generation sequencing provides a powerful approach for discovering fiber developmental mechanisms by comparing gene expression in mutant vs wild-type plants [11,13,14,15]. Phytohormones such as auxins [13,16,17], ethylene [11,18] and brassinosteroids [18,19] are involved in fiber development. Transcription factors such as MYB25 and MYB25like are involved in fiber development [27,28,29]

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