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Transcriptomic analysis of fiber strength in upland cotton chromosome introgression lines carrying different Gossypium barbadense chromosomal segments.

ABSTRACT: Fiber strength is the key trait that determines fiber quality in cotton, and it is closely related to secondary cell wall synthesis. To understand the mechanism underlying fiber strength, we compared fiber transcriptomes from different G. barbadense chromosome introgression lines (CSILs) that had higher fiber strengths than their recipient, G. hirsutum acc. TM-1. A total of 18,288 differentially expressed genes (DEGs) were detected between CSIL-35431 and CSIL-31010, two CSILs with stronger fiber and TM-1 during secondary cell wall synthesis. Functional classification and enrichment analysis revealed that these DEGs were enriched for secondary cell wall biogenesis, glucuronoxylan biosynthesis, cellulose biosynthesis, sugar-mediated signaling pathways, and fatty acid biosynthesis. Pathway analysis showed that these DEGs participated in starch and sucrose metabolism (328 genes), glycolysis/gluconeogenesis (122 genes), phenylpropanoid biosynthesis (101 genes), and oxidative phosphorylation (87 genes), etc. Moreover, the expression of MYB- and NAC-type transcription factor genes were also dramatically different between the CSILs and TM-1. Being different to those of CSIL-31134, CSIL-35431 and CSIL-31010, there were many genes for fatty acid degradation and biosynthesis, and also for carbohydrate metabolism that were down-regulated in CSIL-35368. Metabolic pathway analysis in the CSILs showed that different pathways were changed, and some changes at the same developmental stage in some pathways. Our results extended our understanding that carbonhydrate metabolic pathway and secondary cell wall biosynthesis can affect the fiber strength and suggested more genes and/or pathways be related to complex fiber strength formation process.

SUBMITTER: Fang L

PROVIDER: S-EPMC3998979 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Transcriptomic analysis of fiber strength in upland cotton chromosome introgression lines carrying different Gossypium barbadense chromosomal segments.

Fang Lei L Tian Ruiping R Chen Jiedan J Wang Sen S Li Xinghe X Wang Peng P Zhang Tianzhen T

PloS one 20140424 4

Fiber strength is the key trait that determines fiber quality in cotton, and it is closely related to secondary cell wall synthesis. To understand the mechanism underlying fiber strength, we compared fiber transcriptomes from different G. barbadense chromosome introgression lines (CSILs) that had higher fiber strengths than their recipient, G. hirsutum acc. TM-1. A total of 18,288 differentially expressed genes (DEGs) were detected between CSIL-35431 and CSIL-31010, two CSILs with stronger fiber ...[more]

PMID: 24762562

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Project description: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.

Project description:BackgroundHow to develop new cotton varieties possessing high yield traits of Upland cotton and superior fiber quality traits of Sea Island cotton remains a key task for cotton breeders and researchers. While multiple attempts bring in little significant progresses, the development of Chromosome Segment Substitution Lines (CSSLs) from Gossypium barbadense in G. hirsutum background provided ideal materials for aforementioned breeding purposes in upland cotton improvement. Based on the excellent fiber performance and relatively clear chromosome substitution segments information identified by Simple Sequence Repeat (SSR) markers, two CSSLs, MBI9915 and MBI9749, together with the recurrent parent CCRI36 were chosen to conduct transcriptome sequencing during the development stages of fiber elongation and Secondary Cell Wall (SCW) synthesis (from 10DPA and 28DPA), aiming at revealing the mechanism of fiber development and the potential contribution of chromosome substitution segments from Sea Island cotton to fiber development of Upland cotton.ResultsIn total, 15 RNA-seq libraries were constructed and sequenced separately, generating 705.433 million clean reads with mean GC content of 45.13% and average Q30 of 90.26%. Through multiple comparisons between libraries, 1801 differentially expressed genes (DEGs) were identified, of which the 902 up-regulated DEGs were mainly involved in cell wall organization and response to oxidative stress and auxin, while the 898 down-regulated ones participated in translation, regulation of transcription, DNA-templated and cytoplasmic translation based on GO annotation and KEGG enrichment analysis. Subsequently, STEM software was performed to explicate the temporal expression pattern of DEGs. Two peroxidases and four flavonoid pathway-related genes were identified in the "oxidation-reduction process", which could play a role in fiber development and quality formation. Finally, the reliability of RNA-seq data was validated by quantitative real-time PCR of randomly selected 20 genes.ConclusionsThe present report focuses on the similarities and differences of transcriptome profiles between the two CSSLs and the recurrent parent CCRI36 and provides novel insights into the molecular mechanism of fiber development, and into further exploration of the feasible contribution of G. barbadense substitution segments to fiber quality formation, which will lay solid foundation for simultaneously improving fiber yield and quality of upland cotton through CSSLs.

Project description:Leaf shape is a vital agronomic trait that affects plant and canopy architecture, yield, and other production attributes of upland cotton. Compared with normal leaves, lobed leaves have potential advantages in improving canopy structure and increasing cotton yield. A chromosomal introgression segment from Gossypium barbadense L. conferring sub-okra leaf shape to Gossypium hirsutum L. was identified on chromosome D01. To determine the effects of this transferred sub-okra leaf shape on the leaf anatomical characteristics, photosynthesis-related traits, and yield of short-season cotton, we performed a field experiment with three sets of near-isogenic lines carrying okra, sub-okra, and normal leaf shape in Lu54 (L54) and Shizao 2 (SZ2) backgrounds. Compared with normal leaves, sub-okra leaves exhibited reduced leaf thickness and smaller leaf mass per area; moreover, the deeper lobes of sub-okra leaves improved the plant canopy structure by decreasing leaf area index by 11.24%-22.84%. Similarly, the intercepted PAR rate of lines with sub-okra leaf shape was also reduced. The chlorophyll content of sub-okra leaves was lower than that of okra and normal leaf shapes; however, the net photosynthetic rate of sub-okra leaves was 8.17%-29.81% higher than that of other leaf shapes at most growth stages. Although the biomass of lines with sub-okra leaf shape was less than that of lines with normal leaves, the average first harvest yield and total yield of lines with the sub-okra leaf shape increased by 6.36% and 5.72%, respectively, compared with those with normal leaves. Thus, improvements in the canopy structure and photosynthetic and physiological characteristics contributed to optimizing the light environment, thereby increasing the yield of lines with sub-okra leaf shape. Our results suggest that the sub-okra leaf trait from G. barbadense L. may have practical applications for cultivating short-season varieties with high photosynthetic efficiency, and improving yield, which will be advantageous for short-season varieties.

Dataset Information

Transcriptomic analysis of fiber strength in upland cotton chromosome introgression lines carrying different Gossypium barbadense chromosomal segments.

Publications

Transcriptomic analysis of fiber strength in upland cotton chromosome introgression lines carrying different Gossypium barbadense chromosomal segments.

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