Transcriptome analysis reveals differences in the mechanisms of fiber initiation and elongation between long- and short-fiber cotton (Gossypium hirsutum L.) lines

BMC Genomics
Yuan QinShuxun Yu

Abstract

Improving the yield and fiber quality of upland cotton is a goal of plant breeders. However, increasing the yield and quality of cotton fibers is becoming more urgent. While the growing human population needs more cotton fiber, climate change is reducing the amount of land on which cotton can be planted, or making it difficult to ensure that water and other resources will be available in optimal quantities. The most logical means of improving yield and quality is understanding and manipulating the genes involved. Here, we used comparative transcriptomics to explore differences in gene expression between long- and short-fiber cotton lines to identify candidate genes useful for cotton improvement. Light and electron microscopy revealed that the initial fiber density was significantly greater in our short-fiber group (SFG) than in our long-fiber group (LFG). Compared with the SFG fibers, the LFG fibers were longer at all developmental stages. Comparison of the LFG and SFG transcriptomes revealed a total of 3538 differentially expressed genes (DEGs). Notably, at all three developmental stages examined, two expression patterns, consistently downregulated (profile 0) and consistently upregulated (profile 7), were identified, and both...Continue Reading

References

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Methods Mentioned

BETA
transgenic
scanning electron microscopy
electrophoresis
RNA-seq
PCR
PCA
GTPase
proteomic profiling

Software Mentioned

HTSeq
OmicShare
ArabDesc
Short Time - series Expression Miner ( STEM )

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