Abstract
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.
Highlights
How 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
The present report focuses on the similarities and differences of transcriptome profiles between the two Chromosome Segment Substitution Lines (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
The results indicated that the candidate genes bound up with fiber formation would contribute to the comprehension of the mechanism of cotton fiber elongation and Secondary Cell Wall (SCW) synthesis, and further make a significant difference in the cotton breeding and genomics research
Summary
How 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. The allotetraploid cotton species, Upland cotton (G. hirsutum) and Sea Island cotton (G. barbadense), derived from a natural hybridization event between A-genome and Dgenome 1–2 million years ago [2], contribute over 95% of cotton fiber yield. Heterozygous segment percentage expression similarity alterations between MBI9915/ MBI9749 and the recurrent parent CCRI36 might result from the distinct G. barbadense chromosomal segments contained in the CSSLs. For further confirming the relationship of the three lines at different stages, Principal Component Analysis (PCA) was performed on the above-mentioned expressed genes (Fig. 2). The dynamically varied DEGs identified from the comparisons among the three lines might reveal a key gene expression regulating mechanism in fiber development and quality formation
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