TITLE:
Transcriptome Analysis of Ten Days Post Anthesis Elongating Fiber in the Upland Cotton (Gossypium hirsutum) Chromosome Substitution Line CS-B25
AUTHORS:
Chuan-Yu Hsu, Mark A. Arick II, Qing Miao, Sukumar Saha, Johnie N. Jenkins, Mirzakamol S. Ayubov, Ibrokhim Y. Abdurakhmonov, Daniel G. Peterson, Din-Pow Ma
KEYWORDS:
Chromosome Substitution Lines, Differentially Expressed Genes, Fiber Development, Quantitative Real-Time PCR, RNA Sequencing, Upland Cotton
JOURNAL NAME:
American Journal of Plant Sciences,
Vol.9 No.6,
May
30,
2018
ABSTRACT: A chromosome substitution line, CS-B25, was
developed by the substitution of chromosome pair 25 of Gossypium hirsutum TM-1 with the homologous pair of chromosome 25 from G. barbadense, a double haploid Pima 3-79 line. CS-B25
has improved fiber traits compared to its parent TM-1. To explore the molecule
mechanisms underlying improved fiber traits, deep sequencing of total RNA was
used to compare gene expression in fibers of CS-B25 and TM-1 at 10 days post
anthesis (10-DPA). A total of 1872 differentially expressed genes (DEGs) were
detected between the two lines, with 1175 up-regulated and 697 down-regulated
in CS-B25. Gene Ontology (GO) enrichment analysis of the expression data by Generally
Applicable Gene-set Enrichment (GAGE) and ReviGO indicated that the most
prevalent Biological Process GO terms associated with DEGs included
DNA-templated transcription, response to oxidative stress, and cellulose
biosynthesis. Enriched Molecular Function GO terms included structural
constituents of cytoskeleton, peroxidase activity, cellulose synthase
(UDP-forming) activity, and transcription regulatory region sequence-specific
DNA binding factors. GAGE was also used to find enriched KEGG pathways, and the
highly represented pathways were Biosynthesis of Amino Acids, Starch and
Sucrose Metabolism, Phenylpropanoid Biosynthesis, Protein Processing in
Endoplasmic Reticulum, and Plant Hormone Signal Transduction. Many of the
identified DEGs are involved in cytoskeleton and cell wall metabolism. The
results of gene expression data have provided new insight into the molecular
mechanisms of fiber development during the fiber elongation stage and would
offer novel candidate genes that may be utilized in cotton fiber quality
improvement.