Author(s)

Chuan-Yu Hsu¹, Mark A. Arick II¹, Qing Miao^2,3, Sukumar Saha⁴, Johnie N. Jenkins⁴, Mirzakamol S. Ayubov⁵, Ibrokhim Y. Abdurakhmonov⁵, Daniel G. Peterson¹, Din-Pow Ma^2*

¹Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS, USA.
²Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, USA.
³Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY, USA.
⁴USDA-ARS, Crop Science Research Laboratory, Mississippi State, MS, USA.
⁵Center of Genomics and Bioinformatics, Academy Sciences of Uzbekistan, Tashkent, Uzbekistan.

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.

Chromosome Substitution Lines, Differentially Expressed Genes, Fiber Development, Quantitative Real-Time PCR, RNA Sequencing, Upland Cotton

Hsu, C. , Arick II, M. , Miao, Q. , Saha, S. , Jenkins, J. , Ayubov, M. , Abdurakhmonov, I. , Peterson, D. and Ma, D. (2018) Transcriptome Analysis of Ten Days Post Anthesis Elongating Fiber in the Upland Cotton (Gossypium hirsutum) Chromosome Substitution Line CS-B25. American Journal of Plant Sciences, 9, 1334-1361. doi: 10.4236/ajps.2018.96098.