|Yang, S. Samuel - TEXAS A&M UNIVERSITY|
|Cheung, Foo - INST. FOR GENOMIC RESEARC|
|Wei, Nig - DELTA RESEARCH & EXTEN.|
|Lee, Jinsuk - TEXAS A&M UNIVERSITY|
|Sze, Sing-Hui - TEXAS A&M UNIVERSITY|
|Stelly, David - TEXAS A&M UNIVERSITY|
|Thaxton, Peggy - DELTA RESEARCH & EXTEN.|
|Town, Christopher - INST. FOR GENOMIC RESEACH|
|Chen, Jeffrey - TEXAS A&M UNIVERSITY|
Submitted to: Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: March 3, 2006
Publication Date: June 1, 2006
Citation: Yang, S., Cheung, F., Wei, N.E., Lee, J.J., Sze, S., Stelly, D.M., Thaxton, P., Triplett, B.A., Town, C.D., Chen, J. 2006. Accumulation of genome-specific transcripts, transciption factors and phytohormonal regulators during early stages of fiber cell development in allotetraploid cotton.. Plant Journal. 47. p. 761-775. Interpretive Summary: Not all of the cells on a cottonseed develop into fibers and the signals required to initiate fiber development are poorly understood. This project was envisioned to catalog all of the genes that are "turned on" from three days prior to flowering until three days after flowering, critical time points for fiber initiation. The sequence of nucleotides encoding active genes was determined for 8,272 unique genes, 20% of which had not previously been reported. Comparison of these new sequences to the sequences of other plant genes in public databases revealed many genes that control gene expression and that regulate plant hormone signaling. This advance will permit more detailed analysis of the biochemistry of cotton fiber cell initiation that may lead to enhanced numbers of fibers per seed. In addition, the sequences were evaluated for the presence of specific types of molecular markers that are suitable for use by plant breeders. Two different types of analyses were conducted to demonstrate that a sub-set of putative fiber initiation genes were active in cotton with normal fiber and inactive in a fiber mutant that produces a very low level of fiber. The genomic tools developed by this study will prove useful for a variety of applications from plant breeding to molecular analysis of plant growth and development.
Technical Abstract: Gene expression during early stages of cotton fiber development is poorly understood. Here we report the development of a full-length cDNA library derived from Gossypium hirsutum L. Texas Marker-1 (TM1) immature ovules (TMO) collected from 3 days pre-anthesis, the day of anthesis, and 3 days post-anthesis (DPA). We generated 32,789 high-quality ESTs that were assembled into 8,272 unique sequences including 4,036 tentative consensus sequences (TCs) and 4,504 singletons, representing ~20% unique sequences in the cotton EST collection. Compared to ~128,000 existing ESTs derived from elongated fibers and non-fiber tissues, TMO ESTs showed a significant increase in the percentage of genes encoding putative transcription factors and other regulators involved in trichome development such as WRKY, AP2/EREBP, C2H2, MYB, and bHLH transcription factors and the genes encoding proteins involved in auxin, brassinosteroid, gibberellic acid, and ABA signaling pathways. These activities coincide with predicted biological activities during fiber cell initiation. With the addition of the new ESTs, the Cotton Gene Index (CGI7) was revised using a total of ~161,000 ESTs that contained genome-specific SNPs and SSRs, many of which may be developed as portable molecular markers for cotton breeding. G. hirsutum L. is an allotetraploid derived from polyploidization between A and D-subgenome species. In silico analysis of gene expression in five libraries derived from fiber and non-fiber tissues revealed a large number of A-subgenome genes that were differentially enriched in the TMO library, consistent with the production of lint fibers in A-subgenome species. SSCP and qRT-PCR analyses demonstrated genome-specific expression patterns of a subset of genes during fiber cell initiation but not in the fiberless (naked seed) mutant (N1N1). The data provide new insights into the roles of phytohormonal, transcriptional and genome-specific regulation in the early stages of cotton fiber cell development.