Submitted to: Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/16/2008
Publication Date: 7/10/2008
Citation: Xu, Z., Kohel, R.J., Song, G., Cho, J., Alabady, M., Yu, J., Poo, K., Chu, J., Yu, S., Wilkins, T.A., Zhu, Y., Yu, J. 2008. Gene-rich islands for fiber development in the cotton genome. Genomics. 92:173-183.
Interpretive Summary: The textile industry extensively uses cotton, the world's leading natural fiber. Genetic improvement of cotton fiber yield and quality relies largely on the knowledge and understanding of genetic networks in the cotton genome that are responsible for cotton fiber development. This report elucidates the genomic organization and distribution of fiber genes, and identifies ten gene-rich islands for fiber development. Three gene-rich islands on chromosome 5 were associated with fiber initiation, three on chromosome 10 for early to middle elongation of the fiber cell, three on chromosome 14 for middle to late elongation, and one on chromosome 15 for secondary cell wall deposition. The information presented in this report reveals for the first time the existence of functional coupling gene clusters in the cotton genome. These functionally related gene clusters display similar transcriptional regulation and they are valuable for genetic improvement of cotton fiber traits and for basic studies of genetic mechanisms involved in cotton fiber development.
Technical Abstract: Cotton fiber is an economically important seed trichome and the world's leading natural fiber used in the manufacture of textiles. As a step towards elucidating the genomic organization and distribution of gene networks responsible for cotton fiber development, we investigated the distribution of fiber genes in the cotton genome. Results revealed the presence of gene-rich islands for fiber genes with a biased distribution in the tetraploid cotton (Gossypium hirsutum L.) genome that was also linked to discrete fiber developmental stages based on expression profiles. There were three fiber gene-rich islands associated with fiber initiation on chromosome 5, three islands for the early to middle elongation stage on chromosome 10, three islands for middle to late elongation stage on chromosome 14, and one island on chromosome 15 for secondary cell wall deposition (SCWD) for a total of ten fiber gene-rich islands. Clustering of functionally related gene clusters in the cotton genome displaying similar transcriptional regulation indicates an organizational hierarchy with significant implications for the genetic enhancement of particular fiber quality traits. The relationship between gene-island distribution and functional expression profiling suggests for the first time the existence of functional coupling gene clusters in the cotton genome.