Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: November 4, 2010
Publication Date: December 16, 2010
Citation: Xu, Z., Yu, J., Cho, J., Yu, J., Kohel, R.J., Percy, R.G. 2010. Polyploidization altered gene functions in cotton (Gossypium spp.). PLoS One. 5(12):e14351. doi:10.1371/journal.pone.0014351. Interpretive Summary: Cotton fiber is the world's leading natural material used in the manufacture of textiles. The development of cotton fiber is determined by large numbers of genetic factors that are distributed in the tetraploid cotton genome (AD). To investigate the organization of over 500 genes whose functions were previously verified and confirmed, an integrated genome map of fiber genes was constructed. Among them were 259 fiber development genes and 103 fiber transcription factors. Mapping analysis indicates more fiber development genes from one subgenome (At) that is similar to its probable fiber-producing ancestor (A). On the other hand, there are more transcription factors from the other subgenome (Dt) that is similar to its probable non-fiber ancestor (D). It is suggested that the expression of the fiber development genes is regulated by the transcription factors to enhance the fiber development in the tetraploid cotton. The integrated map of fiber genes resulting from the research provides a framework to study individual fiber genes and their dynamic gene networks during the process of fiber development in the tetraploid cotton.
Technical Abstract: Cotton fibers are seed trichomes derived from individual cells of the epidermal layer of the seed coat. It has been known for a long time that a large set of genes determine the development of cotton fiber, and more recently it has been determined that these genes are distributed across the At and Dt subgenomes of tetraploid AD cottons. In the present study, we investigated the organization and evolution of 535 fiber genes whose functions have been verified and confirmed. An integrated genetic and physical map was constructed of these genes that included 259 fiber development genes, 103 fiber transcription factors, and 173 SSR-contained fiber ESTs. A total of 499 fiber related contigs were selected and assembled, covering about 151 Mb in physical length, or representing about 6.7% of the tetraploid cotton genome. Among these contigs, 397 were anchored onto individual chromosomes. Results from comparison of the distribution of the fiber development genes and transcription factors between the At and Dt subgenomes showed that more fiber development genes were from At subgenome than Dt, whereas more transcription factors were from Dt subgenome than At. Combining our results with previous reports that more fiber QTLs mapped in Dt subgenome than At, a new functional hypothesis is suggested for tetraploid cotton. After the merging of the two diploid Gossypium genomes, the At subgenome has provided more genes for fiber development, because it continues to function similar to its fiber producing diploid probable ancestor (G. arboreum). On the other hand, the Dt subgenome, with its probable non-fiber producing D genome ancestor (G. raimondii), provides more transcription factors that regulate the expression of the fiber genes in the At subgenome. This hypothesis would explain previously published results. The integrated map of fiber genes provides a framework to clone individual full-length fiber genes and to systematically study the functional network of these genes that interact during the process of fiber development in the tetraploid Upland cotton.