Submitted to: Plant and Animal Genome
Publication Type: Abstract Only
Publication Acceptance Date: 1/14/2006
Publication Date: 1/14/2006
Citation: Xu, Z., Song, G., Cho, J., Jianmin, D., Koo, P., Kohel, R.J., Yu, J. 2006. Distribution of fiber elongation genes in the upland cotton genome [abstract]. Proceedings of Plant and Animal Genome XIV Conference. Paper No. P684.
Technical Abstract: Based on cotton fiber transcriptome EST analysis, at least 36,000 genes are needed to produce a fiber. To understand where these genes are located in chromosomes and how they interact is crucial for improving fiber yield and quality. Our goals were to put all the fiber ESTs into integrated genetic and physical map, to evaluate distribution of the fiber genes, and to understand how these genes interact by use of structural and functional genomic tools. All the EST sequences were collected from the public domain, and these ESTs were put into a map by two means: blast analysis and overgo hybridization. Totally, 14,172 fiber unigenes were collected, and 2,556 of them were put in the chromosomes by blast analysis, and each of 1,182 from the 2,556 hit one position in the chromosomes. Of the 2,556, 1,374 hit more than two positions with an average 2.90 loci/unigene. Totally, there are 5,167 loci were hit by 2,556 ESTs, with an average 2.02 loci/per EST. Chromosome 9 and 14 hold highest ESTs, 473 ESTs in chromosome 9, and 436 ESTs in chromosome 14, respectively. A total of 2,556 fiber unigenes were clustered into three functional groups that are similar to the result from functional analysis of 14,000 EST. Six hundred unmapped EST unigenes were used to design overgo hybridization and there were 5.4 BACs/EST. About 46.24% of the contigs could be assigned to subgenome A or D. The gene islands deduced from the distribution of the fiber EST clusters will be discussed.