ARS | Publication request: Analysis of ESTs from Multiple Gossypium hirsutum Tissues and Identification of SSRs

Submitted to: Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 31, 2006
Publication Date: March 28, 2006
Citation: Taliercio, E.W., Allen, R.D., Essenberg, M., Nguyen, H., Patil, M., Payton, P.R., Phillips, A., Pierce, M., Scheffler, B.E., Turley, R.B., Wang, J., Zhang, D., Scheffler, J.A. 2006. Analysis of ESTs from Multiple Gossypium hirsutum Tissues and Identification of SSRs. Genome. 49:306-319.

Interpretive Summary: Compared to other species, cotton research is relatively poor in knowledge of genes, in which tissue specific genes are expressed and the position of genes in the cotton genome (DNA). To address these problems the DNA sequences of 17,000 genes expressed in a variety of tissues were determined. The function of many of the genes was determined by comparing their sequences with the sequences of known genes from other plant species. These gene sequences are an excellent tool to allow the localization of these genes in the cotton genome. Localization of genes in a genome is called gene mapping. Small sequences that are consecutively repeated have been used as markers for mapping in many species. One hundred ninety two of these repeats were evaluated and about 69 were found to be useful as markers in cotton. Lack of available markers is the major limiting factor in the development of cotton gene maps. These new markers will provide cotton researchers and plant breeders with tools to identify important agricultural traits and facilitate selection for these traits.

Technical Abstract: In an effort to expand the Gossypium hirsutum L. (cotton) EST database, ESTs representing a variety of tissues and treatments were sequenced. Assembly of these sequences with ESTs already in dbEST (GenBank) identified 9675 cotton sequences not present in GenBank. Statistical analysis of a subset of these ESTs identified genes likely to be differentially expressed in stems, cotyledons and drought stressed tissues. Annotation of the differentially expressed cDNAs tentatively identified genes involved in lignin metabolism, starch biosynthesis and stress response, consistent with pathways likely to be active in the tissues under investigation. Simple Sequence Repeats (SSRs) were identified among these ESTs, and an inexpensive method was developed to screen genomic DNA for presence of these SSRs. At least 69 SSRs potentially useful in mapping were identified. Selected amplified SSRs were isolated and sequenced. The sequences corresponded to the EST containing the SSRs, confirming that these SSRs will potentially map the gene represented by the EST. The ESTs containing SSRs were annotated to help identify the genes that may be mapped using these markers.