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Analysis of ESTs from multiple Gossypium hirsutum tissues and identification of SSRs

Authors :
Paxton Payton
Mohini A. Patil
Margaret L. Pierce
Ana Cecilia Millena
Natalya Klueva
Angela L. Phillips
Margaret Essenberg
Rickie B. Turley
Randy D. Allen
Earl Taliercio
Henry T. Nguyen
Jodi A. Scheffler
Deshui Zhang
Jing Wang
Brian E. Scheffler
Source :
Genome. 49(4)
Publication Year :
2006

Abstract

In an effort to expand the Gossypium hirsutum L. (cotton) expressed sequence tag (EST) database, ESTs representing a variety of tissues and treatments were sequenced. Assembly of these sequences with ESTs already in the EST database (dbEST, GenBank) identified 9675 cotton sequences not present in GenBank. Statistical analysis of a subset of these ESTs identified genes likely 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 the 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.Key words: drought stress, gene annotation, gene mapping, tentative consensus sequence (TC), Xanthomonas campestris.

Details

ISSN :
08312796
Volume :
49
Issue :
4
Database :
OpenAIRE
Journal :
Genome
Accession number :
edsair.doi.dedup.....cb357c93985d40056f379a17a1d3e17e