title: Analysis of ESTs from multiple Gossypium hirsutum tissues and identification of SSRs.
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.
authors.affiliation: USDA-ARS, 141 Experiment Station Rd., Stoneville, MS 38756, USA. etaliercio@msa-stoneville.ars.usda.gov
authors.forename: Earl
authors.initials: E
authors.lastname: Taliercio
authors.forename: Randy D
authors.initials: RD
authors.lastname: Allen
authors.forename: Margaret
authors.initials: M
authors.lastname: Essenberg
authors.forename: Natalya
authors.initials: N
authors.lastname: Klueva
authors.forename: Henry
authors.initials: H
authors.lastname: Nguyen
authors.forename: Mohini A
authors.initials: MA
authors.lastname: Patil
authors.forename: Paxton
authors.initials: P
authors.lastname: Payton
authors.forename: Ana Cecilia M
authors.initials: AC
authors.lastname: Millena
authors.forename: Angela L
authors.initials: AL
authors.lastname: Phillips
authors.forename: Margaret L
authors.initials: ML
authors.lastname: Pierce
authors.forename: Brian
authors.initials: B
authors.lastname: Scheffler
authors.forename: Rickie
authors.initials: R
authors.lastname: Turley
authors.forename: Jing
authors.initials: J
authors.lastname: Wang
authors.forename: Deshui
authors.initials: D
authors.lastname: Zhang
authors.forename: Jodi
authors.initials: J
authors.lastname: Scheffler
mesh_terms: D002874:Chromosome Mapping / Q000379:methods; D016384:Consensus Sequence / Q000235:genetics; D030561:Databases, Nucleic Acid; D020224:Expressed Sequence Tags / Q000737:chemistry*; D015723:Gene Library; D017343:Genes, Plant; D008040:Genetic Linkage; D005819:Genetic Markers; D003368:Gossypium / Q000235:genetics*; D018598:Minisatellite Repeats / Q000235:genetics*; D018514:Plant Structures / Q000235:genetics* / Q000382:microbiology; D011110:Polymorphism, Genetic; D016959:Xanthomonas campestris / Q000472:pathogenicity
chemical_list: D005819:Genetic Markers