Analyses of expressed sequence tags from apple

Show simple item record Newcomb, Richard en Crowhurst, RN en Gleave, AP en Rikkerink, EHA en Allan, Andrew en Beuning, LL en Bowen, JH en Gera, E en Jamieson, KR en Janssen, BJ en Laing, WA en McArtney, S en Nain, B en Ross, GS en Snowden, Kimberley en Souleyre, EJF en Walton, EF en Yauk, YK en 2012-03-08T23:02:36Z en 2006 en
dc.identifier.citation Plant Physiology 141(1):147-166 2006 en
dc.identifier.issn 0032-0889 en
dc.identifier.uri en
dc.description.abstract The domestic apple (Malus domestica; also known as Malus pumila Mill.) has become a model fruit crop in which to study commercial traits such as disease and pest resistance, grafting, and flavor and health compound biosynthesis. To speed the discovery of genes involved in these traits, develop markers to map genes, and breed new cultivars, we have produced a substantial expressed sequence tag collection from various tissues of apple, focusing on fruit tissues of the cultivar Royal Gala. Over 150,000 expressed sequence tags have been collected from 43 different cDNA libraries representing 34 different tissues and treatments. Clustering of these sequences results in a set of 42,938 nonredundant sequences comprising 17,460 tentative contigs and 25,478 singletons, together representing what we predict are approximately one-half the expressed genes from apple. Many potential molecular markers are abundant in the apple transcripts. Dinucleotide repeats are found in 4,018 nonredundant sequences, mainly in the 5'-untranslated region of the gene, with a bias toward one repeat type (containing AG, 88%) and against another (repeats containing CG, 0.1%). Trinucleotide repeats are most common in the predicted coding regions and do not show a similar degree of sequence bias in their representation. Bi-allelic single-nucleotide polymorphisms are highly abundant with one found, on average, every 706 bp of transcribed DNA. Predictions of the numbers of representatives from protein families indicate the presence of many genes involved in disease resistance and the biosynthesis of flavor and health-associated compounds. Comparisons of some of these gene families with Arabidopsis (Arabidopsis thaliana) suggest instances where there have been duplications in the lineages leading to apple of biosynthetic and regulatory genes that are expressed in fruit. This resource paves the way for a concerted functional genomics effort in this important temperate fruit crop. en
dc.language EN en
dc.publisher American Society of Plant Biologists en
dc.relation.ispartofseries Plant Physiology en
dc.rights Items in ResearchSpace are protected by copyright, with all rights reserved, unless otherwise indicated. Previously published items are made available in accordance with the copyright policy of the publisher. Details obtained from en
dc.rights.uri en
dc.subject FLAVOR COMPOUNDS en
dc.subject DNA MICROARRAYS en
dc.subject ALPHA-FARNESENE en
dc.subject GENE-EXPRESSION en
dc.subject RICE GENOME en
dc.subject PEEL TISSUE en
dc.subject FRUIT en
dc.title Analyses of expressed sequence tags from apple en
dc.type Journal Article en
dc.identifier.doi 10.1104/pp.105.076208 en
pubs.issue 1 en
pubs.begin-page 147 en
pubs.volume 141 en
dc.rights.holder Copyright: American Society of Plant Biologists en
dc.identifier.pmid 16531485 en
pubs.end-page 166 en
dc.rights.accessrights en
pubs.subtype Article en
pubs.elements-id 223127 en Science en Biological Sciences en
pubs.record-created-at-source-date 2012-02-17 en
pubs.dimensions-id 16531485 en

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