Analysis of expressed sequence tags from <it>Actinidia</it>: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening

BMC Genomics. 2008;9(1):351 DOI 10.1186/1471-2164-9-351


Journal Homepage

Journal Title: BMC Genomics

ISSN: 1471-2164 (Online)

Publisher: BMC

LCC Subject Category: Technology: Chemical technology: Biotechnology | Science: Biology (General): Genetics

Country of publisher: United Kingdom

Language of fulltext: English

Full-text formats available: PDF, HTML



Richardson Annette C

Rassam Maysoon

McNeilage Mark A

Nain Bhawana

MacDiarmid Robin M

Lo Kim R

Klages Karin

Janssen Bart J

Hellens Roger P

Gera Emma

Fraser Lena G

Ferguson A Ross

Eckloff Rheinhart

Davy Marcus W

Bowen Judith H

Boldingh Helen L

Allan Andrew C

Usadel Björn

Schaffer Robert J

Newcomb Richard D

Montefiori Mirco

Matich Adam J

Marsh Ken B

Chagne David

Bulley Sean M

Beuning Lesley L

Atkinson Ross G

Ampomah-Dwamena Charles

MacRae Elspeth A

Gleave Andrew P

Crowhurst Ross N

Rikkerink Erik HA

Ross Gavin S

Schröder Roswitha

Snowden Kimberley C

Souleyre Edwige JF

Templeton Matt D

Walton Eric F

Wang Daisy

Wang Mindy Y

Wang Yanming Y

Wood Marion

Wu Rongmei

Yauk Yar-Khing

Laing William A


Blind peer review

Editorial Board

Instructions for authors

Time From Submission to Publication: 17 weeks


Abstract | Full Text

<p>Abstract</p> <p>Background</p> <p>Kiwifruit (Actinidia spp.) are a relatively new, but economically important crop grown in many different parts of the world. Commercial success is driven by the development of new cultivars with novel consumer traits including flavor, appearance, healthful components and convenience. To increase our understanding of the genetic diversity and gene-based control of these key traits in Actinidia, we have produced a collection of 132,577 expressed sequence tags (ESTs).</p> <p>Results</p> <p>The ESTs were derived mainly from four <it>Actinidia </it>species (<it>A. chinensis, A. deliciosa, A. arguta </it>and <it>A. eriantha</it>) and fell into 41,858 non redundant clusters (18,070 tentative consensus sequences and 23,788 EST singletons). Analysis of flavor and fragrance-related gene families (acyltransferases and carboxylesterases) and pathways (terpenoid biosynthesis) is presented in comparison with a chemical analysis of the compounds present in <it>Actinidia </it>including esters, acids, alcohols and terpenes. ESTs are identified for most genes in color pathways controlling chlorophyll degradation and carotenoid biosynthesis. In the health area, data are presented on the ESTs involved in ascorbic acid and quinic acid biosynthesis showing not only that genes for many of the steps in these pathways are represented in the database, but that genes encoding some critical steps are absent. In the convenience area, genes related to different stages of fruit softening are identified.</p> <p>Conclusion</p> <p>This large EST resource will allow researchers to undertake the tremendous challenge of understanding the molecular basis of genetic diversity in the <it>Actinidia </it>genus as well as provide an EST resource for comparative fruit genomics. The various bioinformatics analyses we have undertaken demonstrates the extent of coverage of ESTs for genes encoding different biochemical pathways in <it>Actinidia</it>.</p>