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Open Access Highly Accessed Research article

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

Ross N Crowhurst1, Andrew P Gleave1, Elspeth A MacRae1, Charles Ampomah-Dwamena1, Ross G Atkinson1, Lesley L Beuning1, Sean M Bulley1, David Chagne1, Ken B Marsh1, Adam J Matich1, Mirco Montefiori1, Richard D Newcomb1, Robert J Schaffer1, Björn Usadel2, Andrew C Allan1, Helen L Boldingh1, Judith H Bowen1, Marcus W Davy1, Rheinhart Eckloff1, A Ross Ferguson1, Lena G Fraser1, Emma Gera1, Roger P Hellens1, Bart J Janssen1, Karin Klages1, Kim R Lo1, Robin M MacDiarmid1, Bhawana Nain1, Mark A McNeilage1, Maysoon Rassam1, Annette C Richardson1, Erik HA Rikkerink1, Gavin S Ross1, Roswitha Schröder1, Kimberley C Snowden1, Edwige JF Souleyre1, Matt D Templeton1, Eric F Walton1, Daisy Wang1, Mindy Y Wang1, Yanming Y Wang1, Marion Wood1, Rongmei Wu1, Yar-Khing Yauk1 and William A Laing1*

Author Affiliations

1 The Horticultural and Food Research Institute of New Zealand, PB 92169, Auckland, New Zealand

2 Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany

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BMC Genomics 2008, 9:351  doi:10.1186/1471-2164-9-351

Published: 27 July 2008

Abstract

Background

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).

Results

The ESTs were derived mainly from four Actinidia species (A. chinensis, A. deliciosa, A. arguta and A. eriantha) 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 Actinidia 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.

Conclusion

This large EST resource will allow researchers to undertake the tremendous challenge of understanding the molecular basis of genetic diversity in the Actinidia 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 Actinidia.