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

Crowhurst, R.N., Gleave, A.P., MacRae, E.A., Ampomah-Dwamena, C., Atkinson, R.G., Beuning, L.L., Bulley, S.M., Chagne, D., Marsh, K.B., Matich, A.J., Montefiori, M., Newcomb, R.D., Schaffer, R.J., Usadel, B., Allan, A.C., Boldingh, H.L., Bowen, J.H., Davy, M.W., Eckloff, R., Ross, A.R., Fraser, L.G., Gera, E., Hellens, R.P., Janssen, B.J., Klages, K., Lo, K.R., MacDiarmid, R.M., Nain, B., McNeilage, M.A., Rassam, M., Richardson, A.C., Rikkerink, E.H.A., Ross, G.S., Schröder, R., Snowden, K.C., Souleyre, E.J.F., Templeton, M.D., Walton, E.F., Wang, D., Wang, M.Y., Wang, Y.Y., Wood, M., Wu, R., Yauk, Y.K., & Laing, W.A. (2008) 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. BMC Genomics, 9(351).

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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.

Impact and interest:

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ID Code: 71300
Item Type: Journal Article
Refereed: Yes
Additional Information: Cited By (since 1996):80
Export Date: 6 May 2014
Source: Scopus
Art. No.: 351
PubMed ID: 18655731
DOI: 10.1186/1471-2164-9-351
ISSN: 1471-2164
Divisions: Current > QUT Faculties and Divisions > Science & Engineering Faculty
Copyright Owner: 2008 Crowhurst et al; licensee BioMed Central Ltd.
Copyright Statement: This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Deposited On: 09 May 2014 03:32
Last Modified: 06 Jun 2014 06:33

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