Chestnut resistance to the blight disease: insights from transcriptome analysis

doi:10.1186/1471-2229-12-38

BMC Plant Biol. 2012; 12: 38.

Published online 2012 March 19. doi: 10.1186/1471-2229-12-38

PMCID: PMC3376029

Chestnut resistance to the blight disease: insights from transcriptome analysis

Abdelali Barakat,^1,⁶ Meg Staton,² Chun-Huai Cheng,² Joseph Park,¹ Norzawani Buang M Yassin,¹ Stephen Ficklin,² Chia-Chun Yeh,¹ Fred Hebard,³ Kathleen Baier,⁷ William Powell,⁷ Stephan C Schuster,⁴ Nicholas Wheeler,⁵ Albert Abbott,⁶ John E Carlson,^1,⁸ and Ronald Sederoff⁵

¹The School of Forest Resources, and The Huck Institutes of the Life Sciences, Pennsylvania State University, 326 Forest Resources Building, University Park, PA 16802, USA

²Clemson University Genomics Institute, Clemson University, 310 Biosystems Research Complex, 51 New Cherry Street,, Clemson, SC 29631, USA

³Meadowview Research Farms, Meadowview, VA 24361-3349, USA

⁴Department Biochemistry and Molecular Biology, Pennsylvania State University, 310 Wartik laboratory, University Park, PA 16802, USA

⁵Department of Forestry and Environmental Resources, North Carolina State University, Campus Box, 7247, Raleigh, NC 27695, USA

⁶Department of Biochemistry and Genetics, Clemson University, 116 Jordan Hall, Clemson, SC 29631, USA

⁷College of Environmental Science & Forestry, State University of New York, One Forestry Drive, Syracuse, NY 13210-2788, USA

⁸Department of Bioenergy Science and Technology, Chonnam National University, Buk-Gu, Gwangju 500-757, Korea

Corresponding author.

Abdelali Barakat: abaraka/at/clemson.edu; Meg Staton: mestato/at/yahoo.com; Chun-Huai Cheng: chunhuaicheng/at/wsu.edu; Joseph Park: enceunki/at/gmail.com; Norzawani Buang M Yassin: norzawanibuang/at/gmail.com; Stephen Ficklin: spficklin/at/gmail.com; Chia-Chun Yeh: yeh0104/at/gmail.com; Fred Hebard: fred/at/acf.org; Kathleen Baier: kbaier/at/esf.edu; William Powell: wapowell/at/esf.edu; Stephan C Schuster: scs/at/bx.psu.edu; Nicholas Wheeler: nickwheeler/at/scattercreek.com; Albert Abbott: aalbert/at/clemson.edu; John E Carlson: jec16/at/psu.edu; Ronald Sederoff: ron_sederoff/at/ncsu.edu

Received June 17, 2011; Accepted March 19, 2012.

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.

Abstract

Background

A century ago, Chestnut Blight Disease (CBD) devastated the American chestnut. Backcross breeding has been underway to introgress resistance from Chinese chestnut into surviving American chestnut genotypes. Development of genomic resources for the family Fagaceae, has focused in this project on Castanea mollissima Blume (Chinese chestnut) and Castanea dentata (Marsh.) Borkh (American chestnut) to aid in the backcross breeding effort and in the eventual identification of blight resistance genes through genomic sequencing and map based cloning. A previous study reported partial characterization of the transcriptomes from these two species. Here, further analyses of a larger dataset and assemblies including both 454 and capillary sequences were performed and defense related genes with differential transcript abundance (GDTA) in canker versus healthy stem tissues were identified.

Results

Over one and a half million cDNA reads were assembled into 34,800 transcript contigs from American chestnut and 48,335 transcript contigs from Chinese chestnut. Chestnut cDNA showed higher coding sequence similarity to genes in other woody plants than in herbaceous species. The number of genes tagged, the length of coding sequences, and the numbers of tagged members within gene families showed that the cDNA dataset provides a good resource for studying the American and Chinese chestnut transcriptomes. In silico analysis of transcript abundance identified hundreds of GDTA in canker versus healthy stem tissues. A significant number of additional DTA genes involved in the defense-response not reported in a previous study were identified here. These DTA genes belong to various pathways involving cell wall biosynthesis, reactive oxygen species (ROS), salicylic acid (SA), ethylene, jasmonic acid (JA), abscissic acid (ABA), and hormone signalling. DTA genes were also identified in the hypersensitive response and programmed cell death (PCD) pathways. These DTA genes are candidates for host resistance to the chestnut blight fungus, Cryphonectria parasitica.

Conclusions

Our data allowed the identification of many genes and gene network candidates for host resistance to the chestnut blight fungus, Cryphonectria parasitica. The similar set of GDTAs in American chestnut and Chinese chestnut suggests that the variation in sensitivity to this pathogen between these species may be the result of different timing and amplitude of the response of the two to the pathogen infection. Resources developed in this study are useful for functional genomics, comparative genomics, resistance breeding and phylogenetics in the Fagaceae.

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