Chestnut resistance to the blight disease: Insights from transcriptome analysis

Abdelali Barakat, Meg Staton, Chun Huai Cheng, Joseph Park, Norzawani B.M. Yassin, Stephen Ficklin, Chia Chun Yeh, Fred Hebard, Kathleen Baier, William Powell, Stephan C. Schuster, Nicholas Wheeler, Albert Abbott, John Edward Carlson, Ronald Sederoff

Research output: Contribution to journalArticle

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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.

Original languageEnglish (US)
Article number38
JournalBMC plant biology
Volume12
DOIs
StatePublished - Mar 19 2012

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Castanea
transcriptomics
blight
Castanea dentata
Castanea mollissima
Cryphonectria parasitica
genes
genomics
Fagaceae
backcrossing
transcriptome
fungi
stems
pathogens
hypersensitive response
jasmonic acid
woody plants
salicylic acid
marshes
abscisic acid

All Science Journal Classification (ASJC) codes

  • Plant Science

Cite this

Barakat, A., Staton, M., Cheng, C. H., Park, J., Yassin, N. B. M., Ficklin, S., ... Sederoff, R. (2012). Chestnut resistance to the blight disease: Insights from transcriptome analysis. BMC plant biology, 12, [38]. https://doi.org/10.1186/1471-2229-12-38
Barakat, Abdelali ; Staton, Meg ; Cheng, Chun Huai ; Park, Joseph ; Yassin, Norzawani B.M. ; Ficklin, Stephen ; Yeh, Chia Chun ; Hebard, Fred ; Baier, Kathleen ; Powell, William ; Schuster, Stephan C. ; Wheeler, Nicholas ; Abbott, Albert ; Carlson, John Edward ; Sederoff, Ronald. / Chestnut resistance to the blight disease : Insights from transcriptome analysis. In: BMC plant biology. 2012 ; Vol. 12.
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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.",
author = "Abdelali Barakat and Meg Staton and Cheng, {Chun Huai} and Joseph Park and Yassin, {Norzawani B.M.} and Stephen Ficklin and Yeh, {Chia Chun} and Fred Hebard and Kathleen Baier and William Powell and Schuster, {Stephan C.} and Nicholas Wheeler and Albert Abbott and Carlson, {John Edward} and Ronald Sederoff",
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doi = "10.1186/1471-2229-12-38",
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Barakat, A, Staton, M, Cheng, CH, Park, J, Yassin, NBM, Ficklin, S, Yeh, CC, Hebard, F, Baier, K, Powell, W, Schuster, SC, Wheeler, N, Abbott, A, Carlson, JE & Sederoff, R 2012, 'Chestnut resistance to the blight disease: Insights from transcriptome analysis', BMC plant biology, vol. 12, 38. https://doi.org/10.1186/1471-2229-12-38

Chestnut resistance to the blight disease : Insights from transcriptome analysis. / Barakat, Abdelali; Staton, Meg; Cheng, Chun Huai; Park, Joseph; Yassin, Norzawani B.M.; Ficklin, Stephen; Yeh, Chia Chun; Hebard, Fred; Baier, Kathleen; Powell, William; Schuster, Stephan C.; Wheeler, Nicholas; Abbott, Albert; Carlson, John Edward; Sederoff, Ronald.

In: BMC plant biology, Vol. 12, 38, 19.03.2012.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Chestnut resistance to the blight disease

T2 - Insights from transcriptome analysis

AU - Barakat, Abdelali

AU - Staton, Meg

AU - Cheng, Chun Huai

AU - Park, Joseph

AU - Yassin, Norzawani B.M.

AU - Ficklin, Stephen

AU - Yeh, Chia Chun

AU - Hebard, Fred

AU - Baier, Kathleen

AU - Powell, William

AU - Schuster, Stephan C.

AU - Wheeler, Nicholas

AU - Abbott, Albert

AU - Carlson, John Edward

AU - Sederoff, Ronald

PY - 2012/3/19

Y1 - 2012/3/19

N2 - 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.

AB - 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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Barakat A, Staton M, Cheng CH, Park J, Yassin NBM, Ficklin S et al. Chestnut resistance to the blight disease: Insights from transcriptome analysis. BMC plant biology. 2012 Mar 19;12. 38. https://doi.org/10.1186/1471-2229-12-38