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Chestnut resistance to the blight disease: insights from transcriptome analysis.

Barakat A, Staton M, Cheng CH, Park J, Yassin NB, Ficklin S, Yeh CC, Hebard F, Baier K, Powell W, Schuster SC, Wheeler N, Abbott A, Carlson JE, Sederoff R - BMC Plant Biol. (2012)

Bottom Line: A significant number of additional DTA genes involved in the defense-response not reported in a previous study were identified here.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: The School of Forest Resources, and The Huck Institutes of the Life Sciences, Pennsylvania State University, 326 Forest Resources Building, University Park, PA 16802, USA. abaraka@clemson.edu

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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Expression profiles of defense related genes in Cryphonectria parasitica inoculated and control plants in American and Chinese chestnut. The names of genes studied are indicated on the bottom of diagrams. The tissues analyzed are indicated on the right of the figure. CC CTL, Chinese chestnut control; CC INO, Chinese chestnut inoculated plants; AC CTL, American chestnut control; AC INO, American chestnut inoculated.
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Figure 6: Expression profiles of defense related genes in Cryphonectria parasitica inoculated and control plants in American and Chinese chestnut. The names of genes studied are indicated on the bottom of diagrams. The tissues analyzed are indicated on the right of the figure. CC CTL, Chinese chestnut control; CC INO, Chinese chestnut inoculated plants; AC CTL, American chestnut control; AC INO, American chestnut inoculated.

Mentions: The list of the identified defense-related genes showing DTA involves several related pathways (Tables 3 and 4, Additional file 2: Table S1, Additional file 3: Table S2, and Additional file 4: Table S3). The first category includes genes involved in the biosynthesis of lignin and other cell wall components such as 4-coumarate:CoA ligase (4CL), Cinnamyl-Alcohol Dehydrogenase (CAD), cinnamoyl CoA reductase (CCR), peroxidase, Myb transcription factor, and UDP-glucose:thiohydroximate S-glucosyltransferase. Genes involved in programmed cell death and hypersensitivity such as Myo-inositol-1-phosphate, ATPase transporter, voltage-dependent anion channel, 2-deoxy-D-arabino-heptulosonate 7-phosphate, and cysteine proteinase precursor-like protein were also identified in canker tissues. However, one of the highly represented categories was phytohormone signaling including ethylene, jasmonic acid (JA), salicyc acid (SA), and abscisic acid (ABA) (Tables 3 and 4, Additional file 1: Figure S1, Additional file 2: Table S1). For example, transcripts of 12 genes involved in JA response were differentially abundant in Chinese chestnut. These include allene oxide cyclase, JAZ1, lipoxygenase, 12-oxophytodienoate reductase, 3-ketoacyl-CoA thiolase, chitinase, plastidic fatty acid desaturase, and others. Lipooxygenase, chitinase, and ACC oxidase are among genes with the most DTA in canker versus healthy stem (Additional file 3: Table S3). Genes involved in the response to SA include alpha-dioxygenase, mitochondrial chaperonin HSP, senescence-associated gene, and others. Genes related to the ABA response include ABA 8'-hydroxylase, 26S proteasome regulatory subunit, protein phosphatase 2 C, hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP) synthase and others. Several other genes involved were identified such as MYB transcription factors, proteases, and kinases. Comparison of GDTAs from American and Chinese chestnut showed that similar set of genes were induced in American and Chinese chestnut (Additional file 4: Table S3). Few genes were induced in American versus Chinese and vice versa (Additional file 4: Table S3). Analyses of a small set of these candidate genes using quantitative RT-PCR in healthy stem tissue versus Cryphonectria parasitica inoculated stem tissues from American and Chinese chestnut confirmed the differential expression of several of these candidates (Figure 6).


Chestnut resistance to the blight disease: insights from transcriptome analysis.

Barakat A, Staton M, Cheng CH, Park J, Yassin NB, Ficklin S, Yeh CC, Hebard F, Baier K, Powell W, Schuster SC, Wheeler N, Abbott A, Carlson JE, Sederoff R - BMC Plant Biol. (2012)

Expression profiles of defense related genes in Cryphonectria parasitica inoculated and control plants in American and Chinese chestnut. The names of genes studied are indicated on the bottom of diagrams. The tissues analyzed are indicated on the right of the figure. CC CTL, Chinese chestnut control; CC INO, Chinese chestnut inoculated plants; AC CTL, American chestnut control; AC INO, American chestnut inoculated.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3376029&req=5

Figure 6: Expression profiles of defense related genes in Cryphonectria parasitica inoculated and control plants in American and Chinese chestnut. The names of genes studied are indicated on the bottom of diagrams. The tissues analyzed are indicated on the right of the figure. CC CTL, Chinese chestnut control; CC INO, Chinese chestnut inoculated plants; AC CTL, American chestnut control; AC INO, American chestnut inoculated.
Mentions: The list of the identified defense-related genes showing DTA involves several related pathways (Tables 3 and 4, Additional file 2: Table S1, Additional file 3: Table S2, and Additional file 4: Table S3). The first category includes genes involved in the biosynthesis of lignin and other cell wall components such as 4-coumarate:CoA ligase (4CL), Cinnamyl-Alcohol Dehydrogenase (CAD), cinnamoyl CoA reductase (CCR), peroxidase, Myb transcription factor, and UDP-glucose:thiohydroximate S-glucosyltransferase. Genes involved in programmed cell death and hypersensitivity such as Myo-inositol-1-phosphate, ATPase transporter, voltage-dependent anion channel, 2-deoxy-D-arabino-heptulosonate 7-phosphate, and cysteine proteinase precursor-like protein were also identified in canker tissues. However, one of the highly represented categories was phytohormone signaling including ethylene, jasmonic acid (JA), salicyc acid (SA), and abscisic acid (ABA) (Tables 3 and 4, Additional file 1: Figure S1, Additional file 2: Table S1). For example, transcripts of 12 genes involved in JA response were differentially abundant in Chinese chestnut. These include allene oxide cyclase, JAZ1, lipoxygenase, 12-oxophytodienoate reductase, 3-ketoacyl-CoA thiolase, chitinase, plastidic fatty acid desaturase, and others. Lipooxygenase, chitinase, and ACC oxidase are among genes with the most DTA in canker versus healthy stem (Additional file 3: Table S3). Genes involved in the response to SA include alpha-dioxygenase, mitochondrial chaperonin HSP, senescence-associated gene, and others. Genes related to the ABA response include ABA 8'-hydroxylase, 26S proteasome regulatory subunit, protein phosphatase 2 C, hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP) synthase and others. Several other genes involved were identified such as MYB transcription factors, proteases, and kinases. Comparison of GDTAs from American and Chinese chestnut showed that similar set of genes were induced in American and Chinese chestnut (Additional file 4: Table S3). Few genes were induced in American versus Chinese and vice versa (Additional file 4: Table S3). Analyses of a small set of these candidate genes using quantitative RT-PCR in healthy stem tissue versus Cryphonectria parasitica inoculated stem tissues from American and Chinese chestnut confirmed the differential expression of several of these candidates (Figure 6).

Bottom Line: A significant number of additional DTA genes involved in the defense-response not reported in a previous study were identified here.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: The School of Forest Resources, and The Huck Institutes of the Life Sciences, Pennsylvania State University, 326 Forest Resources Building, University Park, PA 16802, USA. abaraka@clemson.edu

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.

Show MeSH
Related in: MedlinePlus