title: Chestnut resistance to the blight disease: insights from transcriptome analysis.
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.
authors.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
authors.forename: Abdelali
authors.initials: A
authors.lastname: Barakat
authors.forename: Meg
authors.initials: M
authors.lastname: Staton
authors.forename: Chun-Huai
authors.initials: CH
authors.lastname: Cheng
authors.forename: Joseph
authors.initials: J
authors.lastname: Park
authors.forename: Norzawani Buang M
authors.initials: NB
authors.lastname: Yassin
authors.forename: Stephen
authors.initials: S
authors.lastname: Ficklin
authors.forename: Chia-Chun
authors.initials: CC
authors.lastname: Yeh
authors.forename: Fred
authors.initials: F
authors.lastname: Hebard
authors.forename: Kathleen
authors.initials: K
authors.lastname: Baier
authors.forename: William
authors.initials: W
authors.lastname: Powell
authors.forename: Stephan C
authors.initials: SC
authors.lastname: Schuster
authors.forename: Nicholas
authors.initials: N
authors.lastname: Wheeler
authors.forename: Albert
authors.initials: A
authors.lastname: Abbott
authors.forename: John E
authors.initials: JE
authors.lastname: Carlson
authors.forename: Ronald
authors.initials: R
authors.lastname: Sederoff
mesh_terms: D001203:Ascomycota / Q000276:immunology / Q000472:pathogenicity*; D001947:Breeding; D003001:Cloning, Molecular; D020451:Contig Mapping; D018076:DNA, Complementary / Q000235:genetics; D030541:Databases, Genetic; D060467:Disease Resistance; D029962:Fagaceae / Q000235:genetics / Q000276:immunology / Q000382:microbiology*; D020869:Gene Expression Profiling / Q000379:methods*; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D017343:Genes, Plant; D007178:Inbreeding; D010802:Phylogeny; D010935:Plant Diseases / Q000276:immunology* / Q000382:microbiology; D018547:Plant Stems / Q000235:genetics / Q000276:immunology / Q000382:microbiology; D020543:Proteome / Q000032:analysis / Q000235:genetics; D018749:RNA, Plant / Q000032:analysis / Q000235:genetics; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D013045:Species Specificity; D013997:Time Factors; D059467:Transcriptome
chemical_list: D018076:DNA, Complementary; D020543:Proteome; D018749:RNA, Plant