Chestnut resistance to the blight disease: insights from transcriptome analysis

Abstract

BackgroundA 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.ResultsOver 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.ConclusionsOur 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.

Transcriptome of Teak (Tectona grandis, L.f) in Vegetative to Generative Stages Development

“…Following 2 chloroform extractions, RNA was precipitated with LiCl 2 ,again extracted with chloroform and precipitated with ethanol. The resulting RNA pellet was resuspended in 20-100 μL of DEPC-treated water (Barakat et al, 2012). RNA concentration analysis on a Qubit TM fluorometer (www.invitrogen.com/qubit) to showed a total yield of RNA sample.…”

“…The high number of reads generated per run together with the low sequencing error rate in the contigs obtained makes it a good tool to deeply sequence the transcriptome of plants. This approach has been used successfully for analyzing the transcriptomes of maize and Arabidopsis and have applied it to the non-model tree species Castanea dentata and C. mollissima (Collins et al, 2008;Barakat et al, 2009Barakat et al, , 2012.…”

“…Top hit species results use for homology based annotations of teak (Rosero et al, 2011;Barakat et al, 2009Barakat et al, , 2012.…”

“…DEGseq analysis was used to identify flowering development genes in transcript abundance because it integrates several statistical methods (Barakat et al, 2009(Barakat et al, , 2012. The number of reads per contig for each gene was compared between vegetative stage as control and generative tissues in teak separately.…”

A physical map of the Chinese chestnut (Castanea mollissima) genome and its integration with the genetic map

“…Computational analysis of the transcriptomes generated from chestnut blight cankers and healthy tissues revealed ESTs preferentially expressed during canker development in both Chinese chestnut and American chestnut and provided a list of potential candidate genes for blight resistance (Barakat et al 2009(Barakat et al , 2012. The collection of ESTs was analyzed for both SSR and SNP markers to develop a highly informative genetic map.…”