Dynamics in the resistant and susceptible peanut (Arachis hypogaea L.) root transcriptome on infection with the Ralstonia solanacearum

BMC Genomics, Dec 2014

Background Bacterial wilt caused by Ralstonia solanacearum is a serious soil-borne disease of peanut (Arachis hypogaea L). The molecular basis of peanut response to R. solanacearum remains unknown. To understand the resistance mechanism behind peanut resistance to R. solanacearum, we used RNA-Seq to perform global transcriptome profiling on the roots of peanut resistant (R) and susceptible (S) genotypes under R. solanacearum infection. Results A total of 4.95 x 108 raw sequence reads were generated and subsequently assembled into 271, 790 unigenes with an average length of 890 bp and a N50 of 1, 665 bp. 179, 641 unigenes could be annotated by public protein databases. The pairwise transcriptome comparsions of time course (6, 12, 24, 48 and 72 h post inoculation) were conducted 1) between inoculated and control samples of each genotype, 2) between inoculated samples of R and S genotypes. The linear dynamics of transcriptome profile was observed between adjacent samples for each genotype, two genotypes shared similar transcriptome pattern at early time points with most significant up regulation at 12 hour, and samples from R genotype at 24 h and S genotype at 48 h showed similar transcriptome pattern, significant differences of transcriptional profile were observed in pairwise comparisons between R and S genotypes. KEGG analysis showed that the primary metabolisms were inhibited in both genotypes and stronger inhibition in R genotype post inoculation. The defense related genes (R gene, LRR-RLK, cell wall genes, etc.) generally showed a genotype-specific down regulation and different expression between both genotypes. Conclusion This transcriptome profiling provided the largest data set that explores the dynamic in crosstalk between peanut and R. solanacearum. The results suggested that the down-regulation of primary metabolism is contributed to the resistance difference between R and S genotypes. The genotype-specific expression pattern of defense related DEGs also contributed to the resistance difference between R and S genotype. This study will strongly contribute to better understand the molecular interaction between plant and R. solanacearum.

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Dynamics in the resistant and susceptible peanut (Arachis hypogaea L.) root transcriptome on infection with the Ralstonia solanacearum

Yuning Chen 0 Xiaoping Ren 0 Xiaojing Zhou 0 Li Huang 0 Liying Yan 0 Yong Lei 0 Boshou Liao 0 Jinyong Huang Shunmou Huang 0 Wenhui Wei 0 Huifang Jiang 0 0 Oil Crop Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture , No 2 Xudong Second Road, Wuhan 430062 , P.R. China Background: Bacterial wilt caused by Ralstonia solanacearum is a serious soil-borne disease of peanut (Arachis hypogaea L). The molecular basis of peanut response to R. solanacearum remains unknown. To understand the resistance mechanism behind peanut resistance to R. solanacearum, we used RNA-Seq to perform global transcriptome profiling on the roots of peanut resistant (R) and susceptible (S) genotypes under R. solanacearum infection. Results: A total of 4.95 x 108 raw sequence reads were generated and subsequently assembled into 271, 790 unigenes with an average length of 890 bp and a N50 of 1, 665 bp. 179, 641 unigenes could be annotated by public protein databases. The pairwise transcriptome comparsions of time course (6, 12, 24, 48 and 72 h post inoculation) were conducted 1) between inoculated and control samples of each genotype, 2) between inoculated samples of R and S genotypes. The linear dynamics of transcriptome profile was observed between adjacent samples for each genotype, two genotypes shared similar transcriptome pattern at early time points with most significant up regulation at 12 hour, and samples from R genotype at 24 h and S genotype at 48 h showed similar transcriptome pattern, significant differences of transcriptional profile were observed in pairwise comparisons between R and S genotypes. KEGG analysis showed that the primary metabolisms were inhibited in both genotypes and stronger inhibition in R genotype post inoculation. The defense related genes (R gene, LRR-RLK, cell wall genes, etc.) generally showed a genotype-specific down regulation and different expression between both genotypes. Conclusion: This transcriptome profiling provided the largest data set that explores the dynamic in crosstalk between peanut and R. solanacearum. The results suggested that the down-regulation of primary metabolism is contributed to the resistance difference between R and S genotypes. The genotype-specific expression pattern of defense related DEGs also contributed to the resistance difference between R and S genotype. This study will strongly contribute to better understand the molecular interaction between plant and R. solanacearum. - Background Peanut (Arachis hypogaea L.) is an important crop for oil and protein production in the tropical and subtropical regions of the world, Asia is the top region of peanut planting with the growing area of 11 million ha (http://faostat. fao.org/site/339/default.aspx). The bacterial wilt caused by Ralstonia solanacearum is a destructive soil borne peanut disease in Asia. It could cause peanut production reduction at least of 10% even a mass extinction. R. solanacearum has a wide host range expanding over more than 200 plant species [1]. The process of R. solanacearum infecting plant had been well characterized in model crop, briefly, the R. solanacearum penetrated into cortical tissue of host roots, colonized and exploded in numbers, caused a sudden deadly wilt of plant [2-4]. The resistant breeding is the most ideal strategy for controlling bacterial wilt with great benefit of economy and environmental protection [1]. However, even in the resistance varieties, R. solanacearum can multiply in a high level of number and caused the symptoms of stunted growth, weak wilting and reduced resistance to other pathogens, finally resulted in a potential crop failure [5]. Up to now, the molecular basis of peanut resistance to R. solanacearum is poorly understood. Understanding the complexity of disease resistance will contribute to the development of peanut resistance to bacterial wilt. In the past few decades, the molecular cross-talk between plants and pathogens had been characterized, the intrinsic mechanism of plant resistance to pathogens had been well documented [6-8]. During plantpathogen interactions, plant evolved a two-tiered innate immunity system to defend against pathogens attack. The host cell surface localized pattern-recognition receptors (PRRs) recognizes pathogen-associated molecular patterns (PAMPs), then activated the PAMP-triggered immunity (PTI) followed by pathogen effector-triggered immunity (ETI). In PTI and ETI, a set of defense response on transcriptome level were activated, and resulted in the arrest of pathogen clone [9-12]. However, the molecular reaction between plant and R. solanacearum have received far less attentions. Efforts had been made in discovering the molecular mechanisms underlying interactions between Arabidopsis, tomato, potato R. solanacearum, several resistance related genes and enzymes had been well characterized [13-18]. The significant changes on level o (...truncated)


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Yuning Chen, Xiaoping Ren, Xiaojing Zhou, Li Huang, Liying Yan, Yong Lei, Boshou Liao, Jinyong Huang, Shunmou Huang, Wenhui Wei, Huifang Jiang. Dynamics in the resistant and susceptible peanut (Arachis hypogaea L.) root transcriptome on infection with the Ralstonia solanacearum, BMC Genomics, 2014, pp. 1078, 15, DOI: 10.1186/1471-2164-15-1078