title: Identification of Ramie Genes in Response to Pratylenchus coffeae Infection Challenge by Digital Gene Expression Analysis.
abstract: Root lesion disease, caused by Pratylenchus coffeae, seriously impairs the growth and yield of ramie, an important natural fiber crop. The ramie defense mechanism against P. coffeae infection is poorly understood, which hinders efforts to improve resistance via breeding programs. In this study, the transcriptome of the resistant ramie cultivar Qingdaye was characterized using Illumina sequence technology. About 46.3 million clean pair end (PE) reads were generated and assembled into 40,826 unigenes with a mean length of 830 bp. Digital gene expression (DGE) analysis was performed on both the control roots (CK) and P. coffeae-challenged roots (CH), and the differentially expressed genes (DEGs) were identified. Approximately 10.16 and 8.07 million cDNA reads in the CK and CH cDNA libraries were sequenced, respectively. A total of 137 genes exhibited different transcript abundances between the two libraries. Among them, the expressions of 117 and 20 DEGs were up- and down-regulated in P. coffeae-challenged ramie, respectively. The expression patterns of 15 candidate genes determined by qRT-PCR confirmed the results of DGE analysis. Time-course expression profiles of eight defense-related genes in susceptible and resistant ramie cultivars were different after P. coffeae inoculation. The differential expression of protease inhibitors, pathogenesis-related proteins (PRs), and transcription factors in resistant and susceptible ramie during P. coffeae infection indicated that cystatin likely plays an important role in nematode resistance.
authors.affiliation: Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China. yuyongting@caas.cn.
authors.forename: Yongting
authors.initials: Y
authors.lastname: Yu
authors.affiliation: Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China. zengliangbin@caas.cn.
authors.forename: Liangbin
authors.initials: L
authors.lastname: Zeng
authors.affiliation: Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China. yanzhuntoronto@gmail.com.
authors.forename: Zhun
authors.initials: Z
authors.lastname: Yan
authors.affiliation: Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China. liutouming@caas.cn.
authors.forename: Touming
authors.initials: T
authors.lastname: Liu
authors.affiliation: Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China. sunkai@caas.cn.
authors.forename: Kai
authors.initials: K
authors.lastname: Sun
authors.affiliation: Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China. zhtt1988@126.com.
authors.forename: Taotao
authors.initials: T
authors.lastname: Zhu
authors.affiliation: Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China. zhuaiguo@caas.cn.
authors.forename: Aiguo
authors.initials: A
authors.lastname: Zhu
mesh_terms: D000818:Animals; D032402:Boehmeria / Q000235:genetics* / Q000469:parasitology*; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D006790:Host-Parasite Interactions / Q000235:genetics*; D058977:Molecular Sequence Annotation; D009348:Nematoda; D059467:Transcriptome
keywords: Boehmeria nivea (L.) Gaudich; cystatin; digital gene expression; resistance related genes; root lesion nematode