title: Large-scale identification of wheat genes resistant to cereal cyst nematode Heterodera avenae using comparative transcriptomic analysis.
abstract: BACKGROUND
  Cereal cyst nematode Heterodera avenae, an important soil-borne pathogen in wheat, causes numerous annual yield losses worldwide, and use of resistant cultivars is the best strategy for control. However, target genes are not readily available for breeding resistant cultivars. Therefore, comparative transcriptomic analyses were performed to identify more applicable resistance genes for cultivar breeding.
  
  
  METHODS
  The developing nematodes within roots were stained with acid fuchsin solution. Transcriptome assemblies and redundancy filteration were obtained by Trinity, TGI Clustering Tool and BLASTN, respectively. Gene Ontology annotation was yielded by Blast2GO program, and metabolic pathways of transcripts were analyzed by Path_finder. The ROS levels were determined by luminol-chemiluminescence assay. The transcriptional gene expression profiles were obtained by quantitative RT-PCR.
  
  
  RESULTS
  The RNA-sequencing was performed using an incompatible wheat cultivar VP1620 and a compatible control cultivar WEN19 infected with H. avenae at 24 h, 3 d and 8 d. Infection assays showed that VP1620 failed to block penetration of H. avenae but disturbed the transition of developmental stages, leading to a significant reduction in cyst formation. Two types of expression profiles were established to predict candidate resistance genes after developing a novel strategy to generate clean RNA-seq data by removing the transcripts of H. avenae within the raw data before assembly. Using the uncoordinated expression profiles with transcript abundance as a standard, 424 candidate resistance genes were identified, including 302 overlapping genes and 122 VP1620-specific genes. Genes with similar expression patterns were further classified according to the scales of changed transcript abundances, and 182 genes were rescued as supplementary candidate resistance genes. Functional characterizations revealed that diverse defense-related pathways were responsible for wheat resistance against H. avenae. Moreover, phospholipase was involved in many defense-related pathways and localized in the connection position. Furthermore, strong bursts of reactive oxygen species (ROS) within VP1620 roots infected with H. avenae were induced at 24 h and 3 d, and eight ROS-producing genes were significantly upregulated, including three class III peroxidase and five lipoxygenase genes.
  
  
  CONCLUSIONS
  Large-scale identification of wheat resistance genes were processed by comparative transcriptomic analysis. Functional characterization showed that phospholipases associated with ROS production played vital roles in early defense responses to H. avenae via involvement in diverse defense-related pathways as a hub switch. This study is the first to investigate the early defense responses of wheat against H. avenae, not only provides applicable candidate resistance genes for breeding novel wheat cultivars, but also enables a better understanding of the defense mechanisms of wheat against H. avenae.
authors.affiliation: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China. konglingan@caas.cn.
authors.forename: Ling-An
authors.initials: LA
authors.lastname: Kong
authors.affiliation: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China. wuduqing@126.com.
authors.forename: Du-Qing
authors.initials: DQ
authors.lastname: Wu
authors.affiliation: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China. wkhuang2002@163.com.
authors.forename: Wen-Kun
authors.initials: WK
authors.lastname: Huang
authors.affiliation: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China. hpeng83@126.com.
authors.forename: Huan
authors.initials: H
authors.lastname: Peng
authors.affiliation: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China. jksgo@126.com.
authors.forename: Gao-Feng
authors.initials: GF
authors.lastname: Wang
authors.affiliation: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China. jk_cui@163.com.
authors.forename: Jiang-Kuan
authors.initials: JK
authors.lastname: Cui
authors.affiliation: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China. smliuhn@yahoo.com.
authors.forename: Shi-Ming
authors.initials: SM
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Plant Pathology, China Agricultural University, Beijing, 100193, China. lzg0063@126.com.
authors.forename: Zhi-Gang
authors.initials: ZG
authors.lastname: Li
authors.affiliation: State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Plant Pathology, China Agricultural University, Beijing, 100193, China. yangj@cau.edu.cn.
authors.forename: Jun
authors.initials: J
authors.lastname: Yang
authors.affiliation: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China. pengdeliang@caas.cn.
authors.forename: De-Liang
authors.initials: DL
authors.lastname: Peng
mesh_terms: D000818:Animals; D060467:Disease Resistance / Q000235:genetics*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D058977:Molecular Sequence Annotation; D010935:Plant Diseases / Q000235:genetics* / Q000469:parasitology; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000235:genetics*; D014908:Triticum / Q000235:genetics* / Q000469:parasitology; D014431:Tylenchoidea / Q000472:pathogenicity