title: Expression patterns, molecular markers and genetic diversity of insect-susceptible and resistant Barbarea genotypes by comparative transcriptome analysis.
abstract: BACKGROUND
  Barbarea vulgaris contains two genotypes: the glabrous type (G-type), which confers resistance to the diamondback moth (DBM) and other insect pests, and the pubescent type (P-type), which is susceptible to the DBM. Herein, the transcriptomes of P-type B. vulgaris before and after DBM infestation were subjected to Illumina (Solexa) pyrosequencing and comparative analysis.
  
  
  RESULTS
  5.0 gigabase pairs of clean nucleotides were generated. Non-redundant unigenes (33,721) were assembled and 94.1 % of them were annotated. Compared with our previous G-type transcriptome, the expression patterns of many insect responsive genes, including those related to secondary metabolism, phytohormones and transcription factors, which were significantly induced by DBM in G-type plants, were less sensitive to DBM infestation in P-type plants. The genes of the triterpenoid saponin pathway were identified in both G- and P-type plants. The upstream genes of the pathway showed similar expression patterns between the two genotypes. However, gene expression for two downstream enzymes, the glucosyl transferase (UGT73C11) and an oxidosqualene cyclase (OSC), were significantly upregulated in the P-type compared with the G-type plant. The homologous genes from P- and G-type plants were detected by BLAST unigenes with a cutoff level E-value < e(-10). 12,980 gene families containing 26,793 P-type and 36,944 G-type unigenes were shared by the two types of B. vulgaris. 38,397 single nucleotide polymorphisms (SNPs) were found in 9,452 orthologous genes between the P- and G-type plants. We also detected 5,105 simple sequence repeats (SSRs) in the B. vulgaris transcriptome, comprising mono-nucleotide-repeats (2,477; 48.5 %) and triple-nucleotide-repeats (1,590; 31.1 %). Of these, 1,657 SSRs displayed polymorphisms between the P- and G-type. Consequently, 913 SSR primer pairs were designed with a resolution of more than two nucleotides. We randomly chose 30 SSRs to detect the genetic diversity of 32 Barbarea germplasms. The distance tree showed that these accessions were clearly divided into groups, with the G-type grouping with available Western and Central European B. vulgaris accessions in contrast to the P-type accession, B. stricta and B. verna.
  
  
  CONCLUSIONS
  These data represent useful information for pest-resistance gene mining and for the investigation of the molecular basis of plant-pest interactions.
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China. zhangxiaohui01@caas.cn.
authors.forename: Xiaohui
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China. tongjinliu@163.com.
authors.forename: Tongjin
authors.initials: T
authors.lastname: Liu
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China. jweixiaochun@126.com.|Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China. jweixiaochun@126.com.
authors.forename: Xiaochun
authors.initials: X
authors.lastname: Wei
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China. qiuyang@caas.cn.
authors.forename: Yang
authors.initials: Y
authors.lastname: Qiu
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China. songjiangping@caas.cn.
authors.forename: Jiangping
authors.initials: J
authors.lastname: Song
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China. wanghaiping@caas.cn.
authors.forename: Haiping
authors.initials: H
authors.lastname: Wang
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China. shendi@caas.cn.
authors.forename: Di
authors.initials: D
authors.lastname: Shen
authors.affiliation: Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark. nia@plen.ku.dk.
authors.forename: Niels
authors.initials: N
authors.lastname: Agerbirk
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China. lixixiang@caas.cn.
authors.forename: Xixiang
authors.initials: X
authors.lastname: Li
mesh_terms: D000818:Animals; D031216:Barbarea / Q000145:classification* / Q000235:genetics* / Q000469:parasitology; D060467:Disease Resistance; D020869:Gene Expression Profiling / Q000379:methods*; D018506:Gene Expression Regulation, Plant; D014644:Genetic Variation; D059014:High-Throughput Nucleotide Sequencing; D018895:Microsatellite Repeats; D009036:Moths / Q000469:parasitology*; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*; D017423:Sequence Analysis, RNA
chemical_list: D010940:Plant Proteins