Limits...
Expression patterns, molecular markers and genetic diversity of insect-susceptible and resistant Barbarea genotypes by comparative transcriptome analysis.

Zhang X, Liu T, Wei X, Qiu Y, Song J, Wang H, Shen D, Agerbirk N, Li X - BMC Genomics (2015)

Bottom Line: 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.These data represent useful information for pest-resistance gene mining and for the investigation of the molecular basis of plant-pest interactions.

View Article: PubMed Central - PubMed

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.

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.

No MeSH data available.


Related in: MedlinePlus

Bootstrapped unweighted pair-group method with arithmetic means (UPGMA) tree of Barbarea species. The P-type and G-type used for transcriptomics were compared to 30 seed bank accessions from four Barbarea species. The numbers on the branches indicate bootstraps
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4487577&req=5

Fig5: Bootstrapped unweighted pair-group method with arithmetic means (UPGMA) tree of Barbarea species. The P-type and G-type used for transcriptomics were compared to 30 seed bank accessions from four Barbarea species. The numbers on the branches indicate bootstraps

Mentions: To test the utility of the SSRs produced in this study, 30 randomly chosen SSRs were used to investigate the genetic diversity of germplasms from the Barbarea genus. Thirty accessions assigned by the supplying seedbank to four species (B. intermedia, B. stricta, B. verna, and B. vulgaris) and derived from seven countries (Austria, Belgium, Germany, Ireland, Norway, Poland and Spain) were analyzed in addition to the two G- and P-type accessions used for transcriptomics (Additional file 1: Table S14). On PCR, 99.7 % of the primer pairs produced clear peaks on electrophoresis and generated 957 data points. The three (0.31 %) low-quality reactions were treated as missing values in the analyses. The 30 SSR markers generated 92 alleles in the population. Among these, 88 alleles displayed a frequency of more than 5 % in the total sample. Rare alleles could have been missed because of the small sample size. The summary statistics of the SSRs are shown in Table 6. The unweighted pair-group method with arithmetic means (UPGMA) tree was generated using the SSR data. Based on the tree topology, the germplasms could be clearly divided into 4 groups and the P-type alone (Fig. 5). The G-type and P-type accessions from this and a previous [29] transcriptomics study were widely separated as a logical consequence of their polymorphism for all markers used. The B. verna and B. stricta accessions were also separated onto different branches of the tree. Interestingly, the P-type from transcriptomics did not group with any other tested accession, while the G-type from transcriptomics grouped with all the remaining seed bank accessions of B. vulgaris, including twenty-two Western and Central European B. vulgaris accessions. All seed bank B. vulgaris accessions were also found to be resistant to the DBM. Some substructure was evident in the B. vulgaris group, including a distinct group of three accessions (4, 8, 27). However, the seed-bank assigned B. intermedia accessions were completely embedded in the G-type-like B. vulgaris germplasms. Morphological inspection of the two seed bank assigned B. intermedia accessions (as both rosette plants and flowering plants) revealed only modest morphological difference from B. vulgaris (shape of the top few leaves on the scapes) and both B. intermedia accessions showed full DBM resistance (as for the G-type).Table 6


Expression patterns, molecular markers and genetic diversity of insect-susceptible and resistant Barbarea genotypes by comparative transcriptome analysis.

Zhang X, Liu T, Wei X, Qiu Y, Song J, Wang H, Shen D, Agerbirk N, Li X - BMC Genomics (2015)

Bootstrapped unweighted pair-group method with arithmetic means (UPGMA) tree of Barbarea species. The P-type and G-type used for transcriptomics were compared to 30 seed bank accessions from four Barbarea species. The numbers on the branches indicate bootstraps
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4487577&req=5

Fig5: Bootstrapped unweighted pair-group method with arithmetic means (UPGMA) tree of Barbarea species. The P-type and G-type used for transcriptomics were compared to 30 seed bank accessions from four Barbarea species. The numbers on the branches indicate bootstraps
Mentions: To test the utility of the SSRs produced in this study, 30 randomly chosen SSRs were used to investigate the genetic diversity of germplasms from the Barbarea genus. Thirty accessions assigned by the supplying seedbank to four species (B. intermedia, B. stricta, B. verna, and B. vulgaris) and derived from seven countries (Austria, Belgium, Germany, Ireland, Norway, Poland and Spain) were analyzed in addition to the two G- and P-type accessions used for transcriptomics (Additional file 1: Table S14). On PCR, 99.7 % of the primer pairs produced clear peaks on electrophoresis and generated 957 data points. The three (0.31 %) low-quality reactions were treated as missing values in the analyses. The 30 SSR markers generated 92 alleles in the population. Among these, 88 alleles displayed a frequency of more than 5 % in the total sample. Rare alleles could have been missed because of the small sample size. The summary statistics of the SSRs are shown in Table 6. The unweighted pair-group method with arithmetic means (UPGMA) tree was generated using the SSR data. Based on the tree topology, the germplasms could be clearly divided into 4 groups and the P-type alone (Fig. 5). The G-type and P-type accessions from this and a previous [29] transcriptomics study were widely separated as a logical consequence of their polymorphism for all markers used. The B. verna and B. stricta accessions were also separated onto different branches of the tree. Interestingly, the P-type from transcriptomics did not group with any other tested accession, while the G-type from transcriptomics grouped with all the remaining seed bank accessions of B. vulgaris, including twenty-two Western and Central European B. vulgaris accessions. All seed bank B. vulgaris accessions were also found to be resistant to the DBM. Some substructure was evident in the B. vulgaris group, including a distinct group of three accessions (4, 8, 27). However, the seed-bank assigned B. intermedia accessions were completely embedded in the G-type-like B. vulgaris germplasms. Morphological inspection of the two seed bank assigned B. intermedia accessions (as both rosette plants and flowering plants) revealed only modest morphological difference from B. vulgaris (shape of the top few leaves on the scapes) and both B. intermedia accessions showed full DBM resistance (as for the G-type).Table 6

Bottom Line: 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.These data represent useful information for pest-resistance gene mining and for the investigation of the molecular basis of plant-pest interactions.

View Article: PubMed Central - PubMed

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.

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.

No MeSH data available.


Related in: MedlinePlus