Regulatory Network of Secondary Metabolism in Brassica rapa: Insight into the Glucosinolate Pathway

Carpio, Dunia Pino Del; Basnet, Ram Kumar; Arends, Danny; Lin, Keqin; Vos, Ric C. H. de; Muth, Dorota; Kodde, Jan; Boutilier, Kim; Bucher, Johan; Wang, Xiaowu; Jansen, Ritsert C.; Bonnema, Guusje

doi:10.1371/journal.pone.0107123

Cited by 23 publications

(11 citation statements)

References 57 publications

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“…The GSL metabolic pathway has been extensively investigated in Arabidopsis and has been well studied in B. rapa , broccoli, radish, etc. by genome wide homologous analysis (Wittstock and Halkier, 2002 ; Zang et al, 2009 ; Wang et al, 2011 ; Liu et al, 2014 ; Pino Del Carpio et al, 2014 ; Wiesner et al, 2014 ; Mitsui et al, 2015 ). In S. alba , many GSLs have been identified (Agerbirk et al, 2008 ; Popova and Morra, 2014 ; Vastenhout et al, 2014 ), and many studies on the functions of GSLs have been reported (Abdull Razis et al, 2012 ; Peng et al, 2014 ).…”

Section: Introductionmentioning

confidence: 99%

De novo Transcriptome Analysis of Sinapis alba in Revealing the Glucosinolate and Phytochelatin Pathways

et al. 2016

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Sinapis alba is an important condiment crop and can also be used as a phytoremediation plant. Though it has important economic and agronomic values, sequence data, and the genetic tools are still rare in this plant. In the present study, a de novo transcriptome based on the transcriptions of leaves, stems, and roots was assembled for S. alba for the first time. The transcriptome contains 47,972 unigenes with a mean length of 1185 nt and an N50 of 1672 nt. Among these unigenes, 46,535 (97%) unigenes were annotated by at least one of the following databases: NCBI non-redundant (Nr), Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, Gene Ontology (GO), and Clusters of Orthologous Groups of proteins (COGs). The tissue expression pattern profiles revealed that 3489, 1361, and 8482 unigenes were predominantly expressed in the leaves, stems, and roots of S. alba, respectively. Genes predominantly expressed in the leaf were enriched in photosynthesis- and carbon fixation-related pathways. Genes predominantly expressed in the stem were enriched in not only pathways related to sugar, ether lipid, and amino acid metabolisms but also plant hormone signal transduction and circadian rhythm pathways, while the root-dominant genes were enriched in pathways related to lignin and cellulose syntheses, involved in plant-pathogen interactions, and potentially responsible for heavy metal chelating, and detoxification. Based on this transcriptome, 14,727 simple sequence repeats (SSRs) were identified, and 12,830 pairs of primers were developed for 2522 SSR-containing unigenes. Additionally, the glucosinolate (GSL) and phytochelatin metabolic pathways, which give the characteristic flavor and the heavy metal tolerance of this plant, were intensively analyzed. The genes of aliphatic GSLs pathway were predominantly expressed in roots. The absence of aliphatic GSLs in leaf tissues was due to the shutdown of BCAT4, MAM1, and CYP79F1 expressions. Glutathione was extensively converted into phytochelatin in roots, but it was actively converted to the oxidized form in leaves, indicating the different mechanisms in the two tissues. This transcriptome will not only benefit basic research and molecular breeding of S. alba but also be useful for the molecular-assisted transfer of beneficial traits to other crops.

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Section: Introductionmentioning

confidence: 99%

De novo Transcriptome Analysis of Sinapis alba in Revealing the Glucosinolate and Phytochelatin Pathways

et al. 2016

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“…Cabbage ( Brassica oleracea L.) plants represent one of the major vegetable crops grown worldwide. Most crops of B. oleracea and its sister species Brassica rapa produce a range of phytochemicals with diverse functions for plant defense such as polyphenolic compounds, carotenoids, and glucosinolates [ 1 , 2 ]. The draft genome sequences of B. oleracea (with the CC genome) and B. rapa (with the AA genome) were recently published [ 3 , 4 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Characterization of bZIP Transcription Factors inBrassica oleraceaunder Cold Stress

Hwang

Manoharan

Kang

et al. 2016

BioMed Research International

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Cabbages (Brassica oleracea L.) are an important vegetable crop around world, and cold temperature is among the most significant abiotic stresses causing agricultural losses, especially in cabbage crops. Plant bZIP transcription factors play diverse roles in biotic/abiotic stress responses. In this study, 119 putative BolbZIP transcription factors were identified using amino acid sequences from several bZIP domain consensus sequences. The BolbZIP members were classified into 63 categories based on amino acid sequence similarity and were also compared with BrbZIP and AtbZIP transcription factors. Based on this BolbZIP identification and classification, cold stress-responsive BolbZIP genes were screened in inbred lines, BN106 and BN107, using RNA sequencing data and qRT-PCR. The expression level of the 3 genes, Bol008071, Bol033132, and Bol042729, was significantly increased in BN107 under cold conditions and was unchanged in BN106. The upregulation of these genes in BN107, a cold-susceptible inbred line, suggests that they might be significant components in the cold response. Among three identified genes, Bol033132 has 97% sequence similarity to Bra020735, which was identified in a screen for cold-related genes in B. rapa and a protein containing N-rich regions in LCRs. The results obtained in this study provide valuable information for understanding the potential function of BolbZIP transcription factors in cold stress responses.

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“…Therefore, this approach not only detects the expression of a specific gene and the genotype at that gene's locus, but it also reveals clustered trans -eQTLs that are simultaneously regulated by a large fraction of the transcriptome (Brem et al, 2002; Schadt et al, 2003; Morley et al, 2004). This approach has been successfully used in crop plants to detect transcript-level variation and downstream phenotypic trait variation (Jordan et al, 2007; Shi et al, 2007; West et al, 2007; Potokina et al, 2008; Xiao et al, 2013, 2014; Del Carpio et al, 2014; Basnet et al, 2015, 2016). Although eQTLs have successfully been cloned in plants (Werner et al, 2005; Zhang et al, 2006), global eQTL analysis in a large mapping population of plants has not hitherto been performed.…”

Section: Introductionmentioning

confidence: 99%

Molecular Mapping and QTL for Expression Profiles of Flavonoid Genes in Brassica napus

Zhao

et al. 2016

Front. Plant Sci.

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Flavonoids are secondary metabolites that are extensively distributed in the plant kingdom and contribute to seed coat color formation in rapeseed. To decipher the genetic networks underlying flavonoid biosynthesis in rapeseed, we constructed a high-density genetic linkage map with 1089 polymorphic loci (including 464 SSR loci, 97 RAPD loci, 451 SRAP loci, and 75 IBP loci) using recombinant inbred lines (RILs). The map consists of 19 linkage groups and covers 2775 cM of the B. napus genome with an average distance of 2.54 cM between adjacent markers. We then performed expression quantitative trait locus (eQTL) analysis to detect transcript-level variation of 18 flavonoid biosynthesis pathway genes in the seeds of the 94 RILs. In total, 72 eQTLs were detected and found to be distributed among 15 different linkage groups that account for 4.11% to 52.70% of the phenotypic variance atrributed to each eQTL. Using a genetical genomics approach, four eQTL hotspots together harboring 28 eQTLs associated with 18 genes were found on chromosomes A03, A09, and C08 and had high levels of synteny with genome sequences of A. thaliana and Brassica species. Associated with the trans-eQTL hotspots on chromosomes A03, A09, and C08 were 5, 17, and 1 genes encoding transcription factors, suggesting that these genes have essential roles in the flavonoid biosynthesis pathway. Importantly, bZIP25, which is expressed specifically in seeds, MYC1, which controls flavonoid biosynthesis, and the R2R3-type gene MYB51, which is involved in the synthesis of secondary metabolites, were associated with the eQTL hotspots, and these genes might thus be involved in different flavonoid biosynthesis pathways in rapeseed. Hence, further studies of the functions of these genes will provide insight into the regulatory mechanism underlying flavonoid biosynthesis, and lay the foundation for elaborating the molecular mechanism of seed coat color formation in B. napus.

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Regulatory Network of Secondary Metabolism in Brassica rapa: Insight into the Glucosinolate Pathway

Cited by 23 publications

References 57 publications

De novo Transcriptome Analysis of Sinapis alba in Revealing the Glucosinolate and Phytochelatin Pathways

De novo Transcriptome Analysis of Sinapis alba in Revealing the Glucosinolate and Phytochelatin Pathways

Genome-Wide Identification and Characterization of bZIP Transcription Factors inBrassica oleraceaunder Cold Stress

Molecular Mapping and QTL for Expression Profiles of Flavonoid Genes in Brassica napus

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