Identification of candidate genes for fusarium yellows resistance in Chinese cabbage by differential expression analysis

Shimizu, Mitsuru; Fujimoto, Ryo; Ying, Hua; Pu, Zi-jing; Ebe, Yusuke; Kawanabe, Takahiro; Saeki, Natsumi; Taylor, Jennifer; Kaji, Makoto; Dennis, Elizabeth S.; Okazaki, Keiichi

doi:10.1007/s11103-014-0182-0

Cited by 56 publications

(63 citation statements)

References 46 publications

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“…To identify genomic regions with the active histone marks H3K4me3 or H3K36me3 in B. rapa, we selected five genes with a high expression level using previous RNA-seq data (Shimizu et al, 2014). All five genes showed enrichment of H3K4me3, while two out of the five genes showed enrichment of H3K36me3.…”

Section: Discussionmentioning

confidence: 99%

“…Plant materials and growth conditions Previously, we developed the RJKB series of Chinese cabbage inbred lines (Shimizu et al, 2014). In this study, two of these inbred lines, RJKB-T23 and RJKB-T24, were used as plant material.…”

Section: Methodsmentioning

confidence: 99%

“…We previously examined the transcriptome of 14-day-old 1 st and 2 nd leaves of the Chinese cabbage inbred line RJKB-T24 (Shimizu et al, 2014). Of 41,029 genes, 13,283 (32.4%) did not have any mapped reads; these were categorized as Group-0 (Fig.…”

Section: Classification Of Expression Levels By Rna Sequencing Analysismentioning

confidence: 99%

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Development of primer sets that can verify the enrichment of histone modifications, and their application to examining vernalization-mediated chromatin changes in <i>Brassica rapa</i> L.

et al. 2016

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Epigenetic regulation is crucial for the development of plants and for adaptation to a changing environment. Recently, genome-wide profiles of histone modifications have been determined by a combination of chromatin immunoprecipitation (ChIP) and genomic tiling arrays (ChIP on chip) or ChIP and high-throughput sequencing (ChIP-seq) in species including Arabidopsis thaliana, rice and maize. Validation of ChIP analysis by PCR or qPCR using positive and negative regions of histone modification is necessary. In contrast, information about histone modifications is limited in Chinese cabbage, Brassica rapa. The aim of this study was to develop positive and negative control primer sets for H3K4me3 (trimethylation of the 4 th lysine of H3), H3K9me2, H3K27me3 and H3K36me3 in B. rapa. The expression and histone modification of four FLC paralogs in B. rapa, before and after vernalization, were examined using the method developed here. After vernalization, expression of all four BrFLC genes was reduced, and accumulation of H3K27me3 was observed in three of them. As with A. thaliana, the vernalization response and stability of FLC repression correlated with the accumulation of H3K27me3. These results suggest that the epigenetic state during vernalization is important for high bolting resistance in B. rapa. The positive and negative control primer sets developed here revealed positive and negative histone modifications in B. rapa that can be used as a control for future studies.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Development of primer sets that can verify the enrichment of histone modifications, and their application to examining vernalization-mediated chromatin changes in <i>Brassica rapa</i> L.

et al. 2016

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“…Hypergeometric test (Shimizu et al 2014) with Bonferroni correction (Simes 1986) was applied for selecting these statistically significant terms. In search of comparatively smaller and functionally important gene modules, Markov cluster (MCL) (Van Dongen 2008) algorithm, a systematic graph clustering method, was used to fragmentize the network.…”

Section: Enrichment Analysis and Module Detectionmentioning

confidence: 99%

Computational Analysis of “-omics” Data to Identify Transcription Factors Regulating Secondary Metabolism in Rauvolfia serpentina

Pathania

Acharya

2015

Plant Mol Biol Rep

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Rauvolfia serpentina has been known to produce therapeutically important indole alkaloids used in treatment of various diseases. Despite its medicinal importance, complete understanding of its secondary metabolism is challenging due to complex interplay among various transcription factors (TFs) and genes. However, weighted co-expression analysis of transcriptome along with integration of metabolomics data has proficiency to elucidate topological properties of complex regulatory interactions in secondary metabolism. We aimed to implement an integrative strategy using B-omicsd ata to identify TFs of Bunknown function^and exemplify their role in regulation of valuable metabolites as well as metabolic traits. A total of 69 TFs were identified through significant thresholds and removal of false positives based on cisregulatory motif analysis. Network-biology inspired analysis of co-expression network lead to generation of four statistically significant and biologically robust modules. Similar to known regulatory roles of WRKY and AP2-EREBP TF families in Catharanthus roseus, this study presented them to regulate synthesis of alkaloids in R. serpentina as well.Moreover, TFs in module 4 were observed to be regulating connecting steps between primary and secondary metabolic pathways in the synthesis of terpenoid indole alkaloids. Integration of metabolomics data further highlight the significance of module 1 since it was statistically predicted to be involved in synthesis of specialized metabolites, and associated genes may physically clustered on genome. Importantly, putative TFs in module 1 may modulate the major indole alkaloids synthesis in response to various environmental stimuli. The methodology implemented herein may provide a better reference to identify and explore functions of transcriptional regulators.

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“…Additionally, using doubled haploid (DH) and F 2 cabbage populations, Lv et al (2014a) fine-mapped a CFW resistance gene on an 84-kb interval, and identified a toll/interleukin-1 receptor-nucleotide biding site-leucine rich repeat (TIR–NBS–LRR) like gene (i.e., FOC1 ) as the candidate gene. Moreover, Shimizu et al (2014a,b) determined that FocBo1 may be responsible for CFW resistance in broccoli. These studies have facilitated other investigations into the molecular mechanisms regulating CFW resistance, and have accelerated the breeding of CFW-resistant cabbage varieties using MAS.…”

Section: Introductionmentioning

confidence: 99%

Rapid Introgression of the Fusarium Wilt Resistance Gene into an Elite Cabbage Line through the Combined Application of a Microspore Culture, Genome Background Analysis, and Disease Resistance-Specific Marker Assisted Foreground Selection

et al. 2017

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Cabbage is an economically important vegetable worldwide. Cabbage Fusarium Wilt (CFW) is a destructive disease that results in considerable yield and quality losses in cole crops. The use of CFW-resistant varieties is the most effective strategy to mitigate the effects of CFW. 01-20 is an elite cabbage line with desirable traits and a high combining ability, but it is highly susceptible to CFW. To rapidly transfer a CFW resistance gene into 01-20 plants, we used microspore cultures to develop 230 doubled haploid (DH) lines from a cross between 01-20 (highly susceptible) and 96-100 (highly resistant). One of the generated DH lines (i.e., D134) was highly resistant to CFW and exhibited a phenotypic performance that was similar to that of line 01-20. Therefore, D134 was applied as the resistance donor parent. We generated 24 insertion–deletion markers using whole genome resequencing data for lines 01-20 and 96-100 to analyze the genomic backgrounds of backcross (BC) progenies. Based on the CFW resistance gene FOC1, a simple sequence repeat (SSR) marker (i.e., Frg13) was developed for foreground selections. We screened 240 BC1 individuals and 280 BC2 individuals with these markers and assessed their phenotypic performance. The proportion of recurrent parent genome (PRPG) of the best individuals in BC1 and BC2 were 95.8 and 99.1%. Finally, a best individual designated as YR01-20 was identified from 80 BC2F1 individuals, with homozygous FOC1 allele and genomic background and phenotype almost the same as those of 01-20. Our results may provide a rapid and efficient way of improving elite lines through the combined application of microspore culture, whole-genome background analysis, and disease resistance-specific marker selection. Additionally, the cabbage lines developed in this study represent elite materials useful for the breeding of new CFW-resistant cabbage varieties.

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Identification of candidate genes for fusarium yellows resistance in Chinese cabbage by differential expression analysis

Cited by 56 publications

References 46 publications

Development of primer sets that can verify the enrichment of histone modifications, and their application to examining vernalization-mediated chromatin changes in <i>Brassica rapa</i> L.

Development of primer sets that can verify the enrichment of histone modifications, and their application to examining vernalization-mediated chromatin changes in <i>Brassica rapa</i> L.

Computational Analysis of “-omics” Data to Identify Transcription Factors Regulating Secondary Metabolism in Rauvolfia serpentina

Rapid Introgression of the Fusarium Wilt Resistance Gene into an Elite Cabbage Line through the Combined Application of a Microspore Culture, Genome Background Analysis, and Disease Resistance-Specific Marker Assisted Foreground Selection

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