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Xiaowu Wang - One of the best experts on this subject based on the ideXlab platform.

  • BrFLC5: a weak regulator of flowering time in Brassica Rapa
    Theoretical and Applied Genetics, 2018
    Co-Authors: Keyun Wei, Jianli Liang, Feng Cheng, Baozhen Gao, Jiahe Liu, Xiaowu Wang
    Abstract:

    A splicing site mutation in BrFLC5, a non-syntenic paralogue of FLOWERING LOCUS C, was demonstrated to be related to flowering time variation in Brassica Rapa. Flowering time regulation in Brassica Rapa is more complex than in Arabidopsis, as there are multiple paralogues of flowering time genes in B. Rapa. Brassica Rapa contains four FLOWERING LOCUS C (FLC) genes, three of which are syntenic orthologues of AtFLC, while BrFLC5 is not. BrFLC1, BrFLC2, and BrFLC3 have been reported to be involved in flowering time regulation. However, BrFLC5 has thus far been deemed a pseudogene. We detected two alternative splicing patterns of BrFLC5 resulting from a nucleotide mutation (G/A) at the first nucleotide of intron 3 (named as Pi3+1(G/A)). Genotyping of BrFLC5Pi3 + 1(G/A) for 301 B. Rapa accessions showed that this single nucleotide polymorphism was significantly related to flowering time variation (p 

  • Research Progress on Agrobacterium tumefaciens-based Transgenic Technology in Brassica Rapa
    Horticultural Plant Journal, 2018
    Co-Authors: Lixin Yue, Xiaowu Wang, Shifan Zhang, Hui Zhang, Qian Wei, Zhiyuan Fang, Shujiang Zhang
    Abstract:

    Abstract Brassica Rapa L. is cultivated globally and consumed in many areas worldwide. Using the transgenic Agrobacterium-mediated transformation method, which is a reproducible and efficient technique, genes can be transferred into various B. Rapa species. This review summarizes the processes involved in Agrobacterium-mediated transformation of B. Rapa, including surface seed sterilization, co-cultivation with A. tumefaciens, induction of callus/shoot/root formation, and confirmation of transgenic plants. In addition, factors such as the Agrobacterium strain, plant genotype, explant age, transformation efficiency of the hybrid or inbred line, and the concentrations of N6-benzyl amino purine and naphthalene acetic acid, are discussed. And this review shows clearly how to do it, what to do, and what not to do in the transgenic Agrobacterium-mediated in Brassica Rapa. The information presented here lays the foundation for a simple and efficient method that resolves existing problems and improves overall transgenic B. Rapa production, thereby benefiting both basic and applied research.

  • Background History of the National and International Brassica Rapa Genome Sequencing Initiatives
    Compendium of Plant Genomes, 2015
    Co-Authors: Ian Bancroft, Xiaowu Wang
    Abstract:

    Whole genome sequencing of Brassica Rapa was first launched by the multinational group of Brassica Rapa Genome Sequencing Project (BrGSP). The group planned to perform the assembly using the method called “bacterial artificial chromosome (BAC) by BAC” in the initial stage. However, the progress was limited and only chromosome A03 was finished under this method. Along with the development of the second generation sequencing technology, the Chinese suggest to adopt this new sequencing method and initiative assembled the B. Rapa genome in short time by SOAP-denovo, which integrated the data of pair-ends short reads generated from the Illumina sequencing platform and the data of BAC sequences from BrGSP. This well assembled whole genome sequences of B. Rapa—verified by the comparison to the A03 assembled by BAC sequenced—was then serves as the genome reference for the evolution, gene mapping and function studies of B. Rapa.

  • anthocyanin biosynthetic genes in Brassica Rapa
    BMC Genomics, 2014
    Co-Authors: Ning Guo, Jianli Liang, Feng Cheng, Bo Liu, Shuning Zheng, Xiaowu Wang
    Abstract:

    Anthocyanins are a group of flavonoid compounds. As a group of important secondary metabolites, they perform several key biological functions in plants. Anthocyanins also play beneficial health roles as potentially protective factors against cancer and heart disease. To elucidate the anthocyanin biosynthetic pathway in Brassica Rapa, we conducted comparative genomic analyses between Arabidopsis thaliana and B. Rapa on a genome-wide level. In total, we identified 73 genes in B. Rapa as orthologs of 41 anthocyanin biosynthetic genes in A. thaliana. In B. Rapa, the anthocyanin biosynthetic genes (ABGs) have expanded and most genes exist in more than one copy. The anthocyanin biosynthetic structural genes have expanded through whole genome and tandem duplication in B. Rapa. More structural genes located upstream of the anthocyanin biosynthetic pathway have been retained than downstream. More negative regulatory genes are retained in the anthocyanin biosynthesis regulatory system of B. Rapa. These results will promote an understanding of the genetic mechanism of anthocyanin biosynthesis, as well as help the improvement of the nutritional quality of B. Rapa through the breeding of high anthocyanin content varieties.

Beom-seok Park - One of the best experts on this subject based on the ideXlab platform.

  • Mapping Quantitative Trait Loci for Tissue Culture Response in VCS3M-DH Population of Brassica Rapa
    Plant Cell Reports, 2013
    Co-Authors: Mi-suk Seo, Guusje Bonnema, Soo-jin Kwon, Beom-seok Park, Jeong-hwan Mun, Mina Jin, Soo-seong Lee, Richard G. F. Visser, Seong-han Sohn
    Abstract:

    Key message Quantitative trait loci (QTL) controlling callus induction and plant regeneration were identified in the VCS3M-DH population of Brassica Rapa.

  • The Brassica Rapa tissue-specific EST database
    Korean Journal of Horticultural Science & Technology, 2011
    Co-Authors: Sin-gi Park, Beom-seok Park, Seong-han Sohn, Hyun-ju Hwang, Namshin Kim, Hee Chung, Jeong-hwan Mun
    Abstract:

    Brassica Rapa is an A genome model species for Brassica crop genetics, genomics, and breeding. With the completion of sequencing the B. Rapa genome, functional analysis of the genome is forthcoming issue. The expressed sequence tags are fundamental resources supporting annotation and functional analysis of the genome including identification of tissue-specific genes and promoters. As of July 2011, 147,217 ESTs from 39 cDNA libraries of B. Rapa are reported in the public database. However, little information can be retrieved from the sequences due to lack of organized databases. To leverage the sequence information and to maximize the use of publicly-available EST collections, the Brassica Rapa tissue-specific EST database (BrTED) is developed. BrTED includes sequence information of 23,962 unigenes assembled by StackPack program. The unigene set is used as a query unit for various analyses such as BLAST against TAIR gene model, functional annotation using MIPS and UniProt, gene ontology analysis, and prediction of tissue-specific unigene sets based on statistics test. The database is composed of two main units, EST sequence processing and information retrieving unit and tissue-specific expression profile analysis unit. Information and data in both units are tightly inter-connected to each other using a web based browsing system. RT-PCR evaluation of 29 selected unigene sets successfully amplified amplicons from the target tissues of B. Rapa. BrTED provided here allows the user to identify and analyze the expression of genes of interest and aid efforts to interpret the B. Rapa genome through functional genomics. In addition, it can be used as a public resource in providing reference information to study the genus Brassica and other closely related crop crucifer plants.

  • Isolation and Expression Analysis of Brassica Rapa WRKY 7
    The Plant Pathology Journal, 2008
    Co-Authors: Seon-seol Kim, Ji Young Jang, Theresa Lee, Myung Ho Lim, Sang-yeol Park, Shin-chul Bae, Choong-hyo Yun, Beom-seok Park, Duk-ju Hwang
    Abstract:

    Brassica Genomics Team, National Institute of Agricultural Biotechnology (NIAB), RDA, Suwon, Korea (Received on August 11, 2008; Accepted on November 5, 2008)The cDNA clone of Brassica Rapa WRKY7 (BrWRKY7)was obtained from EST collection in Brassica genomicsteam and its DNA sequence was determined. The cDNAclone is 1,037 bp long in nucleotides and encodes anopen reading frame of 307 amino acids. Based on aphylogenetic tree, BrWRKY7 belongs to group IId.BrWRKY7 was induced by wound and SA. It was alsoinduced by pathogen attack such as Xanthomonascampestris pv. campestris (Xcc), suggesting that thisBrWRKY may play an essential role in defense responseof chinese cabbages. Keywords : Brassica Rapa, WRKY transcription factor Plants have a variety of active defense mechanisms toprotect themselves from pathogen infection. Plant defenseresponses result from the transcriptional activation of alarge number of genes upon pathogen infection or treatmentwith pathogen elicitors (Ruston and Somssich, 1998;Schreiber and Desveaux, 2008; Yang et al., 1997). MostWRKY genes are rapidly induced by pathogens, pathogenelicitors, or salicylic acid (SA) treatment in mostly Arabi-dopsis and rice (Chen and Chen, 2000; Dong et al., 2003;Eulgem et al., 1999; Ryu et al., 2006). Therefore, it hasbeen implicated that WRKY proteins are major transcrip-tional regulators in defense signaling (Chen and Chen,2000, 2002; Chen etal., 2002; Cormack et al., 2002;Deslandes et al., 2002; Du and Chen, 2000; Eulgem et al.,1999; Kim et al., 2000; Liu et al., 2005, 2006; Maleck et al.,2000; Robatzek and Somssich, 2001, 2002; Yoda et al.,2002; Yu et al., 2001). In this study, based on globalexpression profiling analysis of Brassica Rapa genes on25K cDNA oligomer chip, BrWRKY7 was isolated andcharacterized.Chinese cabbage (Brassica Rapa ssp. pekiness cv. chiibu)was grown in a greenhouse for 3 weeks. Three-week oldchinese cabbage seedlings were treated with salicylic acid(SA) at 1 mM or buffer, respectively. Chinese cabbageleaves were harvested at the times indicated in the figures.For bacterial inoculations, a compatible strain of Xcc toBrassica Rapa ssp. pekiness cv. chiibu was grown in PSA

  • Progress in understanding and sequencing the genome of Brassica Rapa.
    International Journal of Plant Genomics, 2008
    Co-Authors: Chang Pyo Hong, Soo-jin Kwon, Beom-seok Park, Jung Sun Kim, Tae-jin Yang, Yong Pyo Lim
    Abstract:

    Brassica Rapa, which is closely related to Arabidopsis thaliana, is an important crop and a model plant for studying genome evolution via polyploidization. We report the current understanding of the genome structure of B. Rapa and efforts for the whole-genome sequencing of the species. The tribe Brassicaceae, which comprises ca. 240 species, descended from a common hexaploid ancestor with a basic genome similar to that of Arabidopsis. Chromosome rearrangements, including fusions and/or fissions, resulted in the present-day “diploid” Brassica species with variation in chromosome number and phenotype. Triplicated genomic segments of B. Rapa are collinear to those of A. thaliana with InDels. The genome triplication has led to an approximately 1.7-fold increase in the B. Rapa gene number compared to that of A. thaliana. Repetitive DNA of B. Rapa has also been extensively amplified and has diverged from that of A. thaliana. For its whole-genome sequencing, the Brassica Rapa Genome Sequencing Project (BrGSP) consortium has developed suitable genomic resources and constructed genetic and physical maps. Ten chromosomes of B. Rapa are being allocated to BrGSP consortium participants, and each chromosome will be sequenced by a BAC-by-BAC approach. Genome sequencing of B. Rapa will offer a new perspective for plant biology and evolution in the context of polyploidization.

Christophe Robaglia - One of the best experts on this subject based on the ideXlab platform.

  • Transformation of Pakchoi (Brassica Rapa L. ssp. chinensis) by Agrobacterium infiltration
    Molecular Breeding, 2000
    Co-Authors: Cao Ming Qing, Liu Fan, Yao Lei, Colette Tourneur, David Bouchez, Li Yan, Christophe Robaglia
    Abstract:

    Transgenic pakchoi (Brassica Rapa L. ssp. chinensis) plants were obtained in the progeny of plants infiltrated by an Agrobacterium tumefaciens strain carrying a gene for resistance to the herbicide phosphinotricin (Basta). Genetic analysis demonstrates the transmission of the herbicide resistant trait to the progeny. Molecular analyses show that the transgene was inserted in the plant genome and expressed. This work demonstrates that the infiltration transformation method originally devised for Arabidopsis thaliana can be adapted for other crucifer species and opens up the possibility of genetic engineering of pakchoi, an important vegetable plant.

Guusje Bonnema - One of the best experts on this subject based on the ideXlab platform.

  • Genetic Dissection of Leaf Development in Brassica Rapa Using a Genetical Genomics Approach
    Plant Physiology, 2014
    Co-Authors: Dong Xiao, Huange Wang, Ram Kumar Basnet, Jianjun Zhao, Ke Lin, Xi Lin Hou, Guusje Bonnema
    Abstract:

    The paleohexaploid crop Brassica Rapa harbors an enormous reservoir of morphological variation, encompassing leafy vegetables, vegetable and fodder turnips (Brassica Rapa, ssp. campestris), and oil crops, with different crops having very different leaf morphologies. In the triplicated B. Rapa genome, many genes have multiple paralogs that may be regulated differentially and contribute to phenotypic variation. Using a genetical genomics approach, phenotypic data from a segregating doubled haploid population derived from a cross between cultivar Yellow sarson (oil type) and cultivar Pak choi (vegetable type) were used to identify loci controlling leaf development. Twenty-five colocalized phenotypic quantitative trait loci (QTLs) contributing to natural variation for leaf morphological traits, leaf number, plant architecture, and flowering time were identified. Genetic analysis showed that four colocalized phenotypic QTLs colocalized with flowering time and leaf trait candidate genes, with their cis-expression QTLs and cis- or trans-expression QTLs for homologs of genes playing a role in leaf development in Arabidopsis (Arabidopsis thaliana). The leaf gene Brassica Rapa KIP-RELATED PROTEIN2_A03 colocalized with QTLs for leaf shape and plant height; Brassica Rapa ERECTA_A09 colocalized with QTLs for leaf color and leaf shape; Brassica Rapa LONGIFOLIA1_A10 colocalized with QTLs for leaf size, leaf color, plant branching, and flowering time; while the major flowering time gene, Brassica Rapa FLOWERING LOCUS C_A02, colocalized with QTLs explaining variation in flowering time, plant architectural traits, and leaf size. Colocalization of these QTLs points to pleiotropic regulation of leaf development and plant architectural traits in B. Rapa.

  • Mapping Quantitative Trait Loci for Tissue Culture Response in VCS3M-DH Population of Brassica Rapa
    Plant Cell Reports, 2013
    Co-Authors: Mi-suk Seo, Guusje Bonnema, Soo-jin Kwon, Beom-seok Park, Jeong-hwan Mun, Mina Jin, Soo-seong Lee, Richard G. F. Visser, Seong-han Sohn
    Abstract:

    Key message Quantitative trait loci (QTL) controlling callus induction and plant regeneration were identified in the VCS3M-DH population of Brassica Rapa.

  • Genetic variation in glucosinolate content within Brassica Rapa vegetables
    Acta Horticulturae, 2012
    Co-Authors: Lou Ping, Guusje Bonnema, Matthijs Dekker, Ruud Verkerk
    Abstract:

    Glucosinolates (GSs) were analyzed in 56 accessions of Brassica Rapa grown in the greenhouse. Eight different glucosinolates were identified in the Brassica Rapa group. They are the aliphatic glucosinolates progoitrin (PRO), gluconapin (NAP), glucoBrassicanapin (GBN), the indolyl glucosinolates 4-hydroxyglucobrassicin (4OH), glucobrassicin (GBC), 4-methoxyglucobrassicin (4ME), neoglucobrassicin (NEO) and the aromatic glucosinolate gluconasturtiin (NAS). Gluconapin, glucoBrassicanapin, progoitrin and gluconasturtiin are the most abundant GSs in the Brassica Rapa, but there is considerable variation in content among accessions. The total glucosinolate contents in Brassica Rapa group varied substantially between the different accessions. The highest amount of GSs (361 µmol/100 g FW) was observed in leaves of vegetable turnip, followed by rapid cycling and yellow sarson, with the amount of 200 and 178 µmol/100 g FW respectively. Whereas the lowest GSs content was found in turnip greens (20.8 µmol/100 g FW) and Wutacai (22.6 µmol/100 g FW). The total aliphatic GSs proportion varied from 50 to 90% of the total GS, while generally the content of indolyl glucosinoloates, especially 4OH glucobrassicin and neoglucobrassicin is low. Gluconasturtiin was found in relatively high concentrations in komastsuna (14.6 µmol/100 g FW), yellow sarson (7.1 µmol/ 100 g FW) and constitutes as much as 24% of the total amount of glucosinolates. Relatively high amounts of gluconapin (281 mmol/100 g FW) and glucoBrassicanapin (60.0 mmol/100 g FW) were observed in the leaves of vegetable turnip. Compared with the Brassica oleracea group, Brassica Rapa lacks glucoraphanin and sinigrin but contains gluconapin and glucoBrassicanapin. Variations in glucosinolate content among genotypes suggest differences in their health-promoting properties and the opportunity for enhancement of their levels through breeding or genetic modification.

  • Quantitative trait loci for glucosinolate accumulation in Brassica Rapa leaves
    New Phytologist, 2008
    Co-Authors: Ping Lou, Ruud Verkerk, Jianjun Zhao, Corrie J. Hanhart, Dunia Pino Del Carpio, Jan B. M. Custers, Maarten Koornneef, Guusje Bonnema
    Abstract:

    Glucosinolates and their breakdown products have been recognized for their effects on plant defense, human health, flavor and taste of cruciferous vegetables. Despite this importance, little is known about the regulation of the biosynthesis and degradation in Brassica Rapa. Here, the identification of quantitative trait loci (QTL) for glucosinolate accumulation in B. Rapa leaves in two novel segregating double haploid (DH) populations is reported: DH38, derived from a cross between yellow sarson R500 and pak choi variety HK Naibaicai; and DH30, from a cross between yellow sarson R500 and Kairyou Hakata, a Japanese vegetable turnip variety. An integrated map of 1068 cM with 10 linkage groups, assigned to the international agreed nomenclature, is developed based on the two individual DH maps with the common parent using amplified fragment length polymorphism (AFLP) and single sequence repeat (SSR) markers. Eight different glucosinolate compounds were detected in parents and F(1)s of the DH populations and found to segregate quantitatively in the DH populations. QTL analysis identified 16 loci controlling aliphatic glucosinolate accumulation, three loci controlling total indolic glucosinolate concentration and three loci regulating aromatic glucosinolate concentrations. Both comparative genomic analyses based on Arabidopsis-Brassica Rapa synteny and mapping of candidate orthologous genes in B. Rapa allowed the selection of genes involved in the glucosinolate biosynthesis pathway that may account for the identified QTL.

Jung Sun Kim - One of the best experts on this subject based on the ideXlab platform.

  • Reduction of GIGANTEA expression in transgenic Brassica Rapa enhances salt tolerance
    Plant Cell Reports, 2016
    Co-Authors: Jin A Kim, Soo-in Lee, Joon Ki Hong, Mi Jeong Jeong, Ha-eun Jung, Victor Hermand, C. Robertson Mcclung, Yeon-hee Lee, Joo Yeol Kim, Jung Sun Kim
    Abstract:

    Here we report the enhancement of tolerance to salt stress in Brassica Rapa (Chinese cabbage) through the RNAi-mediated reduction of GIGANTEA ( GI ) expression. Circadian clocks integrate environmental signals with internal cues to coordinate diverse physiological outputs. The GIGANTEA (GI) gene was first discovered due to its important contribution to photoperiodic flowering and has since been shown to be a critical component of the plant circadian clock and to contribute to multiple environmental stress responses. We show that the GI gene in Brassica Rapa (BrGI) is similar to Arabidopsis GI in terms of both expression pattern and function. BrGI functionally rescued the late-flowering phenotype of the Arabidopsis gi-201 loss-of-function mutant. RNAi-mediated suppression of GI expression in Arabidopsis Col-0 and in the Chinese cabbage, B. Rapa DH03, increased tolerance to salt stress. Our results demonstrate that the molecular functions of GI described in Arabidopsis are conserved in B. Rapa and suggest that manipulation of gene expression through RNAi and transgenic overexpression could enhance tolerance to abiotic stresses and thus improve agricultural crop production.

  • Sequence and structure of Brassica Rapa chromosome A3
    Genome Biology, 2010
    Co-Authors: Jeong-hwan Mun, Soo-jin Kwon, Young-joo Seol, Myung Ho Lim, Jin A Kim, Mina Jin, Jung Sun Kim, Soo-in Lee, Joon Ki Hong, Tae-ho Park
    Abstract:

    Background The species Brassica Rapa includes important vegetable and oil crops. It also serves as an excellent model system to study polyploidy-related genome evolution because of its paleohexaploid ancestry and its close evolutionary relationships with Arabidopsis thaliana and other Brassica species with larger genomes. Therefore, its genome sequence will be used to accelerate both basic research on genome evolution and applied research across the cultivated Brassica species.

  • Progress in understanding and sequencing the genome of Brassica Rapa.
    International Journal of Plant Genomics, 2008
    Co-Authors: Chang Pyo Hong, Soo-jin Kwon, Beom-seok Park, Jung Sun Kim, Tae-jin Yang, Yong Pyo Lim
    Abstract:

    Brassica Rapa, which is closely related to Arabidopsis thaliana, is an important crop and a model plant for studying genome evolution via polyploidization. We report the current understanding of the genome structure of B. Rapa and efforts for the whole-genome sequencing of the species. The tribe Brassicaceae, which comprises ca. 240 species, descended from a common hexaploid ancestor with a basic genome similar to that of Arabidopsis. Chromosome rearrangements, including fusions and/or fissions, resulted in the present-day “diploid” Brassica species with variation in chromosome number and phenotype. Triplicated genomic segments of B. Rapa are collinear to those of A. thaliana with InDels. The genome triplication has led to an approximately 1.7-fold increase in the B. Rapa gene number compared to that of A. thaliana. Repetitive DNA of B. Rapa has also been extensively amplified and has diverged from that of A. thaliana. For its whole-genome sequencing, the Brassica Rapa Genome Sequencing Project (BrGSP) consortium has developed suitable genomic resources and constructed genetic and physical maps. Ten chromosomes of B. Rapa are being allocated to BrGSP consortium participants, and each chromosome will be sequenced by a BAC-by-BAC approach. Genome sequencing of B. Rapa will offer a new perspective for plant biology and evolution in the context of polyploidization.