Genome-wide characterization of the CBF/DREB1 gene family in Brassica rapa

Lee, Sang-Choon; Lim, Myung-Ho; Yu, Jae-Gyeong; Park, Beom-Seok; Yang, Tae-Jin

doi:10.1016/j.plaphy.2012.09.016

Cited by 33 publications

(29 citation statements)

References 46 publications

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“…1), as reported in other plant studies (Dietz et al 2010;Lee et al 2012). Among examined species, total AP2/EREBP gene number was not much different and also gene member number in each group was similar.…”

Section: Discussionsupporting

confidence: 81%

“…This indicated the AP2/EREBP gene family was well conserved in genomes of Cucurbitaceae species and A. thaliana. The conservation of TF genes including AP2/EREBP genes was already well demonstrated in many plant genomes, such as Chinese cabbage (Lee et al 2012) and carrot (Iorizzo et al 2016).…”

Section: Discussionmentioning

confidence: 80%

“…The DREB subfamily itself is composed of six subgroups, of which the A1 subgroup includes C-repeat/dehydration-responsive element (CRT/DRE) binding factor 1 (CBF/DREB1) genes (Dietz et al 2010;Lee et al 2012). The CBF/DREB1 genes are known to play an important role in stress response and tolerance (Lata and Prasad 2011;Lee et al 2012).…”

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Identification and Classification of the AP2/EREBP Gene Family in the Cucurbitaceae Species

Lee

Ali

et al. 2017

Plant Breed. Biotech.

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This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. ABSTRACT AP2/EREBP gene family consists of transcription factor genes with a conserved AP2 DNA-binding domain and is involved in various biological processes. AP2/EREBP gene families were identified through genome-wide searches in five Cucurbitaceae species including cucumber, wild cucumber, melon, watermelon, and bitter gourd, which consisted of more than 100 genes in each of the five species. The gene families were further divided into five groups including four subfamilies (ERF, DREB, AP2 and RAV) and a soloist group. Among the subfamilies, DREB subfamily which is known to be related to abiotic stress response was more analyzed and a total of 25 genes were identified as Cucurbitaceae homologues of Arabidopsis CBF/DREB1 genes which are important for abiotic stress-response and tolerance. In silico expression profiling using RNA-Seq data revealed diverse expression patterns of cucumber AP2/EREBP genes. AP2/EREBP gene families identified in this study will be valuable for understanding the stress response mechanism as well as facilitating molecular breeding in Cucurbitaceae crops.

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Section: Discussionsupporting

confidence: 81%

Section: Discussionmentioning

confidence: 80%

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Genome-Wide Identification and Classification of the AP2/EREBP Gene Family in the Cucurbitaceae Species

Lee

Ali

et al. 2017

Plant Breed. Biotech.

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“…rapa genes belonging to different gene families or having important biological functions have been systematically analyzed. Based on the genome sequencing and comparative genomic study of B. rapa, the evolution of many gene families or categories such as circadian clock genes, 41 resistance genes, 42 stress response genes, [43][44][45] glucosinolate genes, 38 anthocyanin biosynthesis genes, 46 phytohormone-related genes, 47 certain transcript factor families 48 and other genes, [49][50][51][52][53][54] were accurately determined individually and studied in detail. Moreover, some functionally important genes related to self-incompatibility, 55,56 male sterility, 57 flowering regulation, 58-60 leaf heading 61 or color 62 have been identified or cloned, and functional studies have been conducted for some of these genes.…”

Section: Two-step Theory To Illustrate the Wgt Process Inmentioning

confidence: 99%

Genome Triplication Drove the Diversification of Brassica Plants

Cheng¹,

Wu²,

Liang³

et al. 2015

Compendium of Plant Genomes

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The genus Brassica belongs to the plant family Brassicaceae, which includes many important crop species that are used as oilseed, condiments, or vegetables throughout the world. Brassica plants comprise many diverse species, and each species contains rich morphotypes showing extreme traits. Brassica species experienced an extra whole genome triplication (WGT) event compared with the model plant Arabidopsis thaliana. Whole genome sequencing of the Brassica species Brassica rapa, Brassica oleracea and others demonstrated that WGT plays an important role in the speciation and morphotype diversification of Brassica plants. Comparative genomic analysis based on the genome sequences of B. rapa and A. thaliana clearly identified the WGT event and further demonstrated that the translocated Proto-Calepine Karyotype (tPCK, n57) was the diploid ancestor of the three subgenomes in B. rapa. Following WGT, subsequent extensive genome fractionation, block reshuffling and chromosome reduction accompanied by paleocentromere descent from the three tPCK subgenomes during the rediploidization process produced stable diploid species. Genomic rearrangement of the diploid species and their hybridization then contributed to Brassica speciation. The subgenome dominance effect and biased gene retention, such as the over-retention of auxin-related genes after WGT, promoted functional gene evolution and thus propelled the expansion of rich morphotypes in the Brassica species. In conclusion, the WGT event initiated subsequent genomic and gene-level evolution, which further drove Brassica speciation and created rich morphotypes in each species. GENUS BRASSICA IN BRASSICACEAE Plants of the genus Brassica are grouped into the tribe Brassiceae, which belongs to the plant family Brassicaceae. Brassicaceae comprises a large family of plants that exhibit common and distinct features in their flowers. The flowers have cruciform petals and six stamens, two of which are short outer stamens. In total, Brassicaceae is composed of 3709 species and 338 genera, 1 with 308 of the 338 genera further assigned to 44 tribes.2 Among the abundant Brassicaceae species, the genus Brassica is important because it contains many economically valuable crops that are used as oilseeds, condiments, and culinary vegetables. Brassica species share an additional common feature in that they all experienced an extra whole genome triplication (WGT) event, which occurred approximately 9-15 million years ago 3,4 or even approximately 28 million years ago. 5-7THE U'S TRIANGLE MODEL DESCRIBES THE RELATIONSHIP AMONG BRASSICA CROPS Six species of the genus Brassica are used widely throughout the world as oilseed, condiments, fodder or vegetable crops. Three of these species are diploid (Brassica rapa, n510; B. nigra, n58; and B. oleracea, n59), whereas the other three are allotetraploids (B. juncea, n518; B. napus, n519; B. carinata, n517) derived from each pair of the three diploid species. The genetic relationships of these species were identified and confirmed by extensive experi...

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“…들이 활발히 진행되고 있다 (Dubouzet et al, 2003;Fowler and Thomashow, 2002;Jaglo et al, 2001;Lee et al, 2012;Qin et al, 2004;Seki et al, 2002;Yang et al, 2005;Zhang et al, 2006). 예를 들어, 벼에서는 GPAT(arabidopsis glycerol-3P-acyltransferase) (Yokoi et al, 1998), OsCDPK7(rice calciumdependent protein kinase) (Saijo et al, 2000), OsDREB1(rice DRE-binding protein 1) (Ito et al, 2006), HvCBF4(barley Crepeat binding factor) (Oh et al, 2007), OsCIPK03(rice calcineurin B-like protein-interaction protein kinase 03) (Xiang et al, 2007), 및 OsTPP1(trehalose-6-phosphate phosphatase) (Ge et al, 2008) 등이 있으며, 옥수수에서는 NPK1(nicotiana protein kinase) (Shou et al, 2004), 애기장대에서는 MYB15(MYB-like transcription factor) (Agarwal et al, 2006) 등이 대표적인 저 온 저항성 유전자들이다.…”

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confidence: 99%

Characterization of a Cold Tolerance-related Gene, BrCSR, Derived from Brassica rapa

Yu¹,

Park

2014

HST

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The objective of this study is to identify cold-tolerance genes in Brassica rapa. In order to acheive this goal, we analyzed a KBGP-24K oligo chip data [BrEMD (B. rapa EST and Microarray Database)] using B. rapa ssp. pekinensis inbred line 'Chiifu' under cold stress condition (4°C). Among 23,929 unigenes of B. rapa, 417 genes (1.7%) were primarily identified as cold responsive genes that were expressed over 5-fold higher than those of wild type control, and then a gene which has unknown function and has full length sequence was selected. It was named BrCSR (B. rapa Cold Stress Resistance). BrCSR was transformed using expression vector pSL101 to confirm whether BrCSR can enhance cold tolerance in tobacco plants. T1 transgenic tobacco plants expressing BrCSR were selected by PCR and Southern hybridization analyses, and the function of BrCSR was characterized by expression level analysis and phenotype observation under cold stress condition. The expression level of BrCSR in transgenic tobacco plants increased up to about two folds in quantitative real-time RT-PCR assay and this was very similar to Northern blot hybridization analysis. Analysis of phenotypic characteristics clearly elucidated that transgenic tobaccos expressing BrCSR were more cold tolerant than wild type control under 4°C treatment. Based on these results, we conclude that the over-expression of BrCSR might be closely related to the enhancement of cold tolerance.

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Genome-wide characterization of the CBF/DREB1 gene family in Brassica rapa

Cited by 33 publications

References 46 publications

Genome-Wide Identification and Classification of the AP2/EREBP Gene Family in the Cucurbitaceae Species

Genome-Wide Identification and Classification of the AP2/EREBP Gene Family in the Cucurbitaceae Species

Genome Triplication Drove the Diversification of Brassica Plants

Characterization of a Cold Tolerance-related Gene, BrCSR, Derived from Brassica rapa

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