Chromosomal and Gene Expression Changes in<i>Brassica</i>Allopolyploids

Jenczewski, Eric; Chèvre, Anne‐Marie; Alix, Karine

doi:10.1002/9781118552872.ch10

Cited by 15 publications

(14 citation statements)

References 88 publications

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“…In the Brassicaceae, the relationships of three diploid species ( B. rapa , AA, 2 n = 20; B. nigra , BB, 2 n = 16; and B. oleracea , CC, 2 n = 18) and three amphidiploid plants ( B. juncea ; AABB, 2 n = 36; B. napus , AACC, 2 n = 38; and Brassica carinata , BBCC, 2 n = 34) have been thoroughly described according to the “triangle of U” theory [ 26 , 27 ], which also provides an excellent evolutionary model to investigate the expansion of gene families [ 28 , 29 ]. During the course of evolution, the Brassicaceae have experienced ɑ and β duplication events, as well as a triplication event specific to the Brassica clade compared with the model plant A. thaliana [ 30 ]. These whole-genome duplication (WGD) events, along with the merger of the two progenitor genomes, have resulted in copious gene duplication in the B. napus genome, followed by substantial gene loss [ 31 ].…”

Section: Introductionmentioning

confidence: 99%

A Genome-Wide Survey of MATE Transporters in Brassicaceae and Unveiling Their Expression Profiles under Abiotic Stress in Rapeseed

Qiao

Yang

Wan

et al. 2020

Plants

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The multidrug and toxic compound extrusion (MATE) protein family is important in the export of toxins and other substrates, but detailed information on this family in the Brassicaceae has not yet been reported compared to Arabidopsis thaliana. In this study, we identified 57, 124, 81, 85, 130, and 79 MATE genes in A. thaliana, Brassica napus, Brassica oleracea, Brassica rapa, Brassica juncea, and Brassica nigra, respectively, which were unevenly distributed on chromosomes owing to both tandem and segmental duplication events. Phylogenetic analysis showed that these genes could be classified into four subgroups, shared high similarity and conservation within each group, and have evolved mainly through purifying selection. Furthermore, numerous B. napusMATE genes showed differential expression between tissues and developmental stages and between plants treated with heavy metals or hormones and untreated control plants. This differential expression was especially pronounced for the Group 2 and 3 BnaMATE genes, indicating that they may play important roles in stress tolerance and hormone induction. Our results provide a valuable foundation for the functional dissection of the different BnaMATE homologs in B. napus and its parental lines, as well as for the breeding of more stress-tolerant B. napus genotypes.

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Section: Introductionmentioning

confidence: 99%

A Genome-Wide Survey of MATE Transporters in Brassicaceae and Unveiling Their Expression Profiles under Abiotic Stress in Rapeseed

Qiao

Yang

Wan

et al. 2020

Plants

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“…Brassica napus (AACC, 2 n = 38), one of the most important oilseed crops worldwide, originated from hybridization between Brassica rapa (AA, 2 n = 20) and Brassica oleracea (CC, 2 n = 18), which have a common ancestor [ 25 ]. At the most recent, moreover, they have experienced α and β duplication events, and then they have two triplication events during the specific to Brassica clade during the evolutionary process [ 26 ]. For these whole-genome duplication (WGD) events, along with the merger of the two progenitor genomes, have resulted in a large number of gene duplications in the B .…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Structural Analysis of bZIP Transcription Factor Genes in Brassica napus

Zhou

Jia

et al. 2017

Genes

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The basic region/leucine zipper motif (bZIP) transcription factor family is one of the largest families of transcriptional regulators in plants. bZIP genes have been systematically characterized in some plants, but not in rapeseed (Brassica napus). In this study, we identified 247 BnbZIP genes in the rapeseed genome, which we classified into 10 subfamilies based on phylogenetic analysis of their deduced protein sequences. The BnbZIP genes were grouped into functional clades with Arabidopsis genes with similar putative functions, indicating functional conservation. Genome mapping analysis revealed that the BnbZIPs are distributed unevenly across all 19 chromosomes, and that some of these genes arose through whole-genome duplication and dispersed duplication events. All expression profiles of 247 bZIP genes were extracted from RNA-sequencing data obtained from 17 different B. napus ZS11 tissues with 42 various developmental stages. These genes exhibited different expression patterns in various tissues, revealing that these genes are differentially regulated. Our results provide a valuable foundation for functional dissection of the different BnbZIP homologs in B. napus and its parental lines and for molecular breeding studies of bZIP genes in B. napus.

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“…Indeed, B. napus (2n = 4x = 38, genome AACC) is an allotetraploid species formed from the hybridization between Brassica rapa (2n = 2x = 20, A genome) and Brassica oleracea (2n = 2x = 18, C genome) (U, 1935 ). Brassica ancestors have undergone two duplication events (named α and β) and two triplication events of which the most recent is specific to the Brassica clade (Jenczewski et al, 2013 ). These WGD events, along with the merger of the two progenitor genomes, have resulted in a large number of duplicated regions in the B. napus genome.…”

Section: Introductionmentioning

confidence: 99%

Comparative genomic analysis of duplicated homoeologous regions involved in the resistance of Brassica napus to stem canker

et al. 2015

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All crop species are current or ancient polyploids. Following whole genome duplication, structural and functional modifications result in differential gene content or regulation in the duplicated regions, which can play a fundamental role in the diversification of genes underlying complex traits. We have investigated this issue in Brassica napus, a species with a highly duplicated genome, with the aim of studying the structural and functional organization of duplicated regions involved in quantitative resistance to stem canker, a disease caused by the fungal pathogen Leptosphaeria maculans. Genome-wide association analysis on two oilseed rape panels confirmed that duplicated regions of ancestral blocks E, J, R, U, and W were involved in resistance to stem canker. The structural analysis of the duplicated genomic regions showed a higher gene density on the A genome than on the C genome and a better collinearity between homoeologous regions than paralogous regions, as overall in the whole B. napus genome. The three ancestral sub-genomes were involved in the resistance to stem canker and the fractionation profile of the duplicated regions corresponded to what was expected from results on the B. napus progenitors. About 60% of the genes identified in these duplicated regions were single-copy genes while less than 5% were retained in all the duplicated copies of a given ancestral block. Genes retained in several copies were mainly involved in response to stress, signaling, or transcription regulation. Genes with resistance-associated markers were mainly retained in more than two copies. These results suggested that some genes underlying quantitative resistance to stem canker might be duplicated genes. Genes with a hydrolase activity that were retained in one copy or R-like genes might also account for resistance in some regions. Further analyses need to be conducted to indicate to what extent duplicated genes contribute to the expression of the resistance phenotype.

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Chromosomal and Gene Expression Changes inBrassicaAllopolyploids

Cited by 15 publications

References 88 publications

A Genome-Wide Survey of MATE Transporters in Brassicaceae and Unveiling Their Expression Profiles under Abiotic Stress in Rapeseed

A Genome-Wide Survey of MATE Transporters in Brassicaceae and Unveiling Their Expression Profiles under Abiotic Stress in Rapeseed

Genome-Wide Identification and Structural Analysis of bZIP Transcription Factor Genes in Brassica napus

Comparative genomic analysis of duplicated homoeologous regions involved in the resistance of Brassica napus to stem canker

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