AustralieFrV1, Main, Exploration, bibRecordById, PMC:4700566

Co-linearity and divergence of the A subgenome of Brassica juncea compared with other Brassica species carrying different A subgenomes

Identifieur interne : 002216 ( Main/Exploration ); précédent : 002215; suivant : 002217

Co-linearity and divergence of the A subgenome of Brassica juncea compared with other Brassica species carrying different A subgenomes

Auteurs : Jun Zou [République populaire de Chine] ; Dandan Hu [République populaire de Chine] ; Peifa Liu [République populaire de Chine] ; Harsh Raman ; Zhongsong Liu [République populaire de Chine] ; Xianjun Liu [République populaire de Chine] ; Isobel A. P. Parkin ; Boulos Chalhoub [France] ; Jinling Meng [République populaire de Chine]

Source :

BMC Genomics [ 1471-2164 ] ; 2016.

RBID : PMC:4700566

Descripteurs français

English descriptors

KwdEn :
- Arabidopsis (genetics), Brassica napus (genetics), Chromosome Mapping, Diploidy, Genetic Linkage, Genome, Plant (genetics), Genotype, Microsatellite Repeats (genetics), Mustard Plant (genetics), Quantitative Trait Loci (genetics), Sequence Analysis, DNA.
MESH :
- genetics : Arabidopsis, Brassica napus, Genome, Plant, Microsatellite Repeats, Mustard Plant, Quantitative Trait Loci.
- Chromosome Mapping, Diploidy, Genetic Linkage, Genotype, Sequence Analysis, DNA.

Abstract

Background

There are three basic Brassica genomes (A, B, and C) and three parallel sets of subgenomes distinguished in the diploid Brassica (i.e.: B. rapa, A^rA^r; B. nigra, BⁿⁱBⁿⁱ; B. oleracea, C^oC^o) and the derived allotetraploid species (i.e.: B. juncea, A^jA^jB^jB^j; B. napus, AⁿAⁿCⁿCⁿ; B. carinata, B^cB^cC^cC^c). To understand subgenome differentiation in B. juncea in comparison to other A genome-carrying Brassica species (B. rapa and B. napus), we constructed a dense genetic linkage map of B. juncea, and conducted population genetic analysis on diverse lines of the three A-genome carrying Brassica species using a genotyping-by-sequencing approach (DArT-seq).

Results

A dense genetic linkage map of B. juncea was constructed using an F₂ population derived from Sichuan Yellow/Purple Mustard. The map included 3329 DArT-seq markers on 18 linkage groups and covered 1579 cM with an average density of two markers per cM. Based on this map and the alignment of the marker sequences with the physical genome of Arabidopsis thaliana, we observed strong co-linearity of the ancestral blocks among the different A subgenomes but also considerable block variation. Comparative analyses at the level of genome sequences of B. rapa and B. napus, and marker sequence anchored on the genetic map of B. juncea, revealed a total of 30 potential inversion events across large segments and 20 potential translocation events among the three A subgenomes. Population genetic analysis on 26 accessions of the three A genome-carrying Brassica species showed that the highest genetic distance were estimated when comparing A^j-Aⁿ than between Aⁿ-A^r and A^j-A^r subgenome pairs.

Conclusions

The development of the dense genetic linkage map of B. juncea with informative DArT-seq marker sequences and availability of the reference sequences of the A^r, and AⁿCⁿ genomes allowed us to compare the A subgenome structure of B. juncea (A^j) . Our results suggest that strong co-linearity exists among the three A Brassica genomes (A^r, Aⁿ and A^j) but with apparent subgenomic variation. Population genetic analysis on three A-genome carrying Brassica species support the idea that B. juncea has distinct genomic diversity, and/or evolved from a different A genome progenitor of B. napus.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-2343-1) contains supplementary material, which is available to authorized users.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4700566

DOI: 10.1186/s12864-015-2343-1
PubMed: 26728943
PubMed Central: 4700566

Affiliations:

France, République populaire de Chine

Le document en format XML

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 species carrying different A subgenomes</title>
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 species carrying different A subgenomes</title>
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<wicri:noCountry code="subfield">NSW 2650 Australia</wicri:noCountry>
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</affiliation>
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<author><name sortKey="Meng, Jinling" sort="Meng, Jinling" uniqKey="Meng J" first="Jinling" last="Meng">Jinling Meng</name>
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<series><title level="j">BMC Genomics</title>
<idno type="eISSN">1471-2164</idno>
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<term>Brassica napus (genetics)</term>
<term>Chromosome Mapping</term>
<term>Diploidy</term>
<term>Genetic Linkage</term>
<term>Genome, Plant (genetics)</term>
<term>Genotype</term>
<term>Microsatellite Repeats (genetics)</term>
<term>Mustard Plant (genetics)</term>
<term>Quantitative Trait Loci (genetics)</term>
<term>Sequence Analysis, DNA</term>
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<keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN</term>
<term>Arabidopsis (génétique)</term>
<term>Brassica napus (génétique)</term>
<term>Cartographie chromosomique</term>
<term>Diploïdie</term>
<term>Génome végétal (génétique)</term>
<term>Génotype</term>
<term>Liaison génétique</term>
<term>Locus de caractère quantitatif (génétique)</term>
<term>Moutarde (plante) (génétique)</term>
<term>Répétitions microsatellites (génétique)</term>
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<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arabidopsis</term>
<term>Brassica napus</term>
<term>Genome, Plant</term>
<term>Microsatellite Repeats</term>
<term>Mustard Plant</term>
<term>Quantitative Trait Loci</term>
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<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Arabidopsis</term>
<term>Brassica napus</term>
<term>Génome végétal</term>
<term>Locus de caractère quantitatif</term>
<term>Moutarde (plante)</term>
<term>Répétitions microsatellites</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Chromosome Mapping</term>
<term>Diploidy</term>
<term>Genetic Linkage</term>
<term>Genotype</term>
<term>Sequence Analysis, DNA</term>
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<keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term>
<term>Cartographie chromosomique</term>
<term>Diploïdie</term>
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>There are three basic <italic>Brassica</italic>
 genomes (A, B, and C) and three parallel sets of subgenomes distinguished in the diploid <italic>Brassica</italic>
 (i.e.: <italic>B. rapa</italic>
, A<sup>r</sup>
A<sup>r</sup>
; <italic>B. nigra</italic>
, B<sup>ni</sup>
B<sup>ni</sup>
; <italic>B. oleracea</italic>
, C<sup>o</sup>
C<sup>o</sup>
) and the derived allotetraploid species (i.e.: <italic>B. juncea</italic>
, A<sup>j</sup>
A<sup>j</sup>
B<sup>j</sup>
B<sup>j</sup>
; <italic>B. napus</italic>
, A<sup>n</sup>
A<sup>n</sup>
C<sup>n</sup>
C<sup>n</sup>
; <italic>B. carinata,</italic>
 B<sup>c</sup>
B<sup>c</sup>
C<sup>c</sup>
C<sup>c</sup>
). To understand subgenome differentiation in <italic>B. juncea</italic>
 in comparison to other A genome-carrying <italic>Brassica</italic>
 species (<italic>B. rapa</italic>
 and <italic>B. napus</italic>
), we constructed a dense genetic linkage map of <italic>B. juncea</italic>
, and conducted population genetic analysis on diverse lines of the three A-genome carrying <italic>Brassica</italic>
 species using a genotyping-by-sequencing approach (DArT-seq).</p>
</sec>
<sec><title>Results</title>
<p>A dense genetic linkage map of <italic>B. juncea</italic>
 was constructed using an F<sub>2</sub>
 population derived from Sichuan Yellow/Purple Mustard. The map included 3329 DArT-seq markers on 18 linkage groups and covered 1579 cM with an average density of two markers per cM. Based on this map and the alignment of the marker sequences with the physical genome of <italic>Arabidopsis thaliana</italic>
, we observed strong co-linearity of the ancestral blocks among the different A subgenomes but also considerable block variation. Comparative analyses at the level of genome sequences of <italic>B. rapa</italic>
 and <italic>B. napus</italic>
, and marker sequence anchored on the genetic map of <italic>B. juncea</italic>
, revealed a total of 30 potential inversion events across large segments and 20 potential translocation events among the three A subgenomes. Population genetic analysis on 26 accessions of the three A genome-carrying <italic>Brassica</italic>
 species showed that the highest genetic distance were estimated when comparing A<sup>j</sup>
-A<sup>n</sup>
 than between A<sup>n</sup>
-A<sup>r</sup>
 and A<sup>j</sup>
-A<sup>r</sup>
 subgenome pairs.</p>
</sec>
<sec><title>Conclusions</title>
<p>The development of the dense genetic linkage map of <italic>B. juncea</italic>
 with informative DArT-seq marker sequences and availability of the reference sequences of the A<sup>r</sup>
, and A<sup>n</sup>
C<sup>n</sup>
 genomes allowed us to compare the A subgenome structure of <italic>B. juncea</italic>
 (A<sup>j</sup>
) . Our results suggest that strong co-linearity exists among the three A <italic>Brassica</italic>
 genomes (A<sup>r</sup>
, A<sup>n</sup>
 and A<sup>j</sup>
) but with apparent subgenomic variation. Population genetic analysis on three A-genome carrying <italic>Brassica</italic>
 species support the idea that <italic>B. juncea</italic>
 has distinct genomic diversity, and/or evolved from a different A genome progenitor of <italic>B. napus</italic>
.</p>
</sec>
<sec><title>Electronic supplementary material</title>
<p>The online version of this article (doi:10.1186/s12864-015-2343-1) contains supplementary material, which is available to authorized users.</p>
</sec>
</div>
</front>
<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Deokar, Aa" uniqKey="Deokar A">AA Deokar</name>
</author>
<author><name sortKey="Ramsay, L" uniqKey="Ramsay L">L Ramsay</name>
</author>
<author><name sortKey="Sharpe, Ag" uniqKey="Sharpe A">AG Sharpe</name>
</author>
<author><name sortKey="Diapari, M" uniqKey="Diapari M">M Diapari</name>
</author>
<author><name sortKey="Sindhu, A" uniqKey="Sindhu A">A Sindhu</name>
</author>
<author><name sortKey="Bett, K" uniqKey="Bett K">K Bett</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Delourme, R" uniqKey="Delourme R">R Delourme</name>
</author>
<author><name sortKey="Falentin, C" uniqKey="Falentin C">C Falentin</name>
</author>
<author><name sortKey="Fomeju, Bf" uniqKey="Fomeju B">BF Fomeju</name>
</author>
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Serveur d'exploration sur les relations entre la France et l'Australie

Co-linearity and divergence of the A subgenome of Brassica juncea compared with other Brassica species carrying different A subgenomes

Co-linearity and divergence of the A subgenome of Brassica juncea compared with other Brassica species carrying different A subgenomes

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	Serveur d'exploration sur les relations entre la France et l'Australie
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