Co-linearity and divergence of the A subgenome of Brassica juncea compared with other Brassica species carrying different A subgenomes
Identifieur interne : 002216 ( Main/Curation ); précédent : 002215; suivant : 002217Co-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.
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Abstract
There are three basic
A dense genetic linkage map of
The development of the dense genetic linkage map of
The online version of this article (doi:10.1186/s12864-015-2343-1) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12864-015-2343-1
PubMed: 26728943
PubMed Central: 4700566
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Harsh Raman<affiliation><nlm:aff id="Aff2">Graham Centre for Agricultural Innovation (an alliance between the Charles Sturt University and NSW Department of Primary Industries), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650 Australia</nlm:aff>
<wicri:noCountry code="subfield">NSW 2650 Australia</wicri:noCountry>
</affiliation>
<affiliation><nlm:aff id="Aff4">Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2 Canada</nlm:aff>
<wicri:noCountry code="subfield">SK S7N 0X2 Canada</wicri:noCountry>
</affiliation>
Le document en format XML
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compared with other <italic>Brassica</italic>
species carrying different A subgenomes</title>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Co-linearity and divergence of the A subgenome of <italic>Brassica juncea</italic>
compared with other <italic>Brassica</italic>
species carrying different A subgenomes</title>
<author><name sortKey="Zou, Jun" sort="Zou, Jun" uniqKey="Zou J" first="Jun" last="Zou">Jun Zou</name>
<affiliation wicri:level="1"><nlm:aff id="Aff1">National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, 430070 China</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan</wicri:regionArea>
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</affiliation>
</author>
<author><name sortKey="Hu, Dandan" sort="Hu, Dandan" uniqKey="Hu D" first="Dandan" last="Hu">Dandan Hu</name>
<affiliation wicri:level="1"><nlm:aff id="Aff1">National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, 430070 China</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan</wicri:regionArea>
<wicri:noRegion>Wuhan</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Liu, Peifa" sort="Liu, Peifa" uniqKey="Liu P" first="Peifa" last="Liu">Peifa Liu</name>
<affiliation wicri:level="1"><nlm:aff id="Aff1">National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, 430070 China</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan</wicri:regionArea>
<wicri:noRegion>Wuhan</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Raman, Harsh" sort="Raman, Harsh" uniqKey="Raman H" first="Harsh" last="Raman">Harsh Raman</name>
<affiliation><nlm:aff id="Aff2">Graham Centre for Agricultural Innovation (an alliance between the Charles Sturt University and NSW Department of Primary Industries), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650 Australia</nlm:aff>
<wicri:noCountry code="subfield">NSW 2650 Australia</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Liu, Zhongsong" sort="Liu, Zhongsong" uniqKey="Liu Z" first="Zhongsong" last="Liu">Zhongsong Liu</name>
<affiliation wicri:level="1"><nlm:aff id="Aff3">Oilseed Crops Institute, Hunan Agricultural University, Changsha, 410128 China</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Oilseed Crops Institute, Hunan Agricultural University, Changsha</wicri:regionArea>
<wicri:noRegion>Changsha</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Liu, Xianjun" sort="Liu, Xianjun" uniqKey="Liu X" first="Xianjun" last="Liu">Xianjun Liu</name>
<affiliation wicri:level="1"><nlm:aff id="Aff3">Oilseed Crops Institute, Hunan Agricultural University, Changsha, 410128 China</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Oilseed Crops Institute, Hunan Agricultural University, Changsha</wicri:regionArea>
<wicri:noRegion>Changsha</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Parkin, Isobel A P" sort="Parkin, Isobel A P" uniqKey="Parkin I" first="Isobel A. P." last="Parkin">Isobel A. P. Parkin</name>
<affiliation><nlm:aff id="Aff4">Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2 Canada</nlm:aff>
<wicri:noCountry code="subfield">SK S7N 0X2 Canada</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Chalhoub, Boulos" sort="Chalhoub, Boulos" uniqKey="Chalhoub B" first="Boulos" last="Chalhoub">Boulos Chalhoub</name>
<affiliation wicri:level="1"><nlm:aff id="Aff5">Unité de Recherche en Génomique Végétale (Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Université d’Evry Val d’Essonnes), Organization and Evolution of Plant Genomes, 91057 Evry cedex, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>Unité de Recherche en Génomique Végétale (Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Université d’Evry Val d’Essonnes), Organization and Evolution of Plant Genomes, 91057 Evry cedex</wicri:regionArea>
<wicri:noRegion>91057 Evry cedex</wicri:noRegion>
<wicri:noRegion>91057 Evry cedex</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Meng, Jinling" sort="Meng, Jinling" uniqKey="Meng J" first="Jinling" last="Meng">Jinling Meng</name>
<affiliation wicri:level="1"><nlm:aff id="Aff1">National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, 430070 China</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan</wicri:regionArea>
<wicri:noRegion>Wuhan</wicri:noRegion>
</affiliation>
</author>
</analytic>
<series><title level="j">BMC Genomics</title>
<idno type="eISSN">1471-2164</idno>
<imprint><date when="2016">2016</date>
</imprint>
</series>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Arabidopsis (genetics)</term>
<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>
</keywords>
<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>
</keywords>
<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>
</keywords>
<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>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term>
<term>Cartographie chromosomique</term>
<term>Diploïdie</term>
<term>Génotype</term>
<term>Liaison génétique</term>
</keywords>
</textClass>
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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>
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</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>
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</analytic>
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</author>
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<biblStruct><analytic><author><name sortKey="Castillo, A" uniqKey="Castillo A">A Castillo</name>
</author>
<author><name sortKey="Ramirez, Mc" uniqKey="Ramirez M">MC Ramirez</name>
</author>
<author><name sortKey="Martin, Ac" uniqKey="Martin A">AC Martin</name>
</author>
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</author>
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</author>
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