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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Centromere Locations in <italic>Brassica</italic>
A and C Genomes Revealed Through Half-Tetrad Analysis</title>
<author><name sortKey="Mason, Annaliese S" sort="Mason, Annaliese S" uniqKey="Mason A" first="Annaliese S." last="Mason">Annaliese S. Mason</name>
<affiliation><nlm:aff id="aff1">Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, 35392 Giessen, Germany</nlm:aff>
</affiliation>
<affiliation><nlm:aff id="aff2">School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane 4072, Australia</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Rousseau Gueutin, Mathieu" sort="Rousseau Gueutin, Mathieu" uniqKey="Rousseau Gueutin M" first="Mathieu" last="Rousseau-Gueutin">Mathieu Rousseau-Gueutin</name>
<affiliation><nlm:aff id="aff3">IGEPP, Institut National de la Recherche Agronomique, BP35327, 35653 Le Rheu, France</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Morice, Jerome" sort="Morice, Jerome" uniqKey="Morice J" first="Jérôme" last="Morice">Jérôme Morice</name>
<affiliation><nlm:aff id="aff3">IGEPP, Institut National de la Recherche Agronomique, BP35327, 35653 Le Rheu, France</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Bayer, Philipp E" sort="Bayer, Philipp E" uniqKey="Bayer P" first="Philipp E." last="Bayer">Philipp E. Bayer</name>
<affiliation><nlm:aff id="aff2">School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane 4072, Australia</nlm:aff>
</affiliation>
<affiliation><nlm:aff id="aff4">School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Besharat, Naghmeh" sort="Besharat, Naghmeh" uniqKey="Besharat N" first="Naghmeh" last="Besharat">Naghmeh Besharat</name>
<affiliation><nlm:aff id="aff4">School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Cousin, Anouska" sort="Cousin, Anouska" uniqKey="Cousin A" first="Anouska" last="Cousin">Anouska Cousin</name>
<affiliation><nlm:aff id="aff4">School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Pradhan, Aneeta" sort="Pradhan, Aneeta" uniqKey="Pradhan A" first="Aneeta" last="Pradhan">Aneeta Pradhan</name>
<affiliation><nlm:aff id="aff4">School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia</nlm:aff>
</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="aff5">Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon, Saskatchewan, Canada</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Chevre, Anne Marie" sort="Chevre, Anne Marie" uniqKey="Chevre A" first="Anne-Marie" last="Chèvre">Anne-Marie Chèvre</name>
<affiliation><nlm:aff id="aff3">IGEPP, Institut National de la Recherche Agronomique, BP35327, 35653 Le Rheu, France</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Batley, Jacqueline" sort="Batley, Jacqueline" uniqKey="Batley J" first="Jacqueline" last="Batley">Jacqueline Batley</name>
<affiliation><nlm:aff id="aff4">School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia</nlm:aff>
</affiliation>
<affiliation><nlm:aff id="aff2">School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane 4072, Australia</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Nelson, Matthew N" sort="Nelson, Matthew N" uniqKey="Nelson M" first="Matthew N." last="Nelson">Matthew N. Nelson</name>
<affiliation><nlm:aff id="aff4">School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia</nlm:aff>
</affiliation>
<affiliation><nlm:aff id="aff6">Natural Capital and Plant Health, Royal Botanic Gardens Kew, Ardingly, West Sussex, RH17 6TN, United Kingdom</nlm:aff>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">26614742</idno>
<idno type="pmc">4788232</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4788232</idno>
<idno type="RBID">PMC:4788232</idno>
<idno type="doi">10.1534/genetics.115.183210</idno>
<date when="2015">2015</date>
<idno type="wicri:Area/Pmc/Corpus">000440</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000440</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Centromere Locations in <italic>Brassica</italic>
A and C Genomes Revealed Through Half-Tetrad Analysis</title>
<author><name sortKey="Mason, Annaliese S" sort="Mason, Annaliese S" uniqKey="Mason A" first="Annaliese S." last="Mason">Annaliese S. Mason</name>
<affiliation><nlm:aff id="aff1">Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, 35392 Giessen, Germany</nlm:aff>
</affiliation>
<affiliation><nlm:aff id="aff2">School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane 4072, Australia</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Rousseau Gueutin, Mathieu" sort="Rousseau Gueutin, Mathieu" uniqKey="Rousseau Gueutin M" first="Mathieu" last="Rousseau-Gueutin">Mathieu Rousseau-Gueutin</name>
<affiliation><nlm:aff id="aff3">IGEPP, Institut National de la Recherche Agronomique, BP35327, 35653 Le Rheu, France</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Morice, Jerome" sort="Morice, Jerome" uniqKey="Morice J" first="Jérôme" last="Morice">Jérôme Morice</name>
<affiliation><nlm:aff id="aff3">IGEPP, Institut National de la Recherche Agronomique, BP35327, 35653 Le Rheu, France</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Bayer, Philipp E" sort="Bayer, Philipp E" uniqKey="Bayer P" first="Philipp E." last="Bayer">Philipp E. Bayer</name>
<affiliation><nlm:aff id="aff2">School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane 4072, Australia</nlm:aff>
</affiliation>
<affiliation><nlm:aff id="aff4">School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Besharat, Naghmeh" sort="Besharat, Naghmeh" uniqKey="Besharat N" first="Naghmeh" last="Besharat">Naghmeh Besharat</name>
<affiliation><nlm:aff id="aff4">School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Cousin, Anouska" sort="Cousin, Anouska" uniqKey="Cousin A" first="Anouska" last="Cousin">Anouska Cousin</name>
<affiliation><nlm:aff id="aff4">School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Pradhan, Aneeta" sort="Pradhan, Aneeta" uniqKey="Pradhan A" first="Aneeta" last="Pradhan">Aneeta Pradhan</name>
<affiliation><nlm:aff id="aff4">School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia</nlm:aff>
</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="aff5">Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon, Saskatchewan, Canada</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Chevre, Anne Marie" sort="Chevre, Anne Marie" uniqKey="Chevre A" first="Anne-Marie" last="Chèvre">Anne-Marie Chèvre</name>
<affiliation><nlm:aff id="aff3">IGEPP, Institut National de la Recherche Agronomique, BP35327, 35653 Le Rheu, France</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Batley, Jacqueline" sort="Batley, Jacqueline" uniqKey="Batley J" first="Jacqueline" last="Batley">Jacqueline Batley</name>
<affiliation><nlm:aff id="aff4">School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia</nlm:aff>
</affiliation>
<affiliation><nlm:aff id="aff2">School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane 4072, Australia</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Nelson, Matthew N" sort="Nelson, Matthew N" uniqKey="Nelson M" first="Matthew N." last="Nelson">Matthew N. Nelson</name>
<affiliation><nlm:aff id="aff4">School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia</nlm:aff>
</affiliation>
<affiliation><nlm:aff id="aff6">Natural Capital and Plant Health, Royal Botanic Gardens Kew, Ardingly, West Sussex, RH17 6TN, United Kingdom</nlm:aff>
</affiliation>
</author>
</analytic>
<series><title level="j">Genetics</title>
<idno type="ISSN">0016-6731</idno>
<idno type="eISSN">1943-2631</idno>
<imprint><date when="2015">2015</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><p>Locating centromeres on genome sequences can be challenging. The high density of repetitive elements in these regions makes sequence assembly problematic, especially when using short-read sequencing technologies. It can also be difficult to distinguish between active and recently extinct centromeres through sequence analysis. An effective solution is to identify genetically active centromeres (functional in meiosis) by half-tetrad analysis. This genetic approach involves detecting heterozygosity along chromosomes in segregating populations derived from gametes (half-tetrads). Unreduced gametes produced by first division restitution mechanisms comprise complete sets of nonsister chromatids. Along these chromatids, heterozygosity is maximal at the centromeres, and homologous recombination events result in homozygosity toward the telomeres. We genotyped populations of half-tetrad-derived individuals (from <italic>Brassica</italic>
interspecific hybrids) using a high-density array of physically anchored SNP markers (Illumina <italic>Brassica</italic>
60K Infinium array). Mapping the distribution of heterozygosity in these half-tetrad individuals allowed the genetic mapping of all 19 centromeres of the <italic>Brassica</italic>
A and C genomes to the reference <italic>Brassica napus</italic>
genome. Gene and transposable element density across the <italic>B. napus</italic>
genome were also assessed and corresponded well to previously reported genetic map positions. Known centromere-specific sequences were located in the reference genome, but mostly matched unanchored sequences, suggesting that the core centromeric regions may not yet be assembled into the pseudochromosomes of the reference genome. The increasing availability of genetic markers physically anchored to reference genomes greatly simplifies the genetic and physical mapping of centromeres using half-tetrad analysis. We discuss possible applications of this approach, including in species where half-tetrads are currently difficult to isolate.</p>
</div>
</front>
</TEI>
<pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Genetics</journal-id>
<journal-id journal-id-type="iso-abbrev">Genetics</journal-id>
<journal-id journal-id-type="hwp">genetics</journal-id>
<journal-id journal-id-type="pmc">genetics</journal-id>
<journal-id journal-id-type="publisher-id">genetics</journal-id>
<journal-title-group><journal-title>Genetics</journal-title>
</journal-title-group>
<issn pub-type="ppub">0016-6731</issn>
<issn pub-type="epub">1943-2631</issn>
<publisher><publisher-name>Genetics Society of America</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">26614742</article-id>
<article-id pub-id-type="pmc">4788232</article-id>
<article-id pub-id-type="publisher-id">183210</article-id>
<article-id pub-id-type="doi">10.1534/genetics.115.183210</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Investigations</subject>
<subj-group><subject>Genome Integrity and Transmission</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group><article-title>Centromere Locations in <italic>Brassica</italic>
A and C Genomes Revealed Through Half-Tetrad Analysis</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Mason</surname>
<given-names>Annaliese S.</given-names>
</name>
<xref ref-type="aff" rid="aff1">*</xref>
<xref ref-type="aff" rid="aff2"><sup>†</sup>
</xref>
<xref ref-type="corresp" rid="cor1"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Rousseau-Gueutin</surname>
<given-names>Mathieu</given-names>
</name>
<xref ref-type="aff" rid="aff3"><sup>‡</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Morice</surname>
<given-names>Jérôme</given-names>
</name>
<xref ref-type="aff" rid="aff3"><sup>‡</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Bayer</surname>
<given-names>Philipp E.</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>†</sup>
</xref>
<xref ref-type="aff" rid="aff4"><sup>§</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Besharat</surname>
<given-names>Naghmeh</given-names>
</name>
<xref ref-type="aff" rid="aff4"><sup>§</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Cousin</surname>
<given-names>Anouska</given-names>
</name>
<xref ref-type="aff" rid="aff4"><sup>§</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Pradhan</surname>
<given-names>Aneeta</given-names>
</name>
<xref ref-type="aff" rid="aff4"><sup>§</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Parkin</surname>
<given-names>Isobel A. P.</given-names>
</name>
<xref ref-type="aff" rid="aff5">**</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Chèvre</surname>
<given-names>Anne-Marie</given-names>
</name>
<xref ref-type="aff" rid="aff3"><sup>‡</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Batley</surname>
<given-names>Jacqueline</given-names>
</name>
<xref ref-type="aff" rid="aff4"><sup>§</sup>
</xref>
<xref ref-type="aff" rid="aff2"><sup>†</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Nelson</surname>
<given-names>Matthew N.</given-names>
</name>
<xref ref-type="aff" rid="aff4"><sup>§</sup>
</xref>
<xref ref-type="aff" rid="aff6"><sup>††</sup>
</xref>
<xref ref-type="corresp" rid="cor1"><sup>1</sup>
</xref>
</contrib>
<aff id="aff1"><label>*</label>
Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, 35392 Giessen, Germany</aff>
<aff id="aff2"><label>†</label>
School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane 4072, Australia</aff>
<aff id="aff3"><label>‡</label>
IGEPP, Institut National de la Recherche Agronomique, BP35327, 35653 Le Rheu, France</aff>
<aff id="aff4"><label>§</label>
School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia</aff>
<aff id="aff5"><label>**</label>
Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon, Saskatchewan, Canada</aff>
<aff id="aff6"><label>††</label>
Natural Capital and Plant Health, Royal Botanic Gardens Kew, Ardingly, West Sussex, RH17 6TN, United Kingdom</aff>
</contrib-group>
<author-notes><corresp id="cor1"><label>1</label>
Corresponding authors: Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany. E-mail: <email>annaliese.mason@agrar.uni-giessen.de</email>
; and Natural Capital and Plant Health, Royal Botanic Gardens, Kew, Wakehurst Place, Ardingly, West Sussex, RH17 6TN, United Kingdom. E-mail: <email>m.nelson@kew.org</email>
</corresp>
</author-notes>
<pmc-comment>Fake ppub date generated by PMC from publisher
pub-date/@pub-type='epub-ppub' </pmc-comment>
<pub-date pub-type="ppub"><month>2</month>
<year>2016</year>
</pub-date>
<pub-date pub-type="epub"><day>25</day>
<month>11</month>
<year>2015</year>
</pub-date>
<volume>202</volume>
<issue>2</issue>
<fpage>513</fpage>
<lpage>523</lpage>
<history><date date-type="received"><day>28</day>
<month>9</month>
<year>2015</year>
</date>
<date date-type="accepted"><day>23</day>
<month>11</month>
<year>2015</year>
</date>
</history>
<permissions><copyright-statement>Copyright © 2016 by the Genetics Society of America</copyright-statement>
<copyright-year>2016</copyright-year>
</permissions>
<self-uri xlink:title="pdf" xlink:type="simple" xlink:href="513.pdf"></self-uri>
<abstract><p>Locating centromeres on genome sequences can be challenging. The high density of repetitive elements in these regions makes sequence assembly problematic, especially when using short-read sequencing technologies. It can also be difficult to distinguish between active and recently extinct centromeres through sequence analysis. An effective solution is to identify genetically active centromeres (functional in meiosis) by half-tetrad analysis. This genetic approach involves detecting heterozygosity along chromosomes in segregating populations derived from gametes (half-tetrads). Unreduced gametes produced by first division restitution mechanisms comprise complete sets of nonsister chromatids. Along these chromatids, heterozygosity is maximal at the centromeres, and homologous recombination events result in homozygosity toward the telomeres. We genotyped populations of half-tetrad-derived individuals (from <italic>Brassica</italic>
interspecific hybrids) using a high-density array of physically anchored SNP markers (Illumina <italic>Brassica</italic>
60K Infinium array). Mapping the distribution of heterozygosity in these half-tetrad individuals allowed the genetic mapping of all 19 centromeres of the <italic>Brassica</italic>
A and C genomes to the reference <italic>Brassica napus</italic>
genome. Gene and transposable element density across the <italic>B. napus</italic>
genome were also assessed and corresponded well to previously reported genetic map positions. Known centromere-specific sequences were located in the reference genome, but mostly matched unanchored sequences, suggesting that the core centromeric regions may not yet be assembled into the pseudochromosomes of the reference genome. The increasing availability of genetic markers physically anchored to reference genomes greatly simplifies the genetic and physical mapping of centromeres using half-tetrad analysis. We discuss possible applications of this approach, including in species where half-tetrads are currently difficult to isolate.</p>
</abstract>
<kwd-group><kwd>recombination</kwd>
<kwd>molecular karyotyping</kwd>
<kwd><italic>Brassica</italic>
</kwd>
<kwd>centromeres</kwd>
<kwd>unreduced gametes</kwd>
</kwd-group>
<counts><fig-count count="3"></fig-count>
<table-count count="1"></table-count>
<equation-count count="0"></equation-count>
<ref-count count="71"></ref-count>
<page-count count="11"></page-count>
</counts>
</article-meta>
</front>
</pmc>
</record>
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