Genome-Wide Sequence Variation Identification and Floral-Associated Trait Comparisons Based on the Re-sequencing of the ‘Nagafu No. 2’ and ‘Qinguan’ Varieties of Apple (Malus domestica Borkh.)
Identifieur interne : 000163 ( Pmc/Checkpoint ); précédent : 000162; suivant : 000164Genome-Wide Sequence Variation Identification and Floral-Associated Trait Comparisons Based on the Re-sequencing of the ‘Nagafu No. 2’ and ‘Qinguan’ Varieties of Apple (Malus domestica Borkh.)
Auteurs : Libo Xing ; Dong Zhang ; Xiaomin Song ; Kai Weng ; Yawen Shen ; Youmei Li ; Caiping Zhao ; Juanjuan Ma ; Na An ; Mingyu HanSource :
- Frontiers in Plant Science [ 1664-462X ] ; 2016.
Abstract
Apple (
Url:
DOI: 10.3389/fpls.2016.00908
PubMed: 27446138
PubMed Central: 4921462
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Genome-Wide Sequence Variation Identification and Floral-Associated Trait Comparisons Based on the Re-sequencing of the ‘Nagafu No. 2’ and ‘Qinguan’ Varieties of Apple (<italic>Malus domestica</italic> Borkh.)</title><author><name sortKey="Xing, Libo" sort="Xing, Libo" uniqKey="Xing L" first="Libo" last="Xing">Libo Xing</name></author><author><name sortKey="Zhang, Dong" sort="Zhang, Dong" uniqKey="Zhang D" first="Dong" last="Zhang">Dong Zhang</name></author><author><name sortKey="Song, Xiaomin" sort="Song, Xiaomin" uniqKey="Song X" first="Xiaomin" last="Song">Xiaomin Song</name></author><author><name sortKey="Weng, Kai" sort="Weng, Kai" uniqKey="Weng K" first="Kai" last="Weng">Kai Weng</name></author><author><name sortKey="Shen, Yawen" sort="Shen, Yawen" uniqKey="Shen Y" first="Yawen" last="Shen">Yawen Shen</name></author><author><name sortKey="Li, Youmei" sort="Li, Youmei" uniqKey="Li Y" first="Youmei" last="Li">Youmei Li</name></author><author><name sortKey="Zhao, Caiping" sort="Zhao, Caiping" uniqKey="Zhao C" first="Caiping" last="Zhao">Caiping Zhao</name></author><author><name sortKey="Ma, Juanjuan" sort="Ma, Juanjuan" uniqKey="Ma J" first="Juanjuan" last="Ma">Juanjuan Ma</name></author><author><name sortKey="An, Na" sort="An, Na" uniqKey="An N" first="Na" last="An">Na An</name></author><author><name sortKey="Han, Mingyu" sort="Han, Mingyu" uniqKey="Han M" first="Mingyu" last="Han">Mingyu Han</name></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27446138</idno><idno type="pmc">4921462</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4921462</idno><idno type="RBID">PMC:4921462</idno><idno type="doi">10.3389/fpls.2016.00908</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000330</idno><idno type="wicri:Area/Pmc/Curation">000329</idno><idno type="wicri:Area/Pmc/Checkpoint">000163</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Genome-Wide Sequence Variation Identification and Floral-Associated Trait Comparisons Based on the Re-sequencing of the ‘Nagafu No. 2’ and ‘Qinguan’ Varieties of Apple (<italic>Malus domestica</italic> Borkh.)</title><author><name sortKey="Xing, Libo" sort="Xing, Libo" uniqKey="Xing L" first="Libo" last="Xing">Libo Xing</name></author><author><name sortKey="Zhang, Dong" sort="Zhang, Dong" uniqKey="Zhang D" first="Dong" last="Zhang">Dong Zhang</name></author><author><name sortKey="Song, Xiaomin" sort="Song, Xiaomin" uniqKey="Song X" first="Xiaomin" last="Song">Xiaomin Song</name></author><author><name sortKey="Weng, Kai" sort="Weng, Kai" uniqKey="Weng K" first="Kai" last="Weng">Kai Weng</name></author><author><name sortKey="Shen, Yawen" sort="Shen, Yawen" uniqKey="Shen Y" first="Yawen" last="Shen">Yawen Shen</name></author><author><name sortKey="Li, Youmei" sort="Li, Youmei" uniqKey="Li Y" first="Youmei" last="Li">Youmei Li</name></author><author><name sortKey="Zhao, Caiping" sort="Zhao, Caiping" uniqKey="Zhao C" first="Caiping" last="Zhao">Caiping Zhao</name></author><author><name sortKey="Ma, Juanjuan" sort="Ma, Juanjuan" uniqKey="Ma J" first="Juanjuan" last="Ma">Juanjuan Ma</name></author><author><name sortKey="An, Na" sort="An, Na" uniqKey="An N" first="Na" last="An">Na An</name></author><author><name sortKey="Han, Mingyu" sort="Han, Mingyu" uniqKey="Han M" first="Mingyu" last="Han">Mingyu Han</name></author></analytic><series><title level="j">Frontiers in Plant Science</title><idno type="eISSN">1664-462X</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Apple (<italic>Malus domestica</italic> Borkh.) is a commercially important fruit worldwide. Detailed information on genomic DNA polymorphisms, which are important for understanding phenotypic traits, is lacking for the apple. We re-sequenced two elite apple varieties, ‘Nagafu No. 2’ and ‘Qinguan,’ which have different characteristics. We identified many genomic variations, including 2,771,129 single nucleotide polymorphisms (SNPs), 82,663 structural variations (SVs), and 1,572,803 insertion/deletions (INDELs) in ‘Nagafu No. 2’ and 2,262,888 SNPs, 63,764 SVs, and 1,294,060 INDELs in ‘Qinguan.’ The ‘SNP,’ ‘INDEL,’ and ‘SV’ distributions were non-random, with variation-rich or -poor regions throughout the genomes. In ‘Nagafu No. 2’ and ‘Qinguan’ there were 171,520 and 147,090 non-synonymous SNPs spanning 23,111 and 21,400 genes, respectively; 3,963 and 3,196 SVs in 3,431 and 2,815 genes, respectively; and 1,834 and 1,451 INDELs in 1,681 and 1,345 genes, respectively. Genetic linkage maps of 190 flowering genes associated with multiple flowering pathways in ‘Nagafu No. 2,’ ‘Qinguan,’ and ‘Golden Delicious,’ identified complex regulatory mechanisms involved in floral induction, flower bud formation, and flowering characteristics, which might reflect the genetic variation of the flowering genes. Expression profiling of key flowering genes in buds and leaves suggested that the photoperiod and autonomous flowering pathways are major contributors to the different floral-associated traits between ‘Nagafu No. 2’ and ‘Qinguan.’ The genome variation data provided a foundation for the further exploration of apple diversity and gene–phenotype relationships, and for future research on molecular breeding to improve apple and related species.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Amasino, R" uniqKey="Amasino R">R. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Front Plant Sci</journal-id><journal-id journal-id-type="iso-abbrev">Front Plant Sci</journal-id><journal-id journal-id-type="publisher-id">Front. Plant Sci.</journal-id><journal-title-group><journal-title>Frontiers in Plant Science</journal-title></journal-title-group><issn pub-type="epub">1664-462X</issn><publisher><publisher-name>Frontiers Media S.A.</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">27446138</article-id><article-id pub-id-type="pmc">4921462</article-id><article-id pub-id-type="doi">10.3389/fpls.2016.00908</article-id><article-categories><subj-group subj-group-type="heading"><subject>Plant Science</subject><subj-group><subject>Original Research</subject></subj-group></subj-group></article-categories><title-group><article-title>Genome-Wide Sequence Variation Identification and Floral-Associated Trait Comparisons Based on the Re-sequencing of the ‘Nagafu No. 2’ and ‘Qinguan’ Varieties of Apple (<italic>Malus domestica</italic> Borkh.)</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Xing</surname><given-names>Libo</given-names></name><xref ref-type="author-notes" rid="fn002"><sup>†</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/224545/overview"></uri></contrib><contrib contrib-type="author"><name><surname>Zhang</surname><given-names>Dong</given-names></name><xref ref-type="author-notes" rid="fn002"><sup>†</sup></xref></contrib><contrib contrib-type="author"><name><surname>Song</surname><given-names>Xiaomin</given-names></name><xref ref-type="author-notes" rid="fn002"><sup>†</sup></xref></contrib><contrib contrib-type="author"><name><surname>Weng</surname><given-names>Kai</given-names></name></contrib><contrib contrib-type="author"><name><surname>Shen</surname><given-names>Yawen</given-names></name></contrib><contrib contrib-type="author"><name><surname>Li</surname><given-names>Youmei</given-names></name></contrib><contrib contrib-type="author"><name><surname>Zhao</surname><given-names>Caiping</given-names></name></contrib><contrib contrib-type="author"><name><surname>Ma</surname><given-names>Juanjuan</given-names></name></contrib><contrib contrib-type="author"><name><surname>An</surname><given-names>Na</given-names></name></contrib><contrib contrib-type="author"><name><surname>Han</surname><given-names>Mingyu</given-names></name><xref ref-type="author-notes" rid="fn001"><sup>*</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/326166/overview"></uri></contrib></contrib-group><aff><institution>College of Horticulture, Northwest Agriculture and Forestry University</institution><country>Yangling, China</country></aff><author-notes><fn fn-type="edited-by"><p>Edited by: <italic>Juan Antonio Vidales, Universidad Autónoma de Nuevo León, Mexico</italic></p></fn><fn fn-type="edited-by"><p>Reviewed by: <italic>Thomas Dandekar, University of Würzburg, Germany; Andrea Mazzucato, University of Tuscia, Italy</italic></p></fn><corresp id="fn001">*Correspondence: <italic>Mingyu Han, <email xlink:type="simple">hanmy@nwsuaf.edu.cn</email></italic></corresp><fn fn-type="other" id="fn002"><p><sup>†</sup><italic>Co-first authors</italic></p></fn><fn fn-type="other" id="fn003"><p>This article was submitted to Crop Science and Horticulture, a section of the journal Frontiers in Plant Science</p></fn></author-notes><pub-date pub-type="epub"><day>27</day><month>6</month><year>2016</year></pub-date><pub-date pub-type="collection"><year>2016</year></pub-date><volume>7</volume><elocation-id>908</elocation-id><history><date date-type="received"><day>07</day><month>12</month><year>2015</year></date><date date-type="accepted"><day>08</day><month>6</month><year>2016</year></date></history><permissions><copyright-statement>Copyright © 2016 Xing, Zhang, Song, Weng, Shen, Li, Zhao, Ma, An and Han.</copyright-statement><copyright-year>2016</copyright-year><copyright-holder>Xing, Zhang, Song, Weng, Shen, Li, Zhao, Ma, An and Han</copyright-holder><license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</license-p></license></permissions><abstract><p>Apple (<italic>Malus domestica</italic> Borkh.) is a commercially important fruit worldwide. Detailed information on genomic DNA polymorphisms, which are important for understanding phenotypic traits, is lacking for the apple. We re-sequenced two elite apple varieties, ‘Nagafu No. 2’ and ‘Qinguan,’ which have different characteristics. We identified many genomic variations, including 2,771,129 single nucleotide polymorphisms (SNPs), 82,663 structural variations (SVs), and 1,572,803 insertion/deletions (INDELs) in ‘Nagafu No. 2’ and 2,262,888 SNPs, 63,764 SVs, and 1,294,060 INDELs in ‘Qinguan.’ The ‘SNP,’ ‘INDEL,’ and ‘SV’ distributions were non-random, with variation-rich or -poor regions throughout the genomes. In ‘Nagafu No. 2’ and ‘Qinguan’ there were 171,520 and 147,090 non-synonymous SNPs spanning 23,111 and 21,400 genes, respectively; 3,963 and 3,196 SVs in 3,431 and 2,815 genes, respectively; and 1,834 and 1,451 INDELs in 1,681 and 1,345 genes, respectively. Genetic linkage maps of 190 flowering genes associated with multiple flowering pathways in ‘Nagafu No. 2,’ ‘Qinguan,’ and ‘Golden Delicious,’ identified complex regulatory mechanisms involved in floral induction, flower bud formation, and flowering characteristics, which might reflect the genetic variation of the flowering genes. Expression profiling of key flowering genes in buds and leaves suggested that the photoperiod and autonomous flowering pathways are major contributors to the different floral-associated traits between ‘Nagafu No. 2’ and ‘Qinguan.’ The genome variation data provided a foundation for the further exploration of apple diversity and gene–phenotype relationships, and for future research on molecular breeding to improve apple and related species.</p></abstract><kwd-group><kwd>genome variation</kwd><kwd>INDELs</kwd><kwd>re-sequencing</kwd><kwd>flowering genes</kwd><kwd>apple (<italic>Malus domestica</italic> Borkh.)</kwd></kwd-group><funding-group><award-group><funding-source id="cn001">China Postdoctoral Science Foundation<named-content content-type="fundref-id">10.13039/501100002858</named-content></funding-source><award-id rid="cn001">2014T70939</award-id><award-id rid="cn001">2014M56806</award-id></award-group></funding-group><counts><fig-count count="7"></fig-count><table-count count="3"></table-count><equation-count count="0"></equation-count><ref-count count="57"></ref-count><page-count count="13"></page-count><word-count count="0"></word-count></counts></article-meta></front></pmc><affiliations><list></list><tree><noCountry><name sortKey="An, Na" sort="An, Na" uniqKey="An N" first="Na" last="An">Na An</name><name sortKey="Han, Mingyu" sort="Han, Mingyu" uniqKey="Han M" first="Mingyu" last="Han">Mingyu Han</name><name sortKey="Li, Youmei" sort="Li, Youmei" uniqKey="Li Y" first="Youmei" last="Li">Youmei Li</name><name sortKey="Ma, Juanjuan" sort="Ma, Juanjuan" uniqKey="Ma J" first="Juanjuan" last="Ma">Juanjuan Ma</name><name sortKey="Shen, Yawen" sort="Shen, Yawen" uniqKey="Shen Y" first="Yawen" last="Shen">Yawen Shen</name><name sortKey="Song, Xiaomin" sort="Song, Xiaomin" uniqKey="Song X" first="Xiaomin" last="Song">Xiaomin Song</name><name sortKey="Weng, Kai" sort="Weng, Kai" uniqKey="Weng K" first="Kai" last="Weng">Kai Weng</name><name sortKey="Xing, Libo" sort="Xing, Libo" uniqKey="Xing L" first="Libo" last="Xing">Libo Xing</name><name sortKey="Zhang, Dong" sort="Zhang, Dong" uniqKey="Zhang D" first="Dong" last="Zhang">Dong Zhang</name><name sortKey="Zhao, Caiping" sort="Zhao, Caiping" uniqKey="Zhao C" first="Caiping" last="Zhao">Caiping Zhao</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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