Identifying the genome-wide genetic variation between precocious trifoliate orange and its wild type and developing new markers for genetics research
Identifieur interne : 000136 ( Pmc/Checkpoint ); précédent : 000135; suivant : 000137Identifying the genome-wide genetic variation between precocious trifoliate orange and its wild type and developing new markers for genetics research
Auteurs : Jin-Zhi Zhang ; Sheng-Rui Liu ; Chun-Gen HuSource :
- DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes [ 1340-2838 ] ; 2016.
Abstract
To increase our understanding of the genes involved in flowering in citrus, we performed genome resequencing of an early flowering trifoliate orange mutant (
Url:
DOI: 10.1093/dnares/dsw017
PubMed: 27106267
PubMed Central: 4991830
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Identifying the genome-wide genetic variation between precocious trifoliate orange and its wild type and developing new markers for genetics research</title><author><name sortKey="Zhang, Jin Zhi" sort="Zhang, Jin Zhi" uniqKey="Zhang J" first="Jin-Zhi" last="Zhang">Jin-Zhi Zhang</name></author><author><name sortKey="Liu, Sheng Rui" sort="Liu, Sheng Rui" uniqKey="Liu S" first="Sheng-Rui" last="Liu">Sheng-Rui Liu</name></author><author><name sortKey="Hu, Chun Gen" sort="Hu, Chun Gen" uniqKey="Hu C" first="Chun-Gen" last="Hu">Chun-Gen Hu</name></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27106267</idno><idno type="pmc">4991830</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4991830</idno><idno type="RBID">PMC:4991830</idno><idno type="doi">10.1093/dnares/dsw017</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000E74</idno><idno type="wicri:Area/Pmc/Curation">000E73</idno><idno type="wicri:Area/Pmc/Checkpoint">000136</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Identifying the genome-wide genetic variation between precocious trifoliate orange and its wild type and developing new markers for genetics research</title><author><name sortKey="Zhang, Jin Zhi" sort="Zhang, Jin Zhi" uniqKey="Zhang J" first="Jin-Zhi" last="Zhang">Jin-Zhi Zhang</name></author><author><name sortKey="Liu, Sheng Rui" sort="Liu, Sheng Rui" uniqKey="Liu S" first="Sheng-Rui" last="Liu">Sheng-Rui Liu</name></author><author><name sortKey="Hu, Chun Gen" sort="Hu, Chun Gen" uniqKey="Hu C" first="Chun-Gen" last="Hu">Chun-Gen Hu</name></author></analytic><series><title level="j">DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes</title><idno type="ISSN">1340-2838</idno><idno type="eISSN">1756-1663</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>To increase our understanding of the genes involved in flowering in citrus, we performed genome resequencing of an early flowering trifoliate orange mutant (<italic>Poncirus trifoliata</italic> L. Raf.) and its wild type. At the genome level, 3,932,628 single nucleotide polymorphisms (SNPs), 1,293,383 insertion/deletion polymorphisms (InDels), and 52,135 structural variations were identified between the mutant and its wild type based on the citrus reference genome. Based on integrative analysis of resequencing and transcriptome analysis, 233,998 SNPs and 75,836 InDels were also identified between the mutant and its wild type at the transcriptional level. Also, 272 citrus homologous flowering-time transcripts containing genetic variation were also identified. Gene Ontology and Kyoto Encyclopaedia of Genes and Genomes annotation revealed that the transcripts containing the mutant- and the wild-type-specific InDel were involved in diverse biological processes and molecular function. Among these transcripts, there were 131 transcripts that were expressed differently in the two genotypes. When 268 selected InDels were tested on 32 genotypes of the three genera of Rutaceae for the genetic diversity assessment, these InDel-based markers showed high transferability. This work provides important information that will allow a better understanding of the citrus genome and that will be helpful for dissecting the genetic basis of important traits in citrus.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Liu, C" uniqKey="Liu C">C. Liu</name></author><author><name sortKey="Xi, W" uniqKey="Xi W">W. Xi</name></author><author><name sortKey="Shen, L" uniqKey="Shen L">L. Shen</name></author><author><name sortKey="Tan, C" uniqKey="Tan C">C. Tan</name></author><author><name sortKey="Yu, H" uniqKey="Yu H">H. Yu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Khan, M R G" uniqKey="Khan M">M.R.G. Khan</name></author><author><name sortKey="Ai, X Y" uniqKey="Ai X">X.-Y. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">DNA Res</journal-id><journal-id journal-id-type="iso-abbrev">DNA Res</journal-id><journal-id journal-id-type="publisher-id">dnares</journal-id><journal-id journal-id-type="hwp">dnares</journal-id><journal-title-group><journal-title>DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes</journal-title></journal-title-group><issn pub-type="ppub">1340-2838</issn><issn pub-type="epub">1756-1663</issn><publisher><publisher-name>Oxford University Press</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">27106267</article-id><article-id pub-id-type="pmc">4991830</article-id><article-id pub-id-type="doi">10.1093/dnares/dsw017</article-id><article-id pub-id-type="publisher-id">dsw017</article-id><article-categories><subj-group subj-group-type="heading"><subject>Full Papers</subject></subj-group></article-categories><title-group><article-title>Identifying the genome-wide genetic variation between precocious trifoliate orange and its wild type and developing new markers for genetics research</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Zhang</surname><given-names>Jin-Zhi</given-names></name></contrib><contrib contrib-type="author"><name><surname>Liu</surname><given-names>Sheng-Rui</given-names></name></contrib><contrib contrib-type="author"><name><surname>Hu</surname><given-names>Chun-Gen</given-names></name><xref ref-type="corresp" rid="cor1">*</xref></contrib><aff><addr-line>Key Laboratory of Horticultural Plant Biology (Ministry of Education)</addr-line>,<institution>College of Horticulture and Forestry Science, Huazhong Agricultural University</institution>,<addr-line>Wuhan 430070</addr-line>,<country>China</country></aff></contrib-group><author-notes><corresp id="cor1"><label>*</label>To whom correspondence should be addressed. Tel. +86 27-87281826. Fax. +86 27-87281826. E-mail: <email>chungen@mail.hzau.edu.cn</email></corresp><fn fn-type="con" id="TN1"><p>Edited by Dr Satoshi Tabata</p></fn></author-notes><pub-date pub-type="ppub"><month>8</month><year>2016</year></pub-date><pub-date pub-type="epub"><day>21</day><month>4</month><year>2016</year></pub-date><pub-date pub-type="pmc-release"><day>21</day><month>4</month><year>2016</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>23</volume><issue>4</issue><fpage>403</fpage><lpage>414</lpage><history><date date-type="received"><day>13</day><month>12</month><year>2015</year></date><date date-type="accepted"><day>21</day><month>3</month><year>2016</year></date></history><permissions><copyright-statement>© The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.</copyright-statement><copyright-year>2016</copyright-year><license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by-nc/4.0/"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc/4.0/">http://creativecommons.org/licenses/by-nc/4.0/</ext-link>), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com</license-p></license></permissions><self-uri content-type="pdf" xlink:href="dsw017.pdf"></self-uri><abstract><p>To increase our understanding of the genes involved in flowering in citrus, we performed genome resequencing of an early flowering trifoliate orange mutant (<italic>Poncirus trifoliata</italic> L. Raf.) and its wild type. At the genome level, 3,932,628 single nucleotide polymorphisms (SNPs), 1,293,383 insertion/deletion polymorphisms (InDels), and 52,135 structural variations were identified between the mutant and its wild type based on the citrus reference genome. Based on integrative analysis of resequencing and transcriptome analysis, 233,998 SNPs and 75,836 InDels were also identified between the mutant and its wild type at the transcriptional level. Also, 272 citrus homologous flowering-time transcripts containing genetic variation were also identified. Gene Ontology and Kyoto Encyclopaedia of Genes and Genomes annotation revealed that the transcripts containing the mutant- and the wild-type-specific InDel were involved in diverse biological processes and molecular function. Among these transcripts, there were 131 transcripts that were expressed differently in the two genotypes. When 268 selected InDels were tested on 32 genotypes of the three genera of Rutaceae for the genetic diversity assessment, these InDel-based markers showed high transferability. This work provides important information that will allow a better understanding of the citrus genome and that will be helpful for dissecting the genetic basis of important traits in citrus.</p></abstract><kwd-group><kwd>citrus</kwd><kwd>flowering</kwd><kwd>genome resequencing</kwd><kwd>genetic variation</kwd><kwd>SNP</kwd></kwd-group><funding-group><award-group id="funding-1"><funding-source>National Natural Science Foundation of China <named-content content-type="funder-id">http://dx.doi.org/10.13039/501100001809</named-content></funding-source><award-id>31130046</award-id><award-id>31471863</award-id><award-id>31372046</award-id><award-id>31221062</award-id><award-id>31101528</award-id></award-group><award-group id="funding-2"><funding-source>Fundamental Research Funds for the Central Universities</funding-source><award-id>2013PY083</award-id></award-group><award-group id="funding-3"><funding-source>International Foundation for Science <named-content content-type="funder-id">http://dx.doi.org/10.13039/501100001724</named-content></funding-source><award-id>C/5148-2</award-id></award-group><award-group id="funding-4"><funding-source>National Science Foundation of China</funding-source><award-id>31130046</award-id></award-group></funding-group><counts><page-count count="12"></page-count></counts></article-meta></front></pmc><affiliations><list></list><tree><noCountry><name sortKey="Hu, Chun Gen" sort="Hu, Chun Gen" uniqKey="Hu C" first="Chun-Gen" last="Hu">Chun-Gen Hu</name><name sortKey="Liu, Sheng Rui" sort="Liu, Sheng Rui" uniqKey="Liu S" first="Sheng-Rui" last="Liu">Sheng-Rui Liu</name><name sortKey="Zhang, Jin Zhi" sort="Zhang, Jin Zhi" uniqKey="Zhang J" first="Jin-Zhi" last="Zhang">Jin-Zhi Zhang</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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