Leaf Transcriptome Sequencing for Identifying Genic-SSR Markers and SNP Heterozygosity in Crossbred Mango Variety ‘Amrapali’ (Mangifera indica L.)
Identifieur interne : 002202 ( Ncbi/Merge ); précédent : 002201; suivant : 002203Leaf Transcriptome Sequencing for Identifying Genic-SSR Markers and SNP Heterozygosity in Crossbred Mango Variety ‘Amrapali’ (Mangifera indica L.)
Auteurs : Ajay Kumar Mahato [Inde] ; Nimisha Sharma [Inde] ; Akshay Singh [Inde] ; Manish Srivastav [Inde] ; Sanjay Kumar Singh [Inde] ; Anand Kumar Singh [Inde] ; Tilak Raj Sharma [Inde] ; Nagendra Kumar Singh [Inde]Source :
- PLoS ONE [ 1932-6203 ] ; 2016.
Abstract
Mango (
Url:
DOI: 10.1371/journal.pone.0164325
PubMed: 27736892
PubMed Central: 5063295
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Leaf Transcriptome Sequencing for Identifying Genic-SSR Markers and SNP Heterozygosity in Crossbred Mango Variety ‘Amrapali’ (<italic>Mangifera indica</italic> L.)</title><author><name sortKey="Mahato, Ajay Kumar" sort="Mahato, Ajay Kumar" uniqKey="Mahato A" first="Ajay Kumar" last="Mahato">Ajay Kumar Mahato</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi</wicri:regionArea><wicri:noRegion>New Delhi</wicri:noRegion></affiliation></author><author><name sortKey="Sharma, Nimisha" sort="Sharma, Nimisha" uniqKey="Sharma N" first="Nimisha" last="Sharma">Nimisha Sharma</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>The Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>The Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi</wicri:regionArea><wicri:noRegion>New Delhi</wicri:noRegion></affiliation></author><author><name sortKey="Singh, Akshay" sort="Singh, Akshay" uniqKey="Singh A" first="Akshay" last="Singh">Akshay Singh</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi</wicri:regionArea><wicri:noRegion>New Delhi</wicri:noRegion></affiliation></author><author><name sortKey="Srivastav, Manish" sort="Srivastav, Manish" uniqKey="Srivastav M" first="Manish" last="Srivastav">Manish Srivastav</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>The Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>The Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi</wicri:regionArea><wicri:noRegion>New Delhi</wicri:noRegion></affiliation></author><author><name sortKey="Singh, Sanjay Kumar" sort="Singh, Sanjay Kumar" uniqKey="Singh S" first="Sanjay Kumar" last="Singh">Sanjay Kumar Singh</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>The Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>The Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi</wicri:regionArea><wicri:noRegion>New Delhi</wicri:noRegion></affiliation></author><author><name sortKey="Singh, Anand Kumar" sort="Singh, Anand Kumar" uniqKey="Singh A" first="Anand Kumar" last="Singh">Anand Kumar Singh</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>The Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>The Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi</wicri:regionArea><wicri:noRegion>New Delhi</wicri:noRegion></affiliation></author><author><name sortKey="Sharma, Tilak Raj" sort="Sharma, Tilak Raj" uniqKey="Sharma T" first="Tilak Raj" last="Sharma">Tilak Raj Sharma</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi</wicri:regionArea><wicri:noRegion>New Delhi</wicri:noRegion></affiliation></author><author><name sortKey="Singh, Nagendra Kumar" sort="Singh, Nagendra Kumar" uniqKey="Singh N" first="Nagendra Kumar" last="Singh">Nagendra Kumar Singh</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi</wicri:regionArea><wicri:noRegion>New Delhi</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27736892</idno><idno type="pmc">5063295</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5063295</idno><idno type="RBID">PMC:5063295</idno><idno type="doi">10.1371/journal.pone.0164325</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">001100</idno><idno type="wicri:Area/Pmc/Curation">001099</idno><idno type="wicri:Area/Pmc/Checkpoint">000121</idno><idno type="wicri:Area/Ncbi/Merge">002202</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Leaf Transcriptome Sequencing for Identifying Genic-SSR Markers and SNP Heterozygosity in Crossbred Mango Variety ‘Amrapali’ (<italic>Mangifera indica</italic> L.)</title><author><name sortKey="Mahato, Ajay Kumar" sort="Mahato, Ajay Kumar" uniqKey="Mahato A" first="Ajay Kumar" last="Mahato">Ajay Kumar Mahato</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi</wicri:regionArea><wicri:noRegion>New Delhi</wicri:noRegion></affiliation></author><author><name sortKey="Sharma, Nimisha" sort="Sharma, Nimisha" uniqKey="Sharma N" first="Nimisha" last="Sharma">Nimisha Sharma</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>The Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>The Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi</wicri:regionArea><wicri:noRegion>New Delhi</wicri:noRegion></affiliation></author><author><name sortKey="Singh, Akshay" sort="Singh, Akshay" uniqKey="Singh A" first="Akshay" last="Singh">Akshay Singh</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi</wicri:regionArea><wicri:noRegion>New Delhi</wicri:noRegion></affiliation></author><author><name sortKey="Srivastav, Manish" sort="Srivastav, Manish" uniqKey="Srivastav M" first="Manish" last="Srivastav">Manish Srivastav</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>The Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>The Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi</wicri:regionArea><wicri:noRegion>New Delhi</wicri:noRegion></affiliation></author><author><name sortKey="Singh, Sanjay Kumar" sort="Singh, Sanjay Kumar" uniqKey="Singh S" first="Sanjay Kumar" last="Singh">Sanjay Kumar Singh</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>The Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>The Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi</wicri:regionArea><wicri:noRegion>New Delhi</wicri:noRegion></affiliation></author><author><name sortKey="Singh, Anand Kumar" sort="Singh, Anand Kumar" uniqKey="Singh A" first="Anand Kumar" last="Singh">Anand Kumar Singh</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>The Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>The Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi</wicri:regionArea><wicri:noRegion>New Delhi</wicri:noRegion></affiliation></author><author><name sortKey="Sharma, Tilak Raj" sort="Sharma, Tilak Raj" uniqKey="Sharma T" first="Tilak Raj" last="Sharma">Tilak Raj Sharma</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi</wicri:regionArea><wicri:noRegion>New Delhi</wicri:noRegion></affiliation></author><author><name sortKey="Singh, Nagendra Kumar" sort="Singh, Nagendra Kumar" uniqKey="Singh N" first="Nagendra Kumar" last="Singh">Nagendra Kumar Singh</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi</wicri:regionArea><wicri:noRegion>New Delhi</wicri:noRegion></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</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>Mango (<italic>Mangifera indica</italic> L.) is called “king of fruits” due to its sweetness, richness of taste, diversity, large production volume and a variety of end usage. Despite its huge economic importance genomic resources in mango are scarce and genetics of useful horticultural traits are poorly understood. Here we generated deep coverage leaf RNA sequence data for mango parental varieties ‘Neelam’, ‘Dashehari’ and their hybrid ‘Amrapali’ using next generation sequencing technologies. De-novo sequence assembly generated 27,528, 20,771 and 35,182 transcripts for the three genotypes, respectively. The transcripts were further assembled into a non-redundant set of 70,057 unigenes that were used for SSR and SNP identification and annotation. Total 5,465 SSR loci were identified in 4,912 unigenes with 288 type I SSR (n ≥ 20 bp). One hundred type I SSR markers were randomly selected of which 43 yielded PCR amplicons of expected size in the first round of validation and were designated as validated genic-SSR markers. Further, 22,306 SNPs were identified by aligning high quality sequence reads of the three mango varieties to the reference unigene set, revealing significantly enhanced SNP heterozygosity in the hybrid Amrapali. The present study on leaf RNA sequencing of mango varieties and their hybrid provides useful genomic resource for genetic improvement of mango.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Mukherjee, Sk" uniqKey="Mukherjee S">SK Mukherjee</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Arumuganathan, K" uniqKey="Arumuganathan K">K Arumuganathan</name></author><author><name sortKey="Earle, Ed" uniqKey="Earle E">ED Earle</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Tharanathan, Rn" uniqKey="Tharanathan R">RN Tharanathan</name></author><author><name sortKey="Yashoda, Hm" uniqKey="Yashoda H">HM Yashoda</name></author><author><name sortKey="Prabha, Tn" uniqKey="Prabha T">TN Prabha</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Singh, Nk" uniqKey="Singh N">NK 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<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id><journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">plosone</journal-id><journal-title-group><journal-title>PLoS ONE</journal-title></journal-title-group><issn pub-type="epub">1932-6203</issn><publisher><publisher-name>Public Library of Science</publisher-name><publisher-loc>San Francisco, CA USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">27736892</article-id><article-id pub-id-type="pmc">5063295</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0164325</article-id><article-id pub-id-type="publisher-id">PONE-D-16-26531</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Computational Biology</subject><subj-group><subject>Genome Analysis</subject><subj-group><subject>Transcriptome Analysis</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Genetics</subject><subj-group><subject>Genomics</subject><subj-group><subject>Genome Analysis</subject><subj-group><subject>Transcriptome Analysis</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Computational Biology</subject><subj-group><subject>Genome Analysis</subject><subj-group><subject>Gene Ontologies</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Genetics</subject><subj-group><subject>Genomics</subject><subj-group><subject>Genome Analysis</subject><subj-group><subject>Gene Ontologies</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Genetics</subject><subj-group><subject>Heredity</subject><subj-group><subject>Heterozygosity</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Plant Science</subject><subj-group><subject>Plant Anatomy</subject><subj-group><subject>Leaves</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Research and Analysis Methods</subject><subj-group><subject>Database and Informatics Methods</subject><subj-group><subject>Database Searching</subject></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Research and Analysis Methods</subject><subj-group><subject>Database and Informatics Methods</subject><subj-group><subject>Biological Databases</subject><subj-group><subject>Sequence Databases</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Molecular Biology</subject><subj-group><subject>Molecular Biology Techniques</subject><subj-group><subject>Sequencing Techniques</subject><subj-group><subject>Sequence Analysis</subject><subj-group><subject>Sequence Databases</subject></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Research and Analysis Methods</subject><subj-group><subject>Molecular Biology Techniques</subject><subj-group><subject>Sequencing Techniques</subject><subj-group><subject>Sequence Analysis</subject><subj-group><subject>Sequence Databases</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Molecular Biology</subject><subj-group><subject>Molecular Biology Techniques</subject><subj-group><subject>Artificial Gene Amplification and Extension</subject><subj-group><subject>Polymerase Chain Reaction</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Research and Analysis Methods</subject><subj-group><subject>Molecular Biology Techniques</subject><subj-group><subject>Artificial Gene Amplification and Extension</subject><subj-group><subject>Polymerase Chain Reaction</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and life sciences</subject><subj-group><subject>Biochemistry</subject><subj-group><subject>Proteins</subject><subj-group><subject>DNA-binding proteins</subject><subj-group><subject>Transcription Factors</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Genetics</subject><subj-group><subject>Gene Expression</subject><subj-group><subject>Gene Regulation</subject><subj-group><subject>Transcription Factors</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Biochemistry</subject><subj-group><subject>Proteins</subject><subj-group><subject>Regulatory Proteins</subject><subj-group><subject>Transcription Factors</subject></subj-group></subj-group></subj-group></subj-group></subj-group></article-categories><title-group><article-title>Leaf Transcriptome Sequencing for Identifying Genic-SSR Markers and SNP Heterozygosity in Crossbred Mango Variety ‘Amrapali’ (<italic>Mangifera indica</italic> L.)</article-title><alt-title alt-title-type="running-head">Genic-SSR Markers and SNP Heterozygosity in Mango</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Mahato</surname><given-names>Ajay Kumar</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Sharma</surname><given-names>Nimisha</given-names></name><xref ref-type="aff" rid="aff002"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Singh</surname><given-names>Akshay</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Srivastav</surname><given-names>Manish</given-names></name><xref ref-type="aff" rid="aff002"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Jaiprakash</surname><given-names></given-names></name><xref ref-type="aff" rid="aff002"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Singh</surname><given-names>Sanjay Kumar</given-names></name><xref ref-type="aff" rid="aff002"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Singh</surname><given-names>Anand Kumar</given-names></name><xref ref-type="aff" rid="aff002"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Sharma</surname><given-names>Tilak Raj</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Singh</surname><given-names>Nagendra Kumar</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref><xref ref-type="corresp" rid="cor001">*</xref></contrib></contrib-group><aff id="aff001"><label>1</label><addr-line>ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India</addr-line></aff><aff id="aff002"><label>2</label><addr-line>The Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Parida</surname><given-names>Swarup Kumar</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1"><addr-line>National Institute for Plant Genome Research, INDIA</addr-line></aff><author-notes><fn fn-type="COI-statement" id="coi001"><p><bold>Competing Interests: </bold>The authors have declared that no competing interests exist.</p></fn><fn fn-type="con"><p><list list-type="simple"><list-item><p><bold>Conceptualization:</bold> NKS AKM.</p></list-item><list-item><p><bold>Data curation:</bold> AKM NS AS.</p></list-item><list-item><p><bold>Funding acquisition:</bold> NKS AKS.</p></list-item><list-item><p><bold>Methodology:</bold> AKM.</p></list-item><list-item><p><bold>Project administration:</bold> NKS AKM.</p></list-item><list-item><p><bold>Resources:</bold> NKS AKS MS J SKS TRS.</p></list-item><list-item><p><bold>Software:</bold> AKM.</p></list-item><list-item><p><bold>Supervision:</bold> NKS.</p></list-item><list-item><p><bold>Validation:</bold> AKM NS.</p></list-item><list-item><p><bold>Visualization:</bold> AKM.</p></list-item><list-item><p><bold>Writing – original draft:</bold> AKM NS.</p></list-item><list-item><p><bold>Writing – review & editing:</bold> NKS TRS AKM.</p></list-item></list></p></fn><corresp id="cor001">* E-mail: <email>nksingh4@gmail.com</email></corresp></author-notes><pub-date pub-type="epub"><day>13</day><month>10</month><year>2016</year></pub-date><pub-date pub-type="collection"><year>2016</year></pub-date><volume>11</volume><issue>10</issue><elocation-id>e0164325</elocation-id><history><date date-type="received"><day>2</day><month>7</month><year>2016</year></date><date date-type="accepted"><day>25</day><month>9</month><year>2016</year></date></history><permissions><copyright-statement>© 2016 Mahato et al</copyright-statement><copyright-year>2016</copyright-year><copyright-holder>Mahato et al</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 <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</ext-link>, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</license-p></license></permissions><self-uri content-type="pdf" xlink:href="pone.0164325.pdf"></self-uri><abstract><p>Mango (<italic>Mangifera indica</italic> L.) is called “king of fruits” due to its sweetness, richness of taste, diversity, large production volume and a variety of end usage. Despite its huge economic importance genomic resources in mango are scarce and genetics of useful horticultural traits are poorly understood. Here we generated deep coverage leaf RNA sequence data for mango parental varieties ‘Neelam’, ‘Dashehari’ and their hybrid ‘Amrapali’ using next generation sequencing technologies. De-novo sequence assembly generated 27,528, 20,771 and 35,182 transcripts for the three genotypes, respectively. The transcripts were further assembled into a non-redundant set of 70,057 unigenes that were used for SSR and SNP identification and annotation. Total 5,465 SSR loci were identified in 4,912 unigenes with 288 type I SSR (n ≥ 20 bp). One hundred type I SSR markers were randomly selected of which 43 yielded PCR amplicons of expected size in the first round of validation and were designated as validated genic-SSR markers. Further, 22,306 SNPs were identified by aligning high quality sequence reads of the three mango varieties to the reference unigene set, revealing significantly enhanced SNP heterozygosity in the hybrid Amrapali. The present study on leaf RNA sequencing of mango varieties and their hybrid provides useful genomic resource for genetic improvement of mango.</p></abstract><funding-group><award-group id="award001"><funding-source><institution-wrap><institution-id institution-id-type="funder-id">http://dx.doi.org/10.13039/501100001503</institution-id><institution>Indian Council of Agricultural Research</institution></institution-wrap></funding-source><award-id>ICAR-NPTC</award-id><principal-award-recipient>Nagendra K. Singh</principal-award-recipient></award-group><award-group id="award002"><funding-source><institution-wrap><institution-id institution-id-type="funder-id">http://dx.doi.org/10.13039/501100005384</institution-id><institution>Indian Agricultural Research Institute</institution></institution-wrap></funding-source><principal-award-recipient><name><surname>Singh</surname><given-names>Anand Kumar</given-names></name></principal-award-recipient></award-group><funding-statement>This work was supported by the Indian Council of Agriculture Research-Network Project on Transgenics in Crops (ICAR-NPTC-2001-3059) NKS, ICAR-Indian Agricultural Research Institute, New Delhi, AKS.</funding-statement></funding-group><counts><fig-count count="6"></fig-count><table-count count="3"></table-count><page-count count="16"></page-count></counts><custom-meta-group><custom-meta id="data-availability"><meta-name>Data Availability</meta-name><meta-value>Data are available from the following NCBI databases: NCBI Sequence Read Archive (SRA) accession numbers: SRR1298995, SRR1297075, SRR1956775; NCBI BioProject accession numbers: PRJNA193591, PRJNA193588, PRJNA279829; NCBI Transcriptome Shotgun Assembly (TSA) accession numbers: GBVX00000000, GBVW00000000, GEEEC00000000.</meta-value></custom-meta></custom-meta-group></article-meta><notes><title>Data Availability</title><p>Data are available from the following NCBI databases: NCBI Sequence Read Archive (SRA) accession numbers: SRR1298995, SRR1297075, SRR1956775; NCBI BioProject accession numbers: PRJNA193591, PRJNA193588, PRJNA279829; NCBI Transcriptome Shotgun Assembly (TSA) accession numbers: GBVX00000000, GBVW00000000, GEEEC00000000.</p></notes></front></pmc><affiliations><list><country><li>Inde</li></country></list><tree><country name="Inde"><noRegion><name sortKey="Mahato, Ajay Kumar" sort="Mahato, Ajay Kumar" uniqKey="Mahato A" first="Ajay Kumar" last="Mahato">Ajay Kumar Mahato</name></noRegion><name sortKey="Sharma, Nimisha" sort="Sharma, Nimisha" uniqKey="Sharma N" first="Nimisha" last="Sharma">Nimisha Sharma</name><name sortKey="Sharma, Tilak Raj" sort="Sharma, Tilak Raj" uniqKey="Sharma T" first="Tilak Raj" last="Sharma">Tilak Raj Sharma</name><name sortKey="Singh, Akshay" sort="Singh, Akshay" uniqKey="Singh A" first="Akshay" last="Singh">Akshay Singh</name><name sortKey="Singh, Anand Kumar" sort="Singh, Anand Kumar" uniqKey="Singh A" first="Anand Kumar" last="Singh">Anand Kumar Singh</name><name sortKey="Singh, Nagendra Kumar" sort="Singh, Nagendra Kumar" uniqKey="Singh N" first="Nagendra Kumar" last="Singh">Nagendra Kumar Singh</name><name sortKey="Singh, Sanjay Kumar" sort="Singh, Sanjay Kumar" uniqKey="Singh S" first="Sanjay Kumar" last="Singh">Sanjay Kumar Singh</name><name sortKey="Srivastav, Manish" sort="Srivastav, Manish" uniqKey="Srivastav M" first="Manish" last="Srivastav">Manish Srivastav</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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