Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus.
Identifieur interne : 000102 ( Main/Corpus ); précédent : 000101; suivant : 000103Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus.
Auteurs : Cheng Zou ; Avinash Karn ; Bruce Reisch ; Allen Nguyen ; Yongming Sun ; Yun Bao ; Michael S. Campbell ; Deanna Church ; Stephen Williams ; Xia Xu ; Craig A. Ledbetter ; Sagar Patel ; Anne Fennell ; Jeffrey C. Glaubitz ; Matthew Clark ; Doreen Ware ; Jason P. Londo ; Qi Sun ; Lance Cadle-DavidsonSource :
- Nature communications [ 2041-1723 ] ; 2020.
English descriptors
- KwdEn :
- Alleles (MeSH), Chromosome Mapping (methods), DNA, Plant (genetics), DNA, Plant (isolation & purification), Genetic Markers (genetics), Genome, Plant (MeSH), Genotyping Techniques (methods), Haplotypes (MeSH), High-Throughput Nucleotide Sequencing (MeSH), Microsatellite Repeats (genetics), Phylogeny (MeSH), Plant Breeding (MeSH), Polymorphism, Single Nucleotide (MeSH), Sequence Analysis, DNA (methods), Vitis (genetics).
- MESH :
- chemical , genetics : DNA, Plant, Genetic Markers.
- chemical , isolation & purification : DNA, Plant.
- genetics : Microsatellite Repeats, Vitis.
- methods : Chromosome Mapping, Genotyping Techniques, Sequence Analysis, DNA.
- Alleles, Genome, Plant, Haplotypes, High-Throughput Nucleotide Sequencing, Phylogeny, Plant Breeding, Polymorphism, Single Nucleotide.
Abstract
Transferable DNA markers are essential for breeding and genetics. Grapevine (Vitis) breeders utilize disease resistance alleles from congeneric species ~20 million years divergent, but existing Vitis marker platforms have cross-species transfer rates as low as 2%. Here, we apply a marker strategy targeting the inferred Vitis core genome. Incorporating seven linked-read de novo assemblies and three existing assemblies, the Vitis collinear core genome is estimated to converge at 39.8 Mb (8.67% of the genome). Adding shotgun genome sequences from 40 accessions enables identification of conserved core PCR primer binding sites flanking polymorphic haplotypes with high information content. From these target regions, we develop 2,000 rhAmpSeq markers as a PCR multiplex and validate the panel in four biparental populations spanning the diversity of the Vitis genus, showing transferability increases to 91.9%. This marker development strategy should be widely applicable for genetic studies in many taxa, particularly those ~20 million years divergent.
DOI: 10.1038/s41467-019-14280-1
PubMed: 31964885
PubMed Central: PMC6972940
Links to Exploration step
pubmed:31964885Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus.</title><author><name sortKey="Zou, Cheng" sort="Zou, Cheng" uniqKey="Zou C" first="Cheng" last="Zou">Cheng Zou</name><affiliation><nlm:affiliation>BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Karn, Avinash" sort="Karn, Avinash" uniqKey="Karn A" first="Avinash" last="Karn">Avinash Karn</name><affiliation><nlm:affiliation>School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY, 14456, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Reisch, Bruce" sort="Reisch, Bruce" uniqKey="Reisch B" first="Bruce" last="Reisch">Bruce Reisch</name><affiliation><nlm:affiliation>School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY, 14456, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Nguyen, Allen" sort="Nguyen, Allen" uniqKey="Nguyen A" first="Allen" last="Nguyen">Allen Nguyen</name><affiliation><nlm:affiliation>Integrated DNA Technologies, Redwood City, CA, 94063, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Sun, Yongming" sort="Sun, Yongming" uniqKey="Sun Y" first="Yongming" last="Sun">Yongming Sun</name><affiliation><nlm:affiliation>Integrated DNA Technologies, Redwood City, CA, 94063, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Bao, Yun" sort="Bao, Yun" uniqKey="Bao Y" first="Yun" last="Bao">Yun Bao</name><affiliation><nlm:affiliation>Integrated DNA Technologies, Redwood City, CA, 94063, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Campbell, Michael S" sort="Campbell, Michael S" uniqKey="Campbell M" first="Michael S" last="Campbell">Michael S. 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Glaubitz</name><affiliation><nlm:affiliation>BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Clark, Matthew" sort="Clark, Matthew" uniqKey="Clark M" first="Matthew" last="Clark">Matthew Clark</name><affiliation><nlm:affiliation>Department of Horticultural Science, University of Minnesota, Saint Paul, MN, 55108, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Ware, Doreen" sort="Ware, Doreen" uniqKey="Ware D" first="Doreen" last="Ware">Doreen Ware</name><affiliation><nlm:affiliation>Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Londo, Jason P" sort="Londo, Jason P" uniqKey="Londo J" first="Jason P" last="Londo">Jason P. Londo</name><affiliation><nlm:affiliation>USDA-ARS, Grape Genetics Research Unit, Geneva, NY, 14456, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Sun, Qi" sort="Sun, Qi" uniqKey="Sun Q" first="Qi" last="Sun">Qi Sun</name><affiliation><nlm:affiliation>BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Cadle Davidson, Lance" sort="Cadle Davidson, Lance" uniqKey="Cadle Davidson L" first="Lance" last="Cadle-Davidson">Lance Cadle-Davidson</name><affiliation><nlm:affiliation>USDA-ARS, Grape Genetics Research Unit, Geneva, NY, 14456, USA. Lance.CadleDavidson@ars.usda.gov.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno type="RBID">pubmed:31964885</idno><idno type="pmid">31964885</idno><idno type="doi">10.1038/s41467-019-14280-1</idno><idno type="pmc">PMC6972940</idno><idno type="wicri:Area/Main/Corpus">000102</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000102</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus.</title><author><name sortKey="Zou, Cheng" sort="Zou, Cheng" uniqKey="Zou C" first="Cheng" last="Zou">Cheng Zou</name><affiliation><nlm:affiliation>BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Karn, Avinash" sort="Karn, Avinash" uniqKey="Karn A" first="Avinash" last="Karn">Avinash Karn</name><affiliation><nlm:affiliation>School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY, 14456, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Reisch, Bruce" sort="Reisch, Bruce" uniqKey="Reisch B" first="Bruce" last="Reisch">Bruce Reisch</name><affiliation><nlm:affiliation>School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY, 14456, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Nguyen, Allen" sort="Nguyen, Allen" uniqKey="Nguyen A" first="Allen" last="Nguyen">Allen Nguyen</name><affiliation><nlm:affiliation>Integrated DNA Technologies, Redwood City, CA, 94063, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Sun, Yongming" sort="Sun, Yongming" uniqKey="Sun Y" first="Yongming" last="Sun">Yongming Sun</name><affiliation><nlm:affiliation>Integrated DNA Technologies, Redwood City, CA, 94063, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Bao, Yun" sort="Bao, Yun" uniqKey="Bao Y" first="Yun" last="Bao">Yun Bao</name><affiliation><nlm:affiliation>Integrated DNA Technologies, Redwood City, CA, 94063, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Campbell, Michael S" sort="Campbell, Michael S" uniqKey="Campbell M" first="Michael S" last="Campbell">Michael S. Campbell</name><affiliation><nlm:affiliation>10x Genomics, Inc., Pleasanton, CA, 94566, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Church, Deanna" sort="Church, Deanna" uniqKey="Church D" first="Deanna" last="Church">Deanna Church</name><affiliation><nlm:affiliation>10x Genomics, Inc., Pleasanton, CA, 94566, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Williams, Stephen" sort="Williams, Stephen" uniqKey="Williams S" first="Stephen" last="Williams">Stephen Williams</name><affiliation><nlm:affiliation>10x Genomics, Inc., Pleasanton, CA, 94566, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Xu, Xia" sort="Xu, Xia" uniqKey="Xu X" first="Xia" last="Xu">Xia Xu</name><affiliation><nlm:affiliation>USDA-ARS, Grape Genetics Research Unit, Geneva, NY, 14456, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Ledbetter, Craig A" sort="Ledbetter, Craig A" uniqKey="Ledbetter C" first="Craig A" last="Ledbetter">Craig A. Ledbetter</name><affiliation><nlm:affiliation>USDA-ARS, Crop Diseases, Pests and Genetics Research, Parlier, CA, 93648, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Patel, Sagar" sort="Patel, Sagar" uniqKey="Patel S" first="Sagar" last="Patel">Sagar Patel</name><affiliation><nlm:affiliation>Agronomy, Horticulture and Plant Science Department, South Dakota State University, Brookings, SD, 57007, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Fennell, Anne" sort="Fennell, Anne" uniqKey="Fennell A" first="Anne" last="Fennell">Anne Fennell</name><affiliation><nlm:affiliation>Agronomy, Horticulture and Plant Science Department, South Dakota State University, Brookings, SD, 57007, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Glaubitz, Jeffrey C" sort="Glaubitz, Jeffrey C" uniqKey="Glaubitz J" first="Jeffrey C" last="Glaubitz">Jeffrey C. Glaubitz</name><affiliation><nlm:affiliation>BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Clark, Matthew" sort="Clark, Matthew" uniqKey="Clark M" first="Matthew" last="Clark">Matthew Clark</name><affiliation><nlm:affiliation>Department of Horticultural Science, University of Minnesota, Saint Paul, MN, 55108, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Ware, Doreen" sort="Ware, Doreen" uniqKey="Ware D" first="Doreen" last="Ware">Doreen Ware</name><affiliation><nlm:affiliation>Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Londo, Jason P" sort="Londo, Jason P" uniqKey="Londo J" first="Jason P" last="Londo">Jason P. Londo</name><affiliation><nlm:affiliation>USDA-ARS, Grape Genetics Research Unit, Geneva, NY, 14456, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Sun, Qi" sort="Sun, Qi" uniqKey="Sun Q" first="Qi" last="Sun">Qi Sun</name><affiliation><nlm:affiliation>BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Cadle Davidson, Lance" sort="Cadle Davidson, Lance" uniqKey="Cadle Davidson L" first="Lance" last="Cadle-Davidson">Lance Cadle-Davidson</name><affiliation><nlm:affiliation>USDA-ARS, Grape Genetics Research Unit, Geneva, NY, 14456, USA. Lance.CadleDavidson@ars.usda.gov.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Nature communications</title><idno type="eISSN">2041-1723</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Alleles (MeSH)</term><term>Chromosome Mapping (methods)</term><term>DNA, Plant (genetics)</term><term>DNA, Plant (isolation & purification)</term><term>Genetic Markers (genetics)</term><term>Genome, Plant (MeSH)</term><term>Genotyping Techniques (methods)</term><term>Haplotypes (MeSH)</term><term>High-Throughput Nucleotide Sequencing (MeSH)</term><term>Microsatellite Repeats (genetics)</term><term>Phylogeny (MeSH)</term><term>Plant Breeding (MeSH)</term><term>Polymorphism, Single Nucleotide (MeSH)</term><term>Sequence Analysis, DNA (methods)</term><term>Vitis (genetics)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Plant</term><term>Genetic Markers</term></keywords><keywords scheme="MESH" type="chemical" qualifier="isolation & purification" xml:lang="en"><term>DNA, Plant</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Microsatellite Repeats</term><term>Vitis</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Chromosome Mapping</term><term>Genotyping Techniques</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Alleles</term><term>Genome, Plant</term><term>Haplotypes</term><term>High-Throughput Nucleotide Sequencing</term><term>Phylogeny</term><term>Plant Breeding</term><term>Polymorphism, Single Nucleotide</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Transferable DNA markers are essential for breeding and genetics. Grapevine (Vitis) breeders utilize disease resistance alleles from congeneric species ~20 million years divergent, but existing Vitis marker platforms have cross-species transfer rates as low as 2%. Here, we apply a marker strategy targeting the inferred Vitis core genome. Incorporating seven linked-read de novo assemblies and three existing assemblies, the Vitis collinear core genome is estimated to converge at 39.8 Mb (8.67% of the genome). Adding shotgun genome sequences from 40 accessions enables identification of conserved core PCR primer binding sites flanking polymorphic haplotypes with high information content. From these target regions, we develop 2,000 rhAmpSeq markers as a PCR multiplex and validate the panel in four biparental populations spanning the diversity of the Vitis genus, showing transferability increases to 91.9%. This marker development strategy should be widely applicable for genetic studies in many taxa, particularly those ~20 million years divergent.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">31964885</PMID><DateCompleted><Year>2020</Year><Month>05</Month><Day>11</Day></DateCompleted><DateRevised><Year>2020</Year><Month>05</Month><Day>11</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">2041-1723</ISSN><JournalIssue CitedMedium="Internet"><Volume>11</Volume><Issue>1</Issue><PubDate><Year>2020</Year><Month>01</Month><Day>21</Day></PubDate></JournalIssue><Title>Nature communications</Title><ISOAbbreviation>Nat Commun</ISOAbbreviation></Journal><ArticleTitle>Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus.</ArticleTitle><Pagination><MedlinePgn>413</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1038/s41467-019-14280-1</ELocationID><Abstract><AbstractText>Transferable DNA markers are essential for breeding and genetics. Grapevine (Vitis) breeders utilize disease resistance alleles from congeneric species ~20 million years divergent, but existing Vitis marker platforms have cross-species transfer rates as low as 2%. Here, we apply a marker strategy targeting the inferred Vitis core genome. Incorporating seven linked-read de novo assemblies and three existing assemblies, the Vitis collinear core genome is estimated to converge at 39.8 Mb (8.67% of the genome). Adding shotgun genome sequences from 40 accessions enables identification of conserved core PCR primer binding sites flanking polymorphic haplotypes with high information content. From these target regions, we develop 2,000 rhAmpSeq markers as a PCR multiplex and validate the panel in four biparental populations spanning the diversity of the Vitis genus, showing transferability increases to 91.9%. This marker development strategy should be widely applicable for genetic studies in many taxa, particularly those ~20 million years divergent.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Zou</LastName><ForeName>Cheng</ForeName><Initials>C</Initials><Identifier Source="ORCID">0000-0001-9325-9465</Identifier><AffiliationInfo><Affiliation>BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Karn</LastName><ForeName>Avinash</ForeName><Initials>A</Initials><Identifier Source="ORCID">0000-0001-9730-8922</Identifier><AffiliationInfo><Affiliation>School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY, 14456, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Reisch</LastName><ForeName>Bruce</ForeName><Initials>B</Initials><Identifier Source="ORCID">0000-0003-0197-7123</Identifier><AffiliationInfo><Affiliation>School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY, 14456, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nguyen</LastName><ForeName>Allen</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Integrated DNA Technologies, Redwood City, CA, 94063, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sun</LastName><ForeName>Yongming</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Integrated DNA Technologies, Redwood City, CA, 94063, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bao</LastName><ForeName>Yun</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Integrated DNA Technologies, Redwood City, CA, 94063, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Campbell</LastName><ForeName>Michael S</ForeName><Initials>MS</Initials><AffiliationInfo><Affiliation>10x Genomics, Inc., Pleasanton, CA, 94566, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Church</LastName><ForeName>Deanna</ForeName><Initials>D</Initials><Identifier Source="ORCID">0000-0003-4264-1853</Identifier><AffiliationInfo><Affiliation>10x Genomics, Inc., Pleasanton, CA, 94566, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Williams</LastName><ForeName>Stephen</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>10x Genomics, Inc., Pleasanton, CA, 94566, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Xia</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>USDA-ARS, Grape Genetics Research Unit, Geneva, NY, 14456, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ledbetter</LastName><ForeName>Craig A</ForeName><Initials>CA</Initials><AffiliationInfo><Affiliation>USDA-ARS, Crop Diseases, Pests and Genetics Research, Parlier, CA, 93648, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Patel</LastName><ForeName>Sagar</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Agronomy, Horticulture and Plant Science Department, South Dakota State University, Brookings, SD, 57007, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fennell</LastName><ForeName>Anne</ForeName><Initials>A</Initials><Identifier Source="ORCID">0000-0002-4234-6419</Identifier><AffiliationInfo><Affiliation>Agronomy, Horticulture and Plant Science Department, South Dakota State University, Brookings, SD, 57007, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Glaubitz</LastName><ForeName>Jeffrey C</ForeName><Initials>JC</Initials><AffiliationInfo><Affiliation>BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Clark</LastName><ForeName>Matthew</ForeName><Initials>M</Initials><Identifier Source="ORCID">0000-0002-1771-1955</Identifier><AffiliationInfo><Affiliation>Department of Horticultural Science, University of Minnesota, Saint Paul, MN, 55108, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ware</LastName><ForeName>Doreen</ForeName><Initials>D</Initials><Identifier Source="ORCID">0000-0002-8125-3821</Identifier><AffiliationInfo><Affiliation>Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Londo</LastName><ForeName>Jason P</ForeName><Initials>JP</Initials><AffiliationInfo><Affiliation>USDA-ARS, Grape Genetics Research Unit, Geneva, NY, 14456, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sun</LastName><ForeName>Qi</ForeName><Initials>Q</Initials><AffiliationInfo><Affiliation>BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cadle-Davidson</LastName><ForeName>Lance</ForeName><Initials>L</Initials><Identifier Source="ORCID">0000-0003-4241-4634</Identifier><AffiliationInfo><Affiliation>USDA-ARS, Grape Genetics Research Unit, Geneva, NY, 14456, USA. Lance.CadleDavidson@ars.usda.gov.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>2017- 51181-26829</GrantID><Agency>United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)</Agency><Country>International</Country></Grant><Grant><GrantID>SD00R668-18</GrantID><Agency>United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)</Agency><Country>International</Country></Grant><Grant><GrantID>8060-21220-007-00-D</GrantID><Agency>United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)</Agency><Country>International</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>01</Month><Day>21</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Nat Commun</MedlineTA><NlmUniqueID>101528555</NlmUniqueID><ISSNLinking>2041-1723</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018744">DNA, Plant</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005819">Genetic Markers</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000483" MajorTopicYN="N">Alleles</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002874" MajorTopicYN="N">Chromosome Mapping</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018744" MajorTopicYN="N">DNA, Plant</DescriptorName><QualifierName UI="Q000235" 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