High-quality SNP Linkage Maps Improved QTL Mapping and Genome Assembly in Populus.
Identifieur interne : 000351 ( Main/Exploration ); précédent : 000350; suivant : 000352High-quality SNP Linkage Maps Improved QTL Mapping and Genome Assembly in Populus.
Auteurs : Chunfa Tong [République populaire de Chine] ; Dan Yao [République populaire de Chine] ; Hainan Wu [République populaire de Chine] ; Yuhua Chen [République populaire de Chine] ; Wenguo Yang [République populaire de Chine] ; Wei Zhao [République populaire de Chine]Source :
- The Journal of heredity [ 1465-7333 ] ; 2020.
Abstract
With the advances in high-throughput sequencing technologies and the development of new software for extracting SNPs across a mapping population, it is possible to construct high-quality genetic maps with thousands of SNPs in outbred forest trees. Two parent-specific linkage maps were constructed with restriction site-associated DNA sequencing data from an F1 hybrid population derived from Populus deltoides and Populus simonii, and applied in QTL mapping and genome assembly. The female Populus deltoides map contained 4,018 SNPs, which were divided into 19 linkage groups under a wide range of LOD thresholds from 7 to 55. The male Populus simonii map showed similar characteristics, consisting of 2,097 SNPs, which also belonged to 19 linkage groups under LOD thresholds of 7 to 29. The SNP order of each linkage group was optimal among different ordering results from several available software. Moreover, the linkage maps allowed the detection of 39 QTLs underlying tree height and 47 for diameter at breast height. In addition, the linkage maps improved the anchoring of 689 contigs of Populus simonii to chromosomes. The two parental genetic maps of Populus are of high quality, especially in terms of SNP data quality, the SNP order within linkage groups, and the perfect match between the number of linkage groups and the karyotype of Populus, as well as the excellent performances in QTL mapping and genome assembly. Both approaches for extracting and ordering SNPs could be applied to other species for constructing high-quality genetic maps.
DOI: 10.1093/jhered/esaa039
PubMed: 32930789
Affiliations:
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Nanjing</wicri:regionArea><wicri:noRegion>Nanjing</wicri:noRegion></affiliation></author><author><name sortKey="Yao, Dan" sort="Yao, Dan" uniqKey="Yao D" first="Dan" last="Yao">Dan Yao</name><affiliation wicri:level="1"><nlm:affiliation>Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing</wicri:regionArea><wicri:noRegion>Nanjing</wicri:noRegion></affiliation></author><author><name sortKey="Wu, Hainan" sort="Wu, Hainan" uniqKey="Wu H" first="Hainan" last="Wu">Hainan Wu</name><affiliation wicri:level="1"><nlm:affiliation>Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing</wicri:regionArea><wicri:noRegion>Nanjing</wicri:noRegion></affiliation></author><author><name sortKey="Chen, Yuhua" sort="Chen, Yuhua" uniqKey="Chen Y" first="Yuhua" last="Chen">Yuhua Chen</name><affiliation wicri:level="1"><nlm:affiliation>Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing</wicri:regionArea><wicri:noRegion>Nanjing</wicri:noRegion></affiliation></author><author><name sortKey="Yang, Wenguo" sort="Yang, Wenguo" uniqKey="Yang W" first="Wenguo" last="Yang">Wenguo Yang</name><affiliation wicri:level="1"><nlm:affiliation>Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing</wicri:regionArea><wicri:noRegion>Nanjing</wicri:noRegion></affiliation></author><author><name sortKey="Zhao, Wei" sort="Zhao, Wei" uniqKey="Zhao W" first="Wei" last="Zhao">Wei Zhao</name><affiliation wicri:level="1"><nlm:affiliation>Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing</wicri:regionArea><wicri:noRegion>Nanjing</wicri:noRegion></affiliation></author></analytic><series><title level="j">The Journal of heredity</title><idno type="eISSN">1465-7333</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">With the advances in high-throughput sequencing technologies and the development of new software for extracting SNPs across a mapping population, it is possible to construct high-quality genetic maps with thousands of SNPs in outbred forest trees. Two parent-specific linkage maps were constructed with restriction site-associated DNA sequencing data from an F1 hybrid population derived from Populus deltoides and Populus simonii, and applied in QTL mapping and genome assembly. The female Populus deltoides map contained 4,018 SNPs, which were divided into 19 linkage groups under a wide range of LOD thresholds from 7 to 55. The male Populus simonii map showed similar characteristics, consisting of 2,097 SNPs, which also belonged to 19 linkage groups under LOD thresholds of 7 to 29. The SNP order of each linkage group was optimal among different ordering results from several available software. Moreover, the linkage maps allowed the detection of 39 QTLs underlying tree height and 47 for diameter at breast height. In addition, the linkage maps improved the anchoring of 689 contigs of Populus simonii to chromosomes. The two parental genetic maps of Populus are of high quality, especially in terms of SNP data quality, the SNP order within linkage groups, and the perfect match between the number of linkage groups and the karyotype of Populus, as well as the excellent performances in QTL mapping and genome assembly. Both approaches for extracting and ordering SNPs could be applied to other species for constructing high-quality genetic maps.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">32930789</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>15</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1465-7333</ISSN><JournalIssue CitedMedium="Internet"><PubDate><Year>2020</Year><Month>Sep</Month><Day>15</Day></PubDate></JournalIssue><Title>The Journal of heredity</Title><ISOAbbreviation>J Hered</ISOAbbreviation></Journal><ArticleTitle>High-quality SNP Linkage Maps Improved QTL Mapping and Genome Assembly in Populus.</ArticleTitle><ELocationID EIdType="pii" ValidYN="Y">esaa039</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1093/jhered/esaa039</ELocationID><Abstract><AbstractText>With the advances in high-throughput sequencing technologies and the development of new software for extracting SNPs across a mapping population, it is possible to construct high-quality genetic maps with thousands of SNPs in outbred forest trees. Two parent-specific linkage maps were constructed with restriction site-associated DNA sequencing data from an F1 hybrid population derived from Populus deltoides and Populus simonii, and applied in QTL mapping and genome assembly. The female Populus deltoides map contained 4,018 SNPs, which were divided into 19 linkage groups under a wide range of LOD thresholds from 7 to 55. The male Populus simonii map showed similar characteristics, consisting of 2,097 SNPs, which also belonged to 19 linkage groups under LOD thresholds of 7 to 29. The SNP order of each linkage group was optimal among different ordering results from several available software. Moreover, the linkage maps allowed the detection of 39 QTLs underlying tree height and 47 for diameter at breast height. In addition, the linkage maps improved the anchoring of 689 contigs of Populus simonii to chromosomes. The two parental genetic maps of Populus are of high quality, especially in terms of SNP data quality, the SNP order within linkage groups, and the perfect match between the number of linkage groups and the karyotype of Populus, as well as the excellent performances in QTL mapping and genome assembly. Both approaches for extracting and ordering SNPs could be applied to other species for constructing high-quality genetic maps.</AbstractText><CopyrightInformation>© The American Genetic Association 2020.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Tong</LastName><ForeName>Chunfa</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yao</LastName><ForeName>Dan</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wu</LastName><ForeName>Hainan</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Yuhua</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Wenguo</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhao</LastName><ForeName>Wei</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>09</Month><Day>15</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>J Hered</MedlineTA><NlmUniqueID>0375373</NlmUniqueID><ISSNLinking>0022-1503</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Populus
</Keyword><Keyword MajorTopicYN="N">genetic linkage map</Keyword><Keyword MajorTopicYN="N">genome assembly</Keyword><Keyword MajorTopicYN="N">quantitative trait locus</Keyword><Keyword MajorTopicYN="N">restriction site-associated DNA sequencing</Keyword><Keyword MajorTopicYN="N">single nucleotide polymorphism</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>06</Month><Day>15</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>9</Month><Day>15</Day><Hour>12</Hour><Minute>14</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>9</Month><Day>16</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>9</Month><Day>16</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>aheadofprint</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32930789</ArticleId><ArticleId IdType="pii">5905935</ArticleId><ArticleId IdType="doi">10.1093/jhered/esaa039</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Tong, Chunfa" sort="Tong, Chunfa" uniqKey="Tong C" first="Chunfa" last="Tong">Chunfa Tong</name></noRegion><name sortKey="Chen, Yuhua" sort="Chen, Yuhua" uniqKey="Chen Y" first="Yuhua" last="Chen">Yuhua Chen</name><name sortKey="Wu, Hainan" sort="Wu, Hainan" uniqKey="Wu H" first="Hainan" last="Wu">Hainan Wu</name><name sortKey="Yang, Wenguo" sort="Yang, Wenguo" uniqKey="Yang W" first="Wenguo" last="Yang">Wenguo Yang</name><name sortKey="Yao, Dan" sort="Yao, Dan" uniqKey="Yao D" first="Dan" last="Yao">Dan Yao</name><name sortKey="Zhao, Wei" sort="Zhao, Wei" uniqKey="Zhao W" first="Wei" last="Zhao">Wei Zhao</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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