Identification of recombination events in outbred species with next-generation sequencing data.
Identifieur interne : 000E33 ( Main/Exploration ); précédent : 000E32; suivant : 000E34Identification of recombination events in outbred species with next-generation sequencing data.
Auteurs : Shentong Tao [République populaire de Chine] ; Jiyan Wu [République populaire de Chine] ; Dan Yao [République populaire de Chine] ; Yuhua Chen [République populaire de Chine] ; Wenguo Yang [République populaire de Chine] ; Chunfa Tong [République populaire de Chine]Source :
- BMC genomics [ 1471-2164 ] ; 2018.
Descripteurs français
- KwdFr :
- Cartographie chromosomique (MeSH), Haplotypes (MeSH), Hybridation génétique (MeSH), Marqueurs génétiques (génétique), Méiose (génétique), Polymorphisme de nucléotide simple (MeSH), Populus (cytologie), Populus (génétique), Recombinaison génétique (MeSH), Séquençage nucléotidique à haut débit (MeSH).
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Genetic Markers.
- cytology : Populus.
- genetics : Meiosis, Populus.
- Chromosome Mapping, Haplotypes, High-Throughput Nucleotide Sequencing, Hybridization, Genetic, Polymorphism, Single Nucleotide, Recombination, Genetic.
Abstract
BACKGROUND
Meiotic recombination events include crossovers and non-crossovers or gene conversions. Although the rate of crossovers is often used for genetic mapping, the gene conversion events are not well studied especially in outbred species, which could produce distorted markers and thus affect the precision of genetic maps.
RESULTS
We proposed a strategy for identifying gene conversion events in Populus with the next-generation sequencing (NGS) data from the two parents and their progeny in an F
CONCLUSIONS
The novel strategy and the new developed Perl package permit to identify gene conversion events with the next-generation sequencing technology in a hybrid population of outbred species. The new method revealed that in a genetic mapping population some distorted genetic markers are possibly due to the gene conversion events.
DOI: 10.1186/s12864-018-4791-x
PubMed: 29801431
PubMed Central: PMC5970487
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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wicri:level="1"><nlm:affiliation>Co-Innovation Center for Sustainable Forestry in South China, College of Forestry, Nanjing Forestry University, No.159, Longpan Road, Xuanwu Qu, Nanjing, 210037, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Co-Innovation Center for Sustainable Forestry in South China, College of Forestry, Nanjing Forestry University, No.159, Longpan Road, Xuanwu Qu, Nanjing, 210037</wicri:regionArea><wicri:noRegion>210037</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 South China, College of Forestry, Nanjing Forestry University, No.159, Longpan Road, Xuanwu Qu, Nanjing, 210037, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Co-Innovation Center for Sustainable Forestry 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with next-generation sequencing data.</title><author><name sortKey="Tao, Shentong" sort="Tao, Shentong" uniqKey="Tao S" first="Shentong" last="Tao">Shentong Tao</name><affiliation wicri:level="1"><nlm:affiliation>Co-Innovation Center for Sustainable Forestry in South China, College of Forestry, Nanjing Forestry University, No.159, Longpan Road, Xuanwu Qu, Nanjing, 210037, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Co-Innovation Center for Sustainable Forestry in South China, College of Forestry, Nanjing Forestry University, No.159, Longpan Road, Xuanwu Qu, Nanjing, 210037</wicri:regionArea><wicri:noRegion>210037</wicri:noRegion></affiliation></author><author><name sortKey="Wu, Jiyan" sort="Wu, Jiyan" uniqKey="Wu J" first="Jiyan" last="Wu">Jiyan Wu</name><affiliation wicri:level="1"><nlm:affiliation>Co-Innovation Center for Sustainable Forestry in South China, College of Forestry, Nanjing Forestry University, No.159, Longpan Road, Xuanwu Qu, Nanjing, 210037, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Co-Innovation Center for Sustainable Forestry in South China, College of Forestry, Nanjing Forestry University, No.159, Longpan Road, Xuanwu Qu, Nanjing, 210037</wicri:regionArea><wicri:noRegion>210037</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 South China, College of Forestry, Nanjing Forestry University, No.159, Longpan Road, Xuanwu Qu, Nanjing, 210037, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Co-Innovation Center for Sustainable Forestry in South China, College of Forestry, Nanjing Forestry University, No.159, Longpan Road, Xuanwu Qu, Nanjing, 210037</wicri:regionArea><wicri:noRegion>210037</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 South China, College of Forestry, Nanjing Forestry University, No.159, Longpan Road, Xuanwu Qu, Nanjing, 210037, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Co-Innovation Center for Sustainable Forestry in South China, College of Forestry, Nanjing Forestry University, No.159, Longpan Road, Xuanwu Qu, Nanjing, 210037</wicri:regionArea><wicri:noRegion>210037</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 South China, College of Forestry, Nanjing Forestry University, No.159, Longpan Road, Xuanwu Qu, Nanjing, 210037, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Co-Innovation Center for Sustainable Forestry in South China, College of Forestry, Nanjing Forestry University, No.159, Longpan Road, Xuanwu Qu, Nanjing, 210037</wicri:regionArea><wicri:noRegion>210037</wicri:noRegion></affiliation></author><author><name sortKey="Tong, Chunfa" sort="Tong, Chunfa" uniqKey="Tong C" first="Chunfa" last="Tong">Chunfa Tong</name><affiliation wicri:level="1"><nlm:affiliation>Co-Innovation Center for Sustainable Forestry in South China, College of Forestry, Nanjing Forestry University, No.159, Longpan Road, Xuanwu Qu, Nanjing, 210037, China. tongchf@njfu.edu.cn.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Co-Innovation Center for Sustainable Forestry in South China, College of Forestry, Nanjing Forestry University, No.159, Longpan Road, Xuanwu Qu, Nanjing, 210037</wicri:regionArea><wicri:noRegion>210037</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Chromosome Mapping (MeSH)</term><term>Genetic Markers (genetics)</term><term>Haplotypes (MeSH)</term><term>High-Throughput Nucleotide Sequencing (MeSH)</term><term>Hybridization, Genetic (MeSH)</term><term>Meiosis (genetics)</term><term>Polymorphism, Single Nucleotide (MeSH)</term><term>Populus (cytology)</term><term>Populus (genetics)</term><term>Recombination, Genetic (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Cartographie chromosomique (MeSH)</term><term>Haplotypes (MeSH)</term><term>Hybridation génétique (MeSH)</term><term>Marqueurs génétiques (génétique)</term><term>Méiose (génétique)</term><term>Polymorphisme de nucléotide simple (MeSH)</term><term>Populus (cytologie)</term><term>Populus (génétique)</term><term>Recombinaison génétique (MeSH)</term><term>Séquençage nucléotidique à haut débit (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Genetic Markers</term></keywords><keywords scheme="MESH" qualifier="cytologie" xml:lang="fr"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="cytology" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Meiosis</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Marqueurs génétiques</term><term>Méiose</term><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Chromosome Mapping</term><term>Haplotypes</term><term>High-Throughput Nucleotide Sequencing</term><term>Hybridization, Genetic</term><term>Polymorphism, Single Nucleotide</term><term>Recombination, Genetic</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Cartographie chromosomique</term><term>Haplotypes</term><term>Hybridation génétique</term><term>Polymorphisme de nucléotide simple</term><term>Recombinaison génétique</term><term>Séquençage nucléotidique à haut débit</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>Meiotic recombination events include crossovers and non-crossovers or gene conversions. Although the rate of crossovers is often used for genetic mapping, the gene conversion events are not well studied especially in outbred species, which could produce distorted markers and thus affect the precision of genetic maps.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>We proposed a strategy for identifying gene conversion events in Populus with the next-generation sequencing (NGS) data from the two parents and their progeny in an F</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>The novel strategy and the new developed Perl package permit to identify gene conversion events with the next-generation sequencing technology in a hybrid population of outbred species. The new method revealed that in a genetic mapping population some distorted genetic markers are possibly due to the gene conversion events.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">29801431</PMID><DateCompleted><Year>2018</Year><Month>12</Month><Day>18</Day></DateCompleted><DateRevised><Year>2018</Year><Month>12</Month><Day>18</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>19</Volume><Issue>1</Issue><PubDate><Year>2018</Year><Month>May</Month><Day>25</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>Identification of recombination events in outbred species with next-generation sequencing data.</ArticleTitle><Pagination><MedlinePgn>398</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s12864-018-4791-x</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Meiotic recombination events include crossovers and non-crossovers or gene conversions. Although the rate of crossovers is often used for genetic mapping, the gene conversion events are not well studied especially in outbred species, which could produce distorted markers and thus affect the precision of genetic maps.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We proposed a strategy for identifying gene conversion events in Populus with the next-generation sequencing (NGS) data from the two parents and their progeny in an F<sub>1</sub> hybrid population. The strategy first involved phasing the heterozygous SNPs of the parents to obtain the parental haplotype blocks by NGS analytical tools, permitting to identify the parental gene conversion events with progeny genotypes. By incorporating available genetic linkage maps, longer haplotype blocks each corresponding to a chromosome can be created, not only allowing to detect crossover events but also possibly to locate a crossover in a small region. Our analysis revealed that gene conversions are more abundant than crossovers in Populus, with a higher probability to generate distorted markers in the regions involved than in the other regions on genome. The analytical procedures were implemented with Perl scripts as a freely available package, findGCO at https://github.com/tongchf/findGCO .</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">The novel strategy and the new developed Perl package permit to identify gene conversion events with the next-generation sequencing technology in a hybrid population of outbred species. The new method revealed that in a genetic mapping population some distorted genetic markers are possibly due to the gene conversion events.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Tao</LastName><ForeName>Shentong</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Co-Innovation Center for Sustainable Forestry in South China, College of Forestry, Nanjing Forestry University, No.159, Longpan Road, Xuanwu Qu, Nanjing, 210037, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wu</LastName><ForeName>Jiyan</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Co-Innovation Center for Sustainable Forestry in South China, College of Forestry, Nanjing Forestry University, No.159, Longpan Road, Xuanwu Qu, Nanjing, 210037, 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 South China, College of Forestry, Nanjing Forestry University, No.159, Longpan Road, Xuanwu Qu, Nanjing, 210037, 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 South China, College of Forestry, Nanjing Forestry University, No.159, Longpan Road, Xuanwu Qu, Nanjing, 210037, 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 South China, College of Forestry, Nanjing Forestry University, No.159, Longpan Road, Xuanwu Qu, Nanjing, 210037, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tong</LastName><ForeName>Chunfa</ForeName><Initials>C</Initials><Identifier Source="ORCID">http://orcid.org/0000-0001-9795-211X</Identifier><AffiliationInfo><Affiliation>Co-Innovation Center for Sustainable Forestry in South China, College of Forestry, Nanjing Forestry University, No.159, Longpan Road, Xuanwu Qu, Nanjing, 210037, China. tongchf@njfu.edu.cn.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>No. 31270706</GrantID><Agency>National Natural Science Foundation of China</Agency><Country></Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2018</Year><Month>05</Month><Day>25</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Genomics</MedlineTA><NlmUniqueID>100965258</NlmUniqueID><ISSNLinking>1471-2164</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005819">Genetic Markers</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D002874" MajorTopicYN="N">Chromosome Mapping</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005819" MajorTopicYN="N">Genetic Markers</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006239" MajorTopicYN="N">Haplotypes</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="Y">High-Throughput Nucleotide Sequencing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006824" MajorTopicYN="Y">Hybridization, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008540" MajorTopicYN="N">Meiosis</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="N">Polymorphism, Single Nucleotide</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000166" MajorTopicYN="N">cytology</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011995" MajorTopicYN="Y">Recombination, Genetic</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Crossover</Keyword><Keyword MajorTopicYN="N">Gene conversion</Keyword><Keyword MajorTopicYN="N">Haplotype block</Keyword><Keyword MajorTopicYN="N">Next-generation sequencing</Keyword><Keyword MajorTopicYN="N">Populus</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>01</Month><Day>14</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2018</Year><Month>05</Month><Day>14</Day></PubMedPubDate><PubMedPubDate 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