Single primer enrichment technology as a tool for massive genotyping: a benchmark on black poplar and maize.
Identifieur interne : 000712 ( Main/Exploration ); précédent : 000711; suivant : 000713Single primer enrichment technology as a tool for massive genotyping: a benchmark on black poplar and maize.
Auteurs : Davide Scaglione [Italie] ; Sara Pinosio [Italie] ; Fabio Marroni [Italie] ; Eleonora Di Centa [Italie] ; Alice Fornasiero [Italie] ; Gabriele Magris [Italie] ; Simone Scalabrin [Italie] ; Federica Cattonaro [Italie] ; Gail Taylor [Royaume-Uni] ; Michele Morgante [Italie]Source :
- Annals of botany [ 1095-8290 ] ; 2019.
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Abstract
BACKGROUND AND AIMS
The advent of molecular breeding is advocated to improve the productivity and sustainability of second-generation bioenergy crops. Advanced molecular breeding in bioenergy crops relies on the ability to massively sample the genetic diversity. Genotyping-by-sequencing has become a widely adopted method for cost-effective genotyping. It basically requires no initial investment for design as compared with array-based platforms which have been shown to offer very robust assays. The latter, however, has the drawback of being limited to analyse only the genetic diversity accounted during selection of a set of polymorphisms and design of the assay. In contrast, genotyping-by-sequencing with random sampling of genomic loci via restriction enzymes or random priming has been shown to be fast and convenient but lacks the ability to target specific regions of the genome and to maintain high reproducibility across laboratories.
METHODS
Here we present a first adoption of single-primer enrichment technology (SPET) which provides a highly efficient and scalable system to obtain targeted sequence-based large genotyping data sets, bridging the gaps between array-based systems and traditional sequencing-based protocols. To fully explore SPET performance, we conducted a benchmark study in ten Zea mays lines and a large-scale study of a natural black poplar population of 540 individuals with the aim of discovering polymorphisms associated with biomass-related traits.
KEY RESULTS
Our results showed the ability of this technology to provide dense genotype information on a customized panel of selected polymorphisms, while yielding hundreds of thousands of untargeted variable sites. This provided an ideal resource for association analysis of natural populations harbouring unexplored allelic diversities and structure such as in black poplar.
CONCLUSION
The improvement of sequencing throughput and the development of efficient library preparation methods has made it feasible to carry out targeted genotyping-by-sequencing experiments cost-competitively with either random complexity reduction systems or traditional array-based platforms, while maintaining the key advantages of both technologies.
DOI: 10.1093/aob/mcz054
PubMed: 30932149
PubMed Central: PMC6821380
Affiliations:
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Istituto di Genomica Applicata, via Jacopo Linussio, Udine, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>IGA - Istituto di Genomica Applicata, via Jacopo Linussio, Udine</wicri:regionArea><wicri:noRegion>Udine</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Institute of Biosciences and Bioresources, National Research Council, Via Madonna del Piano, Sesto Fiorentino, Firenze, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Institute of Biosciences and Bioresources, National Research Council, Via Madonna del Piano, Sesto Fiorentino, Firenze</wicri:regionArea><wicri:noRegion>Firenze</wicri:noRegion></affiliation></author><author><name sortKey="Marroni, Fabio" sort="Marroni, Fabio" uniqKey="Marroni F" first="Fabio" last="Marroni">Fabio Marroni</name><affiliation wicri:level="1"><nlm:affiliation>IGA Technology Services s.r.l., via Jacopo Linussio, Udine, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>IGA Technology Services s.r.l., via Jacopo Linussio, Udine</wicri:regionArea><wicri:noRegion>Udine</wicri:noRegion></affiliation></author><author><name sortKey="Di Centa, Eleonora" sort="Di Centa, Eleonora" uniqKey="Di Centa E" first="Eleonora" last="Di Centa">Eleonora Di Centa</name><affiliation wicri:level="1"><nlm:affiliation>IGA Technology Services s.r.l., via Jacopo Linussio, Udine, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>IGA Technology Services s.r.l., via Jacopo Linussio, Udine</wicri:regionArea><wicri:noRegion>Udine</wicri:noRegion></affiliation></author><author><name sortKey="Fornasiero, Alice" sort="Fornasiero, Alice" uniqKey="Fornasiero A" first="Alice" last="Fornasiero">Alice Fornasiero</name><affiliation wicri:level="1"><nlm:affiliation>IGA - Istituto di Genomica Applicata, via Jacopo Linussio, Udine, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>IGA - Istituto di Genomica Applicata, via Jacopo Linussio, Udine</wicri:regionArea><wicri:noRegion>Udine</wicri:noRegion></affiliation></author><author><name sortKey="Magris, Gabriele" sort="Magris, Gabriele" uniqKey="Magris G" first="Gabriele" last="Magris">Gabriele Magris</name><affiliation wicri:level="1"><nlm:affiliation>Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine</wicri:regionArea><wicri:noRegion>Udine</wicri:noRegion></affiliation></author><author><name sortKey="Scalabrin, Simone" sort="Scalabrin, Simone" uniqKey="Scalabrin S" first="Simone" last="Scalabrin">Simone Scalabrin</name><affiliation wicri:level="1"><nlm:affiliation>IGA Technology Services s.r.l., via Jacopo Linussio, Udine, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>IGA Technology Services s.r.l., via Jacopo Linussio, Udine</wicri:regionArea><wicri:noRegion>Udine</wicri:noRegion></affiliation></author><author><name sortKey="Cattonaro, Federica" sort="Cattonaro, Federica" uniqKey="Cattonaro F" first="Federica" last="Cattonaro">Federica Cattonaro</name><affiliation wicri:level="1"><nlm:affiliation>IGA Technology Services s.r.l., via Jacopo Linussio, Udine, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>IGA Technology Services s.r.l., via Jacopo Linussio, Udine</wicri:regionArea><wicri:noRegion>Udine</wicri:noRegion></affiliation></author><author><name sortKey="Taylor, Gail" sort="Taylor, Gail" uniqKey="Taylor G" first="Gail" last="Taylor">Gail Taylor</name><affiliation wicri:level="1"><nlm:affiliation>Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton</wicri:regionArea><wicri:noRegion>Southampton</wicri:noRegion></affiliation></author><author><name sortKey="Morgante, Michele" sort="Morgante, Michele" uniqKey="Morgante M" first="Michele" last="Morgante">Michele Morgante</name><affiliation wicri:level="1"><nlm:affiliation>IGA - Istituto di Genomica Applicata, via Jacopo Linussio, Udine, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>IGA - Istituto di Genomica Applicata, via Jacopo Linussio, Udine</wicri:regionArea><wicri:noRegion>Udine</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine</wicri:regionArea><wicri:noRegion>Udine</wicri:noRegion></affiliation></author></analytic><series><title level="j">Annals of botany</title><idno type="eISSN">1095-8290</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Benchmarking (MeSH)</term><term>Genotype (MeSH)</term><term>Genotyping Techniques (MeSH)</term><term>Humans (MeSH)</term><term>Polymorphism, Single Nucleotide (MeSH)</term><term>Populus (MeSH)</term><term>Reproducibility of Results (MeSH)</term><term>Zea mays (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Génotype (MeSH)</term><term>Humains (MeSH)</term><term>Polymorphisme de nucléotide simple (MeSH)</term><term>Populus (MeSH)</term><term>Reproductibilité des résultats (MeSH)</term><term>Référenciation (MeSH)</term><term>Techniques de génotypage (MeSH)</term><term>Zea mays (MeSH)</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Benchmarking</term><term>Genotype</term><term>Genotyping Techniques</term><term>Humans</term><term>Polymorphism, Single Nucleotide</term><term>Populus</term><term>Reproducibility of Results</term><term>Zea mays</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Génotype</term><term>Humains</term><term>Polymorphisme de nucléotide simple</term><term>Populus</term><term>Reproductibilité des résultats</term><term>Référenciation</term><term>Techniques de génotypage</term><term>Zea mays</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND AND AIMS</b></p><p>The advent of molecular breeding is advocated to improve the productivity and sustainability of second-generation bioenergy crops. Advanced molecular breeding in bioenergy crops relies on the ability to massively sample the genetic diversity. Genotyping-by-sequencing has become a widely adopted method for cost-effective genotyping. It basically requires no initial investment for design as compared with array-based platforms which have been shown to offer very robust assays. The latter, however, has the drawback of being limited to analyse only the genetic diversity accounted during selection of a set of polymorphisms and design of the assay. In contrast, genotyping-by-sequencing with random sampling of genomic loci via restriction enzymes or random priming has been shown to be fast and convenient but lacks the ability to target specific regions of the genome and to maintain high reproducibility across laboratories.</p></div><div type="abstract" xml:lang="en"><p><b>METHODS</b></p><p>Here we present a first adoption of single-primer enrichment technology (SPET) which provides a highly efficient and scalable system to obtain targeted sequence-based large genotyping data sets, bridging the gaps between array-based systems and traditional sequencing-based protocols. To fully explore SPET performance, we conducted a benchmark study in ten Zea mays lines and a large-scale study of a natural black poplar population of 540 individuals with the aim of discovering polymorphisms associated with biomass-related traits.</p></div><div type="abstract" xml:lang="en"><p><b>KEY RESULTS</b></p><p>Our results showed the ability of this technology to provide dense genotype information on a customized panel of selected polymorphisms, while yielding hundreds of thousands of untargeted variable sites. This provided an ideal resource for association analysis of natural populations harbouring unexplored allelic diversities and structure such as in black poplar.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSION</b></p><p>The improvement of sequencing throughput and the development of efficient library preparation methods has made it feasible to carry out targeted genotyping-by-sequencing experiments cost-competitively with either random complexity reduction systems or traditional array-based platforms, while maintaining the key advantages of both technologies.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Automated" Owner="NLM"><PMID Version="1">30932149</PMID><DateCompleted><Year>2020</Year><Month>03</Month><Day>18</Day></DateCompleted><DateRevised><Year>2020</Year><Month>10</Month><Day>29</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1095-8290</ISSN><JournalIssue CitedMedium="Internet"><Volume>124</Volume><Issue>4</Issue><PubDate><Year>2019</Year><Month>10</Month><Day>29</Day></PubDate></JournalIssue><Title>Annals of botany</Title><ISOAbbreviation>Ann Bot</ISOAbbreviation></Journal><ArticleTitle>Single primer enrichment technology as a tool for massive genotyping: a benchmark on black poplar and maize.</ArticleTitle><Pagination><MedlinePgn>543-552</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/aob/mcz054</ELocationID><Abstract><AbstractText Label="BACKGROUND AND AIMS">The advent of molecular breeding is advocated to improve the productivity and sustainability of second-generation bioenergy crops. Advanced molecular breeding in bioenergy crops relies on the ability to massively sample the genetic diversity. Genotyping-by-sequencing has become a widely adopted method for cost-effective genotyping. It basically requires no initial investment for design as compared with array-based platforms which have been shown to offer very robust assays. The latter, however, has the drawback of being limited to analyse only the genetic diversity accounted during selection of a set of polymorphisms and design of the assay. In contrast, genotyping-by-sequencing with random sampling of genomic loci via restriction enzymes or random priming has been shown to be fast and convenient but lacks the ability to target specific regions of the genome and to maintain high reproducibility across laboratories.</AbstractText><AbstractText Label="METHODS">Here we present a first adoption of single-primer enrichment technology (SPET) which provides a highly efficient and scalable system to obtain targeted sequence-based large genotyping data sets, bridging the gaps between array-based systems and traditional sequencing-based protocols. To fully explore SPET performance, we conducted a benchmark study in ten Zea mays lines and a large-scale study of a natural black poplar population of 540 individuals with the aim of discovering polymorphisms associated with biomass-related traits.</AbstractText><AbstractText Label="KEY RESULTS">Our results showed the ability of this technology to provide dense genotype information on a customized panel of selected polymorphisms, while yielding hundreds of thousands of untargeted variable sites. This provided an ideal resource for association analysis of natural populations harbouring unexplored allelic diversities and structure such as in black poplar.</AbstractText><AbstractText Label="CONCLUSION">The improvement of sequencing throughput and the development of efficient library preparation methods has made it feasible to carry out targeted genotyping-by-sequencing experiments cost-competitively with either random complexity reduction systems or traditional array-based platforms, while maintaining the key advantages of both technologies.</AbstractText><CopyrightInformation>© The Author(s) 2019. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Scaglione</LastName><ForeName>Davide</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>IGA Technology Services s.r.l., via Jacopo Linussio, Udine, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pinosio</LastName><ForeName>Sara</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>IGA - Istituto di Genomica Applicata, via Jacopo Linussio, Udine, Italy.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Institute of Biosciences and Bioresources, National Research Council, Via Madonna del Piano, Sesto Fiorentino, Firenze, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Marroni</LastName><ForeName>Fabio</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>IGA Technology Services s.r.l., via Jacopo Linussio, Udine, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Di Centa</LastName><ForeName>Eleonora</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>IGA Technology Services s.r.l., via Jacopo Linussio, Udine, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fornasiero</LastName><ForeName>Alice</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>IGA - Istituto di Genomica Applicata, via Jacopo Linussio, Udine, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Magris</LastName><ForeName>Gabriele</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Scalabrin</LastName><ForeName>Simone</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>IGA Technology Services s.r.l., via Jacopo Linussio, Udine, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cattonaro</LastName><ForeName>Federica</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>IGA Technology Services s.r.l., via Jacopo Linussio, Udine, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Taylor</LastName><ForeName>Gail</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Morgante</LastName><ForeName>Michele</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>IGA - Istituto di Genomica Applicata, via Jacopo Linussio, Udine, Italy.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Dipartimento di Scienze Agro-alimentari, Università di Udine, Ambientali e Animali (DI4A), Udine, Italy.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Ann Bot</MedlineTA><NlmUniqueID>0372347</NlmUniqueID><ISSNLinking>0305-7364</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D019985" MajorTopicYN="N">Benchmarking</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005838" MajorTopicYN="N">Genotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D060005" MajorTopicYN="N">Genotyping Techniques</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="N">Polymorphism, Single Nucleotide</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="Y">Populus</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015203" MajorTopicYN="N">Reproducibility of Results</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003313" MajorTopicYN="Y">Zea mays</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Populus nigra
</Keyword><Keyword MajorTopicYN="Y">Zea mays
</Keyword><Keyword MajorTopicYN="Y">Allegro</Keyword><Keyword MajorTopicYN="Y">GWAS</Keyword><Keyword MajorTopicYN="Y">SNP</Keyword><Keyword MajorTopicYN="Y">SPET</Keyword><Keyword MajorTopicYN="Y">bioenergy crops</Keyword><Keyword MajorTopicYN="Y">genotyping-by-sequencing</Keyword><Keyword MajorTopicYN="Y">targeted genotyping</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>08</Month><Day>23</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2019</Year><Month>03</Month><Day>25</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>4</Month><Day>2</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>3</Month><Day>19</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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