An open-pollinated design for mapping imprinting genes in natural populations
With the increasing recognition of its role in trait and disease development, it is crucial to account for genetic imprinting to illustrate the genetic architecture of complex traits. Genetic mapping can be innovated to test and estimate effects of genetic imprinting in a segregating population deri...
Gespeichert in:
| Veröffentlicht in: | Briefings in bioinformatics 2015-05, Vol.16 (3), p.449-460 |
|---|---|
| Hauptverfasser: | , , , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 460 |
|---|---|
| container_issue | 3 |
| container_start_page | 449 |
| container_title | Briefings in bioinformatics |
| container_volume | 16 |
| creator | Sun, Lidan Zhu, Xuli Bo, Wenhao Xu, Fang Cheng, Tangren Zhang, Qixiang Wu, Rongling |
| description | With the increasing recognition of its role in trait and disease development, it is crucial to account for genetic imprinting to illustrate the genetic architecture of complex traits. Genetic mapping can be innovated to test and estimate effects of genetic imprinting in a segregating population derived from experimental crosses. Here, we describe and assess a design for imprinting detection in natural plant populations. This design is to sample maternal plants at random from a natural population and collect open-pollinated (OP) seeds randomly from each maternal plant and germinate them into seedlings. A two-stage hierarchical platform is constructed to jointly analyze maternal and OP progeny markers. Through tracing the segregation and transmission of alleles from the parental to progeny generation, this platform allows parent-of-origin-dependent gene expression to be discerned, providing an avenue to estimate the effect of imprinting genes on a quantitative trait. The design is derived to estimate imprinting effects expressed at the haplotype level. Its usefulness and utilization were validated through computer simulation. This OP-based design provides a tool to detect the genomic distribution and pattern of imprinting genes as an important component of heritable variation that is neglected in traditional genetic studies of complex traits. |
| doi_str_mv | 10.1093/bib/bbu019 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_1709781684</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>1709781684</sourcerecordid><originalsourceid>FETCH-LOGICAL-c347t-8c6d872d932de733e40348dfee81296aa9a30347fa0f55634dbe9aa64d7d0c163</originalsourceid><addsrcrecordid>eNqN0UtLxDAQB_AgiruuXvwAUvAiQt28msdxWXzBihc9l7RJlyxtUpP24Lc3ZVcPXvQ0w_BjYOYPwCWCdwhKsqxstayqESJ5BOaIcp5TWNDjqWc8LygjM3AW4w5CDLlAp2CGqcRcUjgHLyuX-d64vPdta50ajM60iXbrssaHrFN9b902s10frBumdmuciZl1WcJjUG3W-35s1WC9i-fgpFFtNBeHugDvD_dv66d88_r4vF5t8ppQPuSiZlpwrCXB2nBCDIWECt0YIxCWTCmpSJrwRsGmKBihujJSKUY117BGjCzAzX5vH_zHaOJQdjbWpm2VM36MJeJQpkuZoP-h6WW0IMXflAmMIRFiote_6M6PwaWbJ1VAhFBBkrrdqzr4GINpyvTFToXPEsFyiq5M0ZX76BK-Oqwcq87oH_qdFfkCIueTmw</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1685011153</pqid></control><display><type>article</type><title>An open-pollinated design for mapping imprinting genes in natural populations</title><source>MEDLINE</source><source>EBSCOhost Business Source Complete</source><source>Oxford Journals Open Access Collection</source><source>EZB-FREE-00999 freely available EZB journals</source><source>PubMed Central</source><creator>Sun, Lidan ; Zhu, Xuli ; Bo, Wenhao ; Xu, Fang ; Cheng, Tangren ; Zhang, Qixiang ; Wu, Rongling</creator><creatorcontrib>Sun, Lidan ; Zhu, Xuli ; Bo, Wenhao ; Xu, Fang ; Cheng, Tangren ; Zhang, Qixiang ; Wu, Rongling</creatorcontrib><description>With the increasing recognition of its role in trait and disease development, it is crucial to account for genetic imprinting to illustrate the genetic architecture of complex traits. Genetic mapping can be innovated to test and estimate effects of genetic imprinting in a segregating population derived from experimental crosses. Here, we describe and assess a design for imprinting detection in natural plant populations. This design is to sample maternal plants at random from a natural population and collect open-pollinated (OP) seeds randomly from each maternal plant and germinate them into seedlings. A two-stage hierarchical platform is constructed to jointly analyze maternal and OP progeny markers. Through tracing the segregation and transmission of alleles from the parental to progeny generation, this platform allows parent-of-origin-dependent gene expression to be discerned, providing an avenue to estimate the effect of imprinting genes on a quantitative trait. The design is derived to estimate imprinting effects expressed at the haplotype level. Its usefulness and utilization were validated through computer simulation. This OP-based design provides a tool to detect the genomic distribution and pattern of imprinting genes as an important component of heritable variation that is neglected in traditional genetic studies of complex traits.</description><identifier>ISSN: 1467-5463</identifier><identifier>EISSN: 1477-4054</identifier><identifier>DOI: 10.1093/bib/bbu019</identifier><identifier>PMID: 24927940</identifier><language>eng</language><publisher>England: Oxford Publishing Limited (England)</publisher><subject>Base Sequence ; Chromosome Mapping - methods ; Computer simulation ; Design ; DNA, Plant - genetics ; Estimates ; Gene expression ; Genes ; Genetics ; Genetics, Population ; Genome-Wide Association Study - methods ; Genomic Imprinting - genetics ; Genomics ; Haplotypes ; Haplotypes - genetics ; Mapping ; Molecular Sequence Data ; Natural populations ; Plant populations ; Plant reproduction ; Plants (organisms) ; Platforms ; Pollination - genetics ; Populations ; Progeny ; Quantitative Trait, Heritable ; Seedlings ; Seeds - genetics ; Sequence Alignment - methods ; Sequence Analysis, DNA - methods</subject><ispartof>Briefings in bioinformatics, 2015-05, Vol.16 (3), p.449-460</ispartof><rights>The Author 2014. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.</rights><rights>Copyright Oxford Publishing Limited(England) May 2015</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c347t-8c6d872d932de733e40348dfee81296aa9a30347fa0f55634dbe9aa64d7d0c163</citedby><cites>FETCH-LOGICAL-c347t-8c6d872d932de733e40348dfee81296aa9a30347fa0f55634dbe9aa64d7d0c163</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780,27903,27904</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24927940$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Sun, Lidan</creatorcontrib><creatorcontrib>Zhu, Xuli</creatorcontrib><creatorcontrib>Bo, Wenhao</creatorcontrib><creatorcontrib>Xu, Fang</creatorcontrib><creatorcontrib>Cheng, Tangren</creatorcontrib><creatorcontrib>Zhang, Qixiang</creatorcontrib><creatorcontrib>Wu, Rongling</creatorcontrib><title>An open-pollinated design for mapping imprinting genes in natural populations</title><title>Briefings in bioinformatics</title><addtitle>Brief Bioinform</addtitle><description>With the increasing recognition of its role in trait and disease development, it is crucial to account for genetic imprinting to illustrate the genetic architecture of complex traits. Genetic mapping can be innovated to test and estimate effects of genetic imprinting in a segregating population derived from experimental crosses. Here, we describe and assess a design for imprinting detection in natural plant populations. This design is to sample maternal plants at random from a natural population and collect open-pollinated (OP) seeds randomly from each maternal plant and germinate them into seedlings. A two-stage hierarchical platform is constructed to jointly analyze maternal and OP progeny markers. Through tracing the segregation and transmission of alleles from the parental to progeny generation, this platform allows parent-of-origin-dependent gene expression to be discerned, providing an avenue to estimate the effect of imprinting genes on a quantitative trait. The design is derived to estimate imprinting effects expressed at the haplotype level. Its usefulness and utilization were validated through computer simulation. This OP-based design provides a tool to detect the genomic distribution and pattern of imprinting genes as an important component of heritable variation that is neglected in traditional genetic studies of complex traits.</description><subject>Base Sequence</subject><subject>Chromosome Mapping - methods</subject><subject>Computer simulation</subject><subject>Design</subject><subject>DNA, Plant - genetics</subject><subject>Estimates</subject><subject>Gene expression</subject><subject>Genes</subject><subject>Genetics</subject><subject>Genetics, Population</subject><subject>Genome-Wide Association Study - methods</subject><subject>Genomic Imprinting - genetics</subject><subject>Genomics</subject><subject>Haplotypes</subject><subject>Haplotypes - genetics</subject><subject>Mapping</subject><subject>Molecular Sequence Data</subject><subject>Natural populations</subject><subject>Plant populations</subject><subject>Plant reproduction</subject><subject>Plants (organisms)</subject><subject>Platforms</subject><subject>Pollination - genetics</subject><subject>Populations</subject><subject>Progeny</subject><subject>Quantitative Trait, Heritable</subject><subject>Seedlings</subject><subject>Seeds - genetics</subject><subject>Sequence Alignment - methods</subject><subject>Sequence Analysis, DNA - methods</subject><issn>1467-5463</issn><issn>1477-4054</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqN0UtLxDAQB_AgiruuXvwAUvAiQt28msdxWXzBihc9l7RJlyxtUpP24Lc3ZVcPXvQ0w_BjYOYPwCWCdwhKsqxstayqESJ5BOaIcp5TWNDjqWc8LygjM3AW4w5CDLlAp2CGqcRcUjgHLyuX-d64vPdta50ajM60iXbrssaHrFN9b902s10frBumdmuciZl1WcJjUG3W-35s1WC9i-fgpFFtNBeHugDvD_dv66d88_r4vF5t8ppQPuSiZlpwrCXB2nBCDIWECt0YIxCWTCmpSJrwRsGmKBihujJSKUY117BGjCzAzX5vH_zHaOJQdjbWpm2VM36MJeJQpkuZoP-h6WW0IMXflAmMIRFiote_6M6PwaWbJ1VAhFBBkrrdqzr4GINpyvTFToXPEsFyiq5M0ZX76BK-Oqwcq87oH_qdFfkCIueTmw</recordid><startdate>201505</startdate><enddate>201505</enddate><creator>Sun, Lidan</creator><creator>Zhu, Xuli</creator><creator>Bo, Wenhao</creator><creator>Xu, Fang</creator><creator>Cheng, Tangren</creator><creator>Zhang, Qixiang</creator><creator>Wu, Rongling</creator><general>Oxford Publishing Limited (England)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>7SC</scope><scope>8FD</scope><scope>FR3</scope><scope>JQ2</scope><scope>K9.</scope><scope>L7M</scope><scope>L~C</scope><scope>L~D</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>201505</creationdate><title>An open-pollinated design for mapping imprinting genes in natural populations</title><author>Sun, Lidan ; Zhu, Xuli ; Bo, Wenhao ; Xu, Fang ; Cheng, Tangren ; Zhang, Qixiang ; Wu, Rongling</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c347t-8c6d872d932de733e40348dfee81296aa9a30347fa0f55634dbe9aa64d7d0c163</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Base Sequence</topic><topic>Chromosome Mapping - methods</topic><topic>Computer simulation</topic><topic>Design</topic><topic>DNA, Plant - genetics</topic><topic>Estimates</topic><topic>Gene expression</topic><topic>Genes</topic><topic>Genetics</topic><topic>Genetics, Population</topic><topic>Genome-Wide Association Study - methods</topic><topic>Genomic Imprinting - genetics</topic><topic>Genomics</topic><topic>Haplotypes</topic><topic>Haplotypes - genetics</topic><topic>Mapping</topic><topic>Molecular Sequence Data</topic><topic>Natural populations</topic><topic>Plant populations</topic><topic>Plant reproduction</topic><topic>Plants (organisms)</topic><topic>Platforms</topic><topic>Pollination - genetics</topic><topic>Populations</topic><topic>Progeny</topic><topic>Quantitative Trait, Heritable</topic><topic>Seedlings</topic><topic>Seeds - genetics</topic><topic>Sequence Alignment - methods</topic><topic>Sequence Analysis, DNA - methods</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Sun, Lidan</creatorcontrib><creatorcontrib>Zhu, Xuli</creatorcontrib><creatorcontrib>Bo, Wenhao</creatorcontrib><creatorcontrib>Xu, Fang</creatorcontrib><creatorcontrib>Cheng, Tangren</creatorcontrib><creatorcontrib>Zhang, Qixiang</creatorcontrib><creatorcontrib>Wu, Rongling</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Computer and Information Systems Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>ProQuest Computer Science Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>Computer and Information Systems Abstracts Academic</collection><collection>Computer and Information Systems Abstracts Professional</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Briefings in bioinformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Sun, Lidan</au><au>Zhu, Xuli</au><au>Bo, Wenhao</au><au>Xu, Fang</au><au>Cheng, Tangren</au><au>Zhang, Qixiang</au><au>Wu, Rongling</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>An open-pollinated design for mapping imprinting genes in natural populations</atitle><jtitle>Briefings in bioinformatics</jtitle><addtitle>Brief Bioinform</addtitle><date>2015-05</date><risdate>2015</risdate><volume>16</volume><issue>3</issue><spage>449</spage><epage>460</epage><pages>449-460</pages><issn>1467-5463</issn><eissn>1477-4054</eissn><abstract>With the increasing recognition of its role in trait and disease development, it is crucial to account for genetic imprinting to illustrate the genetic architecture of complex traits. Genetic mapping can be innovated to test and estimate effects of genetic imprinting in a segregating population derived from experimental crosses. Here, we describe and assess a design for imprinting detection in natural plant populations. This design is to sample maternal plants at random from a natural population and collect open-pollinated (OP) seeds randomly from each maternal plant and germinate them into seedlings. A two-stage hierarchical platform is constructed to jointly analyze maternal and OP progeny markers. Through tracing the segregation and transmission of alleles from the parental to progeny generation, this platform allows parent-of-origin-dependent gene expression to be discerned, providing an avenue to estimate the effect of imprinting genes on a quantitative trait. The design is derived to estimate imprinting effects expressed at the haplotype level. Its usefulness and utilization were validated through computer simulation. This OP-based design provides a tool to detect the genomic distribution and pattern of imprinting genes as an important component of heritable variation that is neglected in traditional genetic studies of complex traits.</abstract><cop>England</cop><pub>Oxford Publishing Limited (England)</pub><pmid>24927940</pmid><doi>10.1093/bib/bbu019</doi><tpages>12</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1467-5463 |
| ispartof | Briefings in bioinformatics, 2015-05, Vol.16 (3), p.449-460 |
| issn | 1467-5463 1477-4054 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_1709781684 |
| source | MEDLINE; EBSCOhost Business Source Complete; Oxford Journals Open Access Collection; EZB-FREE-00999 freely available EZB journals; PubMed Central |
| subjects | Base Sequence Chromosome Mapping - methods Computer simulation Design DNA, Plant - genetics Estimates Gene expression Genes Genetics Genetics, Population Genome-Wide Association Study - methods Genomic Imprinting - genetics Genomics Haplotypes Haplotypes - genetics Mapping Molecular Sequence Data Natural populations Plant populations Plant reproduction Plants (organisms) Platforms Pollination - genetics Populations Progeny Quantitative Trait, Heritable Seedlings Seeds - genetics Sequence Alignment - methods Sequence Analysis, DNA - methods |
| title | An open-pollinated design for mapping imprinting genes in natural populations |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-26T06%3A57%3A00IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=An%20open-pollinated%20design%20for%20mapping%20imprinting%20genes%20in%20natural%20populations&rft.jtitle=Briefings%20in%20bioinformatics&rft.au=Sun,%20Lidan&rft.date=2015-05&rft.volume=16&rft.issue=3&rft.spage=449&rft.epage=460&rft.pages=449-460&rft.issn=1467-5463&rft.eissn=1477-4054&rft_id=info:doi/10.1093/bib/bbu019&rft_dat=%3Cproquest_cross%3E1709781684%3C/proquest_cross%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1685011153&rft_id=info:pmid/24927940&rfr_iscdi=true |