Orthogonal contrast based models for quantitative genetic analysis in autotetraploid species
Dissecting the genetic architecture of quantitative traits is a crucial goal for efficient breeding of polyploid plants, including autotetraploid crop species, such as potato and coffee, and ornamentals such as rose. To meet this goal, a quantitative genetic model is needed to link the genetic effec...
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| Veröffentlicht in: | The New phytologist 2018-10, Vol.220 (1), p.332-346 |
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| container_title | The New phytologist |
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| creator | Chen, Jing Zhang, Fengjun Wang, Lin Leach, Lindsey Luo, Zewei |
| description | Dissecting the genetic architecture of quantitative traits is a crucial goal for efficient breeding of polyploid plants, including autotetraploid crop species, such as potato and coffee, and ornamentals such as rose. To meet this goal, a quantitative genetic model is needed to link the genetic effects of genes or genotypes at quantitative trait loci (QTL) to the phenotype of quantitative traits.
We present a statistically tractable quantitative genetic model for autotetraploids based on orthogonal contrast comparisons in the general linear model. The new methods are suitable for autotetraploid species with any population genetic structure and take full account of the essential features of autotetrasomic inheritance. The statistical properties of the new methods are explored and compared to an alternative method in the literature by simulation studies.
We have shown how these methods can be applied for quantitative genetic analysis in autotetraploids by analysing trait phenotype data from an autotetraploid potato segregating population. Using trait segregation analysis, we showed that both highly heritable traits of flowering time and plant height were under the control of major QTL.
The orthogonal model directly dissects genetic variance into independent components and gives consistent estimates of genetic effects provided that tetrasomic gene segregation is considered. |
| doi_str_mv | 10.1111/nph.15284 |
| format | Article |
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We present a statistically tractable quantitative genetic model for autotetraploids based on orthogonal contrast comparisons in the general linear model. The new methods are suitable for autotetraploid species with any population genetic structure and take full account of the essential features of autotetrasomic inheritance. The statistical properties of the new methods are explored and compared to an alternative method in the literature by simulation studies.
We have shown how these methods can be applied for quantitative genetic analysis in autotetraploids by analysing trait phenotype data from an autotetraploid potato segregating population. Using trait segregation analysis, we showed that both highly heritable traits of flowering time and plant height were under the control of major QTL.
The orthogonal model directly dissects genetic variance into independent components and gives consistent estimates of genetic effects provided that tetrasomic gene segregation is considered.</description><identifier>ISSN: 0028-646X</identifier><identifier>EISSN: 1469-8137</identifier><identifier>DOI: 10.1111/nph.15284</identifier><identifier>PMID: 29987874</identifier><language>eng</language><publisher>England: New Phytologist Trust</publisher><subject>Autotetraploid ; autotetraploids ; Coffee ; Computer simulation ; Data processing ; double reduction ; Flowering ; Gene loci ; Genetic analysis ; Genetic diversity ; Genetic effects ; Genetic structure ; Genetic variance ; Genotype & phenotype ; Genotypes ; Heredity ; Methods ; orthogonal contrasts ; Phenotypes ; Plant breeding ; polyploid ; Polyploidy ; Population (statistical) ; Population genetics ; potato ; Potatoes ; quantitative genetic model ; Quantitative genetics ; Quantitative trait loci ; Species ; tetrasomic inheritance</subject><ispartof>The New phytologist, 2018-10, Vol.220 (1), p.332-346</ispartof><rights>2018 New Phytologist Trust</rights><rights>2018 The Authors. New Phytologist © 2018 New Phytologist Trust</rights><rights>2018 The Authors. New Phytologist © 2018 New Phytologist Trust.</rights><rights>Copyright © 2018 New Phytologist Trust</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4104-caffd78022892cc60e5a6e6833132530bfb727822ba717621cf88366c2182bd73</citedby><cites>FETCH-LOGICAL-c4104-caffd78022892cc60e5a6e6833132530bfb727822ba717621cf88366c2182bd73</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/90024555$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/90024555$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>314,780,784,803,1417,1433,27924,27925,45574,45575,46409,46833,58017,58250</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29987874$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Chen, Jing</creatorcontrib><creatorcontrib>Zhang, Fengjun</creatorcontrib><creatorcontrib>Wang, Lin</creatorcontrib><creatorcontrib>Leach, Lindsey</creatorcontrib><creatorcontrib>Luo, Zewei</creatorcontrib><title>Orthogonal contrast based models for quantitative genetic analysis in autotetraploid species</title><title>The New phytologist</title><addtitle>New Phytol</addtitle><description>Dissecting the genetic architecture of quantitative traits is a crucial goal for efficient breeding of polyploid plants, including autotetraploid crop species, such as potato and coffee, and ornamentals such as rose. To meet this goal, a quantitative genetic model is needed to link the genetic effects of genes or genotypes at quantitative trait loci (QTL) to the phenotype of quantitative traits.
We present a statistically tractable quantitative genetic model for autotetraploids based on orthogonal contrast comparisons in the general linear model. The new methods are suitable for autotetraploid species with any population genetic structure and take full account of the essential features of autotetrasomic inheritance. The statistical properties of the new methods are explored and compared to an alternative method in the literature by simulation studies.
We have shown how these methods can be applied for quantitative genetic analysis in autotetraploids by analysing trait phenotype data from an autotetraploid potato segregating population. Using trait segregation analysis, we showed that both highly heritable traits of flowering time and plant height were under the control of major QTL.
The orthogonal model directly dissects genetic variance into independent components and gives consistent estimates of genetic effects provided that tetrasomic gene segregation is considered.</description><subject>Autotetraploid</subject><subject>autotetraploids</subject><subject>Coffee</subject><subject>Computer simulation</subject><subject>Data processing</subject><subject>double reduction</subject><subject>Flowering</subject><subject>Gene loci</subject><subject>Genetic analysis</subject><subject>Genetic diversity</subject><subject>Genetic effects</subject><subject>Genetic structure</subject><subject>Genetic variance</subject><subject>Genotype & phenotype</subject><subject>Genotypes</subject><subject>Heredity</subject><subject>Methods</subject><subject>orthogonal contrasts</subject><subject>Phenotypes</subject><subject>Plant breeding</subject><subject>polyploid</subject><subject>Polyploidy</subject><subject>Population (statistical)</subject><subject>Population genetics</subject><subject>potato</subject><subject>Potatoes</subject><subject>quantitative genetic model</subject><subject>Quantitative genetics</subject><subject>Quantitative trait loci</subject><subject>Species</subject><subject>tetrasomic inheritance</subject><issn>0028-646X</issn><issn>1469-8137</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><recordid>eNp1kE1LHDEch4MoutUe_ABKoJf2MGteJi9zLNJ2BVEPFnooDJnMfzTL7GRMMsp--8auuwfBXHJ5fg_Jg9ApJXOaz8UwPs6pYLrcQzNayqrQlKt9NCOE6UKW8s8R-hTjkhBSCckO0RGrKq20Kmfo721Ij_7BD6bH1g8pmJhwYyK0eOVb6CPufMBPkxmSSya5Z8APMEByFpu8WUcXsRuwmZJPkNdj712L4wjWQTxBB53pI3x-u4_R758_7i8XxfXtr6vL79eFLSkpC2u6rlWaMKYrZq0kIIwEqTmnnAlOmq5RTGnGGqOokozaTmsupWVUs6ZV_Bh93XjH4J8miKleuWih780Afoo1I1JpLbXgGf3yDl36KeSfvFKVyPocLVPfNpQNPsYAXT0GtzJhXVNSvyavc_L6f_LMnr8Zp2YF7Y7cNs7AxQZ4cT2sPzbVN3eLrfJss1jG5MNuUeWnlUII_g-dI5R-</recordid><startdate>20181001</startdate><enddate>20181001</enddate><creator>Chen, Jing</creator><creator>Zhang, Fengjun</creator><creator>Wang, Lin</creator><creator>Leach, Lindsey</creator><creator>Luo, Zewei</creator><general>New Phytologist Trust</general><general>Wiley Subscription Services, Inc</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>7SN</scope><scope>8FD</scope><scope>C1K</scope><scope>F1W</scope><scope>FR3</scope><scope>H95</scope><scope>L.G</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>20181001</creationdate><title>Orthogonal contrast based models for quantitative genetic analysis in autotetraploid species</title><author>Chen, Jing ; Zhang, Fengjun ; Wang, Lin ; Leach, Lindsey ; Luo, Zewei</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4104-caffd78022892cc60e5a6e6833132530bfb727822ba717621cf88366c2182bd73</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>Autotetraploid</topic><topic>autotetraploids</topic><topic>Coffee</topic><topic>Computer simulation</topic><topic>Data processing</topic><topic>double reduction</topic><topic>Flowering</topic><topic>Gene loci</topic><topic>Genetic analysis</topic><topic>Genetic diversity</topic><topic>Genetic effects</topic><topic>Genetic structure</topic><topic>Genetic variance</topic><topic>Genotype & phenotype</topic><topic>Genotypes</topic><topic>Heredity</topic><topic>Methods</topic><topic>orthogonal contrasts</topic><topic>Phenotypes</topic><topic>Plant breeding</topic><topic>polyploid</topic><topic>Polyploidy</topic><topic>Population (statistical)</topic><topic>Population genetics</topic><topic>potato</topic><topic>Potatoes</topic><topic>quantitative genetic model</topic><topic>Quantitative genetics</topic><topic>Quantitative trait loci</topic><topic>Species</topic><topic>tetrasomic inheritance</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Chen, Jing</creatorcontrib><creatorcontrib>Zhang, Fengjun</creatorcontrib><creatorcontrib>Wang, Lin</creatorcontrib><creatorcontrib>Leach, Lindsey</creatorcontrib><creatorcontrib>Luo, Zewei</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Ecology Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ASFA: Aquatic Sciences and Fisheries Abstracts</collection><collection>Engineering Research Database</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) 1: Biological Sciences & Living Resources</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) Professional</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>The New phytologist</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Chen, Jing</au><au>Zhang, Fengjun</au><au>Wang, Lin</au><au>Leach, Lindsey</au><au>Luo, Zewei</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Orthogonal contrast based models for quantitative genetic analysis in autotetraploid species</atitle><jtitle>The New phytologist</jtitle><addtitle>New Phytol</addtitle><date>2018-10-01</date><risdate>2018</risdate><volume>220</volume><issue>1</issue><spage>332</spage><epage>346</epage><pages>332-346</pages><issn>0028-646X</issn><eissn>1469-8137</eissn><abstract>Dissecting the genetic architecture of quantitative traits is a crucial goal for efficient breeding of polyploid plants, including autotetraploid crop species, such as potato and coffee, and ornamentals such as rose. To meet this goal, a quantitative genetic model is needed to link the genetic effects of genes or genotypes at quantitative trait loci (QTL) to the phenotype of quantitative traits.
We present a statistically tractable quantitative genetic model for autotetraploids based on orthogonal contrast comparisons in the general linear model. The new methods are suitable for autotetraploid species with any population genetic structure and take full account of the essential features of autotetrasomic inheritance. The statistical properties of the new methods are explored and compared to an alternative method in the literature by simulation studies.
We have shown how these methods can be applied for quantitative genetic analysis in autotetraploids by analysing trait phenotype data from an autotetraploid potato segregating population. Using trait segregation analysis, we showed that both highly heritable traits of flowering time and plant height were under the control of major QTL.
The orthogonal model directly dissects genetic variance into independent components and gives consistent estimates of genetic effects provided that tetrasomic gene segregation is considered.</abstract><cop>England</cop><pub>New Phytologist Trust</pub><pmid>29987874</pmid><doi>10.1111/nph.15284</doi><tpages>15</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Autotetraploid autotetraploids Coffee Computer simulation Data processing double reduction Flowering Gene loci Genetic analysis Genetic diversity Genetic effects Genetic structure Genetic variance Genotype & phenotype Genotypes Heredity Methods orthogonal contrasts Phenotypes Plant breeding polyploid Polyploidy Population (statistical) Population genetics potato Potatoes quantitative genetic model Quantitative genetics Quantitative trait loci Species tetrasomic inheritance |
| title | Orthogonal contrast based models for quantitative genetic analysis in autotetraploid species |
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