Maternal Transmission Ratio Distortion in Two Iberian Pig Varieties
Transmission ratio distortion (TRD) is defined as the allele transmission deviation from the heterozygous parent to the offspring from the expected Mendelian genotypic frequencies. Although TRD can be a confounding factor in genetic mapping studies, this phenomenon remains mostly unknown in pigs, pa...
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| Veröffentlicht in: | Genes 2020-09, Vol.11 (9), p.1050 |
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| creator | Vázquez-Gómez, Marta Hijas-Villalba, Melani Martín de Varona, Luis Ibañez-Escriche, Noelia Rosas, Juan Pablo Negro, Sara Noguera, José Luis Casellas, Joaquim |
| description | Transmission ratio distortion (TRD) is defined as the allele transmission deviation from the heterozygous parent to the offspring from the expected Mendelian genotypic frequencies. Although TRD can be a confounding factor in genetic mapping studies, this phenomenon remains mostly unknown in pigs, particularly in traditional breeds (i.e., the Iberian pig). We aimed to describe the maternal TRD prevalence and its genomic distribution in two Iberian varieties. Genotypes from a total of 247 families (dam and offspring) of Entrepelado (
= 129) and Retinto (
= 118) Iberian varieties were analyzed. The offspring were sired by both ungenotyped purebred Retinto and Entrepelado Iberian boars, regardless of the dam variety used. After quality control, 16,246 single-nucleotide polymorphisms (SNPs) in the Entrepelado variety and 9744 SNPs in the Retinto variety were analyzed. Maternal TRD was evaluated by a likelihood ratio test under SNP-by-SNP, adapting a previous model solved by Bayesian inference. Results provided 68 maternal TRD loci (TRDLs) in the Entrepelado variety and 24 in the Retinto variety (
< 0.05), with mostly negative TRD values, increasing the transmission of the minor allele. In addition, both varieties shared ten common TRDLs. No strong evidence of biological effects was found in genes with TRDLs. However, some biological processes could be affected by TRDLs, such as embryogenesis at different levels and lipid metabolism. These findings could provide useful insight into the genetic mechanisms to improve the swine industry, particularly in traditional breeds. |
| doi_str_mv | 10.3390/genes11091050 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_7563664</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2441275414</sourcerecordid><originalsourceid>FETCH-LOGICAL-c415t-242916171f35c27b1810290e950ffd2031dbcfb61fc4663c805b023783a7f0a53</originalsourceid><addsrcrecordid>eNpdkctLAzEQxoMottQevcqCFy-rk9c-LoLUV6GiSPUastukpmyTmuwq_vfu0lpa5zLDzI-PmfkQOsVwSWkOV3NlVcAYcgwcDlCfQEpjxgg_3Kl7aBjCAtpgQAD4MepRkuU5S3kfjZ5krbyVVTT10oalCcE4G73K2rjo1oTa-bprGBtNv100LpQ30kYvZh69S29UbVQ4QUdaVkENN3mA3u7vpqPHePL8MB7dTOKSYV7HhJEcJzjFmvKSpAXOMJAcVM5B6xkBimdFqYsE65IlCS0z4AUQmmZUphokpwN0vdZdNcVSzUplay8rsfJmKf2PcNKI_Yk1H2LuvkTKE5okrBW42Ah499moUIv23lJVlbTKNUEQxjBJOcMdev4PXbim-9OaopDTdrcBitdU6V0IXuntMhhE55DYc6jlz3Yv2NJ_ftBfFhmLOg</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2441309302</pqid></control><display><type>article</type><title>Maternal Transmission Ratio Distortion in Two Iberian Pig Varieties</title><source>MDPI - Multidisciplinary Digital Publishing Institute</source><source>MEDLINE</source><source>Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals</source><source>PubMed Central</source><source>PubMed Central Open Access</source><creator>Vázquez-Gómez, Marta ; Hijas-Villalba, Melani Martín de ; Varona, Luis ; Ibañez-Escriche, Noelia ; Rosas, Juan Pablo ; Negro, Sara ; Noguera, José Luis ; Casellas, Joaquim</creator><creatorcontrib>Vázquez-Gómez, Marta ; Hijas-Villalba, Melani Martín de ; Varona, Luis ; Ibañez-Escriche, Noelia ; Rosas, Juan Pablo ; Negro, Sara ; Noguera, José Luis ; Casellas, Joaquim</creatorcontrib><description>Transmission ratio distortion (TRD) is defined as the allele transmission deviation from the heterozygous parent to the offspring from the expected Mendelian genotypic frequencies. Although TRD can be a confounding factor in genetic mapping studies, this phenomenon remains mostly unknown in pigs, particularly in traditional breeds (i.e., the Iberian pig). We aimed to describe the maternal TRD prevalence and its genomic distribution in two Iberian varieties. Genotypes from a total of 247 families (dam and offspring) of Entrepelado (
= 129) and Retinto (
= 118) Iberian varieties were analyzed. The offspring were sired by both ungenotyped purebred Retinto and Entrepelado Iberian boars, regardless of the dam variety used. After quality control, 16,246 single-nucleotide polymorphisms (SNPs) in the Entrepelado variety and 9744 SNPs in the Retinto variety were analyzed. Maternal TRD was evaluated by a likelihood ratio test under SNP-by-SNP, adapting a previous model solved by Bayesian inference. Results provided 68 maternal TRD loci (TRDLs) in the Entrepelado variety and 24 in the Retinto variety (
< 0.05), with mostly negative TRD values, increasing the transmission of the minor allele. In addition, both varieties shared ten common TRDLs. No strong evidence of biological effects was found in genes with TRDLs. However, some biological processes could be affected by TRDLs, such as embryogenesis at different levels and lipid metabolism. These findings could provide useful insight into the genetic mechanisms to improve the swine industry, particularly in traditional breeds.</description><identifier>ISSN: 2073-4425</identifier><identifier>EISSN: 2073-4425</identifier><identifier>DOI: 10.3390/genes11091050</identifier><identifier>PMID: 32899475</identifier><language>eng</language><publisher>Switzerland: MDPI AG</publisher><subject>Alleles ; Animal breeding ; Animals ; Bayes Theorem ; Bayesian analysis ; Chromosomes, Mammalian - genetics ; Deoxyribonucleic acid ; DNA ; Embryogenesis ; Female ; Gene mapping ; Genes ; Genetic Markers ; Genetic testing ; Genome ; Genomes ; Hogs ; Inheritance Patterns - genetics ; Laboratory animals ; Lipid metabolism ; Male ; Maternal Inheritance - genetics ; Polymorphism, Single Nucleotide ; Quality control ; Single-nucleotide polymorphism ; Software ; Swine - classification ; Swine - genetics</subject><ispartof>Genes, 2020-09, Vol.11 (9), p.1050</ispartof><rights>2020. This work is licensed under http://creativecommons.org/licenses/by/3.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2020 by the authors. 2020</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c415t-242916171f35c27b1810290e950ffd2031dbcfb61fc4663c805b023783a7f0a53</citedby><cites>FETCH-LOGICAL-c415t-242916171f35c27b1810290e950ffd2031dbcfb61fc4663c805b023783a7f0a53</cites><orcidid>0000-0002-8916-2086 ; 0000-0001-6256-5478</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7563664/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7563664/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32899475$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Vázquez-Gómez, Marta</creatorcontrib><creatorcontrib>Hijas-Villalba, Melani Martín de</creatorcontrib><creatorcontrib>Varona, Luis</creatorcontrib><creatorcontrib>Ibañez-Escriche, Noelia</creatorcontrib><creatorcontrib>Rosas, Juan Pablo</creatorcontrib><creatorcontrib>Negro, Sara</creatorcontrib><creatorcontrib>Noguera, José Luis</creatorcontrib><creatorcontrib>Casellas, Joaquim</creatorcontrib><title>Maternal Transmission Ratio Distortion in Two Iberian Pig Varieties</title><title>Genes</title><addtitle>Genes (Basel)</addtitle><description>Transmission ratio distortion (TRD) is defined as the allele transmission deviation from the heterozygous parent to the offspring from the expected Mendelian genotypic frequencies. Although TRD can be a confounding factor in genetic mapping studies, this phenomenon remains mostly unknown in pigs, particularly in traditional breeds (i.e., the Iberian pig). We aimed to describe the maternal TRD prevalence and its genomic distribution in two Iberian varieties. Genotypes from a total of 247 families (dam and offspring) of Entrepelado (
= 129) and Retinto (
= 118) Iberian varieties were analyzed. The offspring were sired by both ungenotyped purebred Retinto and Entrepelado Iberian boars, regardless of the dam variety used. After quality control, 16,246 single-nucleotide polymorphisms (SNPs) in the Entrepelado variety and 9744 SNPs in the Retinto variety were analyzed. Maternal TRD was evaluated by a likelihood ratio test under SNP-by-SNP, adapting a previous model solved by Bayesian inference. Results provided 68 maternal TRD loci (TRDLs) in the Entrepelado variety and 24 in the Retinto variety (
< 0.05), with mostly negative TRD values, increasing the transmission of the minor allele. In addition, both varieties shared ten common TRDLs. No strong evidence of biological effects was found in genes with TRDLs. However, some biological processes could be affected by TRDLs, such as embryogenesis at different levels and lipid metabolism. These findings could provide useful insight into the genetic mechanisms to improve the swine industry, particularly in traditional breeds.</description><subject>Alleles</subject><subject>Animal breeding</subject><subject>Animals</subject><subject>Bayes Theorem</subject><subject>Bayesian analysis</subject><subject>Chromosomes, Mammalian - genetics</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Embryogenesis</subject><subject>Female</subject><subject>Gene mapping</subject><subject>Genes</subject><subject>Genetic Markers</subject><subject>Genetic testing</subject><subject>Genome</subject><subject>Genomes</subject><subject>Hogs</subject><subject>Inheritance Patterns - genetics</subject><subject>Laboratory animals</subject><subject>Lipid metabolism</subject><subject>Male</subject><subject>Maternal Inheritance - genetics</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Quality control</subject><subject>Single-nucleotide polymorphism</subject><subject>Software</subject><subject>Swine - classification</subject><subject>Swine - genetics</subject><issn>2073-4425</issn><issn>2073-4425</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNpdkctLAzEQxoMottQevcqCFy-rk9c-LoLUV6GiSPUastukpmyTmuwq_vfu0lpa5zLDzI-PmfkQOsVwSWkOV3NlVcAYcgwcDlCfQEpjxgg_3Kl7aBjCAtpgQAD4MepRkuU5S3kfjZ5krbyVVTT10oalCcE4G73K2rjo1oTa-bprGBtNv100LpQ30kYvZh69S29UbVQ4QUdaVkENN3mA3u7vpqPHePL8MB7dTOKSYV7HhJEcJzjFmvKSpAXOMJAcVM5B6xkBimdFqYsE65IlCS0z4AUQmmZUphokpwN0vdZdNcVSzUplay8rsfJmKf2PcNKI_Yk1H2LuvkTKE5okrBW42Ah499moUIv23lJVlbTKNUEQxjBJOcMdev4PXbim-9OaopDTdrcBitdU6V0IXuntMhhE55DYc6jlz3Yv2NJ_ftBfFhmLOg</recordid><startdate>20200905</startdate><enddate>20200905</enddate><creator>Vázquez-Gómez, Marta</creator><creator>Hijas-Villalba, Melani Martín de</creator><creator>Varona, Luis</creator><creator>Ibañez-Escriche, Noelia</creator><creator>Rosas, Juan Pablo</creator><creator>Negro, Sara</creator><creator>Noguera, José Luis</creator><creator>Casellas, Joaquim</creator><general>MDPI AG</general><general>MDPI</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>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>LK8</scope><scope>M7P</scope><scope>P64</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-8916-2086</orcidid><orcidid>https://orcid.org/0000-0001-6256-5478</orcidid></search><sort><creationdate>20200905</creationdate><title>Maternal Transmission Ratio Distortion in Two Iberian Pig Varieties</title><author>Vázquez-Gómez, Marta ; Hijas-Villalba, Melani Martín de ; Varona, Luis ; Ibañez-Escriche, Noelia ; Rosas, Juan Pablo ; Negro, Sara ; Noguera, José Luis ; Casellas, Joaquim</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c415t-242916171f35c27b1810290e950ffd2031dbcfb61fc4663c805b023783a7f0a53</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Alleles</topic><topic>Animal breeding</topic><topic>Animals</topic><topic>Bayes Theorem</topic><topic>Bayesian analysis</topic><topic>Chromosomes, Mammalian - genetics</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>Embryogenesis</topic><topic>Female</topic><topic>Gene mapping</topic><topic>Genes</topic><topic>Genetic Markers</topic><topic>Genetic testing</topic><topic>Genome</topic><topic>Genomes</topic><topic>Hogs</topic><topic>Inheritance Patterns - genetics</topic><topic>Laboratory animals</topic><topic>Lipid metabolism</topic><topic>Male</topic><topic>Maternal Inheritance - genetics</topic><topic>Polymorphism, Single Nucleotide</topic><topic>Quality control</topic><topic>Single-nucleotide polymorphism</topic><topic>Software</topic><topic>Swine - classification</topic><topic>Swine - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Vázquez-Gómez, Marta</creatorcontrib><creatorcontrib>Hijas-Villalba, Melani Martín de</creatorcontrib><creatorcontrib>Varona, Luis</creatorcontrib><creatorcontrib>Ibañez-Escriche, Noelia</creatorcontrib><creatorcontrib>Rosas, Juan Pablo</creatorcontrib><creatorcontrib>Negro, Sara</creatorcontrib><creatorcontrib>Noguera, José Luis</creatorcontrib><creatorcontrib>Casellas, Joaquim</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Genes</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Vázquez-Gómez, Marta</au><au>Hijas-Villalba, Melani Martín de</au><au>Varona, Luis</au><au>Ibañez-Escriche, Noelia</au><au>Rosas, Juan Pablo</au><au>Negro, Sara</au><au>Noguera, José Luis</au><au>Casellas, Joaquim</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Maternal Transmission Ratio Distortion in Two Iberian Pig Varieties</atitle><jtitle>Genes</jtitle><addtitle>Genes (Basel)</addtitle><date>2020-09-05</date><risdate>2020</risdate><volume>11</volume><issue>9</issue><spage>1050</spage><pages>1050-</pages><issn>2073-4425</issn><eissn>2073-4425</eissn><abstract>Transmission ratio distortion (TRD) is defined as the allele transmission deviation from the heterozygous parent to the offspring from the expected Mendelian genotypic frequencies. Although TRD can be a confounding factor in genetic mapping studies, this phenomenon remains mostly unknown in pigs, particularly in traditional breeds (i.e., the Iberian pig). We aimed to describe the maternal TRD prevalence and its genomic distribution in two Iberian varieties. Genotypes from a total of 247 families (dam and offspring) of Entrepelado (
= 129) and Retinto (
= 118) Iberian varieties were analyzed. The offspring were sired by both ungenotyped purebred Retinto and Entrepelado Iberian boars, regardless of the dam variety used. After quality control, 16,246 single-nucleotide polymorphisms (SNPs) in the Entrepelado variety and 9744 SNPs in the Retinto variety were analyzed. Maternal TRD was evaluated by a likelihood ratio test under SNP-by-SNP, adapting a previous model solved by Bayesian inference. Results provided 68 maternal TRD loci (TRDLs) in the Entrepelado variety and 24 in the Retinto variety (
< 0.05), with mostly negative TRD values, increasing the transmission of the minor allele. In addition, both varieties shared ten common TRDLs. No strong evidence of biological effects was found in genes with TRDLs. However, some biological processes could be affected by TRDLs, such as embryogenesis at different levels and lipid metabolism. These findings could provide useful insight into the genetic mechanisms to improve the swine industry, particularly in traditional breeds.</abstract><cop>Switzerland</cop><pub>MDPI AG</pub><pmid>32899475</pmid><doi>10.3390/genes11091050</doi><orcidid>https://orcid.org/0000-0002-8916-2086</orcidid><orcidid>https://orcid.org/0000-0001-6256-5478</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Alleles Animal breeding Animals Bayes Theorem Bayesian analysis Chromosomes, Mammalian - genetics Deoxyribonucleic acid DNA Embryogenesis Female Gene mapping Genes Genetic Markers Genetic testing Genome Genomes Hogs Inheritance Patterns - genetics Laboratory animals Lipid metabolism Male Maternal Inheritance - genetics Polymorphism, Single Nucleotide Quality control Single-nucleotide polymorphism Software Swine - classification Swine - genetics |
| title | Maternal Transmission Ratio Distortion in Two Iberian Pig Varieties |
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