Assessment of the Genetic Diversity of a Local Pig Breed Using Pedigree and SNP Data
Herein, the genetic diversity of the local Přeštice Black-Pied pig breed was assessed by the simultaneous analysis of the pedigree and single nucleotide polymorphism (SNP) data. The information about sire line, dam, date of birth, sex, breeding line, and herd for 1971 individuals was considered in t...
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| Veröffentlicht in: | Genes 2021-12, Vol.12 (12), p.1972 |
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| creator | Krupa, Emil Moravčíková, Nina Krupová, Zuzana Žáková, Eliška |
| description | Herein, the genetic diversity of the local Přeštice Black-Pied pig breed was assessed by the simultaneous analysis of the pedigree and single nucleotide polymorphism (SNP) data. The information about sire line, dam, date of birth, sex, breeding line, and herd for 1971 individuals was considered in the pedigree analysis. The SNP analysis (
= 181) was performed using the Illumina PorcineSNP60 BeadChip kit. The quality of pedigree and SNPs and the inbreeding coefficients (F) and effective population size (N
) were evaluated. The correlations between inbreeding based on the runs of homozygosity (F
) and pedigree (F
) were also calculated. The average F
for all animals was 3.44%, while the F
varied from 10.81% for a minimum size of 1 Mbp to 3.98% for a minimum size of 16 Mbp. The average minor allele frequency was 0.28 ± 0.11. The observed and expected within breed heterozygosities were 0.38 ± 0.13 and 0.37 ± 0.12, respectively. The N
, obtained using both the data sources, reached values around 50 animals. Moderate correlation coefficients (0.49-0.54) were observed between F
and F
. It is necessary to make decisions that stabilize the inbreeding rate in the long-term using optimal contribution selection based on the available SNP data. |
| doi_str_mv | 10.3390/genes12121972 |
| format | Article |
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= 181) was performed using the Illumina PorcineSNP60 BeadChip kit. The quality of pedigree and SNPs and the inbreeding coefficients (F) and effective population size (N
) were evaluated. The correlations between inbreeding based on the runs of homozygosity (F
) and pedigree (F
) were also calculated. The average F
for all animals was 3.44%, while the F
varied from 10.81% for a minimum size of 1 Mbp to 3.98% for a minimum size of 16 Mbp. The average minor allele frequency was 0.28 ± 0.11. The observed and expected within breed heterozygosities were 0.38 ± 0.13 and 0.37 ± 0.12, respectively. The N
, obtained using both the data sources, reached values around 50 animals. Moderate correlation coefficients (0.49-0.54) were observed between F
and F
. It is necessary to make decisions that stabilize the inbreeding rate in the long-term using optimal contribution selection based on the available SNP data.</description><identifier>ISSN: 2073-4425</identifier><identifier>EISSN: 2073-4425</identifier><identifier>DOI: 10.3390/genes12121972</identifier><identifier>PMID: 34946921</identifier><language>eng</language><publisher>Switzerland: MDPI AG</publisher><subject>Algorithms ; Animals ; Gene frequency ; Gene Frequency - genetics ; Genealogy ; Genetic diversity ; Genetic Variation - genetics ; Genomics - methods ; Genotype ; Hogs ; Homozygote ; Inbreeding ; Inbreeding - methods ; Pedigree ; Polymorphism, Single Nucleotide - genetics ; Population ; Population Density ; Quality control ; Single-nucleotide polymorphism ; Software ; Swine - genetics</subject><ispartof>Genes, 2021-12, Vol.12 (12), p.1972</ispartof><rights>2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2021 by the authors. 2021</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c415t-bcc48b66564d61ef90473893ac17d85a7702ccf0eee3c1edfd9169e38245d3513</citedby><cites>FETCH-LOGICAL-c415t-bcc48b66564d61ef90473893ac17d85a7702ccf0eee3c1edfd9169e38245d3513</cites><orcidid>0000-0002-9366-7802 ; 0000-0001-7848-5122</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/PMC8702119/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8702119/$$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/34946921$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Krupa, Emil</creatorcontrib><creatorcontrib>Moravčíková, Nina</creatorcontrib><creatorcontrib>Krupová, Zuzana</creatorcontrib><creatorcontrib>Žáková, Eliška</creatorcontrib><title>Assessment of the Genetic Diversity of a Local Pig Breed Using Pedigree and SNP Data</title><title>Genes</title><addtitle>Genes (Basel)</addtitle><description>Herein, the genetic diversity of the local Přeštice Black-Pied pig breed was assessed by the simultaneous analysis of the pedigree and single nucleotide polymorphism (SNP) data. The information about sire line, dam, date of birth, sex, breeding line, and herd for 1971 individuals was considered in the pedigree analysis. The SNP analysis (
= 181) was performed using the Illumina PorcineSNP60 BeadChip kit. The quality of pedigree and SNPs and the inbreeding coefficients (F) and effective population size (N
) were evaluated. The correlations between inbreeding based on the runs of homozygosity (F
) and pedigree (F
) were also calculated. The average F
for all animals was 3.44%, while the F
varied from 10.81% for a minimum size of 1 Mbp to 3.98% for a minimum size of 16 Mbp. The average minor allele frequency was 0.28 ± 0.11. The observed and expected within breed heterozygosities were 0.38 ± 0.13 and 0.37 ± 0.12, respectively. The N
, obtained using both the data sources, reached values around 50 animals. Moderate correlation coefficients (0.49-0.54) were observed between F
and F
. It is necessary to make decisions that stabilize the inbreeding rate in the long-term using optimal contribution selection based on the available SNP data.</description><subject>Algorithms</subject><subject>Animals</subject><subject>Gene frequency</subject><subject>Gene Frequency - genetics</subject><subject>Genealogy</subject><subject>Genetic diversity</subject><subject>Genetic Variation - genetics</subject><subject>Genomics - methods</subject><subject>Genotype</subject><subject>Hogs</subject><subject>Homozygote</subject><subject>Inbreeding</subject><subject>Inbreeding - methods</subject><subject>Pedigree</subject><subject>Polymorphism, Single Nucleotide - genetics</subject><subject>Population</subject><subject>Population Density</subject><subject>Quality control</subject><subject>Single-nucleotide polymorphism</subject><subject>Software</subject><subject>Swine - genetics</subject><issn>2073-4425</issn><issn>2073-4425</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNpdkc1LAzEQxYMoWmqPXiXgxctqvvYjF6FWrULRgnoOaTK7pmx3a7IV-t-bUpXWzCEZ5sdjXh5CZ5RccS7JdQUNBMpiyZwdoB4jOU-EYOnhzvsEDUKYk3gEYYSkx-iECykyyWgPvQ1DgBAW0HS4LXH3AXgcRTtn8J37Ah9ct94MNJ60Rtd46ip86wEsfg-uqfAUrKtij3Vj8evzFN_pTp-io1LXAQY_dx-9P9y_jR6Tycv4aTScJEbQtEtmxohilmVpJmxGoZRE5LyQXBua2yLVeU6YMSUBAG4o2NJKmkngBROp5SnlfXSz1V2uZguwJprwulZL7xbar1WrndqfNO5DVe2XKqIypTIKXP4I-PZzBaFTCxcM1LVuoF0FxTIqGKd5KiJ68Q-dtyvfRHsbiuXxOyPaR8mWMr4NwUP5twwlahOZ2oss8ue7Dv7o34D4N7BZkM8</recordid><startdate>20211210</startdate><enddate>20211210</enddate><creator>Krupa, Emil</creator><creator>Moravčíková, Nina</creator><creator>Krupová, Zuzana</creator><creator>Žáková, Eliška</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/0000-0002-9366-7802</orcidid><orcidid>https://orcid.org/0000-0001-7848-5122</orcidid></search><sort><creationdate>20211210</creationdate><title>Assessment of the Genetic Diversity of a Local Pig Breed Using Pedigree and SNP Data</title><author>Krupa, Emil ; Moravčíková, Nina ; Krupová, Zuzana ; Žáková, Eliška</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c415t-bcc48b66564d61ef90473893ac17d85a7702ccf0eee3c1edfd9169e38245d3513</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Algorithms</topic><topic>Animals</topic><topic>Gene frequency</topic><topic>Gene Frequency - genetics</topic><topic>Genealogy</topic><topic>Genetic diversity</topic><topic>Genetic Variation - genetics</topic><topic>Genomics - methods</topic><topic>Genotype</topic><topic>Hogs</topic><topic>Homozygote</topic><topic>Inbreeding</topic><topic>Inbreeding - methods</topic><topic>Pedigree</topic><topic>Polymorphism, Single Nucleotide - genetics</topic><topic>Population</topic><topic>Population Density</topic><topic>Quality control</topic><topic>Single-nucleotide polymorphism</topic><topic>Software</topic><topic>Swine - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Krupa, Emil</creatorcontrib><creatorcontrib>Moravčíková, Nina</creatorcontrib><creatorcontrib>Krupová, Zuzana</creatorcontrib><creatorcontrib>Žáková, Eliška</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)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central</collection><collection>Engineering Research Database</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>Biological Sciences</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>Krupa, Emil</au><au>Moravčíková, Nina</au><au>Krupová, Zuzana</au><au>Žáková, Eliška</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Assessment of the Genetic Diversity of a Local Pig Breed Using Pedigree and SNP Data</atitle><jtitle>Genes</jtitle><addtitle>Genes (Basel)</addtitle><date>2021-12-10</date><risdate>2021</risdate><volume>12</volume><issue>12</issue><spage>1972</spage><pages>1972-</pages><issn>2073-4425</issn><eissn>2073-4425</eissn><abstract>Herein, the genetic diversity of the local Přeštice Black-Pied pig breed was assessed by the simultaneous analysis of the pedigree and single nucleotide polymorphism (SNP) data. The information about sire line, dam, date of birth, sex, breeding line, and herd for 1971 individuals was considered in the pedigree analysis. The SNP analysis (
= 181) was performed using the Illumina PorcineSNP60 BeadChip kit. The quality of pedigree and SNPs and the inbreeding coefficients (F) and effective population size (N
) were evaluated. The correlations between inbreeding based on the runs of homozygosity (F
) and pedigree (F
) were also calculated. The average F
for all animals was 3.44%, while the F
varied from 10.81% for a minimum size of 1 Mbp to 3.98% for a minimum size of 16 Mbp. The average minor allele frequency was 0.28 ± 0.11. The observed and expected within breed heterozygosities were 0.38 ± 0.13 and 0.37 ± 0.12, respectively. The N
, obtained using both the data sources, reached values around 50 animals. Moderate correlation coefficients (0.49-0.54) were observed between F
and F
. It is necessary to make decisions that stabilize the inbreeding rate in the long-term using optimal contribution selection based on the available SNP data.</abstract><cop>Switzerland</cop><pub>MDPI AG</pub><pmid>34946921</pmid><doi>10.3390/genes12121972</doi><orcidid>https://orcid.org/0000-0002-9366-7802</orcidid><orcidid>https://orcid.org/0000-0001-7848-5122</orcidid><oa>free_for_read</oa></addata></record> |
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| ispartof | Genes, 2021-12, Vol.12 (12), p.1972 |
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| source | MDPI - Multidisciplinary Digital Publishing Institute; MEDLINE; PubMed Central; EZB Electronic Journals Library; PubMed Central Open Access |
| subjects | Algorithms Animals Gene frequency Gene Frequency - genetics Genealogy Genetic diversity Genetic Variation - genetics Genomics - methods Genotype Hogs Homozygote Inbreeding Inbreeding - methods Pedigree Polymorphism, Single Nucleotide - genetics Population Population Density Quality control Single-nucleotide polymorphism Software Swine - genetics |
| title | Assessment of the Genetic Diversity of a Local Pig Breed Using Pedigree and SNP Data |
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