Genetic diversity and population structure of four Nigerian indigenous cattle breeds
A total of thirty-eight (38) Nigerian indigenous cattle were used to evaluate the genetic relatedness, diversity, and population structure of four indigenous cattle breeds. Blood samples were collected from the experimental animals into vacutainer tubes containing EDTA, and genomic DNA extracted, qu...
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| Veröffentlicht in: | Tropical animal health and production 2022-04, Vol.54 (2), p.132-132, Article 132 |
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| description | A total of thirty-eight (38) Nigerian indigenous cattle were used to evaluate the genetic relatedness, diversity, and population structure of four indigenous cattle breeds. Blood samples were collected from the experimental animals into vacutainer tubes containing EDTA, and genomic DNA extracted, quantified, and evaluated for integrity. Fourteen (14) microsatellite primers were used for polymerase chain reaction (PCR) and PCR amplification performed under standard conditions followed by electrophoresis in 2.5% Metaphor Agarose gel. Genomic parameter estimates included allele number (Na), observed (H
o
) and expected (H
e
) heterozygosity, polymorphism information content (PIC), test of Hardy–Weinberg equilibrium, and genetic diversity; pairwise Nei’s genetic distance, Wright’s F-statistics (FIT, FST, and FIS), and gene flow (Nm); and breed relationship, population structure, and degree of admixture. A total of 112 alleles were detected and mean number of alleles was 4.02 ± 0.190, while mean fixation index was 0.461 ± 0.068. Mean H
o
and H
e
were 0.352 ± 0.05 and 0.605 ± 0.018, respectively. Pairwise estimates of genetic differentiation, F
ST
, were significantly different (
p
|
| doi_str_mv | 10.1007/s11250-022-03132-8 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_2637582836</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2637582836</sourcerecordid><originalsourceid>FETCH-LOGICAL-c375t-b79d1cd0995eb9f520cfc6a48688f57390bb3d900b7015a24db670d632dc5c6d3</originalsourceid><addsrcrecordid>eNp9kEtrGzEURkVpSBw3f6CLIuimm0mupNFjliG0TsAkG3ctNJKmyIw1rqQJ-N9Hrd0GsshKF3S--zgIfSZwTQDkTSaEcmiA0gYYYbRRH9CCcMka2TL1ES0A2q5pZSsv0GXOW4AaU-IcXTBOBXSMLNBm5aMvwWIXnn3KoRywiQ7vp_08mhKmiHNJsy1z8nga8DDNCT-GXz4FE3GIrpZxmjO2ppTR4z557_IndDaYMfur07tEP39839zdN-un1cPd7bqxTPLS9LJzxDroOu77buAU7GCFaZVQaqhndND3zHUAvQTCDW1dLyQ4waiz3ArHlujbse8-Tb9nn4vehWz9OJro61KaijpHUcVERb--Qbf1lFi3O1GCM14peqRsmnJOftD7FHYmHTQB_ce5PjrX1bn-61yrGvpyaj33O-_-R_5JrgA7Arl-xerudfY7bV8AqHGMUA</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2637586535</pqid></control><display><type>article</type><title>Genetic diversity and population structure of four Nigerian indigenous cattle breeds</title><source>MEDLINE</source><source>SpringerNature Journals</source><creator>Nwachukwu, E. N. ; Kalla, D. J. U. ; Ukwu, H. O. ; Ogbu, C. C. ; Ezea, J. ; Udoh, U. H. ; Ekumankama, O. O.</creator><creatorcontrib>Nwachukwu, E. N. ; Kalla, D. J. U. ; Ukwu, H. O. ; Ogbu, C. C. ; Ezea, J. ; Udoh, U. H. ; Ekumankama, O. O.</creatorcontrib><description>A total of thirty-eight (38) Nigerian indigenous cattle were used to evaluate the genetic relatedness, diversity, and population structure of four indigenous cattle breeds. Blood samples were collected from the experimental animals into vacutainer tubes containing EDTA, and genomic DNA extracted, quantified, and evaluated for integrity. Fourteen (14) microsatellite primers were used for polymerase chain reaction (PCR) and PCR amplification performed under standard conditions followed by electrophoresis in 2.5% Metaphor Agarose gel. Genomic parameter estimates included allele number (Na), observed (H
o
) and expected (H
e
) heterozygosity, polymorphism information content (PIC), test of Hardy–Weinberg equilibrium, and genetic diversity; pairwise Nei’s genetic distance, Wright’s F-statistics (FIT, FST, and FIS), and gene flow (Nm); and breed relationship, population structure, and degree of admixture. A total of 112 alleles were detected and mean number of alleles was 4.02 ± 0.190, while mean fixation index was 0.461 ± 0.068. Mean H
o
and H
e
were 0.352 ± 0.05 and 0.605 ± 0.018, respectively. Pairwise estimates of genetic differentiation, F
ST
, were significantly different (
p
< 0.001) implying distinct breeds. Estimates of Nm were less than 4 but greater than 1, indicating that the cattle breeds do not belong to one panmictic population. Estimates of pairwise genetic distance revealed that White Fulani and Sokoto Gudali were more closely related than Muturu and N’Dama. The results of STRUCTURE, principal coordinate, and phylogenetic analyses revealed four clusters which implies that the breeds were genetically distinct. It is recommended that the four cattle breeds can be used to develop composites with higher genetic potentials for beef production and resistance to endemic diseases and pests. Further efforts should be made to conserve and genetically improve these breeds to meet present and future production and breeding imperatives.</description><identifier>ISSN: 0049-4747</identifier><identifier>EISSN: 1573-7438</identifier><identifier>DOI: 10.1007/s11250-022-03132-8</identifier><identifier>PMID: 35260931</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Alleles ; Animals ; Beef cattle ; Biomedical and Life Sciences ; Cattle ; Cattle - genetics ; Cluster analysis ; Electrophoresis ; Estimates ; Ethylenediaminetetraacetic acids ; Gene flow ; Gene polymorphism ; Genetic distance ; Genetic diversity ; Genetic Variation ; Genomics ; Heterozygosity ; Indigenous animals ; Life Sciences ; Meat production ; Microsatellite Repeats ; Nigeria ; Parameter estimation ; Pests ; Phylogeny ; Polymerase chain reaction ; Polymorphism ; Polymorphism, Genetic ; Population ; Population genetics ; Population structure ; Regular Articles ; Statistical methods ; Tubes ; Veterinary Medicine/Veterinary Science ; Zoology</subject><ispartof>Tropical animal health and production, 2022-04, Vol.54 (2), p.132-132, Article 132</ispartof><rights>The Author(s), under exclusive licence to Springer Nature B.V. 2022</rights><rights>2022. The Author(s), under exclusive licence to Springer Nature B.V.</rights><rights>The Author(s), under exclusive licence to Springer Nature B.V. 2022.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c375t-b79d1cd0995eb9f520cfc6a48688f57390bb3d900b7015a24db670d632dc5c6d3</citedby><cites>FETCH-LOGICAL-c375t-b79d1cd0995eb9f520cfc6a48688f57390bb3d900b7015a24db670d632dc5c6d3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s11250-022-03132-8$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s11250-022-03132-8$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,41488,42557,51319</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/35260931$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Nwachukwu, E. N.</creatorcontrib><creatorcontrib>Kalla, D. J. U.</creatorcontrib><creatorcontrib>Ukwu, H. O.</creatorcontrib><creatorcontrib>Ogbu, C. C.</creatorcontrib><creatorcontrib>Ezea, J.</creatorcontrib><creatorcontrib>Udoh, U. H.</creatorcontrib><creatorcontrib>Ekumankama, O. O.</creatorcontrib><title>Genetic diversity and population structure of four Nigerian indigenous cattle breeds</title><title>Tropical animal health and production</title><addtitle>Trop Anim Health Prod</addtitle><addtitle>Trop Anim Health Prod</addtitle><description>A total of thirty-eight (38) Nigerian indigenous cattle were used to evaluate the genetic relatedness, diversity, and population structure of four indigenous cattle breeds. Blood samples were collected from the experimental animals into vacutainer tubes containing EDTA, and genomic DNA extracted, quantified, and evaluated for integrity. Fourteen (14) microsatellite primers were used for polymerase chain reaction (PCR) and PCR amplification performed under standard conditions followed by electrophoresis in 2.5% Metaphor Agarose gel. Genomic parameter estimates included allele number (Na), observed (H
o
) and expected (H
e
) heterozygosity, polymorphism information content (PIC), test of Hardy–Weinberg equilibrium, and genetic diversity; pairwise Nei’s genetic distance, Wright’s F-statistics (FIT, FST, and FIS), and gene flow (Nm); and breed relationship, population structure, and degree of admixture. A total of 112 alleles were detected and mean number of alleles was 4.02 ± 0.190, while mean fixation index was 0.461 ± 0.068. Mean H
o
and H
e
were 0.352 ± 0.05 and 0.605 ± 0.018, respectively. Pairwise estimates of genetic differentiation, F
ST
, were significantly different (
p
< 0.001) implying distinct breeds. Estimates of Nm were less than 4 but greater than 1, indicating that the cattle breeds do not belong to one panmictic population. Estimates of pairwise genetic distance revealed that White Fulani and Sokoto Gudali were more closely related than Muturu and N’Dama. The results of STRUCTURE, principal coordinate, and phylogenetic analyses revealed four clusters which implies that the breeds were genetically distinct. It is recommended that the four cattle breeds can be used to develop composites with higher genetic potentials for beef production and resistance to endemic diseases and pests. Further efforts should be made to conserve and genetically improve these breeds to meet present and future production and breeding imperatives.</description><subject>Alleles</subject><subject>Animals</subject><subject>Beef cattle</subject><subject>Biomedical and Life Sciences</subject><subject>Cattle</subject><subject>Cattle - genetics</subject><subject>Cluster analysis</subject><subject>Electrophoresis</subject><subject>Estimates</subject><subject>Ethylenediaminetetraacetic acids</subject><subject>Gene flow</subject><subject>Gene polymorphism</subject><subject>Genetic distance</subject><subject>Genetic diversity</subject><subject>Genetic Variation</subject><subject>Genomics</subject><subject>Heterozygosity</subject><subject>Indigenous animals</subject><subject>Life Sciences</subject><subject>Meat production</subject><subject>Microsatellite Repeats</subject><subject>Nigeria</subject><subject>Parameter estimation</subject><subject>Pests</subject><subject>Phylogeny</subject><subject>Polymerase chain reaction</subject><subject>Polymorphism</subject><subject>Polymorphism, Genetic</subject><subject>Population</subject><subject>Population genetics</subject><subject>Population structure</subject><subject>Regular Articles</subject><subject>Statistical methods</subject><subject>Tubes</subject><subject>Veterinary Medicine/Veterinary Science</subject><subject>Zoology</subject><issn>0049-4747</issn><issn>1573-7438</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp9kEtrGzEURkVpSBw3f6CLIuimm0mupNFjliG0TsAkG3ctNJKmyIw1rqQJ-N9Hrd0GsshKF3S--zgIfSZwTQDkTSaEcmiA0gYYYbRRH9CCcMka2TL1ES0A2q5pZSsv0GXOW4AaU-IcXTBOBXSMLNBm5aMvwWIXnn3KoRywiQ7vp_08mhKmiHNJsy1z8nga8DDNCT-GXz4FE3GIrpZxmjO2ppTR4z557_IndDaYMfur07tEP39839zdN-un1cPd7bqxTPLS9LJzxDroOu77buAU7GCFaZVQaqhndND3zHUAvQTCDW1dLyQ4waiz3ArHlujbse8-Tb9nn4vehWz9OJro61KaijpHUcVERb--Qbf1lFi3O1GCM14peqRsmnJOftD7FHYmHTQB_ce5PjrX1bn-61yrGvpyaj33O-_-R_5JrgA7Arl-xerudfY7bV8AqHGMUA</recordid><startdate>20220401</startdate><enddate>20220401</enddate><creator>Nwachukwu, E. 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N.</au><au>Kalla, D. J. U.</au><au>Ukwu, H. O.</au><au>Ogbu, C. C.</au><au>Ezea, J.</au><au>Udoh, U. H.</au><au>Ekumankama, O. O.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genetic diversity and population structure of four Nigerian indigenous cattle breeds</atitle><jtitle>Tropical animal health and production</jtitle><stitle>Trop Anim Health Prod</stitle><addtitle>Trop Anim Health Prod</addtitle><date>2022-04-01</date><risdate>2022</risdate><volume>54</volume><issue>2</issue><spage>132</spage><epage>132</epage><pages>132-132</pages><artnum>132</artnum><issn>0049-4747</issn><eissn>1573-7438</eissn><abstract>A total of thirty-eight (38) Nigerian indigenous cattle were used to evaluate the genetic relatedness, diversity, and population structure of four indigenous cattle breeds. Blood samples were collected from the experimental animals into vacutainer tubes containing EDTA, and genomic DNA extracted, quantified, and evaluated for integrity. Fourteen (14) microsatellite primers were used for polymerase chain reaction (PCR) and PCR amplification performed under standard conditions followed by electrophoresis in 2.5% Metaphor Agarose gel. Genomic parameter estimates included allele number (Na), observed (H
o
) and expected (H
e
) heterozygosity, polymorphism information content (PIC), test of Hardy–Weinberg equilibrium, and genetic diversity; pairwise Nei’s genetic distance, Wright’s F-statistics (FIT, FST, and FIS), and gene flow (Nm); and breed relationship, population structure, and degree of admixture. A total of 112 alleles were detected and mean number of alleles was 4.02 ± 0.190, while mean fixation index was 0.461 ± 0.068. Mean H
o
and H
e
were 0.352 ± 0.05 and 0.605 ± 0.018, respectively. Pairwise estimates of genetic differentiation, F
ST
, were significantly different (
p
< 0.001) implying distinct breeds. Estimates of Nm were less than 4 but greater than 1, indicating that the cattle breeds do not belong to one panmictic population. Estimates of pairwise genetic distance revealed that White Fulani and Sokoto Gudali were more closely related than Muturu and N’Dama. The results of STRUCTURE, principal coordinate, and phylogenetic analyses revealed four clusters which implies that the breeds were genetically distinct. It is recommended that the four cattle breeds can be used to develop composites with higher genetic potentials for beef production and resistance to endemic diseases and pests. Further efforts should be made to conserve and genetically improve these breeds to meet present and future production and breeding imperatives.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><pmid>35260931</pmid><doi>10.1007/s11250-022-03132-8</doi><tpages>1</tpages></addata></record> |
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| subjects | Alleles Animals Beef cattle Biomedical and Life Sciences Cattle Cattle - genetics Cluster analysis Electrophoresis Estimates Ethylenediaminetetraacetic acids Gene flow Gene polymorphism Genetic distance Genetic diversity Genetic Variation Genomics Heterozygosity Indigenous animals Life Sciences Meat production Microsatellite Repeats Nigeria Parameter estimation Pests Phylogeny Polymerase chain reaction Polymorphism Polymorphism, Genetic Population Population genetics Population structure Regular Articles Statistical methods Tubes Veterinary Medicine/Veterinary Science Zoology |
| title | Genetic diversity and population structure of four Nigerian indigenous cattle breeds |
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