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Exploring haplotype block structure, runs of homozygosity, and effective population size among dairy cattle breeds of India
The present study aimed to explore haplotype structure, runs of homozygosity (ROH), effective population size and persistence of gametic phase among three indigenous dairy cattle breeds, viz., Sahiwal ( n = 19), Tharparkar ( n = 17), and Gir ( n = 16) by using BovineHD single nucleotide polymorph...
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| Published in: | Tropical animal health and production 2023-04, Vol.55 (2), p.129-129, Article 129 |
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| container_end_page | 129 |
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| container_title | Tropical animal health and production |
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| creator | Dash, Soumya Singh, Avtar Dixit, S. P. Kumar, Avnish Behera, Rajalaxmi |
| description | The present study aimed to explore haplotype structure, runs of homozygosity (ROH), effective population size and persistence of gametic phase among three indigenous dairy cattle breeds, viz., Sahiwal (
n
= 19), Tharparkar (
n
= 17), and Gir (
n
= 16) by using BovineHD single nucleotide polymorphism (SNP) genotyping assay. The filtered SNPs after quality control ranged from 44% in Sahiwal to 53% in Gir. The highest number of haplotype blocks was observed in Tharparkar (15,640) and the lowest in Sahiwal (8027) spanning 17.3% and 7.8% of genome, respectively. The average block length was found close to 26 kb which suggests that multiple recombination events fragmented the ancestral haplotypes into smaller sizes. Gir cattle had the largest number of runs of homozygosity (ROH) regions (1762) followed by Tharparkar (1528) and Sahiwal (1138). Without pedigree information, inbreeding coefficients estimated from ROH (F
ROH
) revealed that Gir had the highest F
ROH
(0.099) proposing more inbreeding rate in this population. Effective population size (N
e
) decreased slowly over the last 60 generations and at 13 generations ago; N
e
was estimated as 70 for all the three dairy breeds. The highest gametic phase correlation (
r
= 0.78) was observed for Sahiwal and Tharparkar breed pair suggesting formulation of multi-breed reference population for successful implementation of genomic selection among dairy breeds. The decline in effective population size among native Indian cattle breeds may help in formulating strategies for conservation and genetic improvement of native germplasm for future use. |
| doi_str_mv | 10.1007/s11250-023-03534-2 |
| format | article |
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n
= 19), Tharparkar (
n
= 17), and Gir (
n
= 16) by using BovineHD single nucleotide polymorphism (SNP) genotyping assay. The filtered SNPs after quality control ranged from 44% in Sahiwal to 53% in Gir. The highest number of haplotype blocks was observed in Tharparkar (15,640) and the lowest in Sahiwal (8027) spanning 17.3% and 7.8% of genome, respectively. The average block length was found close to 26 kb which suggests that multiple recombination events fragmented the ancestral haplotypes into smaller sizes. Gir cattle had the largest number of runs of homozygosity (ROH) regions (1762) followed by Tharparkar (1528) and Sahiwal (1138). Without pedigree information, inbreeding coefficients estimated from ROH (F
ROH
) revealed that Gir had the highest F
ROH
(0.099) proposing more inbreeding rate in this population. Effective population size (N
e
) decreased slowly over the last 60 generations and at 13 generations ago; N
e
was estimated as 70 for all the three dairy breeds. The highest gametic phase correlation (
r
= 0.78) was observed for Sahiwal and Tharparkar breed pair suggesting formulation of multi-breed reference population for successful implementation of genomic selection among dairy breeds. The decline in effective population size among native Indian cattle breeds may help in formulating strategies for conservation and genetic improvement of native germplasm for future use.</description><identifier>ISSN: 0049-4747</identifier><identifier>EISSN: 1573-7438</identifier><identifier>DOI: 10.1007/s11250-023-03534-2</identifier><identifier>PMID: 36952060</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Animals ; Biomedical and Life Sciences ; Cattle ; Cattle - genetics ; Dairy cattle ; effective population size ; Genetic improvement ; genome ; Genotype ; Genotyping ; Germplasm ; Haplotypes ; Homozygosity ; Homozygote ; Inbreeding ; India ; Life Sciences ; marker-assisted selection ; Nucleotides ; pedigree ; Polymorphism ; Polymorphism, Single Nucleotide ; Population decline ; Population Density ; Population number ; Quality control ; Recombination ; Regular Articles ; Sahiwal ; Single-nucleotide polymorphism ; Veterinary Medicine/Veterinary Science ; Zoology</subject><ispartof>Tropical animal health and production, 2023-04, Vol.55 (2), p.129-129, Article 129</ispartof><rights>The Author(s), under exclusive licence to Springer Nature B.V. 2023. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.</rights><rights>2023. The Author(s), under exclusive licence to Springer Nature B.V.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c403t-86940a9185e3f4c7081827351c1c129985d20235c28de5d2a1ba6ec2c7784dcb3</cites><orcidid>0000-0001-5009-4947</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780,27901,27902</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/36952060$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Dash, Soumya</creatorcontrib><creatorcontrib>Singh, Avtar</creatorcontrib><creatorcontrib>Dixit, S. P.</creatorcontrib><creatorcontrib>Kumar, Avnish</creatorcontrib><creatorcontrib>Behera, Rajalaxmi</creatorcontrib><title>Exploring haplotype block structure, runs of homozygosity, and effective population size among dairy cattle breeds of India</title><title>Tropical animal health and production</title><addtitle>Trop Anim Health Prod</addtitle><addtitle>Trop Anim Health Prod</addtitle><description>The present study aimed to explore haplotype structure, runs of homozygosity (ROH), effective population size and persistence of gametic phase among three indigenous dairy cattle breeds, viz., Sahiwal (
n
= 19), Tharparkar (
n
= 17), and Gir (
n
= 16) by using BovineHD single nucleotide polymorphism (SNP) genotyping assay. The filtered SNPs after quality control ranged from 44% in Sahiwal to 53% in Gir. The highest number of haplotype blocks was observed in Tharparkar (15,640) and the lowest in Sahiwal (8027) spanning 17.3% and 7.8% of genome, respectively. The average block length was found close to 26 kb which suggests that multiple recombination events fragmented the ancestral haplotypes into smaller sizes. Gir cattle had the largest number of runs of homozygosity (ROH) regions (1762) followed by Tharparkar (1528) and Sahiwal (1138). Without pedigree information, inbreeding coefficients estimated from ROH (F
ROH
) revealed that Gir had the highest F
ROH
(0.099) proposing more inbreeding rate in this population. Effective population size (N
e
) decreased slowly over the last 60 generations and at 13 generations ago; N
e
was estimated as 70 for all the three dairy breeds. The highest gametic phase correlation (
r
= 0.78) was observed for Sahiwal and Tharparkar breed pair suggesting formulation of multi-breed reference population for successful implementation of genomic selection among dairy breeds. The decline in effective population size among native Indian cattle breeds may help in formulating strategies for conservation and genetic improvement of native germplasm for future use.</description><subject>Animals</subject><subject>Biomedical and Life Sciences</subject><subject>Cattle</subject><subject>Cattle - genetics</subject><subject>Dairy cattle</subject><subject>effective population size</subject><subject>Genetic improvement</subject><subject>genome</subject><subject>Genotype</subject><subject>Genotyping</subject><subject>Germplasm</subject><subject>Haplotypes</subject><subject>Homozygosity</subject><subject>Homozygote</subject><subject>Inbreeding</subject><subject>India</subject><subject>Life Sciences</subject><subject>marker-assisted selection</subject><subject>Nucleotides</subject><subject>pedigree</subject><subject>Polymorphism</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Population decline</subject><subject>Population Density</subject><subject>Population number</subject><subject>Quality control</subject><subject>Recombination</subject><subject>Regular Articles</subject><subject>Sahiwal</subject><subject>Single-nucleotide polymorphism</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>2023</creationdate><recordtype>article</recordtype><recordid>eNqFkT1v1TAUhi0EopfCH2BAllgYGjj-iu0RVQUqVWKB2fJ1TtqUJA62g0j587i9BSQGkAef4Xkf6_gl5DmD1wxAv8mMcQUNcNGAUEI2_AHZMaVFo6UwD8kOQNpGaqmPyJOcrwFqzLSPyZForeLQwo78OPu-jDEN8yW98nUq24J0P8bwheaS1lDWhCc0rXOmsadXcYo322XMQ9lOqJ87in2PoQzfkC5xWUdfhjjTPNwg9VOs0s4PaaPBlzJWb0Ls7kTnczf4p-RR78eMz-7vY_L53dmn0w_Nxcf356dvL5ogQZTGtFaCt8woFL0MGgwzXAvFQj3cWqM6Xv9ABW46rLNne99i4EFrI7uwF8fk1cG7pPh1xVzcNOSA4-hnjGt23EhrLFNS_h_VFkABM1DRl3-h13FNc12kUsYawy3oSvEDFVLMOWHvljRMPm2Ogbtt0R1adHUDd9ei4zX04l697ifsfkd-1VYBcQDyclsdpj9v_0P7EyWfp8I</recordid><startdate>20230401</startdate><enddate>20230401</enddate><creator>Dash, Soumya</creator><creator>Singh, Avtar</creator><creator>Dixit, S. 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P.</au><au>Kumar, Avnish</au><au>Behera, Rajalaxmi</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Exploring haplotype block structure, runs of homozygosity, and effective population size among dairy cattle breeds of India</atitle><jtitle>Tropical animal health and production</jtitle><stitle>Trop Anim Health Prod</stitle><addtitle>Trop Anim Health Prod</addtitle><date>2023-04-01</date><risdate>2023</risdate><volume>55</volume><issue>2</issue><spage>129</spage><epage>129</epage><pages>129-129</pages><artnum>129</artnum><issn>0049-4747</issn><eissn>1573-7438</eissn><abstract>The present study aimed to explore haplotype structure, runs of homozygosity (ROH), effective population size and persistence of gametic phase among three indigenous dairy cattle breeds, viz., Sahiwal (
n
= 19), Tharparkar (
n
= 17), and Gir (
n
= 16) by using BovineHD single nucleotide polymorphism (SNP) genotyping assay. The filtered SNPs after quality control ranged from 44% in Sahiwal to 53% in Gir. The highest number of haplotype blocks was observed in Tharparkar (15,640) and the lowest in Sahiwal (8027) spanning 17.3% and 7.8% of genome, respectively. The average block length was found close to 26 kb which suggests that multiple recombination events fragmented the ancestral haplotypes into smaller sizes. Gir cattle had the largest number of runs of homozygosity (ROH) regions (1762) followed by Tharparkar (1528) and Sahiwal (1138). Without pedigree information, inbreeding coefficients estimated from ROH (F
ROH
) revealed that Gir had the highest F
ROH
(0.099) proposing more inbreeding rate in this population. Effective population size (N
e
) decreased slowly over the last 60 generations and at 13 generations ago; N
e
was estimated as 70 for all the three dairy breeds. The highest gametic phase correlation (
r
= 0.78) was observed for Sahiwal and Tharparkar breed pair suggesting formulation of multi-breed reference population for successful implementation of genomic selection among dairy breeds. The decline in effective population size among native Indian cattle breeds may help in formulating strategies for conservation and genetic improvement of native germplasm for future use.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><pmid>36952060</pmid><doi>10.1007/s11250-023-03534-2</doi><tpages>1</tpages><orcidid>https://orcid.org/0000-0001-5009-4947</orcidid><oa>free_for_read</oa></addata></record> |
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| ispartof | Tropical animal health and production, 2023-04, Vol.55 (2), p.129-129, Article 129 |
| issn | 0049-4747 1573-7438 |
| language | eng |
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| source | Springer Nature:Jisc Collections:Springer Nature Read and Publish 2023-2025: Springer Reading List |
| subjects | Animals Biomedical and Life Sciences Cattle Cattle - genetics Dairy cattle effective population size Genetic improvement genome Genotype Genotyping Germplasm Haplotypes Homozygosity Homozygote Inbreeding India Life Sciences marker-assisted selection Nucleotides pedigree Polymorphism Polymorphism, Single Nucleotide Population decline Population Density Population number Quality control Recombination Regular Articles Sahiwal Single-nucleotide polymorphism Veterinary Medicine/Veterinary Science Zoology |
| title | Exploring haplotype block structure, runs of homozygosity, and effective population size among dairy cattle breeds of India |
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