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Detection of occurrence of a recent genetic bottleneck event in Indian hill cattle breed Bargur using microsatellite markers
The effective number of breedable individuals is a crucial determinant for maintaining genetic variability within a population. The population of Bargur, the hill cattle of South India, has gone down drastically by more than 93 % in the past three decades, and only a few thousand animals are availab...
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| Published in: | Tropical animal health and production 2012-12, Vol.44 (8), p.2007-2013 |
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| container_end_page | 2013 |
| container_issue | 8 |
| container_start_page | 2007 |
| container_title | Tropical animal health and production |
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| creator | Ganapathi, Palanisamy Rajendran, Ramanujam Kathiravan, Periasamy |
| description | The effective number of breedable individuals is a crucial determinant for maintaining genetic variability within a population. The population of Bargur, the hill cattle of South India, has gone down drastically by more than 93 % in the past three decades, and only a few thousand animals are available at present. The present study was undertaken to evaluate Bargur cattle for mutation drift equilibrium and to detect the occurrence of recent genetic bottleneck event, if any, in this population. About 50 unrelated animals, true to the type, were sampled and genotyped at 25 microsatellite loci. The mean observed heterozygosity (0.808 ± 0.023) was higher than the mean expected heterozygosity (0.762 ± 0.008) with 15 out of 25 microsatellite loci exhibiting heterozygosity excess when assumed under Hardy–Weinberg equilibrium. To evaluate Bargur cattle for mutation drift equilibrium, three tests were performed under three different mutation models, viz., infinite allele model (IAM), stepwise mutation model (SMM) and two-phase model (TPM). The observed gene diversity (
H
e
) and expected equilibrium gene diversity (
H
eq
) were estimated under different models of microsatellite evolution. All the 25 loci were found to exhibit gene diversity excess under IAM and TPM, while 22 loci were having gene diversity excess under SMM. All the three statistical tests, viz., sign test, standardized differences test, and Wilcoxon sign rank test, revealed significant (
P
|
| doi_str_mv | 10.1007/s11250-012-0171-8 |
| format | article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_1171881053</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>1171881053</sourcerecordid><originalsourceid>FETCH-LOGICAL-c405t-ca78954a27aaaa623b88548094a42699fcdf159e4b3940d0f170bba22d6e47783</originalsourceid><addsrcrecordid>eNqNkc9rHSEQx6W0NC9p_4BeitBLLpuOrq56zO8EAr20Z3Hd2VeTfW6qbqDQP74uLy2lUKigo8xnxpn5EvKOwQkDUB8zY1xCA4zXrVijX5ANk6ptlGj1S7IBEKYRSqgDcpjzPUCN0t1rcsC5NNww2JAfF1jQlzBHOo909n5JCaPH9eVoQo-x0C1GLMHTfi5lqnf_QPFpdYRIb-MQXKRfwzRR71Y_7RPiQM9c2i6JLjnELd0Fn-bsCk5TKEh3Lj1gym_Iq9FNGd8-2yPy5ery8_lNc_fp-vb89K7xAmRpvFPaSOG4cnV1vO21lkKDEU7wzpjRDyOTBkXfGgEDjExB3zvOhw6FUro9Isf7vI9p_rZgLnYXsq-1uIjzki2rw9OagWz_A-WSd_UUFf3wF3o_LynWRlaKCy46rirF9tQ6gJxwtI8p1P6_WwZ2VdHuVbRVRbuqaNd63z9nXvodDr8jfslWAb4HcnXFLaY_vv5n1p9mdacm</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1122424627</pqid></control><display><type>article</type><title>Detection of occurrence of a recent genetic bottleneck event in Indian hill cattle breed Bargur using microsatellite markers</title><source>Springer Nature</source><creator>Ganapathi, Palanisamy ; Rajendran, Ramanujam ; Kathiravan, Periasamy</creator><creatorcontrib>Ganapathi, Palanisamy ; Rajendran, Ramanujam ; Kathiravan, Periasamy</creatorcontrib><description>The effective number of breedable individuals is a crucial determinant for maintaining genetic variability within a population. The population of Bargur, the hill cattle of South India, has gone down drastically by more than 93 % in the past three decades, and only a few thousand animals are available at present. The present study was undertaken to evaluate Bargur cattle for mutation drift equilibrium and to detect the occurrence of recent genetic bottleneck event, if any, in this population. About 50 unrelated animals, true to the type, were sampled and genotyped at 25 microsatellite loci. The mean observed heterozygosity (0.808 ± 0.023) was higher than the mean expected heterozygosity (0.762 ± 0.008) with 15 out of 25 microsatellite loci exhibiting heterozygosity excess when assumed under Hardy–Weinberg equilibrium. To evaluate Bargur cattle for mutation drift equilibrium, three tests were performed under three different mutation models, viz., infinite allele model (IAM), stepwise mutation model (SMM) and two-phase model (TPM). The observed gene diversity (
H
e
) and expected equilibrium gene diversity (
H
eq
) were estimated under different models of microsatellite evolution. All the 25 loci were found to exhibit gene diversity excess under IAM and TPM, while 22 loci were having gene diversity excess under SMM. All the three statistical tests, viz., sign test, standardized differences test, and Wilcoxon sign rank test, revealed significant (
P
< 0.01) deviation of Bargur cattle population from mutation-drift equilibrium under all the three models of mutation. Furthermore, the qualitative test of allele frequency distribution in Bargur cattle population revealed a strong mode shift from the normal L-shaped form suggesting that the population had experienced genetic bottleneck in the recent past. The occurrence of genetic bottleneck might have led to the loss of several rare alleles in the population, which point towards the need for efforts to conserve this important cattle germplasm. The present study is the first report in demonstrating the genetic basis of demographic bottleneck in an Indian cattle population.</description><identifier>ISSN: 0049-4747</identifier><identifier>EISSN: 1573-7438</identifier><identifier>DOI: 10.1007/s11250-012-0171-8</identifier><identifier>PMID: 22592910</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Animal populations ; Animals ; Biomedical and Life Sciences ; Cattle ; Cattle - genetics ; Demography ; Drift ; Evolution ; Evolutionary genetics ; Frequency distribution ; Gene frequency ; Genetic Drift ; Genetic markers ; Genotype ; Germplasm ; Heterozygosity ; India ; Life Sciences ; Male ; Microsatellite Repeats ; Microsatellites ; Models, Biological ; Multilocus Sequence Typing - veterinary ; Mutation ; Original Research ; Polymerase Chain Reaction - veterinary ; Population genetics ; Statistical analysis ; Veterinary Medicine/Veterinary Science ; Zoology</subject><ispartof>Tropical animal health and production, 2012-12, Vol.44 (8), p.2007-2013</ispartof><rights>Springer Science+Business Media B.V. 2012</rights><rights>Springer Science+Business Media Dordrecht 2012</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c405t-ca78954a27aaaa623b88548094a42699fcdf159e4b3940d0f170bba22d6e47783</citedby><cites>FETCH-LOGICAL-c405t-ca78954a27aaaa623b88548094a42699fcdf159e4b3940d0f170bba22d6e47783</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780,27903,27904</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22592910$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Ganapathi, Palanisamy</creatorcontrib><creatorcontrib>Rajendran, Ramanujam</creatorcontrib><creatorcontrib>Kathiravan, Periasamy</creatorcontrib><title>Detection of occurrence of a recent genetic bottleneck event in Indian hill cattle breed Bargur using microsatellite markers</title><title>Tropical animal health and production</title><addtitle>Trop Anim Health Prod</addtitle><addtitle>Trop Anim Health Prod</addtitle><description>The effective number of breedable individuals is a crucial determinant for maintaining genetic variability within a population. The population of Bargur, the hill cattle of South India, has gone down drastically by more than 93 % in the past three decades, and only a few thousand animals are available at present. The present study was undertaken to evaluate Bargur cattle for mutation drift equilibrium and to detect the occurrence of recent genetic bottleneck event, if any, in this population. About 50 unrelated animals, true to the type, were sampled and genotyped at 25 microsatellite loci. The mean observed heterozygosity (0.808 ± 0.023) was higher than the mean expected heterozygosity (0.762 ± 0.008) with 15 out of 25 microsatellite loci exhibiting heterozygosity excess when assumed under Hardy–Weinberg equilibrium. To evaluate Bargur cattle for mutation drift equilibrium, three tests were performed under three different mutation models, viz., infinite allele model (IAM), stepwise mutation model (SMM) and two-phase model (TPM). The observed gene diversity (
H
e
) and expected equilibrium gene diversity (
H
eq
) were estimated under different models of microsatellite evolution. All the 25 loci were found to exhibit gene diversity excess under IAM and TPM, while 22 loci were having gene diversity excess under SMM. All the three statistical tests, viz., sign test, standardized differences test, and Wilcoxon sign rank test, revealed significant (
P
< 0.01) deviation of Bargur cattle population from mutation-drift equilibrium under all the three models of mutation. Furthermore, the qualitative test of allele frequency distribution in Bargur cattle population revealed a strong mode shift from the normal L-shaped form suggesting that the population had experienced genetic bottleneck in the recent past. The occurrence of genetic bottleneck might have led to the loss of several rare alleles in the population, which point towards the need for efforts to conserve this important cattle germplasm. The present study is the first report in demonstrating the genetic basis of demographic bottleneck in an Indian cattle population.</description><subject>Animal populations</subject><subject>Animals</subject><subject>Biomedical and Life Sciences</subject><subject>Cattle</subject><subject>Cattle - genetics</subject><subject>Demography</subject><subject>Drift</subject><subject>Evolution</subject><subject>Evolutionary genetics</subject><subject>Frequency distribution</subject><subject>Gene frequency</subject><subject>Genetic Drift</subject><subject>Genetic markers</subject><subject>Genotype</subject><subject>Germplasm</subject><subject>Heterozygosity</subject><subject>India</subject><subject>Life Sciences</subject><subject>Male</subject><subject>Microsatellite Repeats</subject><subject>Microsatellites</subject><subject>Models, Biological</subject><subject>Multilocus Sequence Typing - veterinary</subject><subject>Mutation</subject><subject>Original Research</subject><subject>Polymerase Chain Reaction - veterinary</subject><subject>Population genetics</subject><subject>Statistical analysis</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>2012</creationdate><recordtype>article</recordtype><recordid>eNqNkc9rHSEQx6W0NC9p_4BeitBLLpuOrq56zO8EAr20Z3Hd2VeTfW6qbqDQP74uLy2lUKigo8xnxpn5EvKOwQkDUB8zY1xCA4zXrVijX5ANk6ptlGj1S7IBEKYRSqgDcpjzPUCN0t1rcsC5NNww2JAfF1jQlzBHOo909n5JCaPH9eVoQo-x0C1GLMHTfi5lqnf_QPFpdYRIb-MQXKRfwzRR71Y_7RPiQM9c2i6JLjnELd0Fn-bsCk5TKEh3Lj1gym_Iq9FNGd8-2yPy5ery8_lNc_fp-vb89K7xAmRpvFPaSOG4cnV1vO21lkKDEU7wzpjRDyOTBkXfGgEDjExB3zvOhw6FUro9Isf7vI9p_rZgLnYXsq-1uIjzki2rw9OagWz_A-WSd_UUFf3wF3o_LynWRlaKCy46rirF9tQ6gJxwtI8p1P6_WwZ2VdHuVbRVRbuqaNd63z9nXvodDr8jfslWAb4HcnXFLaY_vv5n1p9mdacm</recordid><startdate>20121201</startdate><enddate>20121201</enddate><creator>Ganapathi, Palanisamy</creator><creator>Rajendran, Ramanujam</creator><creator>Kathiravan, Periasamy</creator><general>Springer Netherlands</general><general>Springer Nature B.V</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>3V.</scope><scope>7QL</scope><scope>7T7</scope><scope>7U7</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>7X8</scope></search><sort><creationdate>20121201</creationdate><title>Detection of occurrence of a recent genetic bottleneck event in Indian hill cattle breed Bargur using microsatellite markers</title><author>Ganapathi, Palanisamy ; Rajendran, Ramanujam ; Kathiravan, Periasamy</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c405t-ca78954a27aaaa623b88548094a42699fcdf159e4b3940d0f170bba22d6e47783</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>Animal populations</topic><topic>Animals</topic><topic>Biomedical and Life Sciences</topic><topic>Cattle</topic><topic>Cattle - 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Academic</collection><jtitle>Tropical animal health and production</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Ganapathi, Palanisamy</au><au>Rajendran, Ramanujam</au><au>Kathiravan, Periasamy</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Detection of occurrence of a recent genetic bottleneck event in Indian hill cattle breed Bargur using microsatellite markers</atitle><jtitle>Tropical animal health and production</jtitle><stitle>Trop Anim Health Prod</stitle><addtitle>Trop Anim Health Prod</addtitle><date>2012-12-01</date><risdate>2012</risdate><volume>44</volume><issue>8</issue><spage>2007</spage><epage>2013</epage><pages>2007-2013</pages><issn>0049-4747</issn><eissn>1573-7438</eissn><abstract>The effective number of breedable individuals is a crucial determinant for maintaining genetic variability within a population. The population of Bargur, the hill cattle of South India, has gone down drastically by more than 93 % in the past three decades, and only a few thousand animals are available at present. The present study was undertaken to evaluate Bargur cattle for mutation drift equilibrium and to detect the occurrence of recent genetic bottleneck event, if any, in this population. About 50 unrelated animals, true to the type, were sampled and genotyped at 25 microsatellite loci. The mean observed heterozygosity (0.808 ± 0.023) was higher than the mean expected heterozygosity (0.762 ± 0.008) with 15 out of 25 microsatellite loci exhibiting heterozygosity excess when assumed under Hardy–Weinberg equilibrium. To evaluate Bargur cattle for mutation drift equilibrium, three tests were performed under three different mutation models, viz., infinite allele model (IAM), stepwise mutation model (SMM) and two-phase model (TPM). The observed gene diversity (
H
e
) and expected equilibrium gene diversity (
H
eq
) were estimated under different models of microsatellite evolution. All the 25 loci were found to exhibit gene diversity excess under IAM and TPM, while 22 loci were having gene diversity excess under SMM. All the three statistical tests, viz., sign test, standardized differences test, and Wilcoxon sign rank test, revealed significant (
P
< 0.01) deviation of Bargur cattle population from mutation-drift equilibrium under all the three models of mutation. Furthermore, the qualitative test of allele frequency distribution in Bargur cattle population revealed a strong mode shift from the normal L-shaped form suggesting that the population had experienced genetic bottleneck in the recent past. The occurrence of genetic bottleneck might have led to the loss of several rare alleles in the population, which point towards the need for efforts to conserve this important cattle germplasm. The present study is the first report in demonstrating the genetic basis of demographic bottleneck in an Indian cattle population.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><pmid>22592910</pmid><doi>10.1007/s11250-012-0171-8</doi><tpages>7</tpages></addata></record> |
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| subjects | Animal populations Animals Biomedical and Life Sciences Cattle Cattle - genetics Demography Drift Evolution Evolutionary genetics Frequency distribution Gene frequency Genetic Drift Genetic markers Genotype Germplasm Heterozygosity India Life Sciences Male Microsatellite Repeats Microsatellites Models, Biological Multilocus Sequence Typing - veterinary Mutation Original Research Polymerase Chain Reaction - veterinary Population genetics Statistical analysis Veterinary Medicine/Veterinary Science Zoology |
| title | Detection of occurrence of a recent genetic bottleneck event in Indian hill cattle breed Bargur using microsatellite markers |
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