Genome-Wide SNP Data Revealed the Extent of Linkage Disequilibrium, Persistence of Phase and Effective Population Size in Purebred and Crossbred Buffalo Populations
Linkage disequilibrium (LD) is a useful parameter for guiding the accuracy and power of both genome-wide association studies (GWAS) and genomic selection (GS) among different livestock species. The present study evaluated the extent of LD, persistence of phase and effective population size (Ne) for...
| Main Authors: | , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2019-01-01
|
| Series: | Frontiers in Genetics |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2018.00688/full |
| _version_ | 1818650096404791296 |
|---|---|
| author | Tingxian Deng Tingxian Deng Aixin Liang Jiajia Liu Guohua Hua Tingzhu Ye Shenhe Liu Giuseppe Campanile Graham Plastow Chunyan Zhang Zhiquan Wang Angela Salzano Bianca Gasparrini Martino Cassandro Hasan Riaz Xianwei Liang Liguo Yang |
| author_facet | Tingxian Deng Tingxian Deng Aixin Liang Jiajia Liu Guohua Hua Tingzhu Ye Shenhe Liu Giuseppe Campanile Graham Plastow Chunyan Zhang Zhiquan Wang Angela Salzano Bianca Gasparrini Martino Cassandro Hasan Riaz Xianwei Liang Liguo Yang |
| author_sort | Tingxian Deng |
| collection | DOAJ |
| description | Linkage disequilibrium (LD) is a useful parameter for guiding the accuracy and power of both genome-wide association studies (GWAS) and genomic selection (GS) among different livestock species. The present study evaluated the extent of LD, persistence of phase and effective population size (Ne) for the purebred (Mediterranean buffalo; n = 411) and crossbred [Mediterranean × Jianghan × Nili-Ravi buffalo, n = 9; Murrah × Nili-Ravi × local (Xilin or Fuzhong) buffalo, n = 36] buffalo populations using the 90K Buffalo SNP genotyping array. The results showed that the average square of correlation coefficient (r2) between adjacent SNP was 0.13 ± 0.19 across all autosomes for purebred and 0.09 ± 0.13 for crossbred, and the most rapid decline in LD was observed over the first 200 kb. Estimated r2 ≥ 0.2 extended up to ~50 kb in crossbred and 170 kb in purebred populations, while average r2 values ≥0.3 were respectively observed in the ~10 and 60 kb in the crossbred and purebred populations. The largest phase correlation (RP, C = 0.47) was observed at the distance of 100 kb, suggesting that this phase was not actively preserved between the two populations. Estimated Ne for the purebred and crossbred population at the current generation was 387 and 113 individuals, respectively. These findings may provide useful information to guide the GS and GWAS in buffaloes. |
| first_indexed | 2024-12-17T01:44:47Z |
| format | Article |
| id | doaj.art-12abf374713045368cb1c9de2d4b3da0 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-17T01:44:47Z |
| publishDate | 2019-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-12abf374713045368cb1c9de2d4b3da02022-12-21T22:08:13ZengFrontiers Media S.A.Frontiers in Genetics1664-80212019-01-01910.3389/fgene.2018.00688411972Genome-Wide SNP Data Revealed the Extent of Linkage Disequilibrium, Persistence of Phase and Effective Population Size in Purebred and Crossbred Buffalo PopulationsTingxian Deng0Tingxian Deng1Aixin Liang2Jiajia Liu3Guohua Hua4Tingzhu Ye5Shenhe Liu6Giuseppe Campanile7Graham Plastow8Chunyan Zhang9Zhiquan Wang10Angela Salzano11Bianca Gasparrini12Martino Cassandro13Hasan Riaz14Xianwei Liang15Liguo Yang16Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, ChinaGuangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, ChinaKey Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, ChinaKey Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, ChinaKey Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, ChinaKey Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, ChinaKey Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, ChinaDepartment of Veterinary Medicine and Animal Productions, University of Naples “Federico II”, Naples, ItalyDepartment of Agricultural, Food, and Nutritional Sciences, University of Alberta, Edmonton, AB, CanadaDepartment of Agricultural, Food, and Nutritional Sciences, University of Alberta, Edmonton, AB, CanadaDepartment of Agricultural, Food, and Nutritional Sciences, University of Alberta, Edmonton, AB, CanadaDepartment of Veterinary Medicine and Animal Productions, University of Naples “Federico II”, Naples, ItalyDepartment of Veterinary Medicine and Animal Productions, University of Naples “Federico II”, Naples, ItalyDepartment of Agronomy Food Natural Resources Animal Environmental, University of Padova, Legnaro, ItalyDepartment of Biosciences, COMSATS Institute of Information Technology, Sahiwal, PakistanGuangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, ChinaKey Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, ChinaLinkage disequilibrium (LD) is a useful parameter for guiding the accuracy and power of both genome-wide association studies (GWAS) and genomic selection (GS) among different livestock species. The present study evaluated the extent of LD, persistence of phase and effective population size (Ne) for the purebred (Mediterranean buffalo; n = 411) and crossbred [Mediterranean × Jianghan × Nili-Ravi buffalo, n = 9; Murrah × Nili-Ravi × local (Xilin or Fuzhong) buffalo, n = 36] buffalo populations using the 90K Buffalo SNP genotyping array. The results showed that the average square of correlation coefficient (r2) between adjacent SNP was 0.13 ± 0.19 across all autosomes for purebred and 0.09 ± 0.13 for crossbred, and the most rapid decline in LD was observed over the first 200 kb. Estimated r2 ≥ 0.2 extended up to ~50 kb in crossbred and 170 kb in purebred populations, while average r2 values ≥0.3 were respectively observed in the ~10 and 60 kb in the crossbred and purebred populations. The largest phase correlation (RP, C = 0.47) was observed at the distance of 100 kb, suggesting that this phase was not actively preserved between the two populations. Estimated Ne for the purebred and crossbred population at the current generation was 387 and 113 individuals, respectively. These findings may provide useful information to guide the GS and GWAS in buffaloes.https://www.frontiersin.org/article/10.3389/fgene.2018.00688/fullbuffaloeffective population sizelinkage disequilibriumpersistence of phasepurebred populationcrossbred population |
| spellingShingle | Tingxian Deng Tingxian Deng Aixin Liang Jiajia Liu Guohua Hua Tingzhu Ye Shenhe Liu Giuseppe Campanile Graham Plastow Chunyan Zhang Zhiquan Wang Angela Salzano Bianca Gasparrini Martino Cassandro Hasan Riaz Xianwei Liang Liguo Yang Genome-Wide SNP Data Revealed the Extent of Linkage Disequilibrium, Persistence of Phase and Effective Population Size in Purebred and Crossbred Buffalo Populations Frontiers in Genetics buffalo effective population size linkage disequilibrium persistence of phase purebred population crossbred population |
| title | Genome-Wide SNP Data Revealed the Extent of Linkage Disequilibrium, Persistence of Phase and Effective Population Size in Purebred and Crossbred Buffalo Populations |
| title_full | Genome-Wide SNP Data Revealed the Extent of Linkage Disequilibrium, Persistence of Phase and Effective Population Size in Purebred and Crossbred Buffalo Populations |
| title_fullStr | Genome-Wide SNP Data Revealed the Extent of Linkage Disequilibrium, Persistence of Phase and Effective Population Size in Purebred and Crossbred Buffalo Populations |
| title_full_unstemmed | Genome-Wide SNP Data Revealed the Extent of Linkage Disequilibrium, Persistence of Phase and Effective Population Size in Purebred and Crossbred Buffalo Populations |
| title_short | Genome-Wide SNP Data Revealed the Extent of Linkage Disequilibrium, Persistence of Phase and Effective Population Size in Purebred and Crossbred Buffalo Populations |
| title_sort | genome wide snp data revealed the extent of linkage disequilibrium persistence of phase and effective population size in purebred and crossbred buffalo populations |
| topic | buffalo effective population size linkage disequilibrium persistence of phase purebred population crossbred population |
| url | https://www.frontiersin.org/article/10.3389/fgene.2018.00688/full |
| work_keys_str_mv | AT tingxiandeng genomewidesnpdatarevealedtheextentoflinkagedisequilibriumpersistenceofphaseandeffectivepopulationsizeinpurebredandcrossbredbuffalopopulations AT tingxiandeng genomewidesnpdatarevealedtheextentoflinkagedisequilibriumpersistenceofphaseandeffectivepopulationsizeinpurebredandcrossbredbuffalopopulations AT aixinliang genomewidesnpdatarevealedtheextentoflinkagedisequilibriumpersistenceofphaseandeffectivepopulationsizeinpurebredandcrossbredbuffalopopulations AT jiajialiu genomewidesnpdatarevealedtheextentoflinkagedisequilibriumpersistenceofphaseandeffectivepopulationsizeinpurebredandcrossbredbuffalopopulations AT guohuahua genomewidesnpdatarevealedtheextentoflinkagedisequilibriumpersistenceofphaseandeffectivepopulationsizeinpurebredandcrossbredbuffalopopulations AT tingzhuye genomewidesnpdatarevealedtheextentoflinkagedisequilibriumpersistenceofphaseandeffectivepopulationsizeinpurebredandcrossbredbuffalopopulations AT shenheliu genomewidesnpdatarevealedtheextentoflinkagedisequilibriumpersistenceofphaseandeffectivepopulationsizeinpurebredandcrossbredbuffalopopulations AT giuseppecampanile genomewidesnpdatarevealedtheextentoflinkagedisequilibriumpersistenceofphaseandeffectivepopulationsizeinpurebredandcrossbredbuffalopopulations AT grahamplastow genomewidesnpdatarevealedtheextentoflinkagedisequilibriumpersistenceofphaseandeffectivepopulationsizeinpurebredandcrossbredbuffalopopulations AT chunyanzhang genomewidesnpdatarevealedtheextentoflinkagedisequilibriumpersistenceofphaseandeffectivepopulationsizeinpurebredandcrossbredbuffalopopulations AT zhiquanwang genomewidesnpdatarevealedtheextentoflinkagedisequilibriumpersistenceofphaseandeffectivepopulationsizeinpurebredandcrossbredbuffalopopulations AT angelasalzano genomewidesnpdatarevealedtheextentoflinkagedisequilibriumpersistenceofphaseandeffectivepopulationsizeinpurebredandcrossbredbuffalopopulations AT biancagasparrini genomewidesnpdatarevealedtheextentoflinkagedisequilibriumpersistenceofphaseandeffectivepopulationsizeinpurebredandcrossbredbuffalopopulations AT martinocassandro genomewidesnpdatarevealedtheextentoflinkagedisequilibriumpersistenceofphaseandeffectivepopulationsizeinpurebredandcrossbredbuffalopopulations AT hasanriaz genomewidesnpdatarevealedtheextentoflinkagedisequilibriumpersistenceofphaseandeffectivepopulationsizeinpurebredandcrossbredbuffalopopulations AT xianweiliang genomewidesnpdatarevealedtheextentoflinkagedisequilibriumpersistenceofphaseandeffectivepopulationsizeinpurebredandcrossbredbuffalopopulations AT liguoyang genomewidesnpdatarevealedtheextentoflinkagedisequilibriumpersistenceofphaseandeffectivepopulationsizeinpurebredandcrossbredbuffalopopulations |