Skip to main content
×
×
Home

Genomic differentiation between swamp and river buffalo using a cattle high-density single nucleotide polymorphisms panel

  • L. Pérez-Pardal (a1), S. Chen (a2), V. Costa (a1), X. Liu (a3), J. Carvalheira (a1) (a4) and A. Beja-Pereira (a1)...
Abstract

Buffalo (Bubalus bubalis) is an important livestock species in many tropical and subtropical regions. In recent decades, the interest in buffalo’s milk have expanded and intensive buffalo farms start to emerge. However, breeding programs and population genetics information for this species is scarce or inexistent. The present study aims to test the suitability of the commercial high-density single nucleotide polymorphisms (SNP) genotyping panel, the Illumina BovineHD BeadChip, to estimate population genetics parameters, pedigree control and identification of common variants in major production candidate genes. From a total of 777 962 SNPs included in the panel, 20 479 were polymorphic in water buffalo at a call rate of 86% and an average expected heterozygosity (HE) of 0.306. From these, 357 were mapped within or around the flanking regions of several major candidate genes. A principal components analysis identified three different clusters, each representing pure swamp buffalo type, pure river buffalo type and admixed river buffalo. The hybrids between swamp and river buffalo were clearly identified as an intermediary cluster. The suitability of these SNPs data set for parentage and identity testing demonstrated that the combination of just 30 to 50 SNPs were enough to attain high probabilities of parentage exclusion (0.9999) in both types and identity (2.3×10−5 and 2.0×10−7) for river and swamp buffalo, respectively. Our analysis confirms the suitability of the BovineHD BeadChip to assess population structure, hybridization and identity of the water buffalo populations.

  • View HTML
    • Send article to Kindle

      To send this article to your Kindle, first ensure no-reply@cambridge.org is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about sending to your Kindle. Find out more about sending to your Kindle.

      Note you can select to send to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be sent to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

      Find out more about the Kindle Personal Document Service.

      Genomic differentiation between swamp and river buffalo using a cattle high-density single nucleotide polymorphisms panel
      Available formats
      ×
      Send article to Dropbox

      To send this article to your Dropbox account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your <service> account. Find out more about sending content to Dropbox.

      Genomic differentiation between swamp and river buffalo using a cattle high-density single nucleotide polymorphisms panel
      Available formats
      ×
      Send article to Google Drive

      To send this article to your Google Drive account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your <service> account. Find out more about sending content to Google Drive.

      Genomic differentiation between swamp and river buffalo using a cattle high-density single nucleotide polymorphisms panel
      Available formats
      ×
Copyright
Corresponding author
E-mail: albanobp@fc.up.pt
Footnotes
Hide All
a

These authors contribute equally to this work.

Footnotes
References
Hide All
Alexander, DH, Novembre, J and Lange, K 2009. Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19, 16551664.
Beja-Pereira, A, Caramelli, D, Lalueza-Fox, C, Vernesi, C, Ferrand, N, Casoli, A, Goyache, F, Royo, LJ, Conti, S, Lari, M, Martini, A, Ouragh, L, Magid, A, Atash, A, Zsolnai, A, Boscato, P, Triantaphylidis, C, Ploumi, K, Sineo, L, Mallegni, F, Taberlet, P, Erhardt, G, Sampietro, L, Bertranpetit, J, Barbujani, G, Luikart, G and Bertorelle, G 2006. The origin of European cattle: evidence from modern and ancient DNA. Proceedings of the National Academy of Sciences of the United States of America 103, 81138118.
Borquis, RR, Baldi, F, de Camargo, GM, Cardoso, DF, Santos, DJ, Lugo, NH, Sargolzaei, M, Schenkel, FS, Albuquerque, LG and Tonhati, H 2014. Water buffalo genome characterization by the Illumina BovineHD BeadChip. Genetics and Molecular Research 13, 42024215.
Cingolani, P, Platts, A, Wang le, L, Coon, M, Nguyen, T, Wang, L, Land, SJ, Lu, X and Ruden, DM 2012. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 6, 8092.
Colli, L, Milanesi, M, Vajana, E, Iamartino, D, Bomba, L, Puglisi, F, Del Corvo, M, Nicolazzi, E, Ahmed, SSE-d, Herrera, JRV, Cruz, L, Zhang, S, Yang, BZ, Hao, X, Zuo, F, Lai, S-J, Wang, S, Liu, R, Gong, Y, Mokhber, M, Shahrbabak, HM, Mao, Y, Guan, F, Vlaic, A, Ramunno, L, Ahmad, A, Soysal, I, Ünal, , Ketudat-Cairns, M, Garcia, JF, Utsunomiya, YT, Parnpai, R, Drummond, MG, Galbusera, P, Burton, J, Hoal, E, Yusnizar, Y, Sumantri, C, Moioli, B, Valentini, A, Stella, A and Williams, J, International Buffalo Consortium and Ajmone Marsan P 2016. Water buffalo genomic diversity and post-domestication migration routes. In Plant & Animal Genome Conference XXIV, San Diego, USA.
de Camargo, GMF, Aspilcueta-Borquis, RR, Fortes, MRS, Porto-Neto, R, Cardoso, DF, Santos, DJA, Lehnert, SA, Reverter, A, Moore, S and Tonhati, H 2015. Prospecting major genes in dairy buffaloes. BMC Genomics 16, 872.
El-Halawanya, N, Abdel-Shafy, H, Shawkya, A-E-MA, Abdel-Latifc, MA, Al-Tohamya, AFM and El-Moneima, OMA 2017. Genome-wide association study for milk production in Egyptian buffalo. Livestock Science 198, 1016.
Harisah, M, Azmi, TI, Hilmi, M, Vidyadaran, MK, Bongso, TA, Nava, ZM, Momongan, V and Basrur, PK 1989. Identification of crossbred buffalo genotypes and their chromosome segregation patterns. Genome 32, 9991002.
Heaton, MP, Leymaster, KA, Kalbfleisch, TS, Kijas, JW, Clarke, SM, McEwan, J, Maddox, JF, Basnayake, V, Petrik, DT, Simpson, B, Smith, TP and Chitko-McKown, CG, International Sheep Genomics C 2014. SNPs for parentage testing and traceability in globally diverse breeds of sheep. PLoS One 9, e94851.
Iamartino, D, Williams, JL, Sonstegard, T, Reecy, J, Cv, Tassell, Nicolazzi, EL, Biffani, S, Biscarini, F, Schroeder, S, de Oliveira, DAA, Coletta, A, Garcia, JF, Ahmad, A, Ramunno, L, Pasquariello, R, Drummond, MG, Bastianetto, E, Fritz, E and Knoltes, J 2013. The buffalo genome and the application of genomics in animal management and improvement. In 10th World Buffalo Congress and 7th Asian Buffalo Congress, Phuket, Thailand, pp. 151–158.
Iannuzzi, LDM, Di Meo G 2009. Water buffalo. In Genome mapping and genomics in domestic animals. (eds. NE Cockett and C Kole), pp. 19–28, Springer-Verlag, Berlin Herdelberg, Germany.
Jamieson, A and Taylor, SC 1997. Comparisons of three probability formulae for parentage exclusion. Animal Genetics 28, 397400.
Jobling, MA and Gill, P 2004. Encoded evidence: DNA in forensic analysis. Nature Reviews in Genetics 5, 739751.
Lei, CZ, Zhang, W, Chen, H, Lu, F, Ge, QL, Liu, RY, Dang, RH, Yao, YY, Yao, LB, Lu, ZF and Zhao, ZL 2007. Two maternal lineages revealed by mitochondrial DNA D-loop sequences in chinese native water buffaloes (Bubalus bubalis). Asian-Australasian Journal of Animal Sciences 20, 471476.
Matukumalli, LK, Lawley, CT, Schnabel, RD, Taylor, JF, Allan, MF, Heaton, MP, O’Connell, J, Moore, SS, Smith, TP, Sonstegard, TS and Van Tassell, CP 2009. Development and characterization of a high density SNP genotyping assay for cattle. PLoS One 4, e5350.
Michelizzi, VN, Wu, X, Dodson, MV, Michal, JJ, Zambrano-Varon, J, McLean, DJ and Jiang, Z 2010. A global view of 54,001 single nucleotide polymorphisms (SNPs) on the Illumina BovineSNP50 BeadChip and their transferability to water buffalo. International Journal of Biological Sciences 7, 1827.
Moioli, B, Georgoudis, A, Napolitano, F, Catillo, G, Giubilei, E, Ligda, C and Hassanane, M 2001. Genetic diversity between Italian, Greek and Egyptian buffalo populations. Livestock Production Science 70, 203211.
Nagarajan, M, Nimisha, K and Kumar, S 2015. Mitochondrial DNA variability of domestic river buffalo (Bubalus bubalis) populations: genetic evidence for domestication of river buffalo in Indian subcontinent. Genome Biology and Evolution 7, 12521259.
Nicolazzi, EL, Iamartino, D and Williams, JL 2014. AffyPipe: an open-source pipeline for affymetrix axiom genotyping workflow. Bioinformatics 30, 31183119.
Patterson, N, Moorjani, P, Luo, Y, Mallick, S, Rohland, N, Zhan, Y, Genschoreck, T, Webster, T and Reich, D 2012. Ancient admixture in human history. Genetics 192, 10651093.
Peakall, R and Smouse, PE 2012. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research – an update. Bioinformatics 28, 25372539.
Purcell, S, Neale, B, Todd-Brown, K, Thomas, L, Ferreira, MA, Bender, D, Maller, J, Sklar, P, de Bakker, PI, Daly, MJ and Sham, PC 2007. PLINK: a tool set for whole-genome association and population-based linkage analyses. American Journal of Human Genetics 81, 559575.
Santiago, CA, Voge, JL, Aad, PY, Allen, DT, Stein, DR, Malayer, JR and Spicer, LJ 2005. Pregnancy-associated plasma protein-A and insulin-like growth factor binding protein mRNAs in granulosa cells of dominant and subordinate follicles of preovulatory cattle. Domestic Animals Endocrinology 28, 4663.
Thomas, PD, Campbell, MJ, Kejariwal, A, Mi, H, Karlak, B, Daverman, R, Diemer, K, Muruganujan, A and Narechania, A 2003. PANTHER: a library of protein families and subfamilies indexed by function. Genome Research 13, 21292141.
Troy, CS, MacHugh, DE, Bailey, JF, Magee, DA, Loftus, RT, Cunningham, P, Chamberlain, AT, Sykes, BC and Bradley, DG 2001. Genetic evidence for near-eastern origins of European cattle. Nature 410, 10881091.
Waits, LP, Luikart, G and Taberlet, P 2001. Estimating the probability of identity among genotypes in natural populations: cautions and guidelines. Molecular Ecology 10, 249256.
Warriach, HM, McGill, DM, Bush, RD, Wynn, PC and Chohan, KR 2015. A review of recent developments in buffalo reproduction – a review. Asian Australasian Journal of Animal Science 28, 451455.
Wu, JJ, Song, LJ, Wu, FJ, Liang, XW, Yang, BZ, Wathes, DC, Pollott, GE, Cheng, Z, Shi de, S, Liu, QY, Yang, LG and Zhang, SJ 2013. Investigation of transferability of BovineSNP50 BeadChip from cattle to water buffalo for genome wide association study. Molecular Biology Reports 40, 743750.
Yang, DY, Liu, L, Chen, X and Speller, CF 2008. Wild or domesticated: DNA analysis of ancient water buffalo remains from north China. Journal of Archaeological Science 35, 27782785.
Yindee, M, Vlamings, BH, Wajjwalku, W, Techakumphu, M, Lohachit, C, Sirivaidyapong, S, Thitaram, C, Amarasinghe, AA, Alexander, PA, Colenbrander, B and Lenstra, JA 2010. Y-chromosomal variation confirms independent domestications of swamp and river buffalo. Animal Genetics 41, 433435.
Zhang, Y, Lu, Y, Yindee, M, Li, KY, Kuo, HY, Ju, YT, Ye, S, Faruque, MO, Li, Q, Wang, Y, Cuong, VC, Pham, LD, Bouahom, B, Yang, B, Liang, X, Cai, Z, Vankan, D, Manatchaiworakul, W, Kowlim, N, Duangchantrasiri, S, Wajjwalku, W, Colenbrander, B, Zhang, Y, Beerli, P, Lenstra, JA and Barker, JS 2016. Strong and stable geographic differentiation of swamp buffalo maternal and paternal lineages indicates domestication in the China/Indochina border region. Molecular Ecology 25, 15301550.
Recommend this journal

Email your librarian or administrator to recommend adding this journal to your organisation's collection.

animal
  • ISSN: 1751-7311
  • EISSN: 1751-732X
  • URL: /core/journals/animal
Please enter your name
Please enter a valid email address
Who would you like to send this to? *
×

Keywords

Type Description Title
PDF
Supplementary materials

Pérez-Pardal supplementary material
Table S1

 PDF (67 KB)
67 KB
PDF
Supplementary materials

Pérez-Pardal supplementary material
Table S2

 PDF (362 KB)
362 KB

Metrics

Altmetric attention score

Full text views

Total number of HTML views: 15
Total number of PDF views: 88 *
Loading metrics...

Abstract views

Total abstract views: 569 *
Loading metrics...

* Views captured on Cambridge Core between 24th July 2017 - 21st August 2018. This data will be updated every 24 hours.