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

Published online by Cambridge University Press:  24 July 2017

L. Pérez-Pardal ,
S. Chen ,
V. Costa ,
X. Liu ,
J. Carvalheira  and
A. Beja-Pereira
L. Pérez-Pardal
Affiliation:
Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-UP), InBIO, Universidade do Porto, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal
S. Chen
Affiliation:
School of Life Sciences, Yunnan University, No. 2 North Cuihu Road, Kunming 650091, Yunnan Province, China
V. Costa
Affiliation:
Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-UP), InBIO, Universidade do Porto, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal
X. Liu
Affiliation:
Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650221, Yunnan Province, China
J. Carvalheira
Affiliation:
Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-UP), InBIO, Universidade do Porto, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
A. Beja-Pereira*
Affiliation:
Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-UP), InBIO, Universidade do Porto, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal
*
†E-mail: [email protected]
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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.

Keywords

water buffaloadmixturegenome-widediversitytraceability
Type
Research Article
Information
animal , Volume 12 , Issue 3 , March 2018 , pp. 464 - 471
Copyright
© The Animal Consortium 2017 

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Footnotes

a

These authors contribute equally to this work.

References

Alexander, DH, Novembre, J and Lange, K 2009. Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19, 1655–1664.Google Scholar
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, 8113–8118.Google Scholar
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, 4202–4215.Google Scholar
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, 80–92.Google Scholar
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, EÖ, 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.Google Scholar
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.Google Scholar
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, 10–16.Google Scholar
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, 999–1002.CrossRefGoogle ScholarPubMed
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.Google Scholar
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.Google Scholar
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.Google Scholar
Jamieson, A and Taylor, SC 1997. Comparisons of three probability formulae for parentage exclusion. Animal Genetics 28, 397–400.Google Scholar
Jobling, MA and Gill, P 2004. Encoded evidence: DNA in forensic analysis. Nature Reviews in Genetics 5, 739–751.Google Scholar
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, 471–476.Google Scholar
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.CrossRefGoogle ScholarPubMed
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, 18–27.Google Scholar
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, 203–211.Google Scholar
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, 1252–1259.CrossRefGoogle ScholarPubMed
Nicolazzi, EL, Iamartino, D and Williams, JL 2014. AffyPipe: an open-source pipeline for affymetrix axiom genotyping workflow. Bioinformatics 30, 3118–3119.Google Scholar
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, 1065–1093.Google Scholar
Peakall, R and Smouse, PE 2012. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research – an update. Bioinformatics 28, 2537–2539.Google Scholar
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, 559–575.CrossRefGoogle ScholarPubMed
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, 46–63.Google Scholar
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, 2129–2141.Google Scholar
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, 1088–1091.CrossRefGoogle ScholarPubMed
Waits, LP, Luikart, G and Taberlet, P 2001. Estimating the probability of identity among genotypes in natural populations: cautions and guidelines. Molecular Ecology 10, 249–256.CrossRefGoogle ScholarPubMed
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, 451–455.Google Scholar
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, 743–750.Google Scholar
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, 2778–2785.CrossRefGoogle ScholarPubMed
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, 433–435.Google Scholar
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, 1530–1550.CrossRefGoogle ScholarPubMed
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