Low levels of taurine introgression in the current Brazilian Nelore and Gir indicine cattle populations
- Ana M Perez O’Brien1,
- Daniela Höller1,
- Solomon A Boison1,
- Marco Milanesi2,
- Lorenzo Bomba2,
- Yuri T Utsunomiya3,
- Roberto Carvalheiro3,
- Haroldo HR Neves3,
- Marcos VB da Silva4,
- Curtis P VanTassell5,
- Tad S Sonstegard5,
- Gábor Mészáros1,
- Paolo Ajmone-Marsan2,
- Fernando Garcia3, 6 and
- Johann Sölkner1Email author
© Perez O'Brien et al.; licensee BioMed Central. 2015
Received: 23 April 2014
Accepted: 27 February 2015
Published: 17 April 2015
Nelore and Gir are the two most important indicine cattle breeds for production of beef and milk in Brazil. Historical records state that these breeds were introduced in Brazil from the Indian subcontinent, crossed to local taurine cattle in order to quickly increase the population size, and then backcrossed to the original breeds to recover indicine adaptive and productive traits. Previous investigations based on sparse DNA markers detected taurine admixture in these breeds. High-density genome-wide analyses can provide high-resolution information on the genetic composition of current Nelore and Gir populations, estimate more precisely the levels and nature of taurine introgression, and shed light on their history and the strategies that were used to expand these breeds.
We used the high-density Illumina BovineHD BeadChip with more than 777 K single nucleotide polymorphisms (SNPs) that were reduced to 697 115 after quality control filtering to investigate the structure of Nelore and Gir populations and seven other worldwide populations for comparison. Multidimensional scaling and model-based ancestry estimation clearly separated the indicine, European taurine and African taurine ancestries. The average level of taurine introgression in the autosomal genome of Nelore and Gir breeds was less than 1% but was 9% for the Brahman breed. Analyses based on the mitochondrial SNPs present in the Illumina BovineHD BeadChip did not clearly differentiate taurine and indicine haplotype groupings.
The low level of taurine ancestry observed for both Nelore and Gir breeds confirms the historical records of crossbreeding and supports a strong directional selection against taurine haplotypes via backcrossing. Random sampling in production herds across the country and subsequent genotyping would be useful for a more complete view of the admixture levels in the commercial Nelore and Gir populations.
Brazil has the second largest bovine population in the world  with more than 211 million heads of cattle as of 2012 , from which about 80% are estimated to be indicine cattle (Bos primigenius indicus) . In the last decade, Brazil has emerged as one of the top beef exporters in the world and has a pivotal role in contributing towards ensuring protein availability for the growing global population, especially in emerging countries, which have increasing demands for animal products . The Nelore breed has the largest population and is the main breed used for beef production in Brazil . The Gir breed represents about 10% of indicine cattle and is recognized as the indicine breed with the highest dairy capacity, which has favored its use in recent years . A better understanding of the genetic composition of these important breeds in Brazil can help to reconstruct their history and open up perspectives for their future management and improvement of bovine production in the Brazilian tropical context.
Cattle were first introduced in Latin America by Spanish and Portuguese colonizers who brought taurine (Bos primigenius taurus) Iberian breeds in this part of the world . Indicine breeds were imported from India during the 19th and 20th centuries, and it is estimated that a maximum of 7000 animals of indicine origin have been introduced in Brazil . Thanks to their ability to adapt to the Brazilian tropical conditions, indicine cattle became popular and their population rapidly expanded up to the current numbers. This quick process was initiated by the use of locally available female cattle, such as Creoles that derive from Iberian cattle. Thereafter, repeated crosses with indicine males were used as a breeding strategy to recover pure indicine breeds . The analysis of mitochondrial (mt) DNA haplotypes confirms this hypothesis. Brazilian indicine breeds possess the T1 and T3 taurine haplotypes that are very frequent in African and European taurine cattle, respectively , and present in Brazilian Creole and Iberian cattle breeds . However, a Y-chromosome analysis of Brazilian cattle suggested an indicine paternal origin in the indicine breeds and indicine male introgression in the taurine creole populations . Very few studies have analyzed the taurine introgression in Brazilian indicine cattle and most available reports are underpowered by the use of low numbers of microsatellite markers . A recent study that was based on an unbiased panel of amplified fragment length polymorphism (AFLP) markers to investigate the genetic structure of several bovine populations at a global scale did not detect significant levels of taurine ancestry in three Brazilian breeds, including Nelore . Several analyses using genome-wide single nucleotide polymorphisms (SNPs) have included Gir and Nelore individuals in their datasets [15-19], but in most cases with very few individuals (<20).
Here, we report a comprehensive analysis of the levels of genome-wide autosomal taurine admixture in Brazilian Nelore and Gir populations, through the use of dense SNPs and a comparison of the data with genotypes of other worldwide cattle breeds.
Genotypes from the Illumina BovineHD BeadChip  (>777 K SNPs) were used. All samples were derived from previous studies, and with the exception of the Fleckvieh, Nelore and Gir breeds, individuals were chosen to represent the diversity within each breed. For the Fleckvieh, Nelore and Gir breeds, animals were selected to represent influential bulls that are widely used for artificial insemination in their respective breed. Nelore bulls representing two different types of breeding systems, pedigree and production, were included in equal proportions. Individuals (figures in brackets represent the number of individuals per breed) were sampled from five European taurine breeds: Holstein (67), Brown Swiss (73), Austrian Simmental Fleckvieh (96), Angus (37) and Hereford (27); one African taurine breed: N’Dama (48); and three indicine breeds: Brahman (35), Nelore (115) and Gir (100). The Nelore population included two groups of animals: 15 individuals that were considered as ancestral since they are first descendants of imported animals from India, and 100 individuals born after 2000 that represent the current population. All Gir individuals were also born after 2000 and represented the current population. Quality control of genotypes was performed within breed to exclude SNPs and individuals with more than 10% missing genotypes, and across all breeds to exclude monomorphic SNPs. After quality control, 697 115 autosomal SNPs and 28 (out of 343) mt SNPs were retained and used for analyses.
To obtain a general overview of the population structure, a multidimensional scaling analysis was performed by converting the genomic kinship coefficients from the identity-by-state (IBS) matrix generated with PLINK  to squared Euclidean distances between individuals via classical multidimensional scaling using the “cmdscale” function from R .The R script applied was cmdscale(as.dist(1-X), eig = TRUE), with X being the IBS full (upper, diagonal, lower triangle) matrix computed from PLINK. Genetic variability and differentiation of populations were also determined using Wright’s F-statistics, FIS and FST [23,24].
Proportions of individual ancestry for K (number of assumed ancestral populations) ranging from 2 to 5 were evaluated using the unsupervised model-based approach implemented in ADMIXTURE v1.22 software . The same analyses were run for a subset of the data after reducing the number of individuals per breed to a maximum of 20 randomly chosen animals, to evaluate the estimated ancestries using a balanced dataset for number of individuals per breed. We performed a small number of runs with different sets of random samples of 20 animals per group, with similar results. This is consistent with our experience from a different admixture study  in which large numbers of subsets of 10 animals per ancestral breed were used. The best ancestry estimates were obtained by using the cross-validation option implemented by ADMIXTURE. The mt SNPs were used to construct haplotypes  and the frequency for each identified haplotype was calculated per breed to evaluate the ability of these SNPs to separate individuals into indicine and taurine European or African clusters.
Results and discussion
Indicators for population variability and differentiation (Wrights F IS on diagonals and F ST on off-diagonals)
With K = 3, the African and European taurine populations were separated and levels of African taurine ancestry were low in some European populations, particularly in the Fleckvieh breed. A very low level of African taurine ancestry was estimated for the indicine populations, i.e. on average 1.5% in the Brahman and 0.4% in the Nelore populations. Indicine ancestry was observed in some of the African N’Dama individuals, but the number of these was smaller than with K = 2. Indeed with K = 3 a better fit of the model is probably obtained i.e. three ancestries are able to explain the larger divergence between African and European taurine ancestry as supported by the findings of Decker et al. .
With K = 4, Brown Swiss and Holstein cattle were clearly separated, with the other three European populations showing intermediate levels of both ancestries. With the addition of one more assumed ancestry (K = 5), the Gir and Nelore breeds were separated into two clusters of indicine ancestry and the Brahman breed had intermediate levels of taurine and indicine ancestries. The separation of the Nelore and Gir breeds into different ancestries is consistent with the fact that they originated from separate Indian populations; the first population derived from gray breeds of Northern and central India, and the second one from the red and white-speckled cattle from the West coast of India, south of the Kathiawar peninsula . The results obtained for the Brahman breed reflect the historical records on the formation of this breed, which indicate that a synthetic indicine population was created in the United States during the early 1900’s by breeding indicine animals of the Nelore, Gir and Guzerat breeds imported mainly from Brazil to intensively upgrade the available taurine cattle from a base population [29,30]. Levels of taurine introgression were higher in the Brahman breed than in the Nelore and Gir breeds, which may indicate the preservation of taurine specific haplotypes through stronger selection for specific productive characteristics as suggested by Bolormaa et al. . Previous analyses based on mt DNA sequence data also confirmed a maternally-derived taurine influence in Brahman cattle since both European and African characteristic mt DNA haplogroups were found in animals from this breed .
When the same analyses were repeated by restricting the number of individuals per breed to a maximum of 20 randomly chosen animals [see Additional file 1], the results differed most with K = 3. European taurine breeds displayed higher levels of African taurine ancestry than those in the full dataset, with the highest level (18%) observed for individuals of the Fleckvieh breed. In addition, the analysis with K = 4 separated the Hereford from the other European taurine breeds, which is more consistent with the results obtained from multidimensional scaling. The lowest cross-validation error for different numbers of ancestries was obtained with 10 assumed ancestries (results not shown) for which each breed was assigned a main ancestry: the N’Dama breed was separated in two different ancestries based on the observed indicine introgression at K values lower than 10, and all Nelore individuals including the ancestral individuals were assigned to a single cluster.
Frequency of estimated mitochondrial haplotypes for each breed
The main objective of this study was to assess the level of admixture in current Nelore and Gir Brazilian populations. Taurine genome admixture events during the initial expansion of these two breeds are reported in historical records and supported by published results on mt DNA. High-resolution genome-wide analyses indicate that the individuals in the current populations of both breeds possess levels of autosomal taurine ancestry lower than 1%, which is consistent with a process of several decades of continuous purifying selection through the use of indicine imported males as suggested by . Assuming a strict upgrading system from a pure Creole population, seven generations would be required to achieve the observed levels of taurine introgression, which considering a generation interval of 7 to 8 years  would correspond to between 50 and 65 years. This is reasonable scenario for both Brazilian breeds, for which official pedigree recording was established in 1936 .
The taurine ancestry observed in both Brazilian breeds derives from individuals that came from both Europe and Africa. This confirms that the Brazilian Creole breeds are likely the source of the introgression. In fact, the South American Creole populations have been reported to have a moderate level of African taurine ancestry  and to be descendants of Spanish and Portuguese cattle that carry mt haplotypes that are frequently found in African taurine populations [10,12]. It is worth noting that the sample of Nelore individuals analyzed here included in equal proportions individuals that are registered as being of pure indicine origin (“PO” in the national registry) and individuals not considered pure by registry, but no difference in the levels of admixture were observed among these two groups of Nelore individuals.
Using a high-resolution genome-wide DNA analysis, we identified very low levels of taurine introgression in Brazilian Nelore and Gir cattle populations, which contradicts the previous observations in [9,13] but supports those in . Our findings indicate that the current Brazilian Nelore and Gir populations are of almost pure indicine ancestry regarding their autosomal genome. The Brahman population used in this analysis showed average levels of taurine ancestry of 9%, which is consistent with the fact that taurine animals were used to develop this breed in the USA. This result also suggests that, in this breed, there has been a stronger selection for production characteristics that derive from the influence of taurine haplotypes. The Nelore and Gir individuals that were genotyped in this study are all bulls used for artificial insemination and reflect the top of the breeding pyramid in these two breeds. Random sampling of animals from production herds across the country would provide a more complete picture and would be useful to evaluate admixture levels in commercial populations. Finally, the mt SNPs available in the Illumina BovineHD BeadChip could not differentiate between the major known mt haplogroups and could not identify subspecies or subpopulation specific haplotypes among the breeds analyzed.
The authors wish to gratefully acknowledge the US Department of Agriculture, ZuchtData EDV-Dienstleistungen GmbH (Austria), Embrapa Gado de Leite (Brazil), and The Bovine HapMap and The Zebu Genome Consortia for providing the genotypes used in this work. We want to express our gratitude to the European Science Foundation and the Advances in Farm Animal Genomic Resources project for supporting this research by providing AMPO with a travel grant from Austria to Italy. This work was supported in part by Projects 1265-31000-104-00D from USDA-ARS, Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) - process 560922/2010-8 and 483590/2010-0; and Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) - process 2014/01095-8 and 2010/52030-2. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture.
- FAO - Food and Agriculture Organization of the United Nations, FAOSTAT. 2012. http://faostat3.fao.org/. Accessed 11 March 2014.
- IBGE - Instituto Brasileiro de Geografia e Estatística: Pesquisa Pecuária Municipal. 2012. http://www.sidra.ibge.gov.br/bda/pecua/default.asp?t=2&z=t&o=24&u1=1&u2=1&u3=1&u4=1&u5=1&u6=1&u7=1. Accessed 11 March 2014.
- ABCZ - Associação Brasileira dos Criadores de Zebu: Pecuária Brasileira - Produção a pasto.2012. http://issuu.com/revista_abcz/docs/documento_abcz_pecuariabrasileira. Accessed 11 March 2014.
- FAO - Food and Agriculture Organization of the United Nations, Food Outlook Global Market Analysis. 2012. http://www.fao.org/docrep/016/al993e/al993e00.pdf. Accessed 11 March 2014.
- Ferraz JBS, de Felício PE. Production systems - an example from Brazil. Meat Sci. 2010;84:238–43.View ArticlePubMedGoogle Scholar
- Sobrinho FDS, Alvim MJ, Botrel MDA, Machado DA. Relatório técnico da Embrapa Gado de Leite 2001–2003. 2003. http://www.infoteca.cnptia.embrapa.br/handle/doc/956553. Accessed 11 March 2014.
- Wilkins JV. Criollo Cattle of the Americas. In: Animal Genetic Resources Information. Rome: FAO - UNEP; 1984. p. 1–19.Google Scholar
- Santiago AA. A raça nelore, Gado Nelore: 100 anos de seleção. Dos Criadores: São Paulo; 1987.Google Scholar
- Dani MAC, Heinneman MB, Dani SU. Brazilian Nelore cattle: a melting pot unfolded by molecular genetics. Genet Mol Res. 2008;7:1127–37.View ArticlePubMedGoogle Scholar
- Magee DA, Meghen C, Harrison S, Troy CS, Cymbron T, Gaillard C, et al. A partial African ancestry for the Creole cattle populations of the Caribbean. J Hered. 2002;93:429–32.View ArticlePubMedGoogle Scholar
- Miretti MM, Dunner S, Naves M, Contel EP, Ferro JA. Predominant African-derived mtDNA in Caribbean and Brazilian Creole cattle is also found in Spanish cattle (Bos taurus). J Hered. 2004;95:450–3.View ArticlePubMedGoogle Scholar
- Ginja C, Penedo MCT, Melucci L, Quiroz J, Martínez López OR, Revidatti MA, et al. Origins and genetic diversity of New World Creole cattle: Inferences from mitochondrial and Y chromosome polymorphisms. Anim Genet. 2010;41:128–41.View ArticlePubMedGoogle Scholar
- Brasil BSAF, Coelho EGA, Drummond MG, Oliveira DAA. Genetic diversity and differentiation of exotic and American commercial cattle breeds raised in Brazil. Genet Mol Res. 2013;12:5516–26.View ArticlePubMedGoogle Scholar
- Utsunomiya YT, Bomba L, Lucente G, Colli L, Negrini R, Lenstra JA, et al. Revisiting AFLP fingerprinting for an unbiased assessment of genetic structure and differentiation of taurine and zebu cattle. BMC Genet. 2014;15:47.View ArticlePubMed CentralPubMedGoogle Scholar
- McKay SD, Schnabel RD, Murdoch BM, Matukumalli LK, Aerts J, Coppieters W, et al. An assessment of population structure in eight breeds of cattle using a whole genome SNP panel. BMC Genet. 2008;9:37.View ArticlePubMed CentralPubMedGoogle Scholar
- Bovine HapMap Consortium, Gibbs RA, Taylor JF, Van Tassell CP, Barendse W, Eversole KA, et al. Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science. 2009;324:528–32.View ArticleGoogle Scholar
- Decker JE, McKay SD, Rolf MM, Kim J, Molina Alcalá A, Sonstegard TS, et al. Worldwide patterns of ancestry, divergence, and admixture in domesticated cattle. PLoS Genet. 2014;10:e1004254.View ArticlePubMed CentralPubMedGoogle Scholar
- Gautier M, Laloë D, Moazami-Goudarzi K. Insights into the genetic history of French cattle from dense SNP data on 47 worldwide breeds. PLoS ONE. 2010;5:e13038.View ArticlePubMed CentralPubMedGoogle Scholar
- Gautier M, Naves M. Footprints of selection in the ancestral admixture of a New World Creole cattle breed. Mol Ecol. 2011;20:3128–43.View ArticlePubMedGoogle Scholar
- Illumina Inc, BovineHD BeadChip Data Sheet. 2012. http://www.illumina.com/documents/products/datasheets/datasheet_bovineHD.pdf. Accessed 11 March 2014.
- Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Amer J Hum Genet. 2007;81:559–75.View ArticlePubMed CentralPubMedGoogle Scholar
- R Core Team. R: A language and environment for statistical computing. 2014. http://www.r-project.org/. Accessed 11 March 2014.
- Wright S. The interpretation of population structure by F-statistics with special regard to systems of mating. Evolution. 1965;19:395–420.View ArticleGoogle Scholar
- Weir BS, Cockerham CC. Estimating F-statistics for the analysis of population structure. Evolution. 1984;38:1358–70.View ArticleGoogle Scholar
- Alexander DH, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 2009;19:1655–64.View ArticlePubMed CentralPubMedGoogle Scholar
- Frkonja A, Gredler B, Schnyder U, Curik I, Solkner J. Prediction of breed composition in an admixed cattle population. Anim Genet. 2012;43:696–703.View ArticlePubMedGoogle Scholar
- Scheet P, Stephens M. A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet. 2006;78:629–44.View ArticlePubMed CentralPubMedGoogle Scholar
- Freeman AR, Meghen CM, MacHugh DE, Loftus RT, Achukwi MD, Bado A, et al. Admixture and diversity in West African cattle populations. Mol Ecol. 2004;13:3477–87.View ArticlePubMedGoogle Scholar
- Sanders JO. History and development of Zebu cattle in the United-States. J Anim Sci. 1980;50:1188–200.Google Scholar
- Department of Animal Science - Oklahoma State University. Breeds of Livestock. 2008. http://www.ansi.okstate.edu/breeds/. Accessed 20 April 2014.
- Bolormaa S, Hayes BJ, Hawken RJ, Zhang Y, Reverter A, Goddard ME. Detection of chromosome segments of zebu and taurine origin and their effect on beef production and growth. J Anim Sci. 2011;89:2050–60.View ArticlePubMedGoogle Scholar
- Troy CS, MacHugh DE, Bailey JF, Magee DA, Loftus RT, Cunningham P, et al. Genetic evidence for Near-Eastern origins of European cattle. Nature. 2001;410:1088–91.View ArticlePubMedGoogle Scholar
- Faria FJ, Filho AE, Madalena FE, Josahkian LA. Pedigree analysis in the Brazilian Zebu breeds. J Anim Breed Genet. 2009;126:148–53.View ArticlePubMedGoogle Scholar
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.