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Dissection of Ancestral Genetic Contributions to Creole Goat Populations

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Dissection of Ancestral Genetic Contributions to Creole Goat Populations Animal, page 1 of 10 © The Animal Consortium 2018 animal doi:10.1017/S1751731117003627 Dissection of ancestral genetic contributions to Creole goat populations N. Sevane1†, O. Cortés1, L. T. Gama2, A. Martínez3,4, P. Zaragoza5, M. Amills6, D. O. Bedotti7, C. Bruno de Sousa8, J. Cañon1, S. Dunner1, C. Ginja9, M. R. Lanari10, V. Landi3,4, P. Sponenberg11, J. V. Delgado3 and The BioGoat Consortiuma 1Departamento de Producción Animal, Universidad Complutense de Madrid, Spain; 2CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Portugal; 3Departamento de Genética, Universidad de Córdoba, Córdoba, Spain; 4Animal Breeding Consulting SL, Cordoba, Spain; 5Laboratorio de Genética Bioquímica, Facultad de Veterinaria, Universidad de Zaragoza, Spain; 6Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Universitat Autònoma de Barcelona, Bellaterra, Spain; 7INTA, EEA Anguil “Ing. Agr. Guillermo Covas”, Argentina; 8Centro de Ciências do Mar, Instituto de Higiene e Medicina Tropical (UPMM) – UNL, Universidade do Algarve, Portugal; 9Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-InBIO), Universidade do Porto, Campus Agrário de Vairão, Portugal; 10Area de Producción Animal, INTA EEA, Bariloche, Argentina; 11Virginia-Maryland Regional College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA (Received 19 September 2017; Accepted 4 December 2017) Goats have played a key role as source of nourishment for humans in their expansion all over the world in long land and sea trips. This has guaranteed a place for this species in the important and rapid episode of livestock expansion triggered by Columbus’ arrival in the Americas in the late 1400s. The aims of this study are to provide a comprehensive perspective on genetic diversity in American goat populations and to assess their origins and evolutionary trajectories. This was achieved by combining data from autosomal neutral genetic markers obtained in more than two thousand samples that encompass a wide range of Iberian, African and Creole goat breeds. In general, even though Creole populations differ clearly from each other, they lack a strong geographical pattern of differentiation, such that populations of different admixed ancestry share relatively close locations throughout the large geographical range included in this study. Important Iberian signatures were detected in most Creole populations studied, and many of them, particularly the Cuban Creole, also revealed an important contribution of African breeds. On the other hand, the Brazilian breeds showed a particular genetic structure and were clearly separated from the other Creole populations, with some influence from Cape Verde goats. These results provide a comprehensive characterisation of the present structure of goat genetic diversity, and a dissection of the Iberian and African influences that gave origin to different Creole caprine breeds, disentangling an important part of their evolutionary history. Creole breeds constitute an important reservoir of genetic diversity that justifies the development of appropriate management systems aimed at improving performance without loss of genomic diversity. Keywords: Capra hircus, Iberia, America, microsatellites, genetic diversity Implications evolutionary history and define adequate conservation priorities to maintain the vast genetic legacy that we have A better understanding of the genetic diversity and structure inherited. The hardiness and adaptiveness that goats display of Creole goat populations is crucial for disentangling their in harsh environments, where other livestock species find it difficult to adapt, make the genetic reservoir of locally † E-mail: [email protected] adapted Creole breeds a valuable source of diversity to a List of the members of the BioGoat Consortium (full information in Supple- maintain and improve caprine performance and welfare mentary Material): Tumininu Adebambo; Lenin Aguirre Riofrío; Luz Angela Alvarez Franco; Jose Atilio Aranguren; Mª Esperanza Camacho Vallejo; Juan Capote; María under expected climatic change models. del Rosario Fresno; Mª Ines Carolino; Fátima Santos Silva; Marcos P. Carrera Menezes; Edilberto Chacón; Ahmed R.A.E Elbeltagy; Gabriel Fernández; Ainhoa Ferrando; Jordi Jordana; Angel Galarza; Angelika Stemmer; Daniel Martín Santana; Mayra Gómez Carpio; Mariano Gómez; Nilton Gómez Urviola; Arianna Introduction Manunza; Inmaculada Martín-Burriel; Clementina Rodellar; Roberto Martínez; The domestic goat (Capra hircus) was one of the earliest Pere-Miquel Parés i Casanova; Edgar C. Pimenta-Filho; Agueda Pons Barro; Mª Antonia Revidatti; Maria Norma Ribeiro; Laura Leandro Rocha; Asmaa animals to be domesticated and remains a species of major Mohammed Aly Abu Shady; Bartomeu Seguí; Jose Luis Vega Pla; Oriol Vidal. importance in poorly developed rural areas. Given their small 1 Sevane et al. size and high versatility, goats were extensively transported and Celtibérica, two well-differentiated varieties of the same among continents, weakening their phylogeographic structure breed, and Tenerife Norte and Tenerife Sur, which are eco- at a worldwide level, such that most genetic variation is types of the Tinerfeña breed (Martínez et al., 2015); six currently found at the within-population level (Cañón et al., breeds from Portugal; 13 breeds from Africa; two breeds 2006; Naderi et al., 2007; Ginja et al., 2018). Columbus’ arrival from New Zealand; the Golden Guernsey breed from the in the Americas triggered a major change, with the expansion United Kingdom, sampled in United States; three cosmo- of European and African livestock species in the New World, politan breeds, that is, Saanen from Switzerland (sampled starting from a limited number of animals brought around in Spain), Alpine from France and Anglo-Nubian from the the beginning of the 16th century (Rodero et al., 1992). The United Kingdom (both sampled in Brazil); and 23 Creole development of goat populations in the American continents breeds distributed throughout the Americas, from the United has thus been shaped by founder effects, genetic drift, and States to Argentina. The number of samples per breed ran- natural and artificial selection, leading to a progressive ged between 11 and 40, with an average of 34 individuals. divergence from their original founder populations. Samples were collected by qualified veterinarians through The study of goat genetic diversity can bring insights into their routine practice, in the framework of official programs their evolutionary history, and can explain the present geo- aimed at identification, health control and parentage con- graphical distribution and genetic structure of this species. firmation. Therefore, no ethical approval was required for Although several studies have been carried out to characterise sampling biological material. Genomic DNA was isolated as the genetic diversity of European, African, and South and described by Walsh et al. (1991). A set of 20 microsatellite Central American goats at the continental level (e.g. Cañón markers was selected (Supplementary Table S2) according to et al., 2006; Naderi et al., 2007; Ginja et al., 2017), a com- the recommendations of the Food and Agriculture Organi- prehensive joint analysis of breeds from the various continents zation of the United Nations (FAO) and the International has not been accomplished so far. Some research on New Society for Animal Genetics (FAO, 2011), and amplified in World goats has relied on mitochondrial DNA sequences multiplex PCRs as described in Martínez et al. (2015). (Amills et al., 2009), which reflect only the history of female- mediated gene flow and thus lack the power to track complex Statistical analyses histories of introgression and admixture. Despite other studies The MICROSATELLITE TOOLKIT software (Park, 2001) was with samples of Portuguese and Brazilian origin (Ribeiro et al., used to calculate allele frequencies for each locus, total 2012), the likely influence that the other Iberian breeds, as well number of alleles per locus (NA), observed (Ho) and expected as African populations, may have had on the current genetic (He) heterozygosities, and mean number of alleles per structure of Creole goats has not been investigated so far. population. Weir and Cockerham (1984) estimates of The aims of this study are to provide a comprehensive F-statistics and allelic richness (Ar) over all loci per breed assessment of the genetic diversity, origins and evolutionary were estimated with FSTAT (Goudet, 2001). The mean trajectories of American goat populations by combining data F-statistics and their 95% confidence interval over loci after from autosomal neutral genetic markers collected in >2000 1000 bootstraps were calculated using the GENETIX 4.05 samples that include a wide range of Iberian, African and software (Belkhir et al., 2004). Compliance to Hardy– Creole caprine breeds. The populations sampled cover a large Weinberg (HW) equilibrium was analysed using Fisher’s geographical distribution (Figure 1) and encompass the exact test with GENEPOP 1.2 (Raymond and Rousset, 1995). majority of the extant caprine breeds from the Americas and Factorial correspondence analysis (FCA) using the function Iberia, and 13 African local breeds spanning from Egypt to ‘AFC 3D by populations’ was performed with GENETIX. South Africa. Using a set of 20 microsatellite markers, we Genetic relationships among populations and breed groups show that some of the diversity displayed by Creole populations were
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