The genetic ancestry of American Creole cattle inferred from uniparental and autosomal genetic markers

Abstract

Cattle imported from the Iberian Peninsula spread throughout America in the early years of discovery and colonization to originate Creole breeds, which adapted to a wide diversity of environments and later received influences from other origins, including zebu cattle in more recent years. We analyzed uniparental genetic markers and autosomal microsatellites in DNA samples from 114 cattle breeds distributed worldwide, including 40 Creole breeds representing the whole American continent, and samples from the Iberian Peninsula, British islands, Continental Europe, Africa and American zebu. We show that Creole breeds differ considerably from each other, and most have their own identity or group with others from neighboring regions. Results with mtDNA indicate that T1c-lineages are rare in Iberia but common in Africa and are well represented in Creoles from Brazil and Colombia, lending support to a direct African influence on Creoles. This is reinforced by the sharing of a unique Y-haplotype between cattle from Mozambique and Creoles from Argentina. Autosomal microsatellites indicate that Creoles occupy an intermediate position between African and European breeds, and some Creoles show a clear Iberian signature. Our results confirm the mixed ancestry of American Creole cattle and the role that African cattle have played in their development.

Figure 1

Geographic and breed distribution of maternal haplogroups in Creole and African cattle. For the Iberian, British, and Continental European cattle, haplogroup frequencies are summarized for each group. The Indicine cattle included in our study were sampled in the American Continent and are not shown in the figure. Different colors indicate major mitochondrial haplogroups and numbers in the figure correspond to the breed codes defined in Table 1. Detailed information on the mitochondrial diversity found in each breed is in Supplementary Table S1.

Figure 2

Median-Joining network representing genetic relationships between the Y-chromosome haplotypes observed across geographic breed groups and within each major haplogroup (Y1, Y2 and Y3). Colors represent the geographic origin. Further details on the haplotype diversity observed in each breed are shown in Supplementary Table S2.

Figure 3

Spatial representation of genetic distances among the breeds analyzed, from the first two axes obtained in the factorial analyses of correspondence based on microsatellite data. Values between brackets on both axes represent the contribution in % of each axis to total inertia. Colors represent the geographic origin as shown in the figure. The names of some breeds that correspond to areas of overlapping between groups are also shown.

Figure 4

Neighbour-joining tree representation of Nei’s DA genetic distances between 109 breeds based on microsatellite data, with colors representing geographic breed groups as defined in Fig. 3. Breed acronyms are as defined in Table 1.

Figure 5

Population structure of 109 cattle breeds inferred by using the STRUCTURE software and based on microsatellite data. Each breed is represented by a single vertical bar divided into K colors, where K is the number of assumed ancestral clusters, which is graphically represented for K = 2, 7 and 41. The colored segment shows the breed’s estimated membership proportions in a given cluster. Breed numerical codes are as defined in Table 1. Ancestral contributions for other values of K ranging from K = 2 to 40 are shown in Supplementary Fig. 2.