Admixed populations represent attractive biological models to study adaptive selection. Originating from several waves of recent introduction from European (EUT), African (AFT) and zebus (ZEB) cattle, New World Creole cattle allow investigating the response to tropical environmental challenges of these three ancestries. We here provide a detailed assessment of their genetic contributions to the Creole breed from Guadeloupe (CGU). We subsequently look for footprints of selection by combining results from tests based on the extent of haplotype homozygosity and the identification of excess/deficiency of local ancestry. To tackle these issues, 140 CGU individuals and 25 Brahman zebus from Martinique were genotyped at 44 057 SNPs. These data were combined to those available on 23 populations representative of EUT, AFT or ZEB. We found average proportions of 26.1%, 36.0% and 37.9% of EUT, AFT and ZEB ancestries in the CGU genome indicating a higher level of African and zebu ancestries than suggested by historical records. We further identified 23 genomic regions displaying strong signal of selection, most of them being characterized by an excess of ZEB local ancestry. Among the candidate gene underlying these regions, several are associated with reproductive functions (RXFP2, PMEPA1, IGFBP3, KDR, PPP1R8, TBXA2R and SLC7A5) and metabolism (PDE1B and CYP46A1). Finally, two genes (CENTD3 and SAMD12) are involved in cellular signalization of immune response. This study illustrates the relevance of admixed populations to identify footprints of selection by combining several tests straightforward to implement on large data sets.

African-derived mitochondrial DNA (mtDNA) have been described in South American and Caribbean native cattle populations, which could have been introduced into America from Iberia or by direct importation from Africa. However, the similarity among described haplotypes is not known. We examined mtDNA variation in Guadeloupe Creole and Spanish cattle in an attempt to identify African-derived mtDNA haplotypes and compare them with those previously described. Eleven haplotypes clustered into the European taurine haplogroup (T3), two haplotypes into the African taurine (T1) haplogroup, and three haplotypes into the African-derived American haplogroup (AA). The AA1 and Eucons haplotypes were the most frequently observed. The presence of the AA haplogroup in Spanish cattle confirms historical records and genetic evidence of Iberian cattle as the main source of American native cattle origin. The possible origin of African-derived mitochondrial haplotypes in Iberian and Creole cattle is discussed, and the accumulated evidence does not support a founder effect from African ancestral cattle by direct importations. The presence of taurine AA and T3 haplotypes in Brazilian Nellore may indicate introgression by local European-derived cattle. Data presented in this work will contribute to the understanding of the origin of Guadeloupe Creole cattle.

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appropriée de tenir compte de telles aptitudes et fonctions des races locales dans une politique publique de gestion des ressources génétiques animales.

SummaryBreed risk status assessment methods are key components of country-based early warning and response systems. In this study, a multi-indicator method was developed to assess the risk status of livestock populations. Six indicators were used: (i) the current number of breeding females; (ii) the change in the number of breeding females over the last 5 years or generations (depending on the species); (iii) percentage of cross-breeding; (iv) effective population size; (v) breeders organization and technical support; and (vi) socio-economic context. To make these indicators comparable, observed values were converted into scores on a six-point scale (from 0 = no threat to 5 = maximum threat); a specific conversion method was used for each indicator. For each breed, the different scores were analysed graphically and an overall score was calculated by averaging the six separate indicator scores. This approach was applied to 178 French local breeds, belonging to ten different species: horse, donkey, goat, pig, chicken, turkey, goose and Pekin duck. A large percentage of local breeds were found to be at risk to be lost for farming, although the results were species dependent. All local equine and pig breeds, as well as almost all local poultry breeds appeared to be endangered. About 80 percent of local goat and cattle breeds, and half local sheep breeds were also found to be at risk. The usefulness of this method with regards to conservation strategies and public policy is discussed.

A specific breeding goal definition was developed for Creole goats in Guadeloupe. This local breed is used for meat production. To ensure a balanced selection outcome, the breeding objective included two production traits, live weight (BW11) and dressing percentage (DP) at 11 months (the mating or selling age), one reproduction trait, fertility (FER), and two traits to assess animal response to parasite infection: packed cell volume (PCV), a resilience trait, and faecal worm eggs count (FEC), a resistance trait. A deterministic bio-economic model was developed to calculate the economic values based on the description of the profit of a Guadeloupean goat farm. The farm income came from the sale of animals for meat or as reproducers. The main costs were feeding and treatments against gastro-intestinal parasites. The economic values were 7.69€ per kg for BW11, 1.38€ per % for FER, 3.53€ per % for DP and 3 × 10−4€ per % for PCV. The economic value for FEC was derived by comparing the expected profit and average FEC in a normal situation and in an extreme situation where parasites had developed resistance to anthelmintics. This method yielded a maximum weighting for FEC, which was −18.85€ per log(eggs per gram). Alternative scenarios were tested to assess the robustness of the economic values to variations in the economic and environmental context. The economic values of PCV and DP were the most stable. Issues involved in paving the way for selective breeding on resistance or resilience to parasites are discussed.

Despite their central economic and cultural role, the origin of cattle populations living in Indian Ocean islands still remains poorly documented. Here, we unravel the demographic and adaptive histories of the extant Zebus from the Mayotte and Madagascar islands using high-density SNP genotyping data. We found that these populations are very closely related and both display a predominant indicine ancestry. They diverged in the 16th century at the arrival of European people who transformed the trade network in the area. Their common ancestral cattle population originates from an admixture between an admixed African zebu population and an Indian zebu that occurred around the 12th century at the time of the earliest contacts between human African populations of the Swahili corridor and Austronesian people from Southeast Asia in Comoros and Madagascar. A steep increase of the estimated population sizes from the beginning of the 16th to the 17th century coincides with the expansion of the cattle trade. By carrying out genome scans for recent selection in the two cattle populations from Mayotte and Madagascar, we identified sets of candidate genes involved in biological functions (cancer, skin structure and UV-protection, nervous system and behavior, organ development, metabolism and immune response) broadly representative of the physiological adaptation to tropical conditions. Overall, the origin of the cattle populations from Western Indian Ocean islands mirrors the complex history of human migrations and trade in this area.

In this study, we used BovineSNP50 Genotyping BeadChip data to estimate the structure, putative ancestral origin as well as to identify regions with selective sweeps that may have had an important role in the adaptation to tropical conditions of the ‘Charolais de Cuba’ (CHCU) breed. According to a principal component analysis, CHCU samples cluster together with taurine breeds with an estimated 93% of taurus ancestral alleles. Despite the short period since importation, we detected differentiation (Fst = 0.049) between the French Charolaise (CHA) and CHCU. However, CHA breed was the closest breed to CHCU followed by other hybrids breed with a clear CHA origin. Linkage disequilibrium (r2) decay tends to be lower in CHCU compared to CHA probably due to a less intense artificial selection programs of CHCU. Signals of recent adaptation to tropical conditions between CHCU and CHA were identified. Genes mapping within those regions reflect different functions related to immunity, metabolic changes and heat tolerance (CHCU) and muscle development and meat quality (CHA) that may have had an important role in the phenotypic differentiation of these breeds. Further studies will expand our knowledge on the molecular basis of adaptation of cattle to tropical conditions and molecular process associated with meat quality traits.