Genome-wide differential DNA methylation in tropically adapted Creole cattle and their Iberian ancestors

Enhancing climate resilience and sustainable production for animals in harsh environments are important goals for the livestock industry given the predicted impacts of climate change. Rapid adaptation to extreme climatic conditions has already been imposed on livestock species, including those exported after Columbus's arrival in the Americas. We compared the methylomes of two Creole cattle breeds living in tropical environments with their putative Spanish ancestors to understand the epigenetic mechanisms underlying rapid adaptation of a domestic species to a new and more physiologically challenging environment. Reduced representation bisulfite sequencing was used to assess differences in methylation in Creole and Spanish samples and revealed 334 differentially methylated regions using high stringency parameters (P‐value 25%) annotated to 263 unique features. Gene ontology analysis revealed candidate genes involved in tropical adaptation processes, including genes differentially hyper‐ or hypomethylated above 80% in Creole samples displaying biological functions related to immune response (IRF6, PTGDR, FAM19A5, PGLYRP1), nervous system (GBX2, NKX2‐8, RPGR), energy management (BTD), heat resistance (CYB561) and skin and coat attributes (LGR6). Our results entail that major environmental changes imposed on Creole cattle have had an impact on their methylomes measurable today, which affects genes implicated in important pathways for adaptation. Although further work is needed, this first characterization of methylation patterns driven by profound environmental change provides a valuable pointer for the identification of biomarkers of resilience for improved cattle performance and welfare under predicted climatic change models

Dissection of ancestral genetic contributions to Creole goat populations

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

Diversity, identity and influence of other breeds in the development of Creole populations of domestic animals

Creole breeds of the various livestock species mainly derive from animals imported to America from the Iberian Peninsula, starting in the early years of discovery and colonization. Creoles have undergone a long period of selective adaptation to a very diverse set of environmental conditions in the American continent, and over the last two centuries some Creole populations have been admixed with breeds originating from other European countries and India. In spite of the various threats undergone, some Creole populations are still maintained nowadays, especially in marginal regions, but they need to be better known, in order to recognize their identity and establish conservation programs. In this paper, we review the results published over the last five years by various Consortia established under the framework of the CONBIAND network, with the goal of studying the genetic diversity, structure and breed relationships in Creole breeds. In all species, Creole breeds reveal high levels of genetic diversity and clear signatures of their Iberian origin, even though many breeds also show signs of genetic erosion, due to either accumulated inbreeding or admixture with exotic breeds. The research conducted until now demonstrates that the vast majority of Creoles still maintain their own identity, even though they are seldom recognized and protected. These results can be used as a basis for recognition, conservation and genetic improvement of Creoles, which are the result of more than 500 years of selective adaptation

On the origins of American Criollo pigs: A common genetic background with a lasting Iberian signature

American Criollo pigs are thought to descend mainly from those imported from the Iberian Peninsula starting in the late 15th century. Criollo pigs subsequently expanded throughout the Americas, adapting to very diverse environments, and possibly receiving influences from other origins. With the intensification of agriculture in the mid-20th century, cosmopolitan breeds largely replaced Criollo pigs, and the few remaining are mostly maintained by rural communities in marginal areas where they still play an important socio-economic and cultural role. In this study, we used 24 microsatellite markers in samples from 1715 pigs representing 46 breeds with worldwide distribution, including 17 American Criollo breeds, with the major focus of investigating their genetic diversity, structure and breed relationships. We also included representatives of the Iberian, Local British, Hungarian, Chinese and Commercial breeds, as well as Wild Boar, in order to investigate their possible influence in the genetic composition of Criollos. Our results show that, when compared with the other breeds, Criollo pigs present higher levels of genetic diversity, both in terms of allelic diversity and expected heterozygosity. The various analyses indicate that breed differentiation overall explains nearly 21% of the total genetic diversity. Criollo breeds showed their own identity and shared a common genetic background, tending to cluster together in various analyses, even though they differ from each other. A close relationship of Criollos with Iberian breeds was revealed by all the different analyses, and the contribution of Iberian breeds, particularly of the Celtic breeds, is still present in various Criollo breeds. No influence of Chinese breeds was detected on Criollos, but a few were influenced by Commercial breeds or by wild pigs. Our results confirm the uniqueness of American Criollo pigs and the role that Iberian breeds have played in their development. © 2021 Revidatti et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Are Farm-Reared Quails for Game Restocking Really Common Quails (Coturnix coturnix)?: A Genetic Approach

The common quail (Coturnix coturnix) is a popular game species for which restocking with farm-reared individuals is a common practice. In some areas, the number of released quails greatly surpasses the number of wild breeding common quail. However, common quail are difficult to raise in captivity and this casts suspicion about a possible hybrid origin of the farmed individuals from crosses with domestic Japanese quail (C. japonica). In this study we used a panel of autosomal microsatellite markers to characterize the genetic origin of quails reared for hunting purposes in game farms in Spain and of quails from an experimental game farm which was founded with hybrids that have been systematically backcrossed with wild common quails. The genotypes of these quail were compared to those of wild common quail and domestic strains of Japanese quail. Our results show that more than 85% of the game farm birds were not common quail but had domestic Japanese quail ancestry. In the experimental farm a larger proportion of individuals could not be clearly separated from pure common quails. We conclude that the majority of quail sold for restocking purposes were not common quail. Genetic monitoring of individuals raised for restocking is indispensable as the massive release of farm-reared hybrids could represent a severe threat for the long term survival of the native species

Polymorphisms in twelve candidate genes are associated with growth, muscle lipid profile and meat quality traits in eleven European cattle breeds

Current customers’ demands focus on the nutritional and sensory quality of cattle meat. Candidate gene approach allows identification of genetic polymorphisms that have a measurable effect on traits of interest. The aim of this work is to identify new molecular markers for beef production through an association study using 27 candidate genes and 314 purebred bulls from 11 European cattle breeds. Twelve genes were found associated with different lipid and meat quality traits, and among these stand out the considerable effect of CAST on fatness score, CGGBP1 on growth traits, HSPB1 on the percentage of lauric acid (12:0) and phospholipid docosahexaenoic acid (DHA 22:6 n − 3), RORA on the ratio of light absorption (K) to light scattering (S) (K/S), and TNFA on lightness (L*). Most of these traits are related to post-mortem muscle biochemical changes, which are key factors controlling meat quality and consumers’ acceptance. Also, the variations produced on muscle fatty acid profiles, such as those of AANAT, CRH, CSN3, HSPB1, and TNFA, give insights into the genetic networks controlling these complex traits and the possibility of future improvement of meat nutritional quality

Association of bovine meat quality traits with genes included in the PPARG and PPARGC1A networks

Understanding which are the genetic variants underlying the nutritional and sensory properties of beef, enables improvement in meat quality. The aim of this study is to identify new molecular markers for meat quality through an association study using candidate genes included in the PPARG and PPARGC1A networks given their master role in coordinating metabolic adaptation in fat tissue, muscle and liver. Amongst the novel associations found in this study, selection of the positive marker variants of genes such as BCL3, LPL, PPARG, SCAP, and SCD will improve meat organoleptic characteristics and health by balancing the n − 6 to n − 3 fatty acid ratio in meat. Also previous results on GDF8 and DGAT1 were validated, and the novel ATF4, HNF4A and PPARGC1A associations, although slightly under the significance threshold, are consistent with their physiological roles. These data contribute insights into the complex gene-networks underlying economically important traits.N. Sevane, E. Armstrong, O. Cortés, P. Wiener, R. Pong Wong, S. Dunner, GemQual Consortiu