Comparison between European and Brazilian cattle molecular diversity and identification of signatures of selection in the Nellore cattle genome

Abstract

Domestic cattle descend from the extinct Auroch (Bos primigenius) and are divided into two subspecies that interbreed: (1) the humpless taurine cattle (Bos primigenius taurus) and (2) the humped zebu (Bos primigenius indicus). Evidences from archaeological and DNA analyses support that Eurasian taurine and zebu cattle have arisen from separate centres of domestication ~8,000 years BC in Fertile Crescent and Indus valley, respectively. From these possible domestication centres, cattle have expanded over Europe, Asia and Africa following complex routes with slow migration rates, accompanying human migration in occasion of agriculture. Eventually, cattle were introduced in the American continent after its discovery in the late 15th century. Migration of taurine cattle to America was mainly due to Iberian and/or African importations and, later on, Indian zebu cattle were introduced in Central and South America in the early 20th century, due to their adaptability to the tropical environment. These bovine populations interbred, and the modern South American cattle are the result of the combination of exquisite germplasm. The comparison of European cattle with the modern zebu and taurine cattle found in South America by molecular tools may reveal differences in the extent of diversity among these cattle populations, and help to shed some light on adaptability to the tropics. Regarding Nellore breed, the major beef cattle breed in Brazil, first importations of Ongole individuals to Brazil occurred in the 1870's, when few Zoo animals were brought from London and Germany. The inborn adaptation of the animals to the Brazilian environment and the impressive morphological aspect of the animals quickly caught breeders' attention and Ongole animals started to be imported from the Indian province of Nellore from the 1880's to the early 1900's. The result of these importations and successive introgression of Ongole cattle with local Iberian and/or African-descent herds in Brazil gave life to the Nellore breed, named after its homeland. Nellore cattle are recognized as a breed since 1930's, when genealogy registration has begun. Currently there are two main genetic evaluation strategies for the breed: one subgroup emphasizes selection for weaning and yearling weight, while the other emphasizes selection for fertility and carcass traits. Recently, with the use of high-density genomic data, these subgroups were found to be correlated with genetic sub-populations within the breed, which may indicate genetic drift and divergence due selection. Thus, the complex history of the breed, associated to the recent artificial selection pressure, may have shaped the genetic diversity within and between these Nellore subgroups, and their present genomes may shelter unique signatures of these phenomena. Importantly, footprints of selection, such as specific patterns of admixture, linkage disequilibrium (LD), and haplotype structure, are currently detectable from genomic data by well established methodologies, which can allow for assessing the response of the genome to selection, and reveal evidences of loci and variants implicated in economically important traits. Therefore, such techniques will be applied to Nellore and other Brazilian Creole cattle genomic data, already in house, to identify signatures of selection within the Nellore breed and its subgroups. Molecular data are already in house, and exploratory analyses are partially accomplished. During the visit, analyses will be completed in a joint effort between graduate students from Prof. Garcia's research team, and one post-doc fellow from Prof. Ajmone Marsan, Dr. Lorenzo Bomba, who will also be in Aracatuba during the same period. In addition, a paper will be drafted with the goal of having a manuscript, potentially submitted before the end of the visit. (AU)