Abstract
Cattle population history, breeding systems, and geographic subdivision may be reflected in runs of homozygosity (ROH), effective population size (Ne), and linkage disequilibrium (LD) patterns. Thus, the assessment of this information has become essential to the implementation of genomic selection on purebred and crossbred cattle breeding programs. In this way, we assessed the genotype of 19 cattle breeds raised in Brazil belonging to taurine, indicine, synthetic crossbreds, and Iberian-derived locally adapted ancestries to evaluate the overall LD decay patterns, Ne, ROH, and breed composition. We were able to obtain a general overview of the genomic architecture of cattle breeds currently raised in Brazil and other tropical countries. We found that, among the evaluated breeds, different marker densities should be used to improve the genomic prediction accuracy and power of genome-wide association studies. Breeds showing low Ne values indicate a recent inbreeding, also reflected by the occurrence of longer ROH, which demand special attention in the matting schemes to avoid extensive inbreeding. Candidate genes (e.g., ABCA7, PENK, SPP1, IFNAR1, IFNAR2, SPEF2, PRLR, LRRTM1, and LRRTM4) located in the identified ROH islands were evaluated, highlighting biological processes involved with milk production, behavior, rusticity, and fertility. Furthermore, we were successful in obtaining the breed composition regarding the taurine and indicine composition using single-nucleotide polymorphism (SNP) data. Our results were able to observe in detail the genomic backgrounds that are present in each breed and allowed to better understand the various contributions of ancestor breeds to the modern breed composition to the Brazilian cattle.
Highlights
Cattle domestication has generated many differentiated phenotypes that evolved into distinct breeds scattered across the globe
Statistical tests for the equality of linkage disequilibrium (LD) decay curves showed that the overall pattern of the inflection point differed among breeds of taurine, indicine, and locally adapted groups, except for synthetic crossbreds (Figure 1)
The LD decay observed in this study among all cattle breeds differed based on LD curves parameter estimates (ß )
Summary
Cattle domestication has generated many differentiated phenotypes that evolved into distinct breeds scattered across the globe. It is estimated that taurine cattle emerged in the Fertile Crescent region spanning modernday Iraq, Syria, Lebanon, Israel, Palestine, Jordan, the northeast and Nile valley regions of Egypt, the south-eastern region of Turkey, and the western fringes of Iran. After several generations of random crossings in distinct and variable ecosystems throughout the country, these animals became adapted to a wide range of environments and showed different levels of improved fitness to local conditions. They become recognized as Iberian-derived locally adapted breeds (Egito et al, 2007; McManus et al, 2009), such as the Caracu lineages (CaracuCaldeano for dairy purpose and Caracu for beef), CriouloLageano, CurraleiroPé-Duro, and CriouloLageano do RS
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