Cross-population selection signatures in Canchim composite beef cattle

Abstract

Analyses of livestock genomes have been used to detect selection signatures, which are genomic regions associated with traits under selection leading to a change in allele frequency. The objective of the present study was to characterize selection signatures in Canchim composite beef cattle using cross-population analyses with the founder Nelore and Charolais breeds. High-density single nucleotide polymorphism genotypes were available on 395 Canchim representing the target population, along with genotypes from 809 Nelore and 897 Charolais animals representing the reference populations. Most of the selection signatures were co-located with genes whose functions agree with the expectations of the breeding programs; these genes have previously been reported to associate with meat quality, as well as reproductive traits. Identified genes were related to immunity, adaptation, morphology, as well as behavior, could give new perspectives for understanding the genetic architecture of Canchim. Some selection signatures identified genes that were recently introduced in Canchim, such as the loci related to the polled trait.

Characterization of the Temperament and Reactivity of Nelore Cattle (Bos indicus) Associated with Behavior Scores during Corral Management in the Humid Tropics

“…Similarly, the positive correlation between MS and TS indicates an individual distress temperament of the animals, with more reactive animals being more likely to move more during situations of distress or discomfort [ 91 , 92 , 93 , 94 ].…”

The Role of SOCS3 in Regulating Meat Quality in Jinhua Pigs

“…In this context, for studying meat quality traits holistically, genomics and transcriptomics data were analyzed and combinedly to identify the candidate genes. The selection signatures method is commonly used for genomic analysis and has observed great progress in pigs [ 1 , 4 ], chickens [ 21 , 22 ], cattle [ 23 , 24 ], etc. Both the F ST and XP-EHH methods are widely used for exploring selection signatures between populations [ 25 ].…”

Inferring Signatures of Positive Selection in Whole-Genome Sequencing Data: An Overview of Haplotype-Based Methods

“…Indeed, several of the methods presented in this manuscript have been applied not only to humans but to many other living organisms and for different purposes. Economically relevant species of animals and plants, such as pigs (Sus domesticus) [74], cattle (Bos taurus) [75][76][77], yaks (Bos grunniens) [78], sheep (Ovis aries) [79], horses (Equus caballus) [80,81], and tomatoes (Solanum lycopersicum) [82] have been researched mainly for commercially favorable instances of selection; pathogens and disease vectors, including Plasmodium falciparum [83,84] and mosquitoes (Anopheles gambiae) [85], for their rapid evolution and resistance to toxic compounds; companion animals, such as dogs (Canis lupus familiaris) [86,87], were the focus of studies to understand the influence of domestication in close contact with humans. For example, Zorc and colleagues [74] applied the iHS test on both SNPs and microsatellites to reveal that six autochthonous Balkan pig breeds present different genes under positive selection, with particular reference to reproductive traits (number of offspring, sperm quality, early pregnancy), muscle mass, fat metabolism, and disease resistance.…”