Abstract
The use of relatively low numbers of sires in cattle breeding programs, particularly on those for carcass and weight traits in Nellore beef cattle (Bos indicus) in Brazil, has always raised concerns about inbreeding, which affects conservation of genetic resources and sustainability of this breed. Here, we investigated the distribution of autozygosity levels based on runs of homozygosity (ROH) in a sample of 1,278 Nellore cows, genotyped for over 777,000 SNPs. We found ROH segments larger than 10 Mb in over 70% of the samples, representing signatures most likely related to the recent massive use of few sires. However, the average genome coverage by ROH (>1 Mb) was lower than previously reported for other cattle breeds (4.58%). In spite of 99.98% of the SNPs being included within a ROH in at least one individual, only 19.37% of the markers were encompassed by common ROH, suggesting that the ongoing selection for weight, carcass and reproductive traits in this population is too recent to have produced selection signatures in the form of ROH. Three short-range highly prevalent ROH autosomal hotspots (occurring in over 50% of the samples) were observed, indicating candidate regions most likely under selection since before the foundation of Brazilian Nellore cattle. The putative signatures of selection on chromosomes 4, 7, and 12 may be involved in resistance to infectious diseases and fertility, and should be subject of future investigation.
Highlights
Autozygosity is the homozygote state of identical-by-descent alleles, which can result from several different phenomena such as genetic drift, population bottleneck, mating of close relatives, and natural and artificial selection (Falconer and Mackay, 1996; Keller et al, 2011; Curik et al, 2014)
Evidence from whole-genome sequencing studies in humans indicate that highly deleterious variants are common across healthy individuals (MacArthur et al, 2012; Xue et al, 2012), and no such systematical survey has been conducted in cattle to the present date, it is highly expected that unfavorable alleles segregate in cattle populations
The average, median, minimum and maximum runs of homozygosity (ROH) length detected across all chromosomes were 1.26, 0.70, 0.50, and 70.91 Mb, respectively, suggesting this specific Nellore cattle population experienced both recent and remote autozygosity events
Summary
Autozygosity is the homozygote state of identical-by-descent alleles, which can result from several different phenomena such as genetic drift, population bottleneck, mating of close relatives, and natural and artificial selection (Falconer and Mackay, 1996; Keller et al, 2011; Curik et al, 2014). In the past 20 years, the heavy use of relatively low number of sires in Brazilian Nellore breeding programs (Bos indicus) is deemed to have mimicked all these triggers of autozygosity, especially considering the increasing use of artificial insemination over the decades. The use of ever-smaller numbers of animals as founders is expected to inadvertently increase autozygosity of such unfavorable alleles (Szpiech et al, 2013), potentially causing economic losses
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