Assessment of autozygosity in Nellore cows (Bos indicus) through high-density SNP genotypes

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.

Keywords: Bos indicus; cattle; disease resistance; fertility; runs of homozygosity; selection.

Figure 1

Frequency distributions of all detected runs of homozygosity (ROH) across samples, percentage of autosomal genome coverage by ROH (F_ROH) of different minimum lengths (>0.5, >1, >2, >4, >8, and >16 Mb), and diagonal elements of the realized genomic relationship matrix (G_{i, i}).

Figure 2

Scatterplots (lower panel) and correlations (upper panel) of percentage of autosomal genome coverage by runs of homozygosity (F_ROH) of different minimum lengths (>0.5, >1, >2, >4, >8, and >16 Mb) and diagonal elements of the realized genomic relationship matrix (G_{i, i}). The last column of panels on the right indicates that the correlation between F_ROH and G_{i, i} decreases as a function of minimum fragment size.

Figure 3

Barplot of average percentage of chromosome coverage by runs of homozygosity (F_ROH) of minimum length of 0.5 Mb.

Figure 4

Manhattan plot of genome-wide locus autozygosity in Nellore cows. The dashed line represents the 50% threshold.