Effect of genotyping density on the detection of runs of homozygosity and heterozygosity in cattle

Runs of homozygosity (ROHom) are contiguous stretches of homozygous regions of the genome. In contrast, runs of heterozygosity (ROHet) are heterozygosity-rich regions. The detection of these two types of genomic regions (ROHom and ROHet) is influenced by the parameters involved in their identification and the number of available single-nucleotide polymorphisms (SNPs). The present study aimed to test the effect of chip density in detecting ROHom and ROHet in the Italian Simmental cattle breed. A sample of 897 animals were genotyped at low density (50k SNP; 397 individuals), medium density (140k SNP; 348 individuals), or high density (800k SNP; 152 individuals). The number of ROHom and ROHet per animal (nROHom and nROHet, respectively) and their average length were calculated. ROHom or ROHet shared by more than one animal and the number of times a particular SNP was inside a run were also computed (SNPROHom and SNPROHet). As the chip density increased, the nROHom increased, whereas their average length decreased. In contrast, the nROHet decreased and the average length increased as the chip density increased. The most repeated ROHom harbored no genes, whereas in the most repeated ROHet four genes (SNRPN, SNURF, UBE3A, and ATP10A) previously associated with reproductive traits were found. Across the 3 datasets, 31 SNP, located on Bos taurus autosome (BTA) 6, and 37 SNP (located on BTA21) exceeded the 99th percentile in the distribution of the SNPROHom and SNPROHet, respectively. The genomic region on BTA6 mapped the SLIT2, PACRGL, and KCNIP4 genes, whereas 19 and 18 genes were mapped on BTA16 and BTA21, respectively. Interestingly, most of genes found through the ROHet analysis were previously reported to be related to health, reproduction, and fitness traits. The results of the present study confirm that the detection of ROHom is more reliable when the chip density increases, whereas the ROHet trend seems to be the opposite. Genes and quantitative trait loci (QTL) mapped in the highlighted regions confirm that ROHet can be due to balancing selection, thus related to fitness traits, health, and reproduction, whereas ROHom are mainly involved in production traits. The results of the present study strengthened the usefulness of these parameters in analyzing the genomes of livestock and their biological meaning. A total of 897 Italian Simmental animals were genotyped at different densities to investigate the impact of the BeadChip density on detection of the runs of homozygosity (ROHom) and heterozygosity (ROHet). The results suggested that ROHom detection becomes more accurate as the density increases and that ROHom and ROHet may be used to identify genomic regions mainly due to directional and balancing selection, respectively. Runs of homozygosity (ROHom), continuous stretches of homozygous loci, and runs of heterozygosity (ROHet), continuous stretches of heterozygous loci, may be due to directional (ROHom) or balancing selection (ROHet) and are interesting to analyze those shared among animals within a population and the genes they harbor. The detection of both types of genomic regions is influenced by genotyping density and involved parameters. Thus, this work aimed to study the impact of the BeadChip density on the ROHom and ROHet detection in the Italian Simmental cattle breed. Results showed that the ROHom detection is more reliable as the density increases, whereas a more cryptic pattern was observed for ROHet. Interestingly, the hypothesis on how these two types of runs arise was supplied by the results of this study. The genes mapped on the highlighted ROHet were mainly associated with fitness traits, health, and reproduction, whereas those found in the ROHom were associated with production traits.