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Runs of homozygosity in Nellore Cattle

Ana Cristina H. Rios ; Gerardo Alves Fernandes Júnior ;  Lúcio Flávio Macedo Mota  ; Danielly Beraldo dos Santos Silva  ; Ana Fabrícia Braga Magalhães  ; Roberto Carvalheiro ; Fernando Baldi ; Lúcia Galvão de Albuquerque
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Runs of homozygosity (ROH) can be defined as continuous stretches of homozygous genotypes resulting from inbreeding. The aim of this study was to identify ROH segments in a population of Nellore cattle in order to better understanding the genomic patterns of homozygosity in this breed. The dataset used in this study was composed of 2,025 cows and 1,760 steers genotyped with the Illumina(R) Bovine HD chip. Only single nucleotide polymorphisms (SNPs) located on autosomes (735,293 SNPs) were considered in this study. The ROH segments were identified using PLINK software, considering a sliding window of 50 consecutive SNPs. There were allowed 2 heterozygous per window and 5 missing calls. The minimum length of a ROH was set to be 1000 kb, the required minimum SNP density considered was 1 SNP per 50 kb, and the maximum gap between two consecutive SNPs was set to 500 kb. For each SNP, it was summed the number of homozygous windows in which that SNP occurs, For each SNP, the number of homozygous windows in which that SNP occurs were summed, as well as the total number of windows. Thus, if a minimum of 50 consecutive SNP had more than 5% of their windows homozygous, a ROH was called. In this study, there were identified 221,271 ROH across the animals. The number of SNPs per window ranged from 50 to 26,070, with 814 SNPs on average. The ROH length identified per individual was 171.7 ? 65.18 Mb, on average, ranging from 1.0 to 707.0 Mb. It was also observed that in this Nellore population, on average, 6.84 % of the genome was covered by ROH. The number and average length of ROH, considering the following length classes (1) <8 Mb; (2) from 8 to 16 Mb and (3) >16 Mb), were, respectively, 205,960 ROH with 2.04 ? 1.44 Mb; 11,167 ROH with 10.93 ? 2.21 Mb; and 4,144 ROH with 24.83 ? 9.51 Mb. According to the literature, there is a close relationship between the ROH length and the number of generations in which inbreeding events had occurred. Shorter ROH have been associated with remote inbreeding, while longer ROH have been associated with a more recent inbreeding. In this way, our results suggest a higher contribution of remote inbreeding to autozigosity in this Nellore population, because short ROH was more frequent in the genome.