Genomic inbreeding estimation in small populations: evaluation of runs of homozygosity in local cattle breeds

Abstract

The availability of high throughput genotyping has facilitated the quantification of inbreeding by genomic markers in farm animals. Run of homozygosity (ROH) are contiguous lengths of homozygous genotypes and represent an estimate of the degree of autozygosity at genome-wide level. The current study aims to quantify the genomic inbreeding derived from ROH (FROH) in three Italian local cattle breeds. Individuals of Cinisara (71), Modicana (72), Reggiana (168) were genotyped with the 50K v2 Illumina BeadChip. Genotypes from 96 animals of the Italian Holstein cattle breed were included in the analysis. The following criteria were used to define a ROH: two missing SNPs; one heterozygous SNP; minimum density of 1 SNP every 100 kb; maximum gap between consecutive SNPs of 1 000 kb. We used a definition of ROH as tracts of homozygous genotypes that were >4 000 kb in length with a minimum number of 40 SNPs included in the run. Across all four breeds, we identified 3,661 ROH. The Modicana breed showed the highest mean number of ROH for individual (11.03) and the highest value of FROH (0.053), whereas the Reggiana showed the lowest values (7.15 and 0.033, respectively). The three most homozygous animals present in our dataset were from the Cinisara (676.9 Mb), Modicana (681.2 Mb) and Reggiana (725.2 Mb), with almost a quarter of their genome classified as ROH. Differences among breeds existed for the ROH length. The individuals of Reggiana and Italian Holstein breeds showed high number of shorter ROH segments, whereas the Sicilian breeds showed ROH characterized by the presence of large segments. In fact, in all breeds, most ROH segment coverage was in the shorter length categories (4-8 Mb), but the Sicilian breeds presented the highest percentage of ROHs (12%) inside the ROH length category >24Mb. Therefore our results showed the presence of inbreeding due to recent consanguineous matings and a lack of gene flow from other herds and breeds. ROH analyses represent an important instrument that may be used in inference of population history and to associate with important production and disease traits. Considering that the increased of inbreeding leads to different negative effects, our results showed the necessity of implementing conservation programs to preserve the local breeds.