Abstract
Genomes of animals harbor not only homozygous (ROH) but also HRR segments of chromosomes. In the current study, the HRRs in Holstein cattle were analyzed using a 50K array. On average, 366 Holstein cows from six herds had 439 ± 7 and 111 ± 3 HRRs per cow when HRRs with a minimum length of 50 kb and 250 kb were detected, respectively. The average HRRs values did not differ between herds. Removal of SNP with an MAF less than 0.01 leads to a noticeable increase in the number of HRRs. The distribution of HRRs in the chromosomes of cows is not uniform and depends on the scanned lengths of the HRR segments. No clear correlations were found between interchromosomal HRR specific density and the occurrence of HRRIs. When HRR segments with a length of 50 kb or more have been detected, the significant HRRIs were located on BTA1, BTA10, BTA20, and BTA21(first set); for HRR segments with a length of 250 kb or more, significant islands were found on BTA9, BTA11, and BTA29 (second set). According to the Tajima D test, the islands on the BTA of the first set have maximum values of 3.47-2.82, while the islands on the BTA of the second set have values of less than 2.49. The genes in the HRRIs are involved in immune response, oogenesis, and reproduction but are not related to milk production traits. These results show that the recognition of HRRIs strongly depends on the length of the scanned HRR segments. No single "mechanism" was identified as the main cause of HRRIs.