Runs of homozygosity are unevenly located across the genome in highly inbred cattle

MOLINA A.; DEMYDA-PEYRÁS S. E.; GIOVAMBATTISTA G.; GOSZCZYNSKI D. E.; MORALES-DURAND H. F.

Dublin

Conferencia; 36th International Society for Animal Genetics Conference; 2017

International Society for Animal Genetics

Inbreeding depression has been recognized as a main cause of deleterious effects in individuals due to the loss of genetic variability. Nowadays, massive genotyping technologies and the analysis of runs of homozygosity (ROH) provide us with valuable tools to further understand this condition. Using in silico methods, it has been recently demonstrated that ROH size is correlated with the number of generations since the common ancestor, although experimental studies focused in this relation are scarce. Hereby, we characterized the ROH patterns of an extremely consanguineous cattle population with very reliable pedigree data (5.2 ECG). For this, 33 Retinta bulls (average Fped = 16.57%; ranging from 10.25% to 30.62%) were genotyped using the BOS 1 SNP Array. Recent inbreeding was estimated using data from the 3 last generations. ROH patterns were classified upon their size (0.5-1Mb; 1-2Mb; 2-4Mb; 4-8Mb; 8-16Mb ;>16MB). FROH values (percentage of the genome covered by ROHs) were also determined per size category and per chromosome.ROHs showed an average size of 2.17 Mb (0.50 to 66.87 Mb), with 3.19 runs longer than 16Mb per individual. FROHs for the longest runs (8-16 and >16Mb) showed the highest values, which is consistent with the recent inbreeding events produced in this population. Interestingly, high FROH values were also observed in the [1-2Mb] cluster, which may be explained by traits fixed at the origin of the breed (50 generations ago). These results were confirmed by Fped3-FROH correlation, which increased towards long ROHs (-0.28 in [0.5-1Mb] to 0.43 in >16Mb). Therefore, we demonstrated for the first time that the association between long ROHs and generations since the common ancestor is conserved in highly inbred cattle.A further analysis showed that FROH values were highly variable among chromosomes (ranging from 0.1198 in BTA21 to 0.2178 in BTA14). Remarkable differences were also observed in the >16Mb runs, where the average FROH was of 0 on BTA19 and BTA22 (no runs) and 0.083 on BTA7. In conclusion, we demonstrated that homozygosity is unevenly distributed across the genome in an inbred cattle population, potentially affecting different metabolic pathways in individuals with similar Fped.