Turkish Journal of Veterinary & Animal Sciences
Abstract
The present study analyses the influence of various parameters on the accuracy and reliability of ROH identification procedures, as well as their relationship with inbreeding and genetic diversity in Duroc pig populations. The genotyping data of 70 Duroc pigs obtained using PorcineSNP80v1 chips were used, and the effects of LD pruning and ROH calling parameters were evaluated. It was found that the use of strict basic filters during the execution of the --homozyg command reduces the likelihood of false positives and contributes to the more accurate identification of ROH. The results show that LD pruning reduces the detection of random segments, allowing for a more accurate identification of the true ROH, and increases their total number through the elimination of errors. It can thus be concluded that the applied ROH search model leads to more reliable results.
Author ORCID Identifier
TIMOFEY ROMANETS: 0000-0002-0690-4217
ANNA KOROBEYNIKOVA: 0009-0003-0556-9343
LYUBOV GETMANTSEVA: 0000-0003-1868-3148
MARIA KOLOSOVA: 0000-0003-2979-7108
ELENA ROMANETS: 0000-0003-2824-9564
ILONA BAKOEVA: 0009-0007-2827-9006
VARVARA SHEVTSOVA: 0000-0001-8046-0223
ANATOLY KOLOSOV: 0000-0002-6583-8942
ALEXANDER MAKSIMOV: 0000-0003-1526-8010
SIROJ BAKOEV: 0000-0002-0324-3580
DOI
10.55730/1300-0128.4400
Keywords
Areas of homozygosity, ROH, inbreeding, genetic diversity, Duroc pigs
First Page
280
Last Page
287
Publisher
The Scientific and Technological Research Council of Türkiye (TÜBİTAK)
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.
Recommended Citation
ROMANETS, T, KOROBEYNIKOVA, A, GETMANTSEVA, L, KOLOSOVA, M, ROMANETS, E, BAKOEVA, I, SHEVTSOVA, V, KOLOSOV, A, MAKSIMOV, A, & BAKOEV, S (2025). Parameter optimization for runs of homozygosity (ROH) detection in the pig genome. Turkish Journal of Veterinary & Animal Sciences 49 (6): 280-287. https://doi.org/10.55730/1300-0128.4400
