Indicators of assessing the breeding value of cattle based on exterior faults depending on the level of homozygosity and genomic inbreeding

Abstract

A study was conducted to assess the influence of homozygosity ( Ca ) and genomic inbreeding ( F ROH ) on the estimated breeding value ( EBV ) for exterior faults. For calculating the inbreeding coefficient ( F x ) 355 bulls and 42 246 daughters were used; and for calculating the level of homozygosity by STR markers 341 bulls and 39 749 daughters were used. The inbreeding coefficient was calculated using the Wright – Kislovsky formula, and the level of homozygosity was measured as the ratio of homozygous loci to the total number of analyzed loci. To assess the impact of geno- mic inbreeding, data on SNP markers from 356 sire bulls were used, and then F ROH was assigned to their daughters ( n = 42,248). The level of genomic inbreeding was calculated as the ratio of the total length of all homozygosity patterns (Mbp) in the bull's genome to the total genome size (Mbp) for 29 autosomes of cattle, covered by SNPs (%). For the exterior profile, they used the 'Mosplem' Union method. Defects like "winged scapulae" and "pinched behind the shoulder" tended to increase as the inbreeding coefficient rose, going from –0.000213 and –0.000022 at F x = 0.00% to 0.00048 and 0.000511 at F x ≥ 6.69%. The "roof-shaped rear" fault, on the other hand, tended to reduce EBV from 0.001083 in the first group to –0.001688 in the fourth. When looking at the effect of the level of homozygosity, calculated using STR markers, on the evaluation of the breeding value, we can point out a group of faults that tended to increase from the first group ( Ca = 0%) to the second ( Ca = 8–50%) and third groups ( Ca = 55–77%): –0.000023/0.000031/0.001002 – soft back; –0.001562/0.00017/0.000563 – weak loin; 0.000026/0.000048/0.000714 – winged shoulder blades; –0.000349/0.000024/0.000637 – pinch behind the shoulders; –0.009635/0.002585/0.10081 – high tail; –0.002816/–0.000761/0.012315 – outward intoedness; 0.000009/0.000031/0.000051 – barrel-shaped set of the hind legs; –0.001549/0.001260/0.009468 – slugged udder bottom. A decrease in EBV was found for the defects "high tail" and "soft pasterns", respectively, from 0.008866 and 0.006780 in the first group at F ROH = 0.05–4.19% to –0.003860 and –0.002448 in the fourth group at F ROH = 10.97–17.71%. Monitoring the level of homozygosity using modern genomic selection methods, along with assessing the breeding value based on traits and exterior faults, will serve as a connecting link in today’s breeding activities, both at the individual and population levels of livestock management.