Assessment of inbreeding coefficients and inbreeding depression on complex traits from genomic and pedigree data in...

Nelore cattle play a key role in tropical production systems due to their resilience to harsh conditions, such as heat stress and seasonally poor nutrition. Monitoring their genetic diversity is essential to manage the negative impacts of inbreeding. Traditionally, inbreeding and inbreeding depression are assessed by pedigree-based coefficients (F), but recently, genetic markers have been preferred for their precision in capturing the inbreeding level and identifying animals at risk of reduced productive and reproductive performance. Hence, we compared the inbreeding and inbreeding depression for productive and reproductive performance traits in Nelore cattle using different inbreeding coefficient estimation methods from pedigree information (F_Ped), the genomic relationship matrix (F_GRM), runs of homozygosity (F_ROH) of different lengths (> 1 Mb (genome), between 1 and 2 Mb - F_{ROH 1-2}; 2-4 Mb F_{ROH 2-4} or > 8 Mb F_{ROH >8}) and excess homozygosity (F_SNP).

The correlation between F_Ped and F_ROH was lower when the latter was based on shorter segments (r = 0.15 with F_{ROH 1-2}, r = 0.20 with F_{ROH 2-4} and r = 0.28 with F_{ROH 4-8}). Meanwhile, the F_Ped had a moderate correlation with F_SNP (r = 0.47) and high correlation with F_{ROH >8} (r = 0.58) and F_ROH-genome (r = 0.60). The F_ROH-genome was highly correlated with inbreeding based on F_ROH>8 (r = 0.93) and F_SNP (r = 0.88). The F_GRM exhibited a high correlation with F_ROH-genome (r = 0.55) and F_{ROH >8} (r = 0.51) and a lower correlation with other inbreeding estimators varying from 0.30 for F_{ROH 2-4} to 0.37 for F_{ROH 1-2}. Increased levels of inbreeding had a negative impact on the productive and reproductive performance of Nelore cattle. The unfavorable inbreeding effect on productive and reproductive traits ranged from 0.12 to 0.51 for F_Ped, 0.19-0.59 for F_GRM, 0.21-0.58 for F_ROH-genome, and 0.19-0.54 for F_SNP per 1% of inbreeding scaled on the percentage of the mean. When scaling the linear regression coefficients on the standard deviation, the unfavorable inbreeding effect varied from 0.43 to 1.56% for F_Ped, 0.49-1.97% for F_GRM, 0.34-2.2% for F_ROH-genome, and 0.50-1.62% for F_SNP per 1% of inbreeding. The impact of the homozygous segments on reproductive and performance traits varied based on the chromosomes. This shows that specific homozygous chromosome segments can be signs of positive selection due to their beneficial effects on the traits.

The low correlation observed between F_Ped and genomic-based inbreeding estimates suggests that the presence of animals with one unknown parent (sire or dam) in the pedigree does not account for ancient inbreeding. The ROH hotspots surround genes related to reproduction, growth, meat quality, and adaptation to environmental stress. Inbreeding depression has adverse effects on productive and reproductive traits in Nelore cattle, particularly on age at puberty in young bulls and heifer calving at 30 months, as well as on scrotal circumference and body weight when scaled on the standard deviation of the trait.