Inbreeding in populations with incomplete pedigrees

Abstract

IntroductionInbreeding has detrimental effects on a number of economically important traits. W iggans et al. (1995) estimated inbreeding depression of −29 kg, −1.08 kg and −0.97 kg for each 1% increase of inbreeding for the traits milk, fat and protein yield, respectively, across several dairy cattle breeds. For post‐weaning gain in Hereford cattle, the depression was −0.24 kg (G engler et al. 1998). For the number of piglets born alive, 21‐day litter weight, and days to 104.5 kg, it was −0.023, −0.052 and 0.21, respectively (C ulbertson et al. 1998). Inbreeding also adversely impacts reproductive traits, such as delayed puberty, reduced conception rates, higher likelihood of losing established pregnancies, increased mortality of calves and lowered bull fertility (Y oung et al. 1969).National genetic evaluations involve animals with incomplete pedigrees. Regular inbreeding algorithms (RA) based on the definition of W right (1922), such as those by Q uaas (1976), calculate the inbreeding of animals with at least one parent missing as zero. Even if an animal has both parents known, its inbreeding will be underestimated if some of its ancestors are unidentified. If the proportion of missing parents is large, the inbreeding trend in a population could be seriously underestimated. Subsequently, losses from inbreeding would be underestimated, and steps to slow the increase of inbreeding, such as using sires that are less related to the general population or mating less‐related animals (T oro and P erez‐E nciso, 1990; G rundy et al. 1994; M euwissen and S onneson 1998; V anR aden and S mith 1999), may be delayed. In particular, use of a mating system can result in matings adjusted for both inbreeding and dominance (M isztal et al. 1999).In populations that use AI substantially, unidentified parents may not differ genetically from identified parents, on average. Therefore the real average inbreeding in animals with unidentified parent(s) may be similar to their contemporaries with both parents known. V anR aden (1992) proposed an algorithm (VRA), where the inbreeding of animals whose parent(s) are unknown is equal to the mean inbreeding of their contemporaries with known parents. Contemporaries are stratified along unknown parent groups (UPG).VRA has been applied to a few US dairy breeds (V anR aden 1992; W iggans et al. 1995). The calculated inbreeding for the youngest Holstein animals was 3.7% with RA and increased to 4.2% with VRA (V anR aden 1992). The increase was small because the number of unidentified animals was small. However, the performance of VRA in recovering inbreeding lost for a range of incomplete pedigrees has not been evaluated. The objectives of this study were (i) to determine average inbreeding coefficients when pedigrees are increasingly more incomplete; (ii) to assess the efficacy of VRA in recovering these inbreeding coefficients; and (iii) to determine the mean inbreeding using the two inbreeding algorithms in a large beef population.