Additive and heterotic effects estimation from a F2 Duroc × Pietrain crossbreed using 60K realized breed composition and heterozygosis

STEIBEL, J. P.; BATES, R. O.; ROGBERG-MUÑOZ, A.; MUNILLA, S.; GIOVAMBATTISTA, G.; FORNERIS, N.S.; ERNST, C. W.; CANTET, R. J. C.

UTAH

Conferencia; 35th International Society for Animal Genetics Conference; 2016

Heterosis is mainly the result of non-additive genetic effects. It is defined as the difference between the average phenotype of the F1 progeny minus the average of the parental lines. If heterosis is caused by dominance, the values of heterosis are proportional to the loss of heterozygosity, which in turn is defined as the average fraction of the genome with heterozygous loci from the parental lines. Assuming a 2-locus model of genetic effects, the expected value of the phenotype in a F2 progeny from 2 breeds (C and T) can be written as follows: E(CT) = µ + kAA + kDD + kAAAA + kDDDD + kADAD. The coefficients kA and kD are functions of the genomic proportion of each breed (S), and of the fraction of the genome in heterozygous state (H), respectively. Usually S and H have been ?estimated,? using individual breed composition such that all animals at the same crossbreeding stage have the same values of S and H. With the development of SNP arrays technology, thousands of positions in the genome could be genotyped and inheritance of genomic segments could be precisely estimated. Thus, S and H can be ?observed? in a specific cross with an adequate method of genotyping. The goal of this research was to estimate the additive and dominance effects from a Duroc × Pietrain F2 crossbred population, using phenotypic data from the F2 animals and genomic data from the F0, F1, and F2. A total of 411 pigs from an outbred 3-generation Duroc × Pietrain resource population were genotyped with the PorcineSNP60 Beadchip. Data on growth (15 traits) and carcass (25 traits) were also collected from the F2 generation (336 animals). For any pair of grandparent?grandson, the identity by descent sharing within the known pedigree, across all SNPs, were inferred with the software PEDIBD and realized values of S and H were estimated in the grandsons by using as reference the breeds of each grandparent. Then, the estimated values of S and H were used to calculate kA and kD for each F2 animal, values that were later included as covariates in a mixed model for estimating the additive and heterotic effects. The realized values of kA and kD ranged between −0.480 to 0.377, and from −0.716 to 0.360, respectively, and allowed estimating A, D, AA, AD, and DD for all 40 traits.