Consequences of paternally inherited effects on the genetic evaluation of maternal effects.
BACKGROUND
Mixed models are commonly used for the estimation of variance components and genetic evaluation of livestock populations. Some evaluation models include two types of additive genetic effects, direct and maternal. Estimates of variance components obtained with models that account for maternal effects have been the subject of a long-standing controversy about strong negative estimates of the covariance between direct and maternal effects. Genomic imprinting is known to be in some cases statistically confounded with maternal effects. In this study, we analysed the consequences of ignoring paternally inherited effects on the partitioning of genetic variance.


RESULTS
We showed that the existence of paternal parent-of-origin effects can bias the estimation of variance components when maternal effects are included in the evaluation model. Specifically, we demonstrated that adding a constraint on the genetic parameters of a maternal model resulted in correlations between relatives that were the same as those obtained with a model that fits only paternally inherited effects for most pairs of individuals, as in livestock pedigrees. The main consequence is an upward bias in the estimates of the direct and maternal additive genetic variances and a downward bias in the direct-maternal genetic covariance. This was confirmed by a simulation study that investigated five scenarios, with the trait affected by (1) only additive genetic effects, (2) only paternally inherited effects, (3) additive genetic and paternally inherited effects, (4) direct and maternal additive genetic effects and (5) direct and maternal additive genetic plus paternally inherited effects. For each scenario, the existence of a paternally inherited effect not accounted for by the estimation model resulted in a partitioning of the genetic variance according to the predicted pattern. In addition, a model comparison test confirmed that direct and maternal additive models and paternally inherited models provided an equivalent fit.


CONCLUSIONS
Ignoring paternally inherited effects in the maternal models for genetic evaluation can lead to a specific pattern of bias in variance component estimates, which may account for the unexpectedly strong negative direct-maternal genetic correlations that are typically reported in the literature.
Unidad de Genética Cuantitativa y Mejora Animal, Universidad de Zaragoza, 50013, Zaragoza, Spain. lvarona@unizar.es.|Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, 50013, Zaragoza, Spain. lvarona@unizar.es.
Luis
L
Varona
Unidad de Genética Cuantitativa y Mejora Animal, Universidad de Zaragoza, 50013, Zaragoza, Spain. munilla@agro.uba.ar.|Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, 1417, Ciudad Autónoma de Buenos Aires, Argentina. munilla@agro.uba.ar.
Sebastián
S
Munilla
Grup de Recerca en Remugants, Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain. joaquim.casellas@uab.cat.
Joaquim
J
Casellas
Unidad de Genética Cuantitativa y Mejora Animal, Universidad de Zaragoza, 50013, Zaragoza, Spain. cmoreno@unizar.es.|Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, 50013, Zaragoza, Spain. cmoreno@unizar.es.
Carlos
C
Moreno
Unidad de Genética Cuantitativa y Mejora Animal, Universidad de Zaragoza, 50013, Zaragoza, Spain. altarrib@unizar.es.|Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, 50013, Zaragoza, Spain. altarrib@unizar.es.
Juan
J
Altarriba
D000704:Analysis of Variance; D000818:Animals; D014644:Genetic Variation; D018392:Genomic Imprinting; D058751:Livestock / Q000235:genetics*; D008957:Models, Genetic; D019655:Quantitative Trait, Heritable