title: Genomic BLUP including additive and dominant variation in purebreds and F1 crossbreds, with an application in pigs.
abstract: BACKGROUND
  Most developments in quantitative genetics theory focus on the study of intra-breed/line concepts. With the availability of massive genomic information, it becomes necessary to revisit the theory for crossbred populations. We propose methods to construct genomic covariances with additive and non-additive (dominance) inheritance in the case of pure lines and crossbred populations.
  
  
  RESULTS
  We describe substitution effects and dominant deviations across two pure parental populations and the crossbred population. Gene effects are assumed to be independent of the origin of alleles and allelic frequencies can differ between parental populations. Based on these assumptions, the theoretical variance components (additive and dominant) are obtained as a function of marker effects and allelic frequencies. The additive genetic variance in the crossbred population includes the biological additive and dominant effects of a gene and a covariance term. Dominance variance in the crossbred population is proportional to the product of the heterozygosity coefficients of both parental populations. A genomic BLUP (best linear unbiased prediction) equivalent model is presented. We illustrate this approach by using pig data (two pure lines and their cross, including 8265 phenotyped and genotyped sows). For the total number of piglets born, the dominance variance in the crossbred population represented about 13 % of the total genetic variance. Dominance variation is only marginally important for litter size in the crossbred population.
  
  
  CONCLUSIONS
  We present a coherent marker-based model that includes purebred and crossbred data and additive and dominant actions. Using this model, it is possible to estimate breeding values, dominant deviations and variance components in a dataset that comprises data on purebred and crossbred individuals. These methods can be exploited to plan assortative mating in pig, maize or other species, in order to generate superior crossbred individuals in terms of performance.
authors.affiliation: GenPhySE (Génétique, Physiologie et Systèmes d'Elevage), Université de Toulouse, INP, ENSAT, 31326, Castanet-Tolosan, France. zulma.vitezica@ensat.fr.|GenPhySE (Génétique, Physiologie et Systèmes d'Elevage), INRA, 31326, Castanet-Tolosan, France. zulma.vitezica@ensat.fr.
authors.forename: Zulma G
authors.initials: ZG
authors.lastname: Vitezica
authors.affiliation: Departamento de Anatomía, Embriología y Genética, Universidad de Zaragoza, 50013, Saragossa, Spain. lvarona@unizar.es.|Instituto Agroalimentario de Aragón (IA2), 50013, Saragossa, Spain. lvarona@unizar.es.
authors.forename: Luis
authors.initials: L
authors.lastname: Varona
authors.affiliation: GenPhySE (Génétique, Physiologie et Systèmes d'Elevage), INRA, 31326, Castanet-Tolosan, France. jmelsen@toulouse.inra.fr.
authors.forename: Jean-Michel
authors.initials: JM
authors.lastname: Elsen
authors.affiliation: Animal and Dairy Science, University of Georgia, Athens, GA, 30602, USA. ignacy@uga.edu.
authors.forename: Ignacy
authors.initials: I
authors.lastname: Misztal
authors.affiliation: PIC North America, 100 Bluegrass Commons Blvd., Suite 2200, Hendersonville, TN, 37075, USA. William.Herring@genusplc.com.
authors.forename: William
authors.initials: W
authors.lastname: Herring
authors.affiliation: GenPhySE (Génétique, Physiologie et Systèmes d'Elevage), INRA, 31326, Castanet-Tolosan, France. andres.legarra@toulouse.inra.fr.
authors.forename: Andrès
authors.initials: A
authors.lastname: Legarra
mesh_terms: D000483:Alleles; D000818:Animals; D003433:Crosses, Genetic; D005260:Female; D005787:Gene Frequency; D005799:Genes, Dominant; D023281:Genomics; D006579:Heterozygote; D008957:Models, Genetic; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D000068618:Selective Breeding; D034421:Sus scrofa / Q000235:genetics*
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