title: A bi-dimensional genome scan for prolificacy traits in pigs shows the existence of multiple epistatic QTL.
abstract: BACKGROUND
  Prolificacy is the most important trait influencing the reproductive efficiency of pig production systems. The low heritability and sex-limited expression of prolificacy have hindered to some extent the improvement of this trait through artificial selection. Moreover, the relative contributions of additive, dominant and epistatic QTL to the genetic variance of pig prolificacy remain to be defined. In this work, we have undertaken this issue by performing one-dimensional and bi-dimensional genome scans for number of piglets born alive (NBA) and total number of piglets born (TNB) in a three generation Iberian by Meishan F(2) intercross.
  
  
  RESULTS
  The one-dimensional genome scan for NBA and TNB revealed the existence of two genome-wide highly significant QTL located on SSC13 (P < 0.001) and SSC17 (P < 0.01) with effects on both traits. This relative paucity of significant results contrasted very strongly with the wide array of highly significant epistatic QTL that emerged in the bi-dimensional genome-wide scan analysis. As much as 18 epistatic QTL were found for NBA (four at P < 0.01 and five at P < 0.05) and TNB (three at P < 0.01 and six at P < 0.05), respectively. These epistatic QTL were distributed in multiple genomic regions, which covered 13 of the 18 pig autosomes, and they had small individual effects that ranged between 3 to 4% of the phenotypic variance. Different patterns of interactions (a x a, a x d, d x a and d x d) were found amongst the epistatic QTL pairs identified in the current work.
  
  
  CONCLUSIONS
  The complex inheritance of prolificacy traits in pigs has been evidenced by identifying multiple additive (SSC13 and SSC17), dominant and epistatic QTL in an Iberian x Meishan F(2) intercross. Our results demonstrate that a significant fraction of the phenotypic variance of swine prolificacy traits can be attributed to first-order gene-by-gene interactions emphasizing that the phenotypic effects of alleles might be strongly modulated by the genetic background where they segregate.
authors.affiliation: Genètica i Millora Animal, IRTA-Lleida, 25198 Lleida, Spain. joseluis.noguera@irta.es
authors.forename: José L
authors.initials: JL
authors.lastname: Noguera
authors.forename: Carmen
authors.initials: C
authors.lastname: Rodríguez
authors.forename: Luis
authors.initials: L
authors.lastname: Varona
authors.forename: Anna
authors.initials: A
authors.lastname: Tomàs
authors.forename: Gloria
authors.initials: G
authors.lastname: Muñoz
authors.forename: Oscar
authors.initials: O
authors.lastname: Ramírez
authors.forename: Carmen
authors.initials: C
authors.lastname: Barragán
authors.forename: Meritxell
authors.initials: M
authors.lastname: Arqué
authors.forename: Jean P
authors.initials: JP
authors.lastname: Bidanel
authors.forename: Marcel
authors.initials: M
authors.lastname: Amills
authors.forename: Cristina
authors.initials: C
authors.lastname: Ovilo
authors.forename: Armand
authors.initials: A
authors.lastname: Sánchez
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D016678:Genome / Q000235:genetics*; D005838:Genotype; D006801:Humans; D008297:Male; D018895:Microsatellite Repeats / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D040641:Quantitative Trait Loci / Q000235:genetics*; D013552:Swine / Q000235:genetics*