Email updates

Keep up to date with the latest news and content from BMC Genomics and BioMed Central.

Open Access Research article

A bi-dimensional genome scan for prolificacy traits in pigs shows the existence of multiple epistatic QTL

José L Noguera1*, Carmen Rodríguez2, Luis Varona1, Anna Tomàs3, Gloria Muñoz2, Oscar Ramírez3, Carmen Barragán2, Meritxell Arqué1, Jean P Bidanel4, Marcel Amills3, Cristina Ovilo2 and Armand Sánchez3

Author Affiliations

1 Genètica i Millora Animal, IRTA-Lleida, 25198 Lleida, Spain

2 Departamento de Mejora Genética Animal, SGIT-INIA, 28040 Madrid, Spain

3 Departament de Ciència Animal i dels Aliments, UAB, 08193 Bellaterra, Spain

4 INRA, UR337 Station de Génétique Quantitative et appliquée F-78350 Jouy-en-Josas, France

For all author emails, please log on.

BMC Genomics 2009, 10:636  doi:10.1186/1471-2164-10-636

Published: 29 December 2009

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 F2 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 × a, a × d, d × a and d × 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 × Meishan F2 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.