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BMC Genomics. 2009; 10: 636.
Published online Dec 29, 2009. doi:  10.1186/1471-2164-10-636
PMCID: PMC2812473
A bi-dimensional genome scan for prolificacy traits in pigs shows the existence of multiple epistatic QTL
José L Noguera,corresponding author1 Carmen Rodríguez,2 Luis Varona,1 Anna Tomàs,3 Gloria Muñoz,2 Oscar Ramírez,3 Carmen Barragán,2 Meritxell Arqué,1 Jean P Bidanel,4 Marcel Amills,3 Cristina Ovilo,2 and Armand Sánchez3
1Genètica i Millora Animal, IRTA-Lleida, 25198 Lleida, Spain
2Departamento de Mejora Genética Animal, SGIT-INIA, 28040 Madrid, Spain
3Departament de Ciència Animal i dels Aliments, UAB, 08193 Bellaterra, Spain
4INRA, UR337 Station de Génétique Quantitative et appliquée F-78350 Jouy-en-Josas, France
corresponding authorCorresponding author.
José L Noguera: joseluis.noguera/at/irta.es; Carmen Rodríguez: valdo/at/inia.es; Luis Varona: lvarona/at/unizar.es; Anna Tomàs: anna.tomas/at/cresa.uab.cat; Gloria Muñoz: gloriammster/at/gmail.com; Oscar Ramírez: oscar.ramirez/at/upf.edu; Carmen Barragán: barragan/at/inia.es; Meritxell Arqué: marqueclemens/at/gmail.com; Jean P Bidanel: jean-pierre.bidanel/at/jouy.inra.fr; Marcel Amills: marcel.amills/at/uab.es; Cristina Ovilo: ovilo/at/inia.es; Armand Sánchez: armand.sanchez/at/uab.es
Received June 15, 2009; Accepted December 29, 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.
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