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2010-Duthie_et_al - Epistatic analysis of carcass...

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C. Duthie, G. Simm, A. Doeschl-Wilson, E. Kalm, P. W. Knap and R. Roehe between quantitative trait loci attributable to additive and dominance genetic effects Epistatic analysis of carcass characteristics in pigs reveals genomic interactions doi: 10.2527/jas.2009-2266 originally published online March 12, 2010 2010, 88:2219-2234. J ANIM SCI http://jas.fass.org/content/88/7/2219 the World Wide Web at: The online version of this article, along with updated information and services, is located on www.asas.org by guest on July 16, 2011 jas.fass.org Downloaded from
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ABSTRACT: The present study focused on the iden- tification of epistatic QTL pairs for body composition traits (carcass cut, lean tissue, and fat tissue weights) measured at slaughter weight (140 kg of BW) in a 3-generation full-sib population developed by crossing Pietrain sires with a crossbred dam line. Depending on the trait, phenotypic observations were available for 306 to 315 F 2 animals. For the QTL analysis, 386 ani- mals were genotyped for 88 molecular markers covering chromosomes SSC1, SSC2, SSC4, SSC6, SSC7, SSC8, SSC9, SSC10, SSC13, and SSC14. In total, 23 significant epistatic QTL pairs were identified, with the additive × additive genetic interaction being the most prevalent. Epistatic QTL were identified across all chromosomes except for SSC13, and epistatic QTL pairs accounted for between 5.8 and 10.2% of the phenotypic variance. Seven epistatic QTL pairs were between QTL that re- sided on the same chromosome, and 16 were between QTL that resided on different chromosomes. Sus scrofa chromosome 1, SSC2, SSC4, SSC6, SSC8, and SSC9 harbored the greatest number of epistatic QTL. The epistatic QTL pair with the greatest effect was for the entire loin weight between 2 locations on SSC7, explain- ing 10.2% of the phenotypic variance. Epistatic associa- tions were identified between regions of the genome that contain the IGF-2 or melanocortin-4 receptor genes, with QTL residing in other genomic locations. Quan- titative trait loci in the region of the melanocortin-4 receptor gene and on SSC7 showed significant positive dominance effects for entire belly weight, which were offset by negative dominance × dominance interactions between these QTL. In contrast, the QTL in the region of the IGF-2 gene showed significant negative domi- nance effects for entire ham weight, which were largely overcompensated for by positive additive × dominance genetic effects with a QTL on SSC9. The study shows that epistasis is of great importance for the genomic regulation of body composition in pigs and contributes substantially to the variation in complex traits. Key words: carcass characteristic, epistasis, fatness, leanness, pig, quantitative trait locus ©2010 American Society of Animal Science. All rights reserved. J. Anim. Sci. 2010. 88:2219–2234 doi:10.2527/jas.2009-2266 INTRODUCTION Numerous QTL have been reported for carcass char- acteristics in pigs (e.g., Geldermann et al., 2003; Karl- skov-Mortensen et al., 2006; Liu et al., 2007). These studies have focused on identifying the individual QTL effects (additive, dominance, and imprinting), without considering interactions between loci (epistasis). When
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