Identification of Carcass and Meat Quality QTL in an F2 Duroc × Pietrain Pig Resource Population Using Different Least-Squares Analysis Models

Nancy E Raney,Ronald O Bates,Juan P Steibel,Janice M Rumph,Igseo Choi,Catherine W Ernst

doi:10.3389/fgene.2011.00018

Abstract

A three-generation resource population was constructed by crossing pigs from the Duroc and Pietrain breeds. In this study, 954 F2 animals were used to identify quantitative trait loci (QTL) affecting carcass and meat quality traits. Based on results of the first scan analyzed with a line-cross (LC) model using 124 microsatellite markers and 510 F2 animals, 9 chromosomes were selected for genotyping of additional markers. Twenty additional markers were genotyped for 954 F2 animals and 20 markers used in the first scan were genotyped for 444 additional F2 animals. Three different Mendelian models using least-squares for QTL analysis were applied for the second scan: a LC model, a half-sib (HS) model, and a combined LC and HS model. Significance thresholds were determined by false discovery rate (FDR). In total, 50 QTL using the LC model, 38 QTL using the HS model, and 3 additional QTL using the combined LC and HS model were identified (q < 0.05). The LC and HS models revealed strong evidence for QTL regions on SSC6 for carcass traits (e.g., 10th-rib backfat; q < 0.0001) and on SSC15 for meat quality traits (e.g., tenderness, color, pH; q < 0.01), respectively. QTL for pH (SSC3), dressing percent (SSC7), marbling score and moisture percent (SSC12), CIE a* (SSC16), and carcass length and spareribs weight (SSC18) were also significant (q < 0.01). Additional marker and animal genotypes increased the statistical power for QTL detection, and applying different analysis models allowed confirmation of QTL and detection of new QTL.

Highlights

Quantitative trait loci (QTL) mapping has been conducted using numerous pig populations to identify genomic regions controlling phenotypic variation for hundreds of traits
The implementation of QTL into breeding programs which is a major goal of QTL mapping has been limited due to insufficient numbers of identified causative mutations, but because of unknown linkage disequilibrium (LD) phase between markers and QTL resulting from cross breeding systems (Spelman and Bovenhuis, 1998; Hayes et al, 2009)
The objective of this study was to confirm previously identified carcass merit and meat quality QTL regions with addition of new marker genotypes and additional F2 animals, and to detect new QTL for carcass merit and meat quality traits using three different least-squares models under different assumptions; (1) founders fixed for alternative QTL alleles (LC model), (2) segregation of QTL alleles at similar frequencies in founders (HS model), and (3) segregation of QTL alleles at different frequencies in founders (CB model)

Summary

Introduction

Quantitative trait loci (QTL) mapping has been conducted using numerous pig populations to identify genomic regions controlling phenotypic variation for hundreds of traits (http://www.animalgenome.org/cgi-bin/QTLdb/SS/index). We have developed a F2 Duroc × Pietrain resource population at Michigan State University (Edwards et al, 2008b) and reported QTL for carcass merit and meat quality traits (Edwards et al, 2008a). The Duroc and Pietrain breeds are used in breeding programs as sire breeds worldwide, and these breeds exhibit variation in carcass merit and meat quality phenotypes. Pietrain pigs have been shown to have less backfat (Affentranger et al, 1996; Edwards et al, 2003) and larger longissimus muscle area (LMA; Edwards et al, 2003). Duroc and Duroc-sired pigs generally have more favorable meat quality (Langlois and Minvielle, 1989; Affentranger et al, 1996; Jeremiah et al, 1999; Edwards et al, 2003), whereas Pietrain and Pietrain-sired pigs are leaner with average meat quality (Edwards et al, 2003)

Objectives

Methods

Results

Conclusion