Use of Genome Sequence Information for Meat Quality Trait QTL Mining for Casual Genes and Mutations on Pig Chromosome 17

Antonio M Ramos,James M Reecy,Jane Rogers,Max F Rothschild,Sean J Humphray,Zhi-Liang Hu

doi:10.3389/fgene.2011.00043

Abstract

The newly available pig genome sequence has provided new information to fine map quantitative trait loci (QTL) in order to eventually identify causal variants. With targeted genomic sequencing efforts, we were able to obtain high quality BAC sequences that cover a region on pig chromosome 17 where a number of meat quality QTL have been previously discovered. Sequences from 70 BAC clones were assembled to form an 8-Mbp contig. Subsequently, we successfully mapped five previously identified QTL, three for meat color and two for lactate related traits, to the contig. With an additional 25 genetic markers that were identified by sequence comparison, we were able to carry out further linkage disequilibrium analysis to narrow down the genomic locations of these QTL, which allowed identification of the chromosomal regions that likely contain the causative variants. This research has provided one practical approach to combine genetic and molecular information for QTL mining.

Highlights

A large number of quantitative trait loci (QTL) for economically important traits has been identified in pigs over the past 15+ years
We have previously identified five meat quality QTL on pig chromosome 17 in a genome scan using an F2 population derived from a Berkshire × Yorkshire (BY) cross (Malek et al, 2001a)
Because of an extensive conservation between SSC17 and HSA20 (Lahbib-Mansais et al, 2005), 15 candidate genes, or open reading frames (ORFs) were selected from the homologous region of the human genome

Summary

Introduction

A large number of quantitative trait loci (QTL) for economically important traits has been identified in pigs over the past 15+ years. More than 6,300 pig QTL have been deposited in the Animal QTLdb (http://www.animalgenome.org/QTLdb/) as of January 1, 2011. The causal variant(s) for any given QTL are likely in strong linkage disequilibrium (LD) with other genetic markers, which makes identification difficult. This may or may not always be the case. Only a limited number of causal or presumed variants for QTL have been discovered in pigs (Milan et al, 2000; Ciobanu et al, 2001; Van Laere et al, 2003)

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