Genome-wide identification of quantitative trait loci in a cross between Hampshire and Landrace II: meat quality traits

Abstract

Background: Meat quality traits are important in pig breeding programs, but they are difficult to include in a traditional selection program. Marker assisted selection (MAS) of meat quality traits is therefore of interest in breeding programs and a Quantitative Trait Locus (QTL) analysis is the key to identifying markers that can be used in MAS. In this study, Landrace and Hampshire intercross and backcross families were used to investigate meat quality traits. Hampshire pigs are commonly used as the sire line in commercial pig breeding. This is the first time a pedigree including Hampshire pigs has been used for a QTL analysis of meat quality traits.

Results: In total, we analyzed 39 meat quality traits and identified eight genome-wide significant QTL peaks in four regions: one on chromosome 3, two on chromosome 6 and one on chromosome 16. At least two of the QTLs do not appear to have been detected in previous studies. On chromosome 6 we identified QTLs for water content in M. longissimus dorsi (LD), drip loss in LD and post mortem pH decline in LD. On chromosomes 3 and 16 we identified previously undetected QTLs for protein content in LD and for freezing and cooking loss respectively.

Conclusion: We identified at least two new meat quality trait QTLs at the genome-wide significance level. We detected two QTLs on chromosome 6 that possibly coincide with QTLs detected in other studies. We were also able to exclude the C1843T mutation in the ryanodine receptor (RYR1) as a causative mutation for one of the chromosome 6 QTLs in this cross.

Figure 1

Test statistic curves for genome-wide significant QTLs. Horizontal lines indicate the 1% and 5% genome-wide significant thresholds applicable at the corresponding graph. Markers and distances in cM are indicated on the x-axis. A. QTL for protein content in LD on SSC3. B. QTLs on SSC6 for ΔpH/h in LD 45 min to 3 h p.m., drip loss in LD day 3–7 (4 days) and protein content in LD. C. QTLs for chewing resistance, chewing time and tenderness on SSC6. D. QTL for freezing and cooking loss in LD on SSC16. LD – M. longissimus dorsi, p.m.-post mortem