Combined line-cross and half-sib QTL analysis in Duroc–Pietrain population
A Duroc–Pietrain resource population was built to detect quantitative trait loci (QTL) that affect growth, carcass composition, and pork quality. The data were analyzed by applying three least-squares Mendelian models: a line-cross (LC) model, a half-sib (HS) model, and a combined LC and HS model (CB), which enabled the detection of QTL that had fixed, equal, and different allele frequencies for alternate breed alleles, respectively. Permutation tests were performed to determine 5% chromosome-wide and 5% genome-wide threshold values. A total of 40 (137) QTL were detected at the 5% genome-wide (chromosome-wide) level for the 35 traits analyzed. Of the 137 QTL detected, 62 were classified as the LC type (LC-QTL), 47 as the HS type (HS-QTL), and 28 as the CB type (CB-QTL). The results indicate that implementation of a series of model-based framework is not only beneficial to detect QTL, but also provides us with a new and more robust interpretation from which further methodology could be developed.
- Alfonso L, Haley CS (1998) Power of different F2 schemes for QTL detection in livestock. Anim Sci 66:1–8Google Scholar
- Dekkers J, Kim JJ, Malek M, Thomsen H, Lee H et al (2003) A genome scan to detect QTL affecting growth, composition, and meat quality trait in a Berkshirer × Yorkshire cross. 28th National Swine Improvement Federation Proc, December 4–5, 2003, Des Moines, IAGoogle Scholar
- Green P, Falls K, Crooks S (1990) Documentation for CRIMAP version 2.4. Washington University School of Medicine, St. Louis, MOGoogle Scholar