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Quantification And Visualization Of Ld Patterns And Identification Of Haplotype Blocks, Yan Wang, Sandrine Dudoit
Quantification And Visualization Of Ld Patterns And Identification Of Haplotype Blocks, Yan Wang, Sandrine Dudoit
U.C. Berkeley Division of Biostatistics Working Paper Series
Classical measures of linkage disequilibrium (LD) between two loci, based only on the joint distribution of alleles at these loci, present noisy patterns. In this paper, we propose a new distance-based LD measure, R, which takes into account multilocus haplotypes around the two loci in order to exploit information from neighboring loci. The LD measure R yields a matrix of pairwise distances between markers, based on the correlation between the lengths of shared haplotypes among chromosomes around these markers. Data analysis demonstrates that visualization of LD patterns through the R matrix reveals more deterministic patterns, with much less noise, than …
New Alleles In Calpastatin Gene Are Associated With Meat Quality Traits In Pigs, Daniel C. Ciobanu, John W. M. Vleck, S. M. Lonergan, H. Thomsen, J. C. M. Dekkers, G. S. Plastows, M. F. Rothschild
New Alleles In Calpastatin Gene Are Associated With Meat Quality Traits In Pigs, Daniel C. Ciobanu, John W. M. Vleck, S. M. Lonergan, H. Thomsen, J. C. M. Dekkers, G. S. Plastows, M. F. Rothschild
Department of Animal Science: Faculty Publications
Suggestive QTL affecting raw firmness scores and average Instron force, tenderness, juiciness, and chewiness on cooked meat were mapped to pig chromosome 2 using a three-generation intercross between Berkshire and Yorkshire pigs. Based on its function and location, the calpastatin (CAST) gene was considered to be a good candidate for the observed effects. Several missense and silent mutations were identified in CAST and haplotypes covering most of the coding region were constructed and used for association analyses with meat quality traits. Results demonstrated that one CAST haplotype was significantly associated with lower Instron force and cooking loss and …