A single nucleotide polymorphism in CAPN1 associated with marbling score in Korean cattle

Abstract

Background: Marbling score (MS) is the major quantitative trait that affects carcass quality in beef cattle. In this study, we examined the association between genetic polymorphisms of the micromolar calcium-activated neutral protease gene (micro-calpain, CAPN1) and carcass traits in Korean cattle (also known as Hanwoo).

Results: By direct DNA sequencing in 24 unrelated Korean cattle, we identified 39 sequence variants within exons and their flanking regions in CAPN1. Among them, 12 common polymorphic sites were selected for genotyping in the beef cattle (n = 421). Statistical analysis revealed that a polymorphism in the 3'UTR (c.2151*479C>T) showed significant association with MS (Pcor. = 0.02).

Conclusion: Our findings suggest that polymorphisms in CAPN1 might be one of the important genetic factors involved in carcass quality in beef cattle, although it could be false positive association.

Figure 1

Gene map, haplotypes, and linkage disequilibrium in CAPN1. A. Gene map and polymorphisms in CAPN1 on chromosome 29. The coding exon is marked by black blocks, and 5' and 3' UTRs by white blocks. The first base of the translational site is denoted as nucleotide +1. Asterisks (*) indicate polymorphisms genotyped in a larger Korean native cattle cohort (n = 421). B. Haplotypes in CAPN1. Haplotypes with frequency >0.02 are presented. Others contain rare haplotypes: (1)AGTA, GACA, and GGCA; and (2) GATCCGGA, GATGCAGA, GGCGCAAA, and GATGCGGA. C. Linkage disequilibrium (LD) and LD blocks among CAPN1 polymorphisms are shown using Haploview. The color code on the Haploview plot follows the standard color scheme: white (|D'| < 1, LOD < 2); shades of pink/red (|D'| < 1, LOD ≥ 2); blue (|D'| = 1, LOD < 2); bright red (|D'| = 1, LOD ≥ 2). The numbers in cells are D' values. However, the D' values of 1.0 are not shown (empty).