RFLP and linkage analysis of the porcine casein loci--CASAS1, CASAS2, CASB and CASK

Characterization of a Novel Porcine CSN2 Polymorphism and Its Distribution in Five European Breeds

Simple Summary

Polymorphisms in genes encoding major milk proteins have been intensely studied, and are used, worldwide, in marker-assisted selection in dairy species: αS1-casein in goats—associated with milk protein content and flavor; κ-casein and β-lactoglobulin in cattle—associated with milk quantity and quality; bovine β-casein—associated with human health, etc. This aspect has scarcely been investigated in pigs. Using an electrophoretic technique, we previously identified a novel porcine β-casein (encoded by CSN2) polymorphism. Here, we fully characterize it at protein and DNA level, propose a genotyping protocol, and investigate its distribution in five European porcine breeds. In brief, a G/A point mutation in position 647 of the porcine CSN2 cDNA leads to an arginine/glutamine substitution in position 201 of the protein. This mutation can be typed via a StyI PCR-RFLP assay. The frequency of the G allele was 0.965 in the investigated Landrace population (number of individuals genotyped n = 67), one in the Pietrain (n = 40), 0.705 in the Large White (n = 36), 0.885 in the Bazna (n = 13), and 0.555 in the Mangalita population (n = 11). Considering that milk protein content still varies widely within (and between) porcine breeds, this and/or other similar polymorphisms may have implications for the dynamics of piglet growth during suckling.

Abstract

Here, we describe a novel porcine β-casein (CNS2) polymorphism, initially identified using the isoelectric focusing (IEF) technique, and provide its distribution in five European breeds. Porcine CSN2 cDNA samples, from sows identified using IEF as carriers of polymorphic variants, were sequenced, and based on the sequence alignments, a genotyping assay was developed. The distribution of the polymorphism was investigated by genotyping 167 sows. Population genetic indexes were computed using POPGENE32 version 1.32. Sequence alignments revealed that the mutation which caused the different β-casein IEF migration profiles was c.647G>A, a substitution located in exon 7, which modifies the amino acid from position 201 of the mature protein from arginine to glutamine. The frequency of the G allele was 0.965 in the investigated Landrace population (number of individuals genotyped n = 67), one in the Pietrain population (n = 40), 0.705 in the Large White population (n = 36), 0.885 in the Bazna population (n = 13), and 0.555 in the Mangalita population (n = 11). For all breeds, except Pietrain (monomorphic), the genotype distribution was in accordance with the Hardy–Weinberg equilibrium. Given that β-casein is the most important protein in sows’ milk, a polymorphism like the one described here may prove interesting for marker-assisted selection.

Utilization of gene mapping information in livestock animals

A number of recent advances in genomic research will change and improve livestock production in the near future. Genetic linkage maps have been developed for a number of livestock species including cattle, sheep, and pigs. These maps allow scientists to identify chromosomal regions that influence traits of economic importance. This information will lead to improved genetic selection practices by identifying animals with superior copies of the chromosomal regions that affect the selected trait. This mapping information will also be used to identify the genes controlling the trait. A number of genomic regions or loci have already been reported that affect production, carcass or disease traits, and in a few cases, a specific gene has been identified. Production of transgenic animals with sequence changes in these genes may be beneficial for evaluating the effect of the gene upon the selected trait and more specifically the effect of certain polymorphisms (mutations) within the gene.

Physical mapping of the murine casein locus reveals the gene order as alpha-beta-gamma-epsilon-kappa

The murine casein locus has been characterized by long-range restriction mapping and the analysis of large fragment genomic clones. Cloned sequences from five mouse casein genes (alpha, beta, gamma, epsilon, kappa) were used to screen a murine (strain 129) genomic library in a bacterial artificial chromosome vector (BAC). Of the nine clones isolated, two contained three casein genes alpha, beta, gamma and gamma, epsilon, kappa, respectively. The following combinations were found in other clones: alpha + beta, beta + gamma; and gamma + epsilon. Thus, the gene order in the locus can be deduced to be alpha-beta-gamma-epsilon-kappa. This order was confirmed by restriction analysis of the clones. A contig map of the clones and flanking sequences has been established by characterizing seven BAC clones, which together span approximately 470 kb. Long-range restriction analysis of genomic DNA indicates that the murine casein locus is confined to a 250-kb partial Xho I fragment. The alpha and beta casein genes were shown to be arranged in a tail-to-tail orientation.

The PiGMaP consortium linkage map of the pig (Sus scrofa)

A linkage map of the porcine genome has been developed by segregation analysis of 239 genetic markers. Eighty-one of these markers correspond to known genes. Linkage groups have been assigned to all 18 autosomes plus the X Chromosome (Chr). As 69 of the markers on the linkage map have also been mapped physically (by others), there is significant integration of linkage and physical map data. Six informative markers failed to show linkage to these maps. As in other species, the genetic map of the heterogametic sex (male) was significantly shorter (approximately 16.5 Morgans) than the genetic map of the homogametic sex (female) (approximately 21.5 Morgans). The sex-averaged genetic map of the pig was estimated to be approximately 18 Morgans in length. Mapping information for 61 Type I loci (genes) enhances the contribution of the pig gene map to comparative gene mapping. Because the linkage map incorporates both highly polymorphic Type II loci, predominantly microsatellites, and Type I loci, it will be useful both for large experiments to map quantitative trait loci and for the subsequent isolation of trait genes following a comparative and candidate gene approach.