Using in silico RFLP method for the study of MC1R gene alleles in the species Sus Scrofa

In the present study we aimed to use a bioinformatics algorithm that predict RFLP fragmentation of swine MC1R alleles simulating the sequence digestion with over 700 restriction enzymes. The results show several restriction enzymes that have the potential to be used for genotyping of Sus scrofa individuals and for differentiation between hybrids and pure line wild boars (WB)/domestic pigs (DP). Genotyping studies of wild boars and domestic pigs in Moldova populations would allow the determination of introgression/backcrossing degree and would contribute to the elaboration of adequate conservation measures

Differentiating Pigs from Wild Boars Based on NR6A1 and MC1R Gene Polymorphisms

This preliminary study aimed to differentiate domestic pigs from wild boars based on MC1R and NR6A1 polymorphisms and to identify admixture between these genomes. We studied samples obtained from wild boars from two regions of Poland and five pig breeds: Polish Landrace, Polish Large White, Złotnicka White, Pulawska and Duroc. Along the MC1R gene sequence, we identified four polymorphic loci comprising three codons. The “wild type” allele was primarily found in wild boar but also in the Duroc and Złotnicka White breeds. Non-wild type alleles were identified in the vast majority of domestic pig samples and in two wild boar samples. Based on MC1R profiles, we conducted a population study, and revealed admixture between both genomes using STRUCTURE and NETWORK Software. Interestingly, an allelic discrimination assay with NR6A1 g.748C > T TaqMan probes revealed a clear separation of samples into two groups: wild boar samples representing the C allele and domestic breeds representing the T allele. Based on the obtained results, we conclude that NR6A1 g.748C > T is an effective marker for differentiating between wild boars and domestic pigs, where this is supported by MC1R data, to identify admixed profiles. We recommend that a larger sample of genomes is studied to verify this method.

Genomic Regions Associated with Variation in Pigmentation Loss in Saddle Tan Beagles

Loss of pigmentation is a hallmark of domestication, and dogs offer a unique model for understanding the genetics of fur coloration. The aim of this study was to use dense genetic mapping to map loci underlying variations in color and whiteness in a population of laboratory beagles. A total of 190 beagles with well-defined pedigrees were phenotyped for the amount of white color in six different body parts, including the saddle. All individuals were genotyped on 85,172 informative and valid SNP-markers and the genome-wide associations for the amount of white in each body part were determined. There was a large variation in the amount of white on different parts of the body, and the whiteness was highly correlated within individuals, except for saddle color which was only moderately correlated with overall whiteness. The GWAS showed significant associations with two loci, one on chromosome 5, containing the MC1R gene, and one on chromosome 20, containing the MITF gene. Our results suggest that the variation in loss of pigmentation is largely a function of regulatory variation related to these genes.

Dorsal Pigmentation and Its Association with Functional Variation in MC1R in a Lizard from Different Elevations on the Qinghai–Tibetan Plateau

Identification of the role of the MC1R gene has provided major insights into variation in skin pigmentation in several organisms, including humans, but the evolutionary genetics of this variation is less well established. Variation in this gene and its relationship with degree of melanism was analyzed in one of the world’s highest-elevation lizards, Phrynocephalus theobaldi from the Qinghai–Tibetan Plateau. Individuals from the low-elevation group were shown to have darker dorsal pigmentation than individuals from a high-elevation group. The existence of climatic variation across these elevations was quantified, with lower elevations exhibiting higher air pressure, temperatures, and humidity, but less wind and insolation. Analysis of the MC1R gene in 214 individuals revealed amino acid differences at five sites between intraspecific sister lineages from different elevations, with two sites showing distinct fixed residues at low elevations. Three of the four single-nucleotide polymorphisms that underpinned these amino acid differences were highly significant outliers, relative to the generalized MC1R population structuring, suggestive of selection. Transfection of cells with an MC1R allele from a lighter high-elevation population caused a 43% reduction in agonist-induced cyclic AMP accumulation, and hence lowered melanin synthesis, relative to transfection with an allele from a darker low-elevation population. The high-elevation allele led to less efficient integration of the MC1R protein into melanocyte membranes. Our study identifies variation in the degree of melanism that can be explained by four or fewer MC1R substitutions. We establish a functional link between these substitutions and melanin synthesis and demonstrate elevation-associated shifts in their frequencies.

Polymorphism of the Melanocortin 1 Receptor (MC1R) Gene and its Role in Determining the Coat Colour of Central European Cattle Breeds

There are many genes responsible for the appearance of different coat colours, among which the melanocortin 1 receptor gene (MC1R) plays an important role. The aim of the study was to characterize genetic variation in Central European cattle breeds based on polymorphism of the MC1R gene and factors determining their coat colour. The study was conducted on 290 individuals of the following breeds: Polish White-Backed (PW), Lithuanian White-Backed (LW), Polish Red (PR), Lithuanian Red (LR), Carpathian Brown (CB), Ukrainian Grey (UG), and Slovak Pinzgau (SP). Polymorphism at the MC1R gene locus was analysed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) using two restriction enzymes: Cfr10I and SsiI. The proportions of alleles and genotypes in the MC1R locus indicates a strong relationship between polymorphism and the coat colour of cattle: The ED allele proved to be characteristic for the breeds with a white-backed coat (PW and LW), while the dominant allele in the red breeds (PR and LR) was E+. It is noteworthy that coat colour in the SP population was determined only by the recessive e allele, which resulted in the formation of a separate clade in the phylogenetic tree.

Evaluation of Coat Color Inheritance and Production Performance for Cossbreed from Chinese Indigenous Chenghua Pig Crossbred with Berkshire

Background: Crossbreeding programs have been used extensively to improve the native pig’s overall production performance while maintaining superior meat quality. Chenghua (CH) pig is a traditional Chinese indigenous breed with superior meat quality characteristic but poor growth and carcass traits. In recent years, we implemented Berkshire × Chenghua (BC) crossbreeding scheme and have bred the new crossbreed BC pig through selection for four generations. The present objective was to determine the black coat inheritance and evaluate production performance for crossbreed BC F4 pigs in comparison with those of control purebred CH pigs. Results: Coat color of crossbreed BC pigs exhibits a “dominant black” hereditary pattern. Twelve mutation sites for MC1R gene were identified between “uniform black type” and “domino black spotting type” pigs and all piglets derived from boars or sows genotyped ED1ED1 homozygous for MC1R gene showed uniform black coat phenotype. The crossbreed BC F4 gilts displayed a relatively good reproductive performance, showing a higher litter (total no. born: 12.06 and no. born alive: 11.14) and tear size (13.14), heavier at farrowing litter (11.92 kg) and at weaning litter (65.87 kg) than purebred CH gilts, but they reached puberty later than CH gilts (178.44 vs.125.45). The crossbreed BC F4 pigs exhibited improved growth and carcass characteristics with a higher average daily live weight gain (535.28 g vs. 447.11 g), lower feed-to-gain ratio (3.06 vs. 4.03), and higher carcass lean meat rate (50.76% vs. 42.58%) than purebred CH pigs. Importantly, similar to those of purebred CH pigs, the crossbreed BC F4 pigs produced super meat-quality characteristics, showing ideal pH and meat-color values, high intramuscular fat content (3.24%) and water-holding capacity (drip loss: 1.68%), and acceptable muscle-fibre parameters. C18:1, C16:0, C18:0, and C18:2 were the main fatty acids in M. longissimus lumborum in the two breeds, and a very high polyunsaturated/saturated fatty acid ratio of ~0.39 was observed in the BC F4 pigs. Conclusion: These results indicate that crossbreed BC F4 pigs exhibit a uniform black coat pattern and acceptable total production performance, and it can be extensively used in commercial pig production to provide high-quality niche products.