Novel Polymorphisms in Porcine 3′UTR of the Leptin Gene, Including a Rare Variant within Target Sequence for MIR-9 Gene in Duroc Breed, not Associated with Production Traits

A comparative investigation on H3K27ac enhancer activities in the brain and liver tissues between wild boars and domesticated pigs

Dramatic phenotypic differences between domestic pigs and wild boars (Sus scrofa) provide opportunities to investigate molecular mechanisms underlying the formation of complex traits, including morphology, physiology and behaviour. Most studies comparing domestic pigs and wild boars have focused on variations in DNA sequences and mRNA expression, but not on epigenetic changes. Here, we present a genome-wide comparative study on H3K27ac enhancer activities and the corresponding mRNA profiling in the brain and liver tissues of adult Bama Xiang pigs (BMXs) and Chinese wild boars (CWBs). We identified a total of 1,29,487 potential regulatory elements, among which 11,241 H3K27ac peaks showed differential activity between CWBs and BMXs in at least one tissue. These peaks were overrepresented by binding motifs of FOXA1, JunB, ATF3 and BATF, and overlapped with differentially expressed genes that are involved in female mating behaviour, response to growth factors and hormones, and lipid metabolism. We also identified 4118 nonredundant super-enhancers from ChIP-Seq data on H3K27ac. Notably, we identified differentially active peaks located close to or within candidate genes, including TBX19, MSTN, AHR and P2RY1, which were identified in DNA sequence-based population differentiation studies. This study generates a valuable dataset on H3K27ac profiles of the brain and liver from domestic pigs and wild boars, which helps gain insights into the changes in enhancer activities from wild boars to domestic pigs.

DNA-type results of Landrace sows for RYR1-gene and its association with productivity

Recently the assessment of QTL genes has been a relevant focus of research. Among other genes, the RYR1 is one of the most important. Research on this gene for Landrace sows of Ukrainian selection has been insufficient. This fact confirms the need for our work. A total of 63 Landrace sows from different families were evaluated by reproductive qualities for two generations. A comprehensive assessment of the sows’ reproductive ability was performed using the SIRQS-index. Determination of polymorphism in the RYR1 gene in pigs was performed by using DNA-typing of animals. Genetic potential was calculated between two generations “mother-daughter”. By assessment of polymorphism of the RYR1 gene, it was found that 6.3% of the Landrace sows were the carriers for the mutant allele of the RYR1 gene. No animals with the RYR1nn genotype were detected. Accordingly, animals with the RYR1NN genotype accounted for 93.6%. The frequency of the N allele of the RYR1 gene was 0.97, the n frequency of the RYR1 gene allele was 0.03. Sows with RYR1NN genotype had a higher level of reproductive ability compared to the RYR1Nn genotype. RYR1NN genotype also had a higher level of genetic potential. The greatest progress was established between generations of Landrace sows which were carriers for the mutant allele. The highest values of this progress were by the NBA, the lowest – by the NW. On the contrary, there was regression between populations for part of the population (Landrace sows of Ukrainian selection of RYR1Nn genotype) by the all estimated indicators of reproductive ability. Sows that were free of the mutant allele of the RYR-1 gene had high SIRQS index. The phenotypic consolidation coefficients by the NBA were lower for sows free of the mutant allele than for its carrier. The advantage of sows free of the mutant allele of the RYR-1 gene over its carrier sows was established in almost all assessed indicators of reproductive ability. No significant differences in the level of consolidation of reproductive ability between sows with different allelic variants of the RYR-1 gene were established. The higher productive level of sows with RYR1NN genotype is reflected in the indicators of economic efficiency of production. It allows higher levels of profitability to be obtained and net profit to be increased by 1093 UAH compared to sows with RYR1Nn genotype. The further monitoring of the studied gene and the gradual elimination of carriers of the mutant allele is a promising direction in breeding work.

Genome-wide SNP data unveils the globalization of domesticated pigs

BACKGROUND

Pigs were domesticated independently in Eastern and Western Eurasia early during the agricultural revolution, and have since been transported and traded across the globe. Here, we present a worldwide survey on 60K genome-wide single nucleotide polymorphism (SNP) data for 2093 pigs, including 1839 domestic pigs representing 122 local and commercial breeds, 215 wild boars, and 39 out-group suids, from Asia, Europe, America, Oceania and Africa. The aim of this study was to infer global patterns in pig domestication and diversity related to demography, migration, and selection.

RESULTS

A deep phylogeographic division reflects the dichotomy between early domestication centers. In the core Eastern and Western domestication regions, Chinese pigs show differentiation between breeds due to geographic isolation, whereas this is less pronounced in European pigs. The inferred European origin of pigs in the Americas, Africa, and Australia reflects European expansion during the sixteenth to nineteenth centuries. Human-mediated introgression, which is due, in particular, to importing Chinese pigs into the UK during the eighteenth and nineteenth centuries, played an important role in the formation of modern pig breeds. Inbreeding levels vary markedly between populations, from almost no runs of homozygosity (ROH) in a number of Asian wild boar populations, to up to 20% of the genome covered by ROH in a number of Southern European breeds. Commercial populations show moderate ROH statistics. For domesticated pigs and wild boars in Asia and Europe, we identified highly differentiated loci that include candidate genes related to muscle and body development, central nervous system, reproduction, and energy balance, which are putatively under artificial selection.

CONCLUSIONS

Key events related to domestication, dispersal, and mixing of pigs from different regions are reflected in the 60K SNP data, including the globalization that has recently become full circle since Chinese pig breeders in the past decades started selecting Western breeds to improve local Chinese pigs. Furthermore, signatures of ongoing and past selection, acting at different times and on different genetic backgrounds, enhance our insight in the mechanism of domestication and selection. The global diversity statistics presented here highlight concerns for maintaining agrodiversity, but also provide a necessary framework for directing genetic conservation.

Genetics of Adiposity in Large Animal Models for Human Obesity-Studies on Pigs and Dogs

The role of domestic mammals in the development of human biomedical sciences has been widely documented. Among these model species the pig and dog are of special importance. Both are useful for studies on the etiology of human obesity. Genome sequences of both species are known and advanced genetic tools [eg, microarray SNP for genome wide association studies (GWAS), next generation sequencing (NGS), etc.] are commonly used in such studies. In the domestic pig the accumulation of adipose tissue is an important trait, which influences meat quality and fattening efficiency. Numerous quantitative trait loci (QTLs) for pig fatness traits were identified, while gene polymorphisms associated with these traits were also described. The situation is different in dog population. Generally, excessive accumulation of adipose tissue is considered, similar to humans, as a complex disease. However, research on the genetic background of canine obesity is still in its infancy. Between-breed differences in terms of adipose tissue accumulation are well known in both animal species. In this review we show recent advances of studies on adipose tissue accumulation in pigs and dogs, and their potential importance for studies on human obesity.

The novel SNPs of leptin gene and their associations with growth traits in Chinese Nanjiang Yellow goat

The leptin (LEP) gene encodes a protein that greatly affects the regulation of body weight, energy balance, and food intake in mammals. The objective of the present work was to identify genetic variants of the caprine LEP gene in 411 individuals from five Chinese goat breeds. Six novel single nucleotide polymorphisms (SNPs) (g.117T > C, g.1642G > A, g.2883G > A, g.3053T > C, g.3190G > A, and g.3314T > C) were detected using DNA sequencing. A chi-squared (χ(2)) test showed that all of the LEP SNPs were in Hardy-Weinberg equilibrium in the studied population (P > 0.05). Six common haplotypes were identified in the five goat populations, with frequencies ranging from 0.083 to 0.244. The r(2) linkage disequilibrium plot of the LEP SNPs indicated linkage disequilibrium only in the cultured breeds (NJ and JY). Statistical analysis revealed that all of the six SNPs of the LEP gene were associated with growth traits. The individuals with the GG genotype at g.1642G>A and g.3190G > A loci showed higher birth weight (2.38 ± 0.03, 2.43 ± 0.05) and weight at 2 months of age (10.59 ± 0.16, 10.71 ± 0.26) than the A-bearing genotypes (AA or GA, P < 0.05). Our findings indicate that polymorphisms of the caprine LEP gene might be important genetic factors influencing growth traits, and these genetic markers may be useful for future marker-assisted selection programs in goat breeding and production.