GWAS and Post-GWAS High-Resolution Mapping Analyses Identify Strong Novel Candidate Genes Influencing the Fatty Acid Composition of the Longissimus dorsi Muscle in Pigs.

Fatty acid (FA) composition is one of the most important parameters for the assessment of meat quality in pigs. The FA composition in pork can also affect human health. Our aim was to identify quantitative trait loci (QTLs) and positional candidate genes affecting the FA profile of the longissimus dorsi muscle in a large F2 intercross between Landrace and Korean native pigs comprising 1105 F2 progeny by genome-wide association studies (GWAS) and post-GWAS high-resolution mapping analyses. We performed GWAS using the PorcineSNP60K BeadChip and a linear mixed model. Four genome-wide significant QTL regions in SSC8, SSC12, SSC14, and SSC16 were detected (p < 2.53 × 10-7). Several co-localizations of QTLs in SSC12 for oleic acid, linoleic acid, arachidonic acid, monounsaturated FAs, polyunsaturated FAs, and the polyunsaturated/saturated FA ratio were observed. To refine the QTL region in SSC12, a linkage and linkage disequilibrium analysis was applied and could narrow down the critical region to a 0.749 Mb region. Of the genes in this region, GAS7, MYH2, and MYH3 were identified as strong novel candidate genes based on further conditional association analyses. These findings provide a novel insight into the genetic basis of FA composition in pork and could contribute to the improvement of pork quality.

Comparative study of nutritional composition and color traits of meats obtained from the horses and Korean native black pigs raised in Jeju Island.

OBJECTIVE: The present study aimed at comparing the nutritional composition and color traits between two meat types: Horse meat and pork from Korean native black pigs raised in Jeju Island. METHODS: After slaughter 24 h, the longissimus dorsi samples were taken from left side carcasses of the 32-mo-old Jeju female breed horses and the 6-mo-old Korean native black pigs (n = 10 each). The samples were then placed into cool boxes containing ice packs and transported to the Laboratory of Meat Science where all visual fats and connective tissues were trimmed off and then the samples were ground. All the samples were analyzed for nutritional composition (proximate composition, minerals, vitamins, fatty acids, and amino acids) and color traits. RESULTS: The horse meat contained significantly higher collagen, moisture and protein than the pork (p<0.05). The Jeju horse meat showed more desirable fatty acid profiles such as containing significantly lower saturated fatty acids (SFA), higher polyunsaturated fatty acids (PUFA) contents and PUFA/SFA ratios than the pork (p<0.05). Differences in concentrations of ten amino acids existed between the two meat types in which the horse meat had higher values for all these amino acids, total amino acids (20.33 g/100 g) and essential amino acids (10.06 g/100 g) than the pork (p<0.05). Also, the horse meat showed significantly higher concentrations of Fe (34.21 mg/100 g) and Cu (2.47 mg/100 g) than the pork (Fe, 17.42 mg/100 g and Cu, 1.51 mg/100 g) (p<0.05). All the vitamins detected showed statistical differences between the two meat types in which the horse meat had higher concentrations of vitamin B1 (25.19 mg/100 g), B2 (92.32 mg/100 g), B3 (2,115.51 mg/100 g), and B5 (67.13 mg/100 g) than the pork (p<0.05). CONCLUSION: Based on the results obtained in the study, it is concluded that the two meat types studied are rich in nutrients and the animal species strongly affected the nutritional values and color traits of the muscle tissues.

Genome-wide analyses of the Jeju, Thoroughbred, and Jeju crossbred horse populations using the high density SNP array.

The Jeju horse is an indigenous Korean horse breed that is currently registered with the Food and Agriculture Organization of the United Nations. However, there is severe lack of genomic studies on Jeju horse. This study was conducted to investigate genetic characteristics of horses including Jeju horse, Thoroughbred and Jeju crossbred (Jeju × Thoroughbred) populations. We compared the genomes of three horse populations using the Equine SNP70 Beadchip array. Short-range Linkage disequilibrium was the highest in Thoroughbred, whereas r2 values were lowest in Jeju horse. Expected heterozygosity was the highest in Jeju crossbred (0.351), followed by the Thoroughbred (0.337) and Jeju horse (0.311). The level of inbreeding was slightly higher in Thoroughbred (- 0.009) than in Jeju crossbred (- 0.035) and Jeju horse (- 0.038). FST value was the highest between Jeju horse and Thoroughbred (0.113), whereas Jeju crossbred and Thoroughbred showed the lowest value (0.031). The genetic relationship was further assessed by principal component analysis, suggesting that Jeju crossbred is more genetically similar to Thoroughbred than Jeju horse population. Additionally, we detected potential selection signatures, for example, in loci located on LCORL/NCAPG and PROP1 genes that are known to influence body. Genome-wide analyses of the three horse populations showed that all the breeds had somewhat a low level of inbreeding within each population. In the population structure analysis, we found that Jeju crossbred was genetically closer to Thoroughbred than Jeju horse. Furthermore, we identified several signatures of selection which might be associated with traits of interest. To our current knowledge, this study is the first genomic research, analyzing genetic relationships of Jeju horse, Thoroughbred and Jeju crossbred.

Estimation of genetic parameters for temperament in Jeju crossbred horses.

OBJECTIVE: Temperament can be defined as a type of behavioral tendency that appears in a relatively stable manner in responses to various external stimuli over time. The aim of this study was to estimate genetic parameters for the records of temperament testing that are used to improve the temperament of Jeju crossbred (Jeju×Thoroughbred) horses. METHODS: This study was conducted using 205 horses (101 females and 104 males) produced between 2010 and 2015. The experimental animals were imprinted and tamed according to the Manual for Horse Taming and Evaluation for Therapeutic Riding Horses and evaluated according to the categories for temperament testing (gentleness, patience, aggressiveness, sensitivity, and friendliness) between 15 months and 18 months of age. Each category was scored on a five-point linear scale. Genetic parameters for the test categories were analyzed using a multi-trait mixed model with repeated records. The ASReml program was used to analyze the data. RESULTS: The heritability of gentleness, patience, aggressiveness, sensitivity and friendliness ranged from 0.08 to 0.53. The standard errors of estimated heritability ranged from 0.13 to 0.17. The test categories showed high genetic correlations with each other, ranging from 0.96 to 0.99 and high repeatability, ranging from 0.70 to 0.73. CONCLUSION: The results of this study showed that the test categories had moderate heritability and high genetic correlations, but additional studies may be necessary to use the results for the improvement programs of the temperament of Jeju crossbred horses.