Background: As the number of households raising companion dogs increases, the pet genetic analysis market also continues to grow. However, most studies have focused on specific purposes or native breeds. This study aimed to collect genomic data through single nucleotide polymorphism (SNP) chip analysis of companion dogs in South Korea and perform genetic diversity analysis and SNP annotation. Methods: We collected samples from 95 dogs belonging to 26 breeds, including mixed breeds, in South Korea. The SNP genotypes were obtained for each sample using an Axiom™ Canine HD Array. Quality control (QC) was performed to enhance the accuracy of the analysis. A genetic diversity analysis was performed for each SNP. Results: QC initially selected SNPs, and after excluding non-diverse ones, 621,672 SNPs were identified. Genetic diversity analysis revealed minor allele frequencies, polymorphism information content, expected heterozygosity, and observed heterozygosity values of 0.220, 0.244, 0.301, and 0.261, respectively. The SNP annotation indicated that most variations had an uncertain or minimal impact on gene function. However, approximately 16,000 non-synonymous SNPs (nsSNPs) have been found to significantly alter gene function or affect exons by changing translated amino acids. Conclusions: This study obtained data on SNP genetic diversity and functional SNPs in companion dogs raised in South Korea. The results suggest that establishing an SNP set for individual identification could enable a gene-based registration system. Furthermore, identifying and researching nsSNPs related to behavior and diseases could improve dog care and prevent abandonment.

Background: The Hanwoo industry must develop technologies that can increase the production of preferred cuts to match changing consumer trends. In this study, we aimed to estimate the genetic parameters for carcass traits (carcass weight, eye muscle area, back fat thickness, and intramuscular fat) and primal cut traits (tenderloin, loin, strip loin, neck, clod, top round, bottom round, brisket, shank, and rib) in a Hanwoo population to obtain basic data for improving primal cut productivity. Methods: Data from 1,905 Hanwoo steers, including carcass traits and primal cut weights, were collected. Genetic parameters were estimated using REMLF90 in a multi-trait analysis. Results: High heritability was found for carcass weight (0.52) and strip loin yield (0.63). Genetic correlations between carcass weight and primal cut weights ranged from 0.52 to 0.93. Conclusions: This study demonstrates the significant potential for genetic improvement in Hanwoo cattle through selective breeding, particularly for traits with high heritability and genetic correlations. These findings provide crucial insights into optimizing breeding programs to improve Hanwoo cattle production efficiency.

Background: Recently, the single-step genomic best linear unbiased prediction (ssGBLUP) method, which incorporates not only genomic information but also phenotypic information of pedigree, is under study. In this study, we performed a ssGBLUP analysis on a commercial Hanwoo population using phenotypic, genotypic, and pedigree data. Methods: The test population comprised Hanwoo 1,740 heads raised in four regions of Korea, while the reference population used Hanwoo 18,499 heads raised across the country and two-generation pedigree data. Analysis was performed using genotype data generated by the Hanwoo 50 K SNP beadchip. Results: The mean Genome estimated breeding values (GEBVs) estimated using the ssGBLUP methods for carcass weight (CWT), eye muscle area (EMA), back fat thickness (BFT), and marbling score (MS) were 7.348, 1.515, -0.355, and 0.040, respectively, while the accuracy of each trait was 0.749, 0.733, 0.769, and 0.768, respectively. When the correlation analysis between the GEBVs as a result of this study and the actual slaughter performance was confirmed, CWT, EMA, BFT, and MS were reported to be 0.519, 0.435, 0.444, and 0.543, respectively. Conclusions: Our results suggest that the ssGBLUP method enables a more accurate evaluation because it conducts a genetic evaluation of an individual using not only genotype information but also phenotypic information of the pedigree. Individual evaluation using the ssGBLUP method is considered effective for enhancing the genetic ability of farms and enabling accurate and rapid improvements. It is considered that if more pedigree information of reference population is collected for analysis, genetic ability can be evaluated more accurately.

Background: Copy number variation (CNV) can be identified using next-generation sequencing and microarray technologies, the research on the analysis of its association with meat traits in livestock breeding has significantly increased in recent years. Hanwoo is an inherent species raised in the Republic of Korea. It is now considered one of the most economically important species and a major food source mainly used for meat (Hanwoo beef). Methods: In this study, CNVs and the relationship between the obtained CNV regions (CNVRs) can be identified in the Hanwoo steer samples (n = 473) using Illumina Hanwoo SNP 50K bead chip and bioinformatic tools, which were used to locate the required data and meat traits were investigated. The PennCNV software was used for the identification of CNVs, followed by the use of the CNV Ruler software for locating the different CNVRs. Furthermore, bioinformatics analysis was performed. Results: We found a total of 2,575 autosomal CNVs (933 losses, 1,642 gains) and 416 CNVRs (289 gains, 111 losses, and 16 mixed), which were established with ranged in size from 2,183 bp to 983,333 bp and 10,004 bp to 381,836 bp, respectively. Upon analyzing the restriction of minor alleles frequency > 0.05 for meat traits association, 6 CNVRs in the carcass weight, 2 CNVRs in the marbling score, 3 CNVRs in the backfat thickness, and 2 CNVRs in the longissimus muscle area were related to the meat traits. In addition, we identified an overlap of 347 CNVRs. Moreover, 3 CNVRs were determined to have a gene that affects meat quality. Conclusions: Our results confirmed the relationship between Hanwoo CNVR and meat traits, and the possibility of overlapping candidate genes, annotations, and quantitative trait loci that results depended on to contribute to the greater understanding of CNVs in Hanwoo and its role in genetic variation among cattle livestock.

This study has evaluated the genomic estimated breeding value (GEBV) of the commercial Hanwoo population using the genomic best linear unbiased prediction (GBLUP) method and genomic information. Furthermore, it analyzed the accuracy and realized accuracy of the GEBV. 1,740 heads of the Hanwoo population which were analyzed using a single nucleotide polymorphism (SNP) Chip has selected as the test population. For carcass weight (CWT), eye muscle area (EMA), back fat thickness (BFT), and marbling score (MS), the mean GEBVs estimated using the GBLUP method were 3.819, 0.740, -0.248, and 0.041, respectively and the accuracy of each trait was 0.743, 0.728, 0.737, and 0.765, respectively. The accuracy of the breeding value was affected by heritability. The accuracy was estimated to be low in EMA with low heritability and high in MS with high heritability. Realized accuracy values of 0.522, 0.404, 0.444, and 0.539 for CWT, EMA, BFT, and MS, respectively, showing the same pattern as the accuracy value. The results of this study suggest that the breeding value of each individual can be estimated with higher accuracy by estimating the GEBV using the genomic information of 18,499 reference populations. If this method is used and applied to individual selection in a commercial Hanwoo population, more precise and economical individual selection is possible. In addition, continuous verification of the GBLUP model and establishment of a reference population suitable for commercial Hanwoo populations in Korea will enable a more accurate evaluation of individuals.

A number of Korean Chicken breeds were registered in Domestic Animal Diversity Information System (DAD-IS, http://dad.fao.org/) of the Food and Agriculture Organization (FAO). Evaluation of genetic diversity and relationship of local breeds is an important factor towards the identification of unique and valuable genetic resources. Therefore, this study aimed to analysis the genetic diversity and relationship of 22 Korean Chicken breeds using 12 microsatellite (MS) markers. The mean number of alleles for each variety was 5.52, ranging from a 3.75 (Leghorn F; NF) to a 7.0 (Ross). The most diverse breed was the Hanhyup3 (HCC), which had the highest expected heterozygosity (HExp) (0.754) and polymorphic information content (PIC) (0.711). The NF was the least diverse population, having the lowest HExp (0.467) and PIC (0.413). As a result of the principal coordinates analysis (PCoA) and factorial correspondence analysis (FCA) confirmed that Hy-line Brown (HL) and Lohmann Brown (LO) are very close to each other and that Leghorn and Rhode Island Red (RIR) are clearly distinguished from other groups. Thus, the reliability and power of identification using 12 types of MS markers were improved, and the genetic diversity and probability of individual discrimination were confirmed through statistical analysis. This study is expected to be used as basic data for the identification of Korean chicken breeds, and our results indicated that these multiplex PCR marker sets will have considerable applications in population genetic structure analysis.

Halla horse is crossbreed between Jeju and Thoroughbred horses and is used for riding, racing and meat production. Thus, molecular genetic studies are needed to establish and preserve the industrially valuable Halla horses. This study aimed to analyses the genetic diversity and population structure through 12 microsatellite (MS) markers for Halla and putatively related 3 breeds (Jeju, Mongolian and Thoroughbred horses). On average, the number of alleles, observed heterozygosity (Hobs), expected heterozygosity (Hexp), and polymorphic information content (PIC) among all horses were 10, 0.767, 0.799, and 0.771, respectively. Neighbor-joining tree and STRUCTURE analysis showed that Halla horses were between Thoroughbred and Jeju horses, tend to more influenced by Thoroughbred horses. Therefore, these results could be considered for use as the basic genetic breed relationships resource among the horse breeds (Jeju, Mongolian, and Thoroughbred horses) related to the origins of the Halla horse.

Meat and carcass quality attributes are important factors influencing consumer preference and profitability in the pork industry. Single nucleotide polymorphisms (SNPs) are essential for livestock breeding and improvement. In the present study, the pig Perilipin 2 (PLIN2 ) gene was characterized with the aim of detecting genetic variation at these loci in relation to economic traits in Berkshire pigs. Four SNPs (G6714C, G6813A, G10340A, and G10632A) were detected in this studied. Statistical analysis indicated that G6714C was significantly associated with the National Pork Producers Council (NPPC) color score, G6813A, and G10340A significantly affected NPPC color score and NPPC marbling score, and G10632A significantly affected backfat thickness (BF) (p < 0.05). Therefore, the molecular markers used in the present study might provide a useful basis for identification and improvement of traits in the Berkshire pigs.

Food and agricultural production sector, especially livestock production is vital for Mongolia’s economic and social development. Domestic sheep play key roles for Mongolians, providing food (meat, milk) and raw materials (wool, sheepskin), but genetic diversity, origin of sheep populations in Mongolia have not been well studied. Studies of population genetic diversity is important research field in conservation and restoration of animal breeds and genetic resources. Therefore, this study aimed to investigate genetic characteristics and estimate origin through the analysis of mitochondrial DNA control region D-loop and Cytochrome b of Mongolian indigenous sheep (Mongolian native, Orkhon and Altanbulag) and one Europe sheep (Suffolk). As a result of there were found, 220 SNPs (Single nucleotide polymorphism) in the D-loop region, 28 SNPs in the Cytochrome B region, furthermore, 77 Haplotypes. The nucleotide diversity was only found in D-loop region (n = 0.0184). Phylogenetic analysis showed that 3 (A, B, and C) of 5 haplogroups of sheep have been identified in our research. Haplogroup C was only found in Mongolian indigenous sheep. Haplogroup D and E were not observed. As a result of haplogroups, haplogroup A was dominant (n = 46 of 94 sheeps), followed by haplogroup B (n = 36) and haplogroup C (n = 12). Sequence analysis showed that T deletion, insertion and heteroplasmy in D-loop region occurred at a high rate in Mongolian indigenous sheep population (T insertion = 47, T deletion = 83). The heteroplasmy, which has never been found in Mongolian sheep, has been newly discovered in this study. As a result, the Mongolian sheep varieties, which mainly derived from Asia, were in hybridization with European sheep varieties.

The aim of this study was to assess the levels of genetic diversity and relationships of Korean native black goat (n = 58), compared with the exotic breed, Boer (n = 97). For the analysis of genetic characterization 11 microsatellite markers (MAF065, INRA063, CSRD247, OarFCB20, SRCRSP5, INRA006, ILSTS008, ILSTS011, INRA005, ILSTS087, SRCRSP8) were genotyped. The number of alleles was observed 3 (INRA005) to 10 (SRCRSP8) each markers. The mean expected and observed heterozygosity (Hexp and Hobs) and polymorphism information content (PIC) for the Korean native black goat breed varied from 0.551 to 0.860, 0.517 to 0.948 and 0.464 to 0.835, respectively. Principal Components Analysis (PCoA) and FCA results showed that Korean native black goat breed was confirmed to be clearly separated from bore breed. These results were scientific evidence that Korean native black goat represents a unique and valuable animal genetic resource.

The KLF(Kruppel-like factors) are transcriptional regulators that including the C2H2 zinc-finger motif and regulation of cell growth, cell differentiation, and development. In this study, mRNA and total DNA was extracted from the meat around the backbone of 130 cattle that has economic traits score. The KLF11 gene was act on the center of the main pathway in associated with the development and growth of cells and the fat metabolism. Genetic polymorphism was detected by DNA sequencing. A total of four SNPs(G9047A, C9104G, G9131A, C9170T) were identified in exon 4 regions, statistical association analysis revealed that the G9131A polymorphism were significantly associated with marbling score. The real time quantitative PCR to investigated gene and miRNA expression patterns and identify the relation of economic trait in Korean Native Beef Cattle. Gene expression level linked to KLF11 genes was investigated by determining its association and variation with the economic traits in Korean Native Beef Cattle. The increment of KLF11 gene expresstion level is resulted in increasing marbling score(MS). We found that expression profile of KLF gene and mir-494 was contrast tendency because the lower expression ratio of gene was the higher marbling score rating was when we analyzed expression profile ofKLF gene and mir-494. Therefore, this result has useful in improvement of livestock in Korean cattle.

소의 14번 염색체에 위치한 2,4-Dienoyl CoA reductase1(DECR1) 유전자는 polyunsaturated fatty enoyl-CoA의 β-oxidation과 연관된 호르몬으로 지질대사조절에 영향을 미치는 유전자로 알려져 있다. 따라서 본 연구는 한우의 경제형질 관련 DNA 마커 개발을 목적으로 DECR1 유전자 내의 single nucleotide polymorphisms(SNPs)를 탐색하고, 경제형질간의 연관성을 분석하고자 수행하였다. 먼저 부모가 서로 다른 한우 종모우에서 DECR1 유전자 내의 SNP를 탐색한 결과 총 13개의 SNPs를 확인하였고, 이 중 G20788A는 valine(Val)에서 methionine(Met)으로, A23262G는 isoleucine(Ile)에서 valine(Val)으로 바뀌는 missense mutation으로 확인되었다. 그리고 도체 성적을 보유한 200두의 한우를 대상으로 missense mutation으로 확인된 G20788A와 A23262G의 유전자형과 경제형질간의 연관성을 분석하였다. 그 결과 G20788A는 근내지방도와 도체중에서 A23262G는 등지방두께, 배최장근단면적, 근내지방도와 도체중에서 통계적 유의성을 확인 할 수 있었고(P<0.05), 이를 통해 missence mutation인 G20788A와 A23262G는 각 경제형질에 영향을 미치는 것을 알 수 있었다. 따라서 본 연구에서 탐색된 한우 DECR1 유전자의 SNP 유전자형은 한우 선발 및 개량을 위한 DNA 마커로 활용 가능할 것으로 기대된다.

Recently, with the increase of meat production, high quality and safety of meat have been strongly emphasized by Korean consumers. Marbling in beef has been regarded as an important criterion deciding meat quality in Korea. The purpose of this study was to identify the transcriptional level of insulin-like growth factor-1 (IGF-1) in longissimus muscle samples of 46 Hanwoo. The level of IGF-1 transcripts was measured by real-time polymerase chain reaction (PCR) and molecular connection of IGF-1 was analyzed using the Pathway Studio program (Ver 9.0). Increase of marbling score (MS) induced increase of IGF-1 transcripts level in the muscle and there is a significant correlation (p<0.05) between IGF-1 mRNA expression and MS. The pathway study showed that IGF-1 genes are regulated in insulin, fatty acid synthase, leptin, and corticotrophin releasing hormone. These results suggest that IGF-1 might be used as a useful marker for the improvement of economic traits in Hanwoo.

닭의 7번 염색체에 위치하고 있는 NRAMP-1(Natural Resistance Associated Macrophage Protein1) 유전자는 면역 반응에서 작용하는 유전자로서 대식세포의 초기 활성화 과정에 영향을 주는 것으로 알려져 있으며, 유전자의 변이에 따라 살모넬라균에 감염되었을 시에 비장의 변화에 영향을 주는 것으로 보고되어져 있다. 본 연구는 3개의 품종(로드아일랜드 레드, 코니쉬, 재래닭)을 대상으로 유전자 변이 지역 중 하나인 C3229T 지역의 유전자형을 확인하고, 경제형질간의 연관성을 분석하기 위하여 실시하였다. 분석결과 C3229T 지역은 변이에 의해 Serine에서 phenyl-alanine으로 변하는 missence mutation으로 확인 되었으며, 로드아일랜드 레드에서 변이지역과 경제형질간의 연관성 분석 결과 150일령 체중에서 유의적인 연관성이 확인 되었다. 본 연구를 통하여 확인된 C3229T 지역의 SNP를 활용하여 추후 닭의 선발 및 육종을 위한 기초자료로 활용 가능할 것으로 사료된다.