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.

Embryos produced with serum show the alterations in their ultrastructure, impaired compaction, abnormal blastulation, aberrant mRNA expression profiles and large calf syndrome with greater incidences of stillbirths and deaths after birth. The aim of the present study was to describe in vitro embryo production by analyzing embryo production, fetal production and pregnancy rate in free-serum medium. The OPU-IVP data used in this study from 2016. Approximately, sixteen cows (Hanwoo), which belonged to the Institute of Gyeongsang National University, were used. Two experimental group is used in this study. Serum groups were conducted in March to July and free-serum group was conducted in September to December. The recovered cumulus-oocyte complexes were morphologically classified to four grades based on the compaction of cumulus cells layers and homogeneity of the cytoplasm. The number of oocyte was significantly greater in serum groups than that in free-serum groups (29.61 ± 0.63 vs. 15.6 ± 0.62; p < 0.05). Between serum and free-serum groups indicate that average of 1st and 2nd grade oocytes were no difference (2.38 ± 1.67 vs. 2.38 ± 1.48; p > 0.05), but number of 3rd and 4th grade oocytes were greater in serum groups than that in free-serum groups (7.31 ± 7.64 vs. 5.60 ± 6.29; p < 0.05). Embryo cleaved competence was higher in rate in free-serum groups than that in serum groups (62.1% vs. 58.3; p < 0.05). However, blastocyst developmental rate was no difference between serum and free-serum groups (33.1% vs. 43.5%; p < 0.05). 986 recipients were used for embryo transfer. Pregnancy rate was indicated that between serum and free-serum group was no difference (54.6% vs. 56.3%; p < 0.05). In conclusion, we developed the free-serum system for production of in vitro bovine embryos in order to meet the developmental and qualitative requirements for large scale commercial use.

Up-to-date artificial insemination (AI) using frozen sperm consider as the most widely using technology for improvement of Korean Native Cow (Hanwoo) embryo production. However, it is time consuming, required at least 15~20 years to make more than 6 generations, and their offspring number is limited. To overcome such limitations, superovulation and in vitro fertilization have been developed. For superovulation, the number of produced embryos are not enough for commercialization and donor cows need rest period. This led to use of slaughterhouse ovary for in vitro fertilization, but it is impossible to repeat the collection from the same individual and it only can improve the genetic merits of offspring for one generation. Production of embryos using Ovum Pick-Up (OPU) technique, where oocytes can be repeatedly collected from living elite donor, might overcome these limitations. In this study, we investigated the possibility of using OPU technique from donors at different age and different session periods for mass-embryo-production. Oocytes were collected from 26 donor cows twice per week, 3 - 4 months per year, between 2013 and 2016. Results showed that, the average number of embryo produced in first year used donor was significantly higher than that in second year used donor (3.89 ± 2.85 vs 3.29 ± 2.70), however, there was no significant difference between third year used donor (3.51 ± 3.32) and other groups. Taken together, our data showed that repeated using of donor up to three years is possible for in vitro embryo mass-production. Moreover, OPU can be used as suitable embryo producing technique for livestock breed improvement.

현재까지 한우개량을 위해 가장 보편적으로 활용되고 있는 기술은 웅성 유전자원의 동결용 정액을 활용하는 인공수정기술로서 개량에 최소 6 세대 이상 즉, 암송아지만을 생산한다는 가정에서 15~20 년 이상의 시간이 소요될 뿐만 아니라 생산되는 산자 수 또한 한정적이다. 가축개량 효율을 높이기 위해 수정란이식 기술이 개발되었으며, 호르몬 투여에 의한 과배란 유래 체내 수정란 및 체외 수정란 생산 방법이 개발되어 활용되어 왔다. 체내 수정란 생산방법은 혈통관리는 정확하나 수정란 생산을 위해 호르몬 과다 투여에 의한 휴식기간 등이 필요하며 수정란의 생산량의 한계로 산업화 적용에 비효율적이고, 근래에 체외수정란을 활용되면서 도축 유래 수정란을 활용하는 경향이 있으나 친자 검정의 한계로 인한 친자 불일치 및 고도근친 위험성 등이 상존하고 있다. 이러한 문제를 극복하고 효율적인 이식 가능한 수정란의 생산이 가능한 OPU 유래 수정란 생산기술은 살아있는 공란우에서 난자를 채취하여 체외수정란을 생산함으로써 혈통관리가 정확하고 우수유전 자원을 선발 활용함으로써 계획 교배에 의한 근친도와 개량의 폭을 예측할 수 있는 장점이 있다. 또한 수정란의 생산 가능 량은 3~4 개월에 약 60 여 개의 이식 가능한 수정란을 대량 생산으로 산업화에 적합한 수정란 생산기술이다. 본 연구에서는 선발된 공란우의 반복 사용으로 우수 유전자원의 수정란을 대량생산에 활용하기 위해서 2013-2016 년까지 매년 3-4 개월 동안 주 2 회 채란 및 수정란을 생산하였고 채란 완료 후 일정 기간의 휴식한 다음 다시 채란에 활용으로 2 회 이상 수정란 생산으로 수정란의 반복 생산 가능성 및 생산 효율에 대하여 조사하였다. 2 반복의 공란우는 총 24 두와 3 반복은 7 두를 3-4 개월 동안/년 매주 2 회 총 1,626 회 채란으로 평균 3.6±2.9 개의 수정란이 생산되었다. 특히 채란 시 생산된 수정란은 채란 횟수당 1 회 반복에서 3.9±2.8 개, 2 회 반복은 3.3±2.7 개 및 3 회 반복은 3.5±3.3 개로 확인되었고, 3 회 이상의 반복 채란된 개체 7 두를 분석한 결과 1 회 반복 채란에서 평균 3.63±2.79 개, 2 회 반복은 평균 3.70±2.84 개 및 3 회 반복은 년 3.51±3.32 개로 반복 채란에 수정란 생산에 활용하였으며 반복 채란에 의한 수정란의 생산효율에는 유의적인 차이를 보이지 않았다. 따라서 가축개량을 위해 산업화에 가장 적합한 수정란 생산방법으로 유전능력이 우수한 한우에서 대량의 수정란을 생산하여 우량한우 집단구축을 위하여 약 3-4 개월 동안 매주 2 회 수정란을 생산하고 일정기간을 휴식한 다음 공란우로써 재활용 가능성을 확인하였고 또한 OPU 유래 수정란 생산방법은 우수한 유전자원을 보유한 개체를 연속적이며 반복적으로 활용할 수 있는 가능성을 확인하였다

Sex preselection has always generated great interest among livestock producers due to an increase in the profitability of the cattle industry through the production of offspring with desired sex, such as females for dairy or males for meat production. Among the prevalent sorting methods, the embryo developmental potential is still very low as expected, and there is distinguished evidence that sex sorting has a negative effect on sperm quality with an altered pattern of sperm motility, ultimately reducing lifespan. The consequence is a very low embryo development rate using sex-sorted semen, and its negative impact influences the progress of the dairy industry. Here, we established a new approach with reduced stress by using WholeMom® and observed no significant differences (P < 0.05) in early cleaving embryos between sorted X sperm and the control group, although there was a remarkable significant difference in embryos of the Y sperm group, 81.82 ± 2.71% vs. 87.44 ± 3.02% vs. 54.21 ± 2.21%, respectively. The percentage of embryos that developed into blastocysts (Day 7) was also significantly (P < 0.05) higher in the control and X Sperm group compared to the Y sperm group, 35.53 ± 1.92% and 29.76 ± 2.38% vs. 21.90 ± 1.54%. Moreover, B-SRY F2 and B-SRY R2 gene expression data exhibited 81.03% accuracy for the female embryos and 72.54% for the male embryos produced in vitro. And also the field trials for the heifer production using WholeMom by Artificial Insemination technique demonstrated 76% female and 24% male in vivo. In conclusion, the combination of pre-selected sex semen and OPU derived elite cattle embryo production is highly recommended to apply to the mass production in the dairy industry with rapid genetic up-gradation.

This study investigated the use of bovine serum albumin (BSA) as alternatives to fetal bovine serum (FBS) in in vitro maturation medium. The oocyte maturation, cumulus cell-oocyte gap junctional communication, and development of bovine embryos were determined by assessing their cell number, lipid content, mitochondrial activity, gene expression and cryo-tolerance. Oocytes were cultured in TCM-199 supplemented with 1 μg/ml estradiol-17ß, 10 μg/ml FSH, 10 ng/ml EGF, 0.6 mM cysteine, 0.2 mM sodium pyruvate and either 8% BSA (BSA group), 10% FBS (FBS group), or neither BSA nor FBS (TCM group), and followed by in vitro fertilization and the zygotes were cultured in SOF-BE1 medium. The differences in embryo development between experimental groups were analyzed by one-way ANOVA. We have shown that the percentages of embryos that underwent cleavage and formed a blastocyst were non significantly different among all experimental groups (37.4 ± 1.5% for FBS group vs. 31.1 ± 3.9% for BSA group and 34.5 ± 1.6% for TCM group, six replicates were performed). Furthermore, there was no significant difference between the percentage of MII oocyte between FBS (71.8 ± 1.9%) and BSA groups (69.3 ± 2.3%). However, culture of oocytes with FBS increased (P < 0.05) the cumulus cell expansion as well as expression of gape junction proteins, CX37 and CX43, at both transcriptional and translation levels. We also found that FBS significantly increased total cell number and decreased the apoptotic index in day-8 blastocyst comparing to BSA group. The beneficial effects of BSA on embryos were associated with significantly reduced intracellular lipid content and increased mitochondrial activity in both oocytes and blastocyst. Taken together, these data suggest that supplementation of maturation medium with BSA, as alternatives to FBS, can be used as defined medium that support consistently the development of IVP bovine embryos.

OPU 유래 수정란 생산 및 이식은 기존의 체내 및 체외 수정란 생산과 이식의 단점을 해결하고 한우 개량을 촉진 시킬 수 있는 기술이다. 특히 살아있는 공란우를 활용하므로 모계와 부계에 대한 혈통관리가 정확하고 또한 선발된 공란우와 계획 교배를 통하여 가장 적합한 동결정액을 사용하여 개량의 효과를 극대화가 가능하고 또한 현재까지 생산효율이 가장 높은 생산기술이다. 따라서 기존의 수정란 생산방법보다 공란우의 선발강도를 더 높일 수 있어 개량의 효과를 극대화 할 수 있는 장점이 있다. 본 연구실에서는 2009 년도부터 OPU 유래 수정란을 생산하여 이식하여 수정란이식이 산업화로 전개될 수 있도록 진행하고 있다. 특히 한우에 대한 우수성 확보, 개량 및 그 다음 세대 후대의 근친적인 문제가 발생되지 않도록 수정란이식에 의해 탄생된 송아지 혈통관리를 위한 친자검정으로 수정란에 대한 신뢰성을 높여 수정란 이식이 산업화가 될 수 있도록 진행하였다. 본 연구에 대한 조사는 2013 년도 7 개의 시·군을 시작으로 ‘14 년도 11 개, ‘15 년도 15 개, ‘16년도 17 개의 시·군으로 점진적으로 확대됨에 따라 공란우의 두수도 ‘13 년도 35 두를 시작으로 ‘16 년도는 71 두로 증가되었다. 조사된 4 년동안 각 지역에서 선발된 유전능력이 우수한 공란우는 총 211 두에서 수정란을 총 18,839 개, 두당 89.3 개를 생산하였다. 두당 생산 효율도 ‘13 도에는 회당 3.0±4.5 개에서 ‘16 년도에는 4.8±2.2 로 회당 이식 가능한 수정란의 생산량이 년도에 따라 꾸준히 향상되었다. 생산된 수정란은 자연발정 또는 발정동기화를 통하여 매주 2 회 이상 이식으로 ‘13 년 49.7%, ‘14 년 51.9%, ‘15 년 52.9%와 ‘16 년 47.9%의 수태율을 확인하였다. 이는 년도가 증가되면서 수정란의 생산성의 향상과 적정 수준의 수태율의 성과는 시술자와 농가의 적극적인 참여에 의한 결과로 판단되고 또한 유전능력이 우수한 수정란의 대량생산 및 공급으로 개량의 효과가 증가되고 우수한 한우 집단 구축으로 한우산업이 지속적으로 발전 할 것으로 판단된다.