Genetic characteristics of Korean Jeju Black cattle with high density single nucleotide polymorphisms

Alam, M. Zahangir,Lee, Yun-Mi,Son, Hyo-Jung,Hanna, Lauren H.,Riley, David G.,Mannen, Hideyuki,Sasazaki, Shinji,Park, Se Pill,Kim, Jong-Joo Asian Australasian Association of Animal Productio 2021 Animal Bioscience Vol.34 No.5

Objective: Conservation and genetic improvement of cattle breeds require information about genetic diversity and population structure of the cattle. In this study, we investigated the genetic diversity and population structure of the three cattle breeds in the Korean peninsula. Methods: Jeju Black, Hanwoo, Holstein cattle in Korea, together with six foreign breeds were examined. Genetic diversity within the cattle breeds was analyzed with minor allele frequency (MAF), observed and expected heterozygosity (HO and HE), inbreeding coefficient (FIS) and past effective population size. Molecular variance and population structure between the nine breeds were analyzed using a model-based clustering method. Genetic distances between breeds were evaluated with Nei's genetic distance and Weir and Cockerham's FST. Results: Our results revealed that Jeju Black cattle had lowest level of heterozygosity (HE = 0.21) among the studied taurine breeds, and an average MAF of 0.16. The level of inbreeding was -0.076 for Jeju Black, while -0.018 to -0.118 for the other breeds. Principle component analysis and neighbor-joining tree showed a clear separation of Jeju Black cattle from other local (Hanwoo and Japanese cattle) and taurine/indicine cattle breeds in evolutionary process, and a distinct pattern of admixture of Jeju Black cattle having no clustering with other studied populations. The FST value between Jeju Black cattle and Hanwoo was 0.106, which was lowest across the pair of breeds ranging from 0.161 to 0.274, indicating some degree of genetic closeness of Jeju Black cattle with Hanwoo. The past effective population size of Jeju Black cattle was very small, i.e. 38 in 13 generation ago, whereas 209 for Hanwoo. Conclusion: This study indicates genetic uniqueness of Jeju Black cattle. However, a small effective population size of Jeju Black cattle indicates the requirement for an implementation of a sustainable breeding policy to increase the population for genetic improvement and future conservation.

Comparisons of Beef Fatty Acid and Amino Acid Characteristics between Jeju Black Cattle, Hanwoo, and Wagyu Breeds

Seung-Hoon Lee,Chung-Nam Kim,Kyoung-Bo Ko,Se-Pill Park,Ho-Kyoung Kim,Jun-Mo Kim,Youn-Chul Ryu 한국축산식품학회 2019 한국축산식품학회지 Vol.39 No.3

Jeju black cattle are known as one of Korea’s traditional cattle. However, Hanwoo is more well-known to Korean meat consumers as representative beef cattle. Despite the popularity of these two breeds, comparison of the nutritional characteristics between Jeju black cattle and Hanwoo have not been studied. Here, we compared the fatty acid and amino acid characteristics between two Korean traditional cattle and Wagyu breeds. A total of 62 cattle were used in this study. The Jeju black cattle beef had significantly higher unsaturated fatty acids than Hanwoo (p<0.05). Savory fatty acids, including oleic acid were also higher than in Hanwoo cattle (p<0.05). The negative flavor fatty acids, such as palmitic acid were significantly lower than in Hanwoo (p<0.001). On the other hand, linoleic acid which imparts a negative flavor was higher than Hanwoo (p<0.05). Amino acids, including alanine and glutamine, usually representative of the umami taste were present in significantly higher proportions in Jeju black cattle (p<0.05). In addition, bitter tasting amino acids, including valine, leucine, isoleucine, and methionine were lower in Jeju black cattle beef than in Hanwoo (p<0.05, p<0.001, p<0.001, and p<0.001 each). Taken together, our results suggest that Jeju black cattle beef had higher savory flavor and umami taste which affected consumers preference for the meat.

Hanwoo cattle: origin, domestication, breeding strategies and genomic selection

Lee, Seung-Hwan,Park, Byoung-Ho,Sharma, Aditi,Dang, Chang-Gwon,Lee, Seung-Soo,Choi, Tae-Jeong,Choy, Yeon-Ho,Kim, Hyeong-Cheol,Jeon, Ki-Jun,Kim, Si-Dong,Yeon, Seong-Heum,Park, Soo-Bong,Kang, Hee-Seol Korean Society of Animal Sciences and Technology 2014 한국축산학회지 Vol.56 No.1

Hanwoo (Korean cattle) is the native, taurine type of cattle breed of Korea and its history as a draft animal dates back to 5000 Years. In earlier times Hanwoo was used extensively for farming, transportation. Over the period of time, Hanwoo has changed to be meat type cattle. Full-scale production of Hanwoo as meat-type cattle has occurred since 1960s with the rapid growth of the Korean economy. Hanwoo is one of the most economically important species in Korea as it is a significant source of nutrition to the Korean people. Hanwoo beef is the most cherished food of Korea. One of the main goals of researchers is to increase the meat quality, quantity and taste of the beef. In this review we describe the origin, domestication of Hanwoo cattle and breeding program initiated from 1980's. Moreover the advent of technological advancement had provided us a platform to perform genome wide selection on economic traits and its implementation into traditional breeding programs.

REVIEW : Open Access ; Hanwoo cattle: origin, domestication, breeding strategies and genomic selection

( Seung Hwan Lee ),( Byoung Ho Park ),( Aditi Sharma ),( Chang Gwon Dang ),( Seung Soo Lee ),( Tae Jeong Choi ),( Yeon Ho Choy ),( Hyeong Cheol Kim ),( Ki Jun Jeon ),( Si Dong Kim ),( Seong Heum Yeon 한국동물자원과학회(구 한국축산학회) 2014 한국축산학회지 Vol.56 No.2

Hanwoo (Korean cattle) is the native, taurine type of cattle breed of Korea and its history as a draft animal dates back to 5000 Years. In earlier times Hanwoo was used extensively for farming, transportation. Over the period of time, Hanwoo has changed to be meat type cattle. Full-scale production of Hanwoo as meat-type cattle has occurred since 1960s with the rapid growth of the Korean economy. Hanwoo is one of the most economically important species in Korea as it is a significant source of nutrition to the Korean people. Hanwoo beef is the most cherished food of Korea. One of the main goals of researchers is to increase the meat quality, quantity and taste of the beef. In this review we describe the origin, domestication of Hanwoo cattle and breeding program initiated from 1980’s. Moreover the advent of technological advancement had provided us a platform to perform genome wide selection on economic traits and its implementation into traditional breeding programs.

Copy number variations in Hanwoo and Yanbian cattle genomes using the massively parallel sequencing data

Choi, J.W.,Chung, W.H.,Lim, K.S.,Lim, W.J.,Choi, B.H.,Lee, S.H.,Kim, H.C.,Lee, S.S.,Cho, E.S.,Lee, K.T.,Kim, N.,Kim, J.D.,Kim, J.B.,Chai, H.H.,Cho, Y.M.,Kim, T.H.,Lim, D. Elsevier/North-Holland 2016 Gene Vol.589 No.1

Hanwoo is an indigenous Korean beef cattle breed, and it shared an ancestor with Yanbian cattle that are found in the Northeast provinces in China until the last century. During recent decades, those cattle breeds experienced different selection pressures. Here, we present genome-wide copy number variations (CNVs) by comparing Hanwoo and Yanbian cattle sequencing data. We used ~3.12 and ~3.07 billion sequence reads from Hanwoo and Yanbian cattle, respectively. A total of 901 putative CNV regions (CNVRs) were identified throughout the genome, representing 5,513,340bp. This is a smaller number than has been reported in previous studies, indicating that Hanwoo are genetically close to Yanbian cattle. Of the CNVRs, 53.2% and 46.8% were found to be gains and losses in Hanwoo. Potential functional roles of each CNVR were assessed by annotating all CNVRs and gene ontology (GO) enrichment analysis. We found that 278 CNVRs overlapped with cattle gene-sets (genic-CNVRs) that could be promising candidates to account for economically important traits in cattle. The enrichment analysis indicated that genes were significantly over-represented in GO terms, including developmental process, multicellular organismal process, reproduction, and response to stimulus. These results provide a valuable genomic resource for determining how CNVs are associated with cattle traits.

한우의 체외수정란으로 생산된 육우의 경제성

이준영(Jun Young Lee),정연길(Yun Gil Jung),김수진(Su Jin Kim),서병부(Byoung Boo Seo) 한국동물보건학회 2023 한국동물보건학회지 Vol.2 No.4

This study seeks to compare the economic feasibility and slaughter weight of beef cattle produced based on in vitro embryo. To this end, the study compared and investigated the grade rate of carcasses based on embryo transfer and artificial insemination; slaughter weight, carcass grading results, meat quality and quantity. With respect to the meat grades of carcass based on embryo transfer and artificial insemination; 50.0% (5/10) of embryo transfer-based carcasses were graded with 1++; and 50.0% (5/10), 1+, indicating that 100% (10/10) received at least 1+ grade. On the other hand, artificial insemination-based castrated cattle had no 1++ grade while 30.0% (6/20) received 1+; 60.0% (12/20), 1; and 10.0% (2/20) 2. This finding showed that embryo-based castrated cattle had higher grades than artificial insemination-based cattle as 100% of the former were graded with 1+ or higher. This study also investigated 10 embryo transfer-based castrated cattle and 20 artificial insemination-based cattle to compare their dressed weight, back fat thickness, sirloin cross section, and meat quantity indication. As a result, the embryo transfer-based castrated cattle showed slaughter weight of 488.4kg on average, heavier by 40.6kg than 447.8kg of artificial insemination-based cattle. Back fat thickness was 15.6㎝ on average in embryo transfer-based cases, 0.9㎝ thinner than 16.5㎝ of artificial insemination-based cases. Sirloin cross section of embryo transfer-based cattle was 99.6㎠ on average, 9.8㎠ wider than 89.8㎠ of artificial insemination cases. Meat quantity indication was found 2.1% higher in the embryo transfer cases (62.8%) than artificial insemination cases (64.9%). With respect to meat quantity grade, 10.0% (2/20) of the artificial insemination cases had Grade A; 50.0% (10/20), Grade B; and 40.0% (8/20), Grade C. Embryo transfer-based cattle showed no Grade A among the 10 carcasses; Grade B in 60.0% (6/10); and Grade C in 40.0% (4/10). Comparing the results of economic profitability in terms of carcass auction prices, the embryo transfer-based castrated cattle was KRW 1,119,453 higher than artificial insemination-based castrated case. Per-head economic gain of embryo transfer-based castrated cattle was KRW 2,282,602, higher than KRW 1,567,149 of artificial insemination-based cattle. Based on the findings, this study examined embryo transfer-based castrated cattle and artificial insemination-based cattle to compare their carcass grade rate, dressed weight, grading result and economic feasibility. Consequentially, this study found that in vitro embryo transfer-based castrated cattle had higher meat quality grade, slaughter weight and economic feasibility. Based on information on pedigree, attribute, and carcass data of individual with blood tie which indicate such meat productivity; high grade cattle genetic resources would be secured to contribute to quality meat production. Subsequent study will need to research industrialization based on in vitro embryo transfer.

Hematological Changes Associated with Theileria orientalis Infection in Korean Indigenous Cattle

김수희,유도현,강성우,채정병,최경성,김현철,박배근,채준석,박진호 대한기생충학ㆍ열대의학회 2017 The Korean Journal of Parasitology Vol.55 No.5

Tick-borne pathogens can cause serious problems in grazing cattle. However, little information is available on tick-mediated diseases in cattle grazing on mountains. Thus, this study aimed to understand the potential problems related to tick-borne diseases in grazing cattle through the investigation of prevalent tick-transmitted infections, and their associated hematological changes, in terms of season and grazing type in Korean indigenous cattle (=Hanwoo). Hanwoo cattle from 3 regions of the Republic of Korea (=Korea) were either maintained indoors or placed on grassy mountains from spring to fall of 2014 and 2015. Cattle that grazed in mountainous areas showed a greater prevalence of tick-borne infections with an increased Theileria orientalis infection rate (54.7%) compared to that in non-grazing cattle (16.3%) (P<0.001). Accordingly, the red blood cell (RBC) count and hematocrit (HCT) values of grazing cattle were significantly lower than those of non-grazing cattle throughout the season (P<0.05). Moreover, RBC, hemoglobin (Hb), and HCT of T. orientalis-positive group were significantly lower than those of T. orientalis-negative group (P<0.05). T. orientalis is a widespread tick-borne pathogen in Korea. Grazing of cattle in mountainous areas is closely associated with an increase in T. orientalis infection (RR=3.4, P<0.001), and with consequent decreases in RBC count and HCT. Thus, these findings suggest that the Hanwoo cattle in mountainous areas of Korea are at a high risk of infection by T. orientalis, which can lead to hematological alterations. This study highlights the necessity of preventive strategies that target T. orientalis infection.

Whole-Genome Resequencing Analysis of Hanwoo and Yanbian Cattle to Identify Genome-Wide SNPs and Signatures of Selection

Choi, Jung-Woo,Choi, Bong-Hwan,Lee, Seung-Hwan,Lee, Seung-Soo,Kim, Hyeong-Cheol,Yu, Dayeong,Chung, Won-Hyong,Lee, Kyung-Tai,Chai, Han-Ha,Cho, Yong-Min,Lim, Dajeong Korean Society for Molecular and Cellular Biology 2015 Molecules and cells Vol.38 No.5

Over the last 30 years, Hanwoo has been selectively bred to improve economically important traits. Hanwoo is currently the representative Korean native beef cattle breed, and it is believed that it shared an ancestor with a Chinese breed, Yanbian cattle, until the last century. However, these two breeds have experienced different selection pressures during recent decades. Here, we whole-genome sequenced 10 animals each of Hanwoo and Yanbian cattle (20 total) using the Illumina HiSeq 2000 sequencer. A total of approximately 3.12 and 3.07 billion sequence reads were mapped to the bovine reference sequence assembly (UMD 3.1) at an average of approximately 10.71- and 10.53-fold coverage for Hanwoo and Yanbian cattle, respectively. A total of 17,936,399 single nucleotide polymorphisms (SNPs) were yielded, of which 22.3% were found to be novel. By annotating the SNPs, we further retrieved numerous nonsynonymous SNPs that may be associated with traits of interest in cattle. Furthermore, we performed whole-genome screening to detect signatures of selection throughout the genome. We located several promising selective sweeps that are potentially responsible for economically important traits in cattle; the PPP1R12A gene is an example of a gene that potentially affects intramuscular fat content. These discoveries provide valuable genomic information regarding potential genomic markers that could predict traits of interest for breeding programs of these cattle breeds.

Whole-Genome Resequencing Analysis of Hanwoo and Yanbian Cattle to Identify Genome-Wide SNPs and Signatures of Selection

최정우,이승환,최봉환,이승수,김형철,유대영,정원형,최한하,이경태,임다정,조영민 한국분자세포생물학회 2015 Molecules and cells Vol.38 No.5

Over the last 30 years, Hanwoo has been selectively bred to improve economically important traits. Hanwoo is currently the representative Korean native beef cattle breed, and it is believed that it shared an ancestor with a Chinese breed, Yanbian cattle, until the last century. However, these two breeds have experienced different selection pressures during recent decades. Here, we whole-genome sequenced 10 animals each of Hanwoo and Yanbian cattle (20 total) using the Illumina HiSeq 2000 sequencer. A total of approximately 3.12 and 3.07 billion sequence reads were mapped to the bovine reference sequence assembly (UMD 3.1) at an average of approximately 10.71- and 10.53- fold coverage for Hanwoo and Yanbian cattle, respectively. A total of 17,936,399 single nucleotide polymorphisms (SNPs) were yielded, of which 22.3% were found to be novel. By annotating the SNPs, we further retrieved numerous nonsynonymous SNPs that may be associated with traits of interest in cattle. Furthermore, we performed whole-genome screening to detect signatures of selection throughout the genome. We located several promising selective sweeps that are potentially responsible for economically important traits in cattle; the PPP1R12A gene is an example of a gene that potentially affects intramuscular fat content. These discoveries provide valuable genomic information regarding potential genomic markers that could predict traits of interest for breeding programs of these cattle breeds.

한우와 칡소의 선발신호 분석을 통한 한우의 인위적 선발 영역 탐색

임다정,이승환,최봉환,채한화,손주환,유다영,김태헌,강희설,조용민 경상대학교 농업생명과학연구원 2013 농업생명과학연구 Vol.47 No.6

Korean cattle (Hanwoo) are categorized into three types of breeds according to their color, brown, brindle and black. Among the three breeds, the brown Hanwoo has been subjected to intensive artificial selection over the past seventy years to improve meat production traits such as carcass weight and marbling. In this study, three methods (Rsb, iHS and FST) were applied to identify genomic regions of artificial selection for traits in Hanwoo. To identify traces driven by the artificial selection process called the Hanwoo breeding program, we scanned the genome of set of brown and brindle Hanwoo using 50K SNP Chip. As a result, we identified 41, 23 and 50 highly homozygous regions that seem to be very strong and/or recent artificial selections in brown Hanwoo compared to the brindle Hanwoo from Rsb, iHS and FST, respectively. To go further in the interpretation of the observed signatures of selection, we subsequently performed functional enrichment analysis using candidate genes. As a result, candidate genes have enriched GO terms such as muscle development or immune response. Artificial selection might have targeted most of these genes was mainly oriented towards improvement of meat production in brown Hanwoo. 우리나라 고유 품종인 한우는 표현형 중 외모에 따라 일반적으로 한우라 불리는 황갈색 한우, 칡소, 흑우로 구분되어 있다. 한우 집단 중, 황갈색 한우만이 육질, 육량 형질을 중심으로 체계적인 개량프로그램에 의해 개량되었다. 본 연구에서는 황갈색 한우와 칡소의 50K 고밀도 칩을 활용하여 선발신호를 검출할 수 있는 세 가지 분석법(Rsb, iHS, FST)에 따라 인위적 선발에 의해 진화적으로 선택된 유전체 영역을 탐색하였다. 그 결과, Rsb, iHS, FST 분석법에 따라 각각 41개, 23개, 50개의 후보유전체 영역이 칡소와 비교하였을 때 황갈색 한우에서 유의적으로 다름을 알 수 있었다. 또한, 후보 유전체 영역 내에 존재하는 유전자군을 대상으로 유전자 기능에 대한 주석 달기를 진행하였을 때, 근육 발달, 면역 반응 등의 기능들이 통계적으로 유의함을 알 수 있었다. 이러한 유전체 영역들이 진화적 관점에서 황갈색 한우의 적응과정에 있어서 육질 등 생산성을 높이는 데에 기여하였다고 사료된다.