• Fisheries and Aquatic Sciences
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• 제15권2호
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• pp.151-155
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• 2012

We used nine microsatellite DNA markers to estimate genetic variation among wild and cultured populations of the sea squirt Halocynthia roretzi. The loci were polymorphic, with 6-32 alleles, and allelic richness ranged from 6.0 to 26.1 in each population. The wild and the cultured populations had similar mean heterozygosities ($H_O$ and $H_E$), allele numbers, and allelic richness. One cultured population with softness syndrome had a lower mean in the observed heterozygosity ($H_O$ = 0.57) and higher mean inbreeding coefficient ($F_{IS}$ = 0.261) than any other populations. This suggests that the loss of genetic variation in the diseased population might be due to increased inbreeding. A neighbor-joining tree and pairwise population estimates of $F_{ST}$ showed moderate genetic differentiation between the wild and the cultured populations. Additionally, the softness syndrome population was genetically divergent from wild populations, but it was genetically close to the cultured populations.

• Asian-Australasian Journal of Animal Sciences
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• 제8권4호
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• pp.357-364
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• 1995

A biochemical genetic study on blood enzyme/protein systems in some breeds/crosses of sheep in Malaysia was carried out using horizontal starch gel electrophoresis. Blood samples were collected from 435 sheep, representing 8 breeds/crosses. These included 5 wool sheep breeds (Thai Longtail, wiltshire, Suffolk, Dorsimal and cMBLx), 1 hair sheep breed (Barbados Blackbelly) and 2 hybrids between wool sheep and hair sheep (Cameroon ${\times}$ Thai Longtail and Bali Bali ${\times}$ Malin). Twenty loci systems were examined. Of these, ten ($HB{\beta}$, ALB, TF, XP, CAT, DIA1, EsA, GPI, ME and NP) exhibited genetic variation whereas the other ten (AAT, CA, DIA2, ${\alpha}GLO$, ${\alpha}GLU$, LDH, MDH, PEP[leu-gly-gly], 6PGD and SOD) were monomorphic. The allelic frequencies which were obtained in 10 polymorphic markers are assessed and compared with the results obtained by previous workers. The estimations of inbreeding coefficient, intrabreed variation and breed relationships have been critically discussed and are used to reveal some important recommendations.

• Proceedings of the National Institute of Ecology of the Republic of Korea
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• 제2권2호
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• pp.120-128
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• 2021

The objective of this study was to analyze the genotype of black-spotted pond frog (Pelophylax nigromaculatus) using seven microsatellite loci to quantify its genetic diversity and population structure throughout the spatial scale of basins of Han, Geum, Yeongsan, and Nakdong Rivers in South Korea. Genetic diversities in these four areas were compared using diversity index and inbreeding coefficient obtained from the number and frequency of alleles as well as heterozygosity. Additionally, the population structure was confirmed with population differentiation, Nei's genetic distance, multivariate analysis, and Bayesian clustering analysis. Interestingly, a negative genetic diversity pattern was observed in the Han River basin, indicating possible recent habitat disturbances or population declines. In contrast, a positive genetic diversity pattern was found for the population in the Nakdong River basin that had remained the most stable. Results of population structure suggested that populations of black-spotted pond frogs distributed in these four river basins were genetically independent. In particular, the population of the Nakdong River basin had the greatest genetic distance, indicating that it might have originated from an independent population. These results support the use of genetics in addition to designations strictly based on geographic stream areas to define the spatial scale of populations for management and conservation practices.

• 한국자원식물학회지
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• 제19권1호
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• pp.76-82
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• 2006

우리나라 고산 지역에 제한적으로 자생하는 희귀 유전자원인 눈향나무(Juniperus chinensis var. sargentii HENRY)의 설악산 및 한라산 집단을 대상으로 동위효소 분석에 의한 유전적 다양성을 조사하였다. 총 7개 동위효소에서 11개의 재현성 있는 유전자좌가 분석되었으며, 이중 Mdh-1, Mdh-2, Mdh-3 및 Pig-1 유전자좌를 제외한 7개 유전자좌에서 다형성이 관찰되었다. 분석된 두 집단의 유전변이량은 각각 A=2.2, $A_e=1.61,\;P_{95}=54.5,\;H_{o}=0.179,\;H_e=0.287$(설악산 집단)과 A=2.1, $A_e=1.48,\;P_{95}=63.6,\;H_{o}=0.270,\;H_e=0.250$(한라산 집단)으로 국내 타 침엽수종으로부터 동위효소 분석을 통해 추정된 유전변이량에 비해 다소 높은 경향을 보였으며, 분석 집단간 유전적 분화 정도는 그리 높지 않은 것으로 나타났다($F_{ST}=0.039$). 설악산 집단의 경우 이형접합도의 관찰치가 기대치에 비해 매우 낮았으며 근교계수 값이 매우 높게 나타나(F=0.376), 전반적으로 근친교배 또는 유전적 부동의 영향을 많이 받고 있는 것으로 추정되었다. 이는 설악산 눈향나무 집단의 분포 면적이나 개체수가 한라산 집단에 비해 매우 적기 때문인 것으로 추정되며, 향후 설악산 집단의 보존을 위한 보다 적극적인 노력이 필요한 것으로 사료된다.

• Animal Bioscience
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• 제34권7호
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• pp.1116-1122
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• 2021

Objective: The aim was to characterize the genetic diversity evolution of the registered Mexican Charolais cattle population by pedigree analysis. Methods: Data consisted of 331,390 pedigree records of animals born from 1934 to 2018. Average complete generation equivalent, generation interval, effective population size (N_e), and effective numbers of founders (f_e), ancestors (f_a), and founder genomes (N_g) were calculated for seven five-year periods. The inbreeding coefficient was calculated per year of birth, from 1984 to 2018, whereas the gene contribution of the most influential ancestors was calculated for the latter period. Results: Average complete generation equivalent consistently increased across periods, from 4.76, for the first period (1984 through 1988), to 7.86, for the last period (2014 through 2018). The inbreeding coefficient showed a relative steadiness across the last seventeen years, oscillating from 0.0110 to 0.0145. During the last period, the average generation interval for the father-offspring pathways was nearly 1 yr. longer than that of the mother-offspring pathways. The effective population size increased steadily since 1984 (105.0) and until 2013 (237.1), but showed a minor decline from 2013 to 2018 (233.2). The population displayed an increase in the f_a since 1984 and until 2008; however, showed a small decrease during the last decade. The effective number of founder genomes increased from 1984 to 2003, but revealed loss of genetic variability during the last fifteen years (from 136.4 to 127.7). The f_a:f_e ratio suggests that the genetic diversity loss was partially caused by formation of genetic bottlenecks in the pedigree; in addition, the N_g:f_a ratio indicates loss of founder alleles due to genetic drift. The most influential ancestor explained 1.8% of the total genetic variability in the progeny born from 2014 to 2018. Conclusion: Inbreeding, N_e, f_a, and N_g are rather beyond critical levels; therefore, the current genetic status of the population is not at risk.

• Animal Bioscience
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• 제34권5호
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• pp.789-800
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• 2021

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.

• 한국조류학회지
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• 제25권2호
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• pp.77-81
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• 2018

세계적으로 멸종위기종인 따오기 (Nipponia Nippon)는 한국에서도 멸종위기종으로 구분되어 있으며, 이를 복원하기 위해 2008년 10월에 중국에서 따오기 1쌍을 도입하여 한국 최초로 인공번식에 성공하였다. 이 후 우포늪 따오기 종 복원을 통해 2017년까지 개체수가 200마리 이상으로 늘어났다. 본 연구에서는 우포늪 따오기 228 개체를 대상으로 성별을 결정하고, microsatellite 마커를 이용하여 유전적 유연관계를 분석하였다. 그 결과, 115마리의 암컷과 113마리의 수컷으로 판별되었으며, 2016년보다 2017년에 서식하고 있는 개체의 이형접합도와 다형성 정보지수가 모두 감소한 것으로 나타났다. 이는 작은 집단으로부터 개체 수를 늘려나가다 보니 2017년에 근친율이 증가한 것으로 사료된다. 향 후 본 연구는 한국 따오기의 번식사업 및 복원사업을 위한 기초자료로 유용하게 활용될 것으로 기대된다.

• Asian-Australasian Journal of Animal Sciences
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• 제31권12호
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• pp.1871-1880
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• 2018

Objective: Recently, there has been an increasing interest in conservation of native genetic resources of chicken on a worldwide basis. Most of the native chicken breeds are threatened by extinction or crossing with ecotypes. Methods: Six Saudi native chicken breeds including black naked neck, brown frizzled, black, black barred, brown and gray were used in the current study. The aim of the current study was to evaluate genetic diversity, relationship and population structure of Saudi native chicken breeds based on 20 microsatellite markers. Results: A total of 172 alleles were detected in Saudi native chicken breeds across all 20 microsatellite loci. The mean number of alleles per breed ranged from 4.35 in gray breed to 5.45 in normally feathered black with an average of 8.6 alleles. All breeds were characterized by a high degree of genetic diversity, with the lowest heterozygosity found in the brown breed (72%) and the greatest in the frizzled and black barred populations (78%). Higher estimate of expected heterozygosity (0.68) was found in both black breeds (normal and naked neck) compared to the other chicken populations. All studied breeds showed no inbreeding within breed (negative inbreeding coefficient [$F_{IS}$]). The phylogenetic relationships of chickens were examined using neighbor-joining trees constructed at the level of breeds and individual samples. The neighbor-joining tree constructed at breed level revealed three main clusters, with naked neck and gray breeds in one cluster, and brown and frizzled in the second cluster leaving black barred in a separate one. Conclusion: It could be concluded that the genetic information derived from the current study can be used as a guide for genetic improvement and conservation in further breeding programs. Our findings indicate that the Saudi native chicken populations have a rich genetic diversity and show a high polymorphism.

• Asian-Australasian Journal of Animal Sciences
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• 제32권1호
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• pp.49-57
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• 2019

Objective: The first stage in both breeding and programs for the conservation of genetic resources are the identification of genetic diversity in the relevant population. The aim of the present study is to identify genetic diversity of six brown layer pure chicken lines (Rhode Island Red [RIRI, RIRII], Barred Rock [BARI, BARII], Columbian Rock [COL], and line 54 [L-54]) with microsatellite markers. Furthermore, the study aims to employ its findings to discuss the possibilities for the conservation and sustainable use of these lines that have been bred as closed populations for a long time. Methods: In the present study, a total number of 180 samples belonging to RIRI (n = 30), RIRII (n = 30), BARI (n = 30), BARII (n = 30), L-54 (n = 30), and COL (n = 30) lines were genotyped using 22 microsatellite loci. Microsatellite markers are extremely useful tools in the identification of genetic diversity since they are distributed throughout the eukaryotic genome in multitudes, demonstrate co-dominant inheritance and they feature a high rate of polymorphism and repeatability. Results: In this study, we found all loci to be polymorphic and identified the average number of alleles per locus to be in the range between 4.41 (BARI) and 5.45 (RIRI); the observed heterozygosity to be in the range between 0.31 (RIRII) and 0.50 (BARII); and $F_{IS}$ (inbreeding coefficient) values in the range between 0.16 (L-54) and 0.46 (RIRII). The $F_{IS}$ values obtained in this context points out to a deviation from Hardy-Weinberg equilibrium due to heterozygote deficiency in six different populations. The Neighbour-Joining tree, Factorial Correspondence Analysis and STRUCTURE clustering analyzes showed that six brown layer lines were separated according to their genetic origins. Conclusion: The results obtained from the study indicate a medium level of genetic diversity, high level inbreeding in chicken lines and high level genetic differentiation between chicken lines.

• Animal Bioscience
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• 제34권4호
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• pp.471-481
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• 2021

Objective: A comprehensive study was conducted to study the effects of partition of variance on accuracy of genetic parameters and genetic trends of economic traits in Vanaraja male line/project directorate-1 (PD-1) chicken. Methods: Variance component analysis utilizing restricted maximum likelihood animal model was carried out with five generations data to delineate the population status, direct additive, maternal genetic, permanent environmental effects, besides genetic trends and performance of economic traits in PD-1 chickens. Genetic trend was estimated by regression of the estimated average breeding values (BV) on generations. Results: The body weight (BW) and shank length (SL) varied significantly (p≤0.01) among the generations, hatches and sexes. The least squares mean of SL at six weeks, the primary trait was 77.44±0.05 mm. All the production traits, viz., BWs, age at sexual maturity, egg production (EP) and egg weight were significantly influenced by generation. Model four with additive, maternal permanent environmental and residual effects was the best model for juvenile growth traits, except for zero-day BW. The heritability estimates for BW and SL at six weeks (SL6) were 0.20±0.03 and 0.17±0.03, respectively. The BV of SL6 in the population increased linearly from 0.03 to 3.62 mm due to selection. Genetic trend was significant (p≤0.05) for SL6, BW6, and production traits. The average genetic gain of EP40 for each generation was significant (p≤0.05) with an average increase of 0.38 eggs per generation. The average inbreeding coefficient was 0.02 in PD-1 line. Conclusion: The population was in ideal condition with negligible inbreeding and the selection was quite effective with significant genetic gains in each generation for primary trait of selection. The animal model minimized the over-estimation of genetic parameters and improved the accuracy of the BV, thus enabling the breeder to select the suitable breeding strategy for genetic improvement.