• 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.

• 식물분류학회지
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• 제53권1호
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• pp.14-24
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• 2023

Saussurea dorogostaiskii Palib. (Asteraceae) is a critically endangered medicinal plant in Mongolia and Russia. We studied the genetic variation of S. dorogostaiskii from three mountains of northern Mongolia. The genetic profile was assessed in 70 individuals from eight populations using five inter-simple sequence repeat markers, producing 53 loci with 96.4% polymorphism across all bands. Shannon's index (I) and Nei's gene diversity (H) value at the species level of S. dorogostaiskii are 0.25 and 0.17, respectively. An AMOVA showed high genetic variation among the populations (22% of populations and 32% of mountains), consistent with the high genetic differentiation (G_ST = 0.49) and low gene flow (N_m = 0.51) in S. dorogostaiskii populations. Eight populations were clustered into two groups, corresponding to their geographic locations. The low within-population genetic diversity and high genetic differentiation among S. dorogostaiskii populations factor into their endangered designation. This genetic analysis reveals that all populations are equally threatened, and community-based conservation is appropriate for these species.

• Asian-Australasian Journal of Animal Sciences
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• 제23권2호
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• pp.154-161
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• 2010

The level of genetic differentiation and genetic structure in a Chinese native chicken breed, Bian chicken, and two controlled chicken populations (Jinghai chicken and Youxi chicken in China) were analysed based on 29 microsatellite markers. A total of 166 distinct alleles were observed across the 3 breeds, and 32 of these alleles (19.3%) were unique to only 1 breed. Bian chicken carried the largest number of private alleles at 15 (46.9%), followed by the Jinghai chicken with 12 private alleles (37.5%). The average polymorphism information content (0.5168) and the average expected heterozygote frequency (0.5750) of the Bian chicken were the highest, and those of the Jinghai chicken were 0.4915 and 0.5505, respectively, which were the lowest. Among 29 microsatellite loci, there were 15 highly informative loci in Bian chicken, and the other 14 were reasonably informative loci. The highly informative loci in Jinghai chicken and Youxi chicken were 17 and 14 respectively. Significant deviations from the Hardy-Weinberg equilibrium were observed at several locus-breed combinations, showing a deficit of heterozygotes in many cases. As a whole, genetic differentiation among the breeds estimated by the fixation index (Fst) were at 6.7% (p<0.001). The heterozygote deficit within population (Fis) was 22.2% (p<0.001), with the highest (0.249) in Bian chicken and lowest (0.159) in Youxi chicken. These results serve as an initial step in the plan for genetic characterization and conservation of the Chinese chicken genetic resource of Bian, as well as Jinghai and Youxi chickens.

• Asian-Australasian Journal of Animal Sciences
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• 제33권4호
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• pp.539-546
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• 2020

Objective: The Jeju native pig (JNP) found on the Jeju Island of Korea is a unique black pig known for high-quality meat. To investigate the genetic uniqueness of JNP, we analyzed the selection signature of the JNP in comparison to commercial pigs such as Berkshire and Yorkshire pigs. Methods: We surveyed the genetic diversity to identify the genetic stability of the JNP, using the linkage disequilibrium method. A selective sweep of the JNP was performed to identify the selection signatures. To do so, the population differentiation measure, Weir-Cockerham's F_st was utilized. This statistic directly measures the population differentiation at the variant level. Additionally, we investigated the gene ontologies (GOs) and genetic features. Results: Compared to the Berkshire and Yorkshire pigs, the JNP had lower genetic diversity in terms of linkage disequilibrium decays. We summarized the selection signatures of the JNP as GO. In the JNP and Berkshire pigs, the most enriched GO terms were epithelium development and neuron-related. Considering the JNP and Yorkshire pigs, cellular response to oxygen-containing compound and generation of neurons were the most enriched GO. Conclusion: The selection signatures of the JNP were identified through the population differentiation statistic. The genes with possible selection signatures are expected to play a role in JNP's unique pork quality.

• 생태와환경
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• 제41권1호
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• pp.98-103
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• 2008

우리나라 멸종위기종 미호종개 3집단(갑천, 백곡천, 지천)의 유전 다양성 및 유전적 구조를 AFLP분석을 통해 조사하였다. 3종의 primer조합형을 이용한 AFLP분석에서 각 집단으로부터 106, 107, 104개의 밴드가 생성되었으며, 집단 내 다형 밴드의 출현 빈도는 3개 집단에서 $21.5\sim24.5%$로 유사하게 나타났고, 이형접합율$(0.067\sim0.084)$및 유전적 다양도$(0.076\sim0.087)$는 매우 낮은 값을 보였다. 집단간 유전적 거리 및 유전적 상동성 분석 역시 유사한 결과를 나타내어 본 연구에서 분석한 미호종개 3개 집단은 유전적으로 매우 밀접한 근연관계를 나타내었다. 비록 pairwise Fst 값은 매우 낮았지만 3집단은 유전적 분화가 진행되고 있었다. 본 연구는 미호종개의 유전적 다양성 및 분화에 대해 처음으로 보고된 연구이며, 미호종개의 보존을 위한 유전적 기초 정보를 제공해 준다.

• BMB Reports
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• 제38권4호
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• pp.491-499
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• 2005

DNA-based molecular markers for differentiation of five penaeid shrimps (Penaeus monodon, P. semisulcatus, Feneropenaeus merguiensis, Litopenaeus vannamei and Marsupenaeus japonicus) were developed based on polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and single-stranded conformation polymorphism (SSCP) of 16S ribosomal (r) DNA. Differentiation of P. monodon, P. semisulcatus and L. vannamei can be unambiguously carried out by PCR-RFLP of 16S $rDNA_{560}$ whereas P. semisulcatus and M. japonicus shared a BABB mitotype. These shrimps were successfully discriminated by SSCP analysis of 16S $rDNA_{560}$. Nevertheless, the amplification success for L. vannamei and F. merguiensis was not consistent when tested against larger sample sizes. As a result, 16S $rDNA_{560}$ of an individual representing the most common mitotype of each species was cloned and sequenced. The new primer pair was designed and tested against the large sample sizes (312 bp product, N = 185). The amplification success was consistent across all species. PCR-RFLP of 16S $rDNA_{312}$ was as effective as that of 16S $rDNA_{560}$. Differentiation of all shrimp species were successfully carried out by SSCP analysis.

• Journal of Life Science
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• 제10권1호
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• pp.14-19
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• 2000

Variation at 25 allozyme loci in Korean wateralder (Alnus hirsuta Rupr.) from nine distinct populations was measured to estimate the amount and pattern of genetic diversity and population structure. The mean genetic diversity within population was 0.166. Korean alder populations have slightly high levels of genetic diversity compared to those present in associated temperature-zone species and two Canadian alder species. Among population s genetic differentiation accounted for an significant 9% of the total variation. High gene flow(Nm=2.63) was observed. Analysis of fixation indices, calculated for all polymorphic loci in each population, showed a substantial deficiency of heterozygotes relative to Hardy-Weinberg expectations. The mean GST value A. hirsuta in Korea (GST = 0.087) is similar to those of A. rogosa in Canada (GST = 0.052). These low values of GST in two countries. reflecting little spatial genetic differentiation, may indicate extensive gene flow (via pollen and/or seeds) and/or recent colonization. These factors reduce the effect of geographic isolation of breeding and the chance for genetic divergence. A pattern of increasing is observed with increasing rainfall per year. Regression analysis indicates that 54% (F = 4.67) of the variability observed can be explained by this relationship.

• 한국응용곤충학회지
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• 제40권3호
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• pp.227-233
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• 2001

네 가지 다형 동위효소를 이용하여 야외 월동세대의 배추좀나방(Plutella xylostella(Linne))의 집단 유전분석이 실시되었다. 세 지역 (안동, 영천, 양산)의 야외집단들은 모든 동위효소 유전좌위에서 서로 다른 대립유전자빈도를 보였다. 특히 두 동위효소(acid phosphatase and phosphoglucomutase)에서 나타나는 유전자 빈도의 불균형은 집단간에 임의교배가 이루어져 있지 않음을 나타냈다. 추정된 집단간 Nei의 유전거리는 0.0151(양산집단과 영천집단)에서 0.0877(안동집단과 영천집단)까지 다양했다. 기존의 배추좀나방 야외집단들의 유전거리 추정치에 비해 이러한 월동 초기세대들이 보인 다소 높은 유전분화는 이들 집단이 월동과정중 지역적 환경요인에 따른 상이한 도태압이 작용하여 유전적 병목현상이 초래되었음을 내포한다.

• Animal cells and systems
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• 제4권1호
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• pp.23-30
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• 2000

Horizontal starch gel electrophoresis for 29 populations (n=543) of the wrinkled frog, Rana rugosa, from Korea and Japan was peformed to assess the degree of genic variation and genetic diversity, and to understand the biogeographic pattern of distribution and speciation. A sum of 22 presumptive loci was screened from 17 enzymes and general proteins. Four loci, Aco, Est-3, Me-2, and Pgm, demonstrated high levels of polymorphism. The degree of average genetic variation of R. rugosa was P=22.7% (9.1-40.9%), Ho=0.086 (0.048-0.165) and He=0.090 (0.042-0.168). In the south-eastern region of the Korean peninsula (Chongsong, Yongchon, Ulsan, Kyongju, Pohang, yongdok and Ulchin), a few unique alleles in the Mpi locus were detected and their biogeographic implications were considered. The degree of genetic differentiation among the Korean populations was moderate (S=0.900), whereas the degree of genetic diversity between Korean and Japanese populations was notably high (S=0.687, D=0.293). This result corresponds with the data obtained by the mitochondrial cytochrome b gene sequence (Lee et al., 1999) suggesting that the Korean and Japanese R. rugosa might have evolved a specific level of genetic differentiation since their geographic isolation.

• Animal Bioscience
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• 제36권1호
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• pp.144-155
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• 2023

Objective: Adipocyte differentiation is regulated by a variety of functional genes and noncoding RNAs. However, the role of miRNAs in lipid deposition of goat white adipose tissue is still unclear. Therefore, this study revealed the miRNA expression profile in goat subcutaneous adipocytes by sRNA-seq. Methods: The miRNA expressed in goat subcutaneous preadipocytes and the mature adipocytes were sequenced by sRNA-seq. The differentially expressed miRNAs (DEm) were screened and gene ontology (GO) and Kyoto encyclopedia for genes and genomes (KEGG) analyses were performed. Gain-of-function and loss-of-function combined with oil red O staining, Bodipy staining, and quantitative reverse-transcription polymerase chain reaction (qPCR) were utilized to determine the effect of miR-133a-3p on adipocyte differentiation. Results: A total of 218 DEm were screened out. The target genes of these DEm were significantly enriched in GO items such as biological regulation and in KEGG terms such as FAK signaling pathway and MAPK signaling pathway. qPCR verified that the expression trend of miRNA was consistent with miRNA-seq. The gain-of-function or loss-of-function of miR-133a-3p showed that it promoted or inhibited the accumulation of lipid droplets, and CCAAT enhancer binding protein α (C/EBPα) and C/EBPβ were extremely significantly up-regulated or down-regulated respectively (p<0.01), the loss-of-function also led to a significant down-regulation of peroxisome proliferator activated receptor gamma (PPARγ) (p<0.01). Conclusion: This study successfully identified miRNAs expression patterns in goat subcutaneous adipocytes, and functional identification indicates that miR-133a-3p is a positive regulator of the differentiation process of goat subcutaneous adipocytes. Our results lay the foundation for the molecular mechanism of lipid deposition in meat-source goats from the perspective of miRNA.