• Proceedings of the National Institute of Ecology of the Republic of Korea
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• v.2 no.2
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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.

• Journal of Life Science
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• v.18 no.2
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• pp.175-179
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• 2008

Cornus controversa is a long-lived woody species mostly distributed in East Asia. Random amplified polymorphic DNA (RAPD) markers were used to investigate the genetic diversity and population structure of Korean populations of this species. A high level of genetic variation was found in seven populations of C. controversa. The mean genetic diversity (H) was 0.222 across populations, varying from 0.200 to 0.238. Eighty of the 93 loci (86.0%) showed detectable polymorphism in at least one population. Total genetic diversity values ($H_T$) varied between 0.192 and 0.231, giving an average overall polymorphic loci of 0.212. The interlocus variation of genetic diversity within populations ($H_S$) was high (0.167). Mean of genetic diversity in C. controversa was higher than average values for species with similar life history traits. The sexual reproduction, perennial habitat, and longevity are proposed as possible factors contributing to high genetic diversity. On a per locus basis, the proportion of total genetic variation due to differences among populations ($G_{ST}$) ranged from 0.169 to 0.278 with a mean of 0.216, indicating that about 21.6% of the total genetic variation was among populations. An indirect estimate of the number of migrants per generation (Nm=1.893) indicated that gene flow was extensive among Korean populations of C. controversa.

• Journal of Life Science
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• v.12 no.1
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• pp.27-32
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• 2002

Enzyme electrophoresis was used to estimate genetic diversity and population structure of maize, Zea mays L. (Graminales) in Korea. In nine populations, fourteen of the 24 loci (58.3 %) showed detectable polymorphism. Genetic diversity (0.205) was higher than average values for species with similar life history traits. Although our data are relatively small and the landraces not direct ancestors of cultivar, apparently the domestication process has eroded the levels of genetic variation of maize. The recent cultivars were found to have fewer alleles per locus (1.42 vs. 1.56), fewer alleles per polymorphic locus (2.27 vs. 2.33), lower percent polymorphic locus (33.3% vs. 41.7%), and lower diversity (0.159 vs. 0.185) than landraces. These genetic diversity parameters indicated that the cultivar populations were genetically depauperate relative to landlaces. The GST value of nine populations was 0.239. Nearly 76% of the total genetic diversity in Zea mays was apportioned within populations. The indirect estimate of gene new based on mean GST was moderate (Nm=0.80).

• Journal of Species Research
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• v.7 no.4
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• pp.354-362
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• 2018

Population genetic assessment is essential for the conservation and management of endangered and rare plants. Neofinetia falcata is endangered epiphyte orchid and protected by law in Korea. In Korea, this species is only found on islands in the South Sea of Korea (including Jeju-do) and the southern coast of the Korean Peninsula. We developed nine microsatellite makers to assess the genetic diversity and population genetic structure of three populations of N. falcata. The genetic diversity at the species level was low, which can be attributed to inbreeding or fragmentation into small, isolated populations. A recent bottleneck was detected in one population, likely due to overcollection. N. falcata exhibited moderated levels of differentiation among populations, with the three populations were divided into two clusters based on genetic structure. The genetic diversity and structure of N. falcata are affected by restricted gene flow by pollen or seeds due to isolation and geographic distance. Strategies for in situ and ex situ conservation of this species are been proposed based on the results of our study.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.9
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• pp.1223-1228
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• 2012

The population sizes of three Korean indigenous cattle populations have been drastically reduced over the past decades. In this study, we examined the extent to which reduction in populations influenced genetic diversity, population structure and demographic history using complete mitochondrial DNA (mtDNA) control region sequences. The complete mtDNA control region was sequenced in 56 individuals from Korean Black (KB), Jeju Black (JEB) and Korean Brindle (BRI) cattle populations. We included 27 mtDNA sequences of Korean Brown (BRO) from the GenBank database. Haplotype diversity estimate for the total population was high (0.870) while nucleotide diversity was low (0.004). The KB showed considerably low nucleotide (${\pi}$ = 0.001) and haplotype (h = 0.368) diversities. Analysis of molecular variance revealed a low level of genetic differentiation but this was highly significant (p<0.001) among the cattle populations. Of the total genetic diversity, 7.6% was attributable to among cattle populations diversity and the rest (92.4%) to differences within populations. The mismatch distribution analysis and neutrality tests revealed that KB population was in genetic equilibrium or decline. Indeed, unless an appropriate breeding management practice is developed, inbreeding and genetic drift will further impoverish genetic diversity of these cattle populations. Rational breed development and conservation strategy is needed to safeguard these cattle population.

• Journal of Life Science
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• v.10 no.1
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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.

• Journal of Animal Science and Technology
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• v.62 no.6
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• pp.790-800
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• 2020

The Yeonsan Ogye (YO) chicken is a natural heritage of Korea, characterized by black feathers, skin, bones, eyes, and comb. The purebred of YO population has been reared under the natural mating system with no systematic selection and breeding plan. The purpose of this study was to identify the genetic diversity and find the optimal number of population sub-division using 12 polymorphic microsatellite (MS) markers to construct a pedigree-based breeding plan for the YO population. A total of 509 YO birds were used for this study. Genetic diversity and population structure analysis were conducted based on the MS marker genotype information. The overall average polymorphic information content value and expected heterozygosity of the population were 0.586, and 0.642, respectively. The K-mean cluster analysis based on the genetic distance result confirmed that the current YO population can be divided into three ancestry groups. Individuals in each group were evaluated based on their genetic distance to identify the potential candidates for a future breeding plan. This study concludes that a future breeding plan with known pedigree information of selected founder animals, which holds high genetic diversity, could be the best strategy to ensure the conservation of the Korean YO chicken population.

• Journal of Life Science
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• v.12 no.1
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• pp.9-13
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• 2002

Crepidiastrum lanceolatum ($H_{OUTT}$) $N_{AKAI}$ (Compositae) is distributed in East Asia including Korea. Genetic diversity and population structure of six C. lanceolatum populations in Korea and two populations in Japan were determined using genetic variation at 19 allozyme loci. The percent of polymorphic loci within the enzymes was 42.1%. Genetic diversity at the species level and at the population level was low (Hes : 0.077; Hep : 0.068, respectively), where-as the extent of the population divergence was relatively low ($G_{ST}$ : 0.093). One of the most striking features of this study was the more significant difference within populations than among populations. An indirect estimate of the number of migrants per generation (Nm : 2.44) indicated that gene flow was moderate among eight populations of the species. In addition, analysis of fixation indices revealed a slight heterozygosity deficiency in some populations and at some loci. Narrow geographic ranges, short-lived perennial herbaceous, and small population sizes are mainly associated with the low level of genetic variation.n.

• Animal Bioscience
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• v.36 no.10
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• pp.1508-1516
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• 2023

Objective: To carry out a comprehensive production planning of the existing Rongchang pig population from both environmental and genetic aspects, and to establish a closed population with stable genetic diversity and strict pathogen control, it is necessary to fully understand the genetic background of the population. Methods: We genotyped 54 specific pathogen free (SPF) Rongchang pigs using the Zhongxin-1 Porcine Breeding Array PLUS, calculated their genetic diversity parameters and constructed their families. In addition, we also counted the runs of homozygosity (ROH) of each individual and calculated the value of inbreeding coefficient based on ROH for each individual. Results: Firstly, the results of genetic diversity analysis showed that the effective population size (N_e) of this population was 3.2, proportion of polymorphic markers (P_N) was 0.515, desired heterozygosity (H_e) and observed heterozygosity (H_o) were 0.315 and 0.335. H_o was higher than H_e, indicating that the heterozygosity of all the selected loci was high. Secondly, combining the results of genomic relatedness analysis and cluster analysis, it was found that the existing Rongchang pig population could be divided into four families. Finally, we also counted the ROH of each individual and calculated the inbreeding coefficient value accordingly, whose mean value was 0.09. Conclusion: Due to the limitation of population size and other factors, the genetic diversity of this Rongchang pig population is low. The results of this study can provide basic data to support the development of Rongchang pig breeding program, the establishment of SPF Rongchang pig closed herd and its experimental utilization.

• Journal of Plant Biotechnology
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• v.50
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• pp.207-214
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• 2023

Lindera obtusiloba (Lauraceae) is a dioecious tree that is widely distributed in the low-altitude montane forests of East Asia, including Korea. Despite its various pharmacological properties and ornamental value, the genetic diversity and population structure of this species in Korea have not been explored. In this study, we selected 6 nuclear and 6 chloroplast microsatellite markers with polymorphism or clean cross-amplification and used these markers to perform genetic diversity and population structure analyses of L. obtusiloba samples collected from 20 geographical regions. Using these 12 markers, we identified a total of 44 alleles, ranging from 1 to 8 per locus, and the average observed and expected heterozygosity values were 0.11 and 0.44, respectively. The average polymorphism information content was 0.39. Genetic relationship and population structure analyses revealed that the natural L. obtusiloba population in Korea is composed of 2 clusters, possibly due to two different plastid genotypes. The same clustering patterns have also been observed in Lindera species in mainland China and Japan.