• Mycobiology
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• v.48 no.2
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• pp.115-121
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• 2020

In this study, the genetic diversity and the population structure of 77 wild strains and 23 cultivars of Lentinula edodes from Korea were analyzed using 20 genomic SSRs, and their genetic relationship was investigated. The tested strains of L. edodes were divided into three sub-groups consisting of only wild strains, mainly wild strains and several cultivars, and mainly cultivars and several wild strains by distance-based analysis. Using model-based analysis, L. edodes strains were divided into two subpopulations; the first one consisting of only wild strains and the second one with mainly cultivars and several wild strains. Moreover, AMOVA analysis revealed that the genetic variation in the cultivars was higher than that in the wild strains. The expected and observed heterozygosity and values indicating the polymorphic information content of L. edodes cultivars from Korea were also higher than that of the wild strains. Based on these results, we presume that the cultivars in Korea have developed by using numerous strains from other countries. In conclusion, the usage of wild strains for the development of new cultivars could improve the adaptability of L. edodes to biotic and abiotic stress.

• Korean Journal of Plant Taxonomy
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• v.52 no.1
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• pp.45-53
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• 2022

Halenia coreana is an endangered, endemic species that is distributed in only a few locations in Korea, such as Mts. Hwaaksan and Daeamsan. It has been recently segregated from H. corniculata, broadly distributed in cold temperate regions that include northern Japan, the Russian Far East, northeastern China, Mongolia, and eastern Europe, where population sizes are usually large. To examine the genetic diversity of H. coreana and evaluate the level of genetic differentiation of the species compared with that of H. corniculata, we surveyed 183 candidate simple sequence repeats (SSR) motif markers for H. coreana and H. corniculata from sequence data of amplified fragments of a specific length in the genome. A total of 17 genomic-SSR markers were selected to examine the levels of genetic diversity and differentiation using 17 samples of H. coreana and 60 samples of three populations of H. corniculata. The results here suggest that the genetic diversity of H. coreana is very low with a high frequency of inbreeding within its population. We found that H. coreana is genetically differentiated from H. corniculata, supporting the recognition of the geographically isolated H. coreana as a distinct species.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.82-82
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• 2017

The production of spring wheat, the major crop in Mongolia, is accounting for 98% of the cultivated area. Collection, conservation and utilization of wheat germplasm resources play an important role in wheat breeding and production in Mongolia. Understanding genetic variability in the existing genebank accessions is important for collection and conservation of wheat germplasms. To determine the genetic diversity and population structure among a representative collection of Mongolian local wheat cultivars and lines, 200 wheat accessions were analyzed with 15 SSR markers distributed throughout the wheat genome. A total of 85 alleles were detected, with 3 to 5 alleles per locus and a mean genetic diversity value of 5.66. The average genetic diversity index was 0.68, with values ranging from 0.37 to 0.80. The 200 Mongolian wheat accessions were divided into two subgroups based on STRUCTURE, un-rooted NJ cluster and principal coordinate analyses. The results from this study will provide important information for future wheat germplasm conservation and improvement programs with Mongolian genebank.

• Fisheries and Aquatic Sciences
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• v.25 no.12
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• pp.601-618
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• 2022

The genus Semisulcospira is an economically and ecologically valuable freshwater resource. Among the species, Semisulcospira coreana, Semisulcospira forticosta and Semisulcospira tegulata are endemic to the Korean peninsula and Semisulcospira gottschei is widespread in Asia. Therefore, maintenance and conservation of wild populations of these snails are important. We investigated the genetic diversity and population structure of Semisulcospira based on the mitochondrial cytochrome c oxidase subunit I (COI), NADH dehydrogenase subunit 4 (ND4), and combined mitochondrial DNA (COI + ND4) sequences. All four species and various genetic makers showed a high level of haplotype diversity and a low level of nucleotide diversity. In addition, Fu's Fs and Tajima's D neutrality tests were performed to assess the variation in size among populations. Neutrality tests of the four species yielded negative Fu's Fs and Tajima's D values, except for populations with one haplotype. The minimum spanning network indicated a common haplotype for populations of S. coreana, S. tegulata and S. gottschei, whereas S. forticosta had a rare haplotype. Also, genetic differences and gene flows between populations were assessed by analysis of molecular variance and using the pairwise fixation index. Our findings provided insight into the degree of preservation of the species' genetic diversity and could be utilized to enhance the management of endemic species.

• Journal of Life Science
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• v.30 no.11
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• pp.1007-1011
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• 2020

This study was conducted to analyze the genetic diversity and relationships that discriminate between Korean native black goat populations (Dangjin, Jangsu, Tongyoung, and Gyeongsang National University strains) and crossbred goats. Monomorphic single nucleotide polymorphisms (SNPs) in each strain were collected, and 133 common SNPs were selected for analysis. These 133 monomorphic SNPs showed differences in the genetic structure of the Korean native black goat and crossbred goats, and results from the principal component analysis (PCA) showed that the two can be clearly separated. Furthermore, analysis of the validation population comprising 70 individuals (Korean native black goats, n = 24; crossbred goats, n = 46) with the reference population showed that Korean native black goat strains and the reference population have the same genetic structure, and the crossbred goats shared only part of the genetic structure with the reference population. The result of the PCA analysis showed that the Korean native black goat strains form one population, whereas the foreign strains form another population which is more widely dispersed than the Korean native black goat strains. Thus, the results from this study can be used as baseline data for the conservation of genetic resources of Korean native black goat communities through utilization of monomorphic SNPs and for the introduction of exotic species for further improvement in genetic diversity. This study can also help reduce unnecessary inbreeding and gene flow between native strains.

• Asian-Australasian Journal of Animal Sciences
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• v.10 no.4
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• pp.428-434
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• 1997

The effect of genetic diversity in sub-populations on breeding efficiency was examined with prospect of potential crossbreeding. Simulation study of selection was performed for 20 generations with 20 replications each, comparing average breeding values and inbreeding coefficients between the two breeding systemes; single population scheme and two population scheme. The different genetic levels were assumed to be caused by different gene frequencies. Phenotypes of two traits generated polygenic effect with additive 36 loci and residuals distributed normally were selected by selection index procedure. High genetic gain with less inbreeding was clearly recognized in the single population scheme, independently of difference in genetic level, economic weight and genetic correlation. Genetic correlation after selection in the single population scheme was lower than the two population scheme. When crossbreeding between the sub-population was taken into account, superiority of the two population scheme was suggested under those restrictions; difference in genetic level is moderate, selection criterion for the two traits is not far from even economic weight, and genetic correlation is positive with low to moderate value. The use of complementarity increased the possibility of the two population scheme.

• Korean Journal of Ichthyology
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• v.36 no.2
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• pp.139-155
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• 2024

Using the cytb gene region of the mitochondrial DNA of eight populations of Sarcocheilichthys nigripinnis morii and five populations of S. variegatus wakiyae, which belong to the genus Sarcocheilichthys from Korea, the genetic diversity and molecular phylogenetic relationships of each population were examined. As a result of the analysis, it was confirmed that the S. variegatus wakiyae population had higher genetic diversity than the S. nigripinnis morii population. In the phylogenetic tree of genus Sarcocheilichthys fish in Korea based on the cytb gene, the Yeongsan River (YSR) population of S. variegatus wakiyae forms a clade with the Tamjin River (TJR), Yeongsan River (YSR), and Seomjin River (SJR) population of S. nigripinnis morii, and genetic relationships that do not align with the current classification system were observed. Meanwhile, on the nuclear DNA phylogenetic tree, S. variegatus wakiyae and S. nigripinnis morii could be clearly distinguished, showing mitonuclear inconsistency where mitochondrial and nuclear DNA conflicted on the phylogenetic tree. The Seomjin River (SJR) population of S. nigripinnis morii was translocated to the Dongjin River (DJR) population, haplotype from which crossbreeding was presumed to have occurred was confirmed. Among the rivers flowing into the East Sea, the S. nigripinnis morii population is known to have been introduced and inhabit only the Hyeongsan River (HSR), and it is presumed to be a population formed by translocation from the Han River (HR) population, with a haplotype representing a unique genetic group also confirmed. The Han River (HR), Geum River (GR), and Mangyeong River (MGR) populations of S. nigripinnis morii formed a genetically identical population with S. czerskii and S. soldatovi distributed north of the Yalu River, and accordingly, a taxonomic reexamination was required through morphological and molecular phylogenetic studies by securing various specimens.

• Journal of Advanced Navigation Technology
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• v.18 no.2
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• pp.170-177
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• 2014

Genetic Algorithms are robust search and optimization techniques but have some problems such as premature convergence and convergence to local extremum. As population diversity converges to low value, the search ability decreases and converges to local extremum but population diversity converges to high value, then the search ability increases and converges to global optimum or genetic algorithm may diverge. To guarantee that genetic algorithms converge to the global optima, the genetic operators should be chosen properly. In this paper, we propose the genetic operators with the hybrid function of the average Hamming distance and the fitness value to maintain the diversity of the GA's population for escaping from the premature convergence. Results of simulation studies verified the effects of the mutation operator for maintaining diversity and the other operators for improving convergence properties as well as the feasibility of using proposed genetic operators on convergence properties to avoid premature convergence and convergence to local extremum.

• Animal Bioscience
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• v.37 no.4
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• pp.591-599
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• 2024

Objective: Sumba Ongole (SO) cattle are valuable breed due to their important role in the development of Indonesian cattle. Despite rapid advances in molecular technology, no genomic studies on SO cattle have been conducted to date. The aim of this study is to provide genomic profile related to the population diversity, admixture, and demographic trends of SO cattle. Methods: Genomic information was gathered from 79 SO cattle using the Illumina Bovine SNP50 v3 Beadchip, and for comparative purposes, additional genotypes from 209 cattle populations worldwide were included. The expected and observed heterozygosity, inbreeding coefficient, pairwise fixation indices between-population, and Nei's genetic distance were examined. Multidimensional scaling, admixture, and treemix analyses were used to investigate the population structure. Based on linkage disequilibrium and effective population size calculations, the demographic trend was observed. Results: The findings indicated that the genetic diversity of SO cattle was similar to that of other indicine breeds. SO cattle were genetically related to indicines but not to taurines or Bali cattle. The study further confirmed the close relationship between SO, Ongole, and Nellore cattle. Additionally, a small portion of the Ongole mixture were identified dominant in the SO population at the moment. The study also discovered that SO and Bali cattle (Bos javanicus) could have been ancestors in the development of Ongole Grade cattle, which corresponds to the documented history of Ongolization. Our finding indicate that SO cattle have maintained stability and possess unique traits separate from their ancestors. Conclusion: In conclusion, the genetic diversity of the SO cattle has been conserved as a result of the growing significance of the present demographic trend. Consistent endeavors are necessary to uphold the fitness of the breed.

• Animal Bioscience
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• v.34 no.7
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• pp.1105-1115
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• 2021

Objective: To conserve and utilize the genetic resources of a traditional Chinese indigenous pig breed, Liangshan pig, we assessed the genetic diversity, genetic structure, and genetic distance in this study. Methods: We used 50K single nucleotide polymorphism (SNP) chip for SNP detection of 139 individuals in the Liangshan Pig Conservation Farm. Results: The genetically closed conserved population consisted of five overlapping generations, and the total effective content of the population (Ne) was 15. The whole population was divided into five boar families and one non-boar family. Among them, the effective size of each generation subpopulation continuously decreased. However, the proportion of polymorphic markers (P_N) first decreased and then increased. The average genetic distance of these 139 Liangshan pigs was 0.2823±0.0259, and the average genetic distance of the 14 boars was 0.2723±0.0384. Thus, it can be deduced that the genetic distance changed from generation to generation. In the conserved population, 983 runs of homozygosity (ROH) were detected, and the majority of ROH (80%) were within 100 Mb. The inbreeding coefficient calculated based on ROH showed an average value of 0.026 for the whole population. In addition, the inbreeding coefficient of each generation subpopulation initially increased and then decreased. In the pedigree of the whole conserved population, the error rate of paternal information was more than 11.35% while the maternal information was more than 2.13%. Conclusion: This molecular study of the population genetic structure of Liangshan pig showed loss of genetic diversity during the closed cross-generation reproduction process. It is necessary to improve the mating plan or introduce new outside blood to ensure long-term preservation of Liangshan pig.