• Animal Bioscience
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• 제34권11호
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• pp.1757-1765
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• 2021

Objective: The swine leukocyte antigen (SLA) gene group, which is closely linked and highly polymorphic, has important biomedical significance in the protection and utilization of germplasm resources. However, genetic polymorphism analyses of SLA microsatellite markers in Chinese miniature pigs are limited. Methods: Eighteen pairs of microsatellite primers were used to amplify the SLA regions of seven miniature pig breeds and three wild boar breeds (n = 346) from different regions of China. The indexes of genetic polymorphism, including expected heterozygosity (He), polymorphic information content (PIC), and haplotype, were analyzed. The genetic differentiation coefficient (Fst) and neighbor-joining methods were used for cluster analysis of the breeds. Results: In miniature pigs, the SLA I region had the highest numbers of polymorphisms, followed by the SLA II and SLA III regions; the region near the centromere had the lowest number of polymorphisms. Among the seven miniature pig breeds, Diannan small-ear pigs had the highest genetic diversity (PIC value = 0.6396), whereas the genetic diversity of the Hebao pig was the lowest (PIC value = 0.4330). The Fst values in the Mingguang small-ear, Diannan small-ear, and Yunnan wild boars were less than 0.05. According to phylogenetic cluster analysis, the South-China-type miniature pigs clustered into one group, among which Mingguang small-ear pigs clustered with Diannan small-ear pigs. Haplotype analysis revealed that the SLA I, II, and III regions could be constructed into 13, 7, and 11 common haplotypes, respectively. Conclusion: This study validates the high genetic diversity of the Chinese miniature pig. Mingguang small-ear pigs have close kinship with Diannan small-ear pigs, implying that they may have similar genetic backgrounds and originate from the same population. This study also provides a foundation for genetic breeding, genetic resource protection, and classification of Chinese miniature pigs.

• Asian-Australasian Journal of Animal Sciences
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• 제27권11호
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• pp.1548-1553
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• 2014

Four Korean native cattle (KNC) breeds-Hanwoo, Chikso, Heugu, and Jeju black-are entered in the Domestic Animal Diversity Information System of the United Nations Food and Agriculture Organization (FAO). The objective of this study was to assess the genetic diversity, phylogenetic relationships and population structure of these KNC breeds (n = 120) and exotic breeds (Holstein and Charolais, n = 56). Thirty microsatellite loci recommended by the International Society for Animal Genetics/FAO were genotyped. These genotypes were used to determine the allele frequencies, allelic richness, heterozygosity and polymorphism information content per locus and breed. Genetic diversity was lower in Heugu and Jeju black breeds. Phylogenetic analysis, Factorial Correspondence Analysis and genetic clustering grouped each breed in its own cluster, which supported the genetic uniqueness of the KNC breeds. These results will be useful for conservation and management of KNC breeds as animal genetic resources.

• Asian-Australasian Journal of Animal Sciences
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• 제25권9호
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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 Ecology and Environment
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• 제36권3호
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• pp.205-210
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• 2013

Cicuta virosa L. (Apiaceae) is a perennial emergent plant designated as an endangered species in South Korea. According to the former records, only four natural habitats remain in South Korea. A former study suggested that three of four populations (Pyeongchang: PC, Hoengseong: HS, Gunsan: GS) would be classified as different ecotypes based on their different morphological characteristics and life cycle under different environmental conditions. To evaluate this suggestion, we estimated genetic diversity in each population and distance among three populations by random amplification of polymorphic DNA. Seven random primers generated a total of 61 different banding positions, 36 (59%) of them were polymorphic. Nei's gene diversity and the Shannon diversity index increased in the order of PC < HS < GS, which is the same order of population size. In the two-dimensional (2D) plot of first two principal components in principal component analysis with the presence of 61 loci, individuals could be grouped as three populations easily (proportion of variance = 0.6125). Nei's genetic distance for the three populations showed the same tendency with the geographical distance within three populations. And it is also similar to the result of discriminant analysis with the morphological or life-cycle factors from the previous study. From the results, we concluded that three different populations of C. virosa should be classified as ecotypes based on not only morphology and phenology but genetic differences in terms of diversity and distance as well.

• ALGAE
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• 제33권3호
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• pp.205-214
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• 2018

Red algae in the genus Portieria produce secondary halogenated monoterpenes, which are effective deterrents against herbivores, as secondary metabolites. Portieria hornemannii samples from various sites contain different concentrations of these metabolites, suggesting the existence of genetic diversity and cryptic species. To evaluate the genetic diversity and species distribution of Portieria in the northwest Pacific, we analyzed rbcL sequences of samples collected from Korea, Japan, and Taiwan. The phylogenetic analysis revealed five distinct lineages at the species level. One was recognized as Portieria japonica and the others were cryptic lineages in P. hornemannii. The rbcL haplotypes of P. japonica were genetically fragmented into two subgroups of geographic origin; Korean and Japanese. The four cryptic lineages within P. hornemannii were also geographically structured at a much finer scale. These results suggest that different genetic lineages in Portieria evolved from variable microhabitats, consequently influencing secondary metabolites. Further study is required to resolve the relationships between genetic and secondary metabolite variations in Portieria.

• Asian-Australasian Journal of Animal Sciences
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• 제29권2호
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• pp.176-183
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• 2016

A study was conducted to assess the genetic diversity among Simmental Cross cattle in West Sumatra using microsatellite DNA markers. A total of 176 individual cattle blood samples was used for obtaining DNA samples. Twelve primers of microsatellite loci as recommended by FAO were used to identify the genetic diversity of the Simmental Cross cattle population. Multiplex DNA fragment analysis method was used for allele identification. All the microsatellite loci in this study were highly polymorphic and all of the identified alleles were able to classify the cattle population into several groups based on their genetic distance. The heterozygosity values of microsatellite loci in this study ranged from 0.556 to 0.782. The polymorphism information content (PIC) value of the 12 observed loci is high (PIC>0.5). The highest PIC value in the Simmental cattle population was 0.893 (locus TGLA53), while the lowest value was 0.529 (locus BM1818). Based on the genetic distance value, the subpopulation of the Simmental Cross-Agam and the Simmental Cross-Limapuluh Kota was exceptionally close to the Simmental Purebred thus indicating that a grading-up process has taken place with the Simmental Purebred. In view of the advantages possessed by the Simmental Cross cattle and the evaluation of the genetic diversity results, a number of subpopulations in this study can be considered as the initial (base) population for the Simmental Cross cattle breeding programs in West Sumatra, Indonesia.

• 한국약용작물학회지
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• 제19권3호
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• pp.149-156
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• 2011

The genetic diversity and the genetic relationship among 30 genetic resources of T. officinale and T. coreanum collected from 20 regions in Korea were evaluated by using ISSR markers. Out of 127 loci detected overall, 122 were identified to be polymorphic with a rate of 96.0% at the 30 individuals. The intraspecific polymorphism between T. officinale and T. coreanum was 92.6% and 88.2%, respectively. The genetic similarity matrix (GSM) revealed a wide range of variablility among the 30 accessions, spanning from 0.179 to 922. According to the clustering analysis, different species T. officinale and T. coreanum, were divided into independent groups and all of the accessions could be classified into 7 categories. Especially, all of the mountain collected accessions belonged to independent groups. The study findings indicate that T. officinale and T. coreanum accessions have a high genetic diversity and accordingly carry a germ-plasm qualifying as good genetic resources for breeding.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2022년도 춘계학술대회
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• pp.110-110
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• 2022

Rice is the world's most important food crop and a major source of nutrition for about two thirds of populations. Northern Vietnam is one of the most important centers of genetic diversity for cultivated rice. In this study, we determined the genetic diversity and population structure of 79 rice landraces collected from northern Vietnam and 19 rice accessions collected from different countries. In total, 98 rice accessions could be differentiated into japonica and indica with moderate genetic diversity and a polymorphism information content of 0.382. We also detected subspecies-specific markers to classify rice (Oryza sativa L.) into indica and japonica. Additionally, we detected five marker-trait associations and rare alleles that can be applied in future breeding programs. Most interestingly, analysis of molecular variance (AMOVA) found genetic differentiation was related to geographical regions with an overall PhiPT (analog of fixation index FST) value of 0.130. More emphasis was given to provide signatures and infer explanations about the role of geographical isolation and environmental heterogeneity in genetic differentiation among regions in landraces from northern Vietnam. Our results suggest that rice landraces in northern Vietnam have a dynamic genetic system that can create different levels of genetic differentiation among regions, but also maintain a balanced genetic diversity between regions.

• International Journal of Industrial Entomology and Biomaterials
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• 제36권2호
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• pp.31-41
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• 2018

The dung beetle, Copris tripartitus (Coleoptera: Scarabaeidae), is an endangered insect in South Korea. Previously, partial mitochondrial COI and CytB gene sequences have been used to infer genetic diversity and gene flow of this species in South Korea. In this study, we additionally collected C. tripartitus (n = 35) from one previous locality and two new localities, sequenced COI and CytB genes, and combined these with preexisting data for population genetic analysis. Sequence divergence of current samples showed slightly lower values [4.86% (32 bp) for COI and 4.16% (18 bp) for CytB] than that in the previous study. Nucleotide diversity (${\pi}$) ranged from 0.005336 (Gulupdo) to 0.020756 (Seogwi-dong) in COI and 0.009060 (Aewol-eup) to 0.017464 (Seogwi-dong) in CytB. Seogwi-dong samples that showed the highest ${\pi}$ in the previous study also showed the highest ${\pi}$ in this study for both gene sequences. The newly investigated Gulupdo samples had the lowest haplotype diversity for both gene sequences. They also had the lowest ${\pi}$ for COI and the second lowest ${\pi}$ for CytB. On the other hand, the newly added Haean-dong sample had relatively higher diversity estimates. Gene flow among populations was high, although significant difference was only detected between Gulupdo and Anmado or between Gulupdo and Seogwi-dong for COI sequences (P < 0.05). Considering the high genetic diversity and gene flow in C. tripartitus populations, one major issue regarding conservation seems not to be recovery of genetic diversity.

• Parasites, Hosts and Diseases
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• 제60권6호
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• pp.393-400
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• 2022

Human infection with simian malaria Plasmodium knowlesi is a cause for concern in Southeast Asian countries, especially in Malaysia. A previous study on Peninsular Malaysia P. knowlesi rhoptry associated protein-1 (PkRAP1) gene has discovered the existence of dimorphism. In this study, genetic analysis of PkRAP1 in a larger number of P. knowlesi samples from Malaysian Borneo was conducted. The PkRAP1 of these P. knowlesi isolates was PCR-amplified and sequenced. The newly obtained PkRAP1 gene sequences (n=34) were combined with those from the previous study (n=26) and analysed for polymorphism and natural selection. Sequence analysis revealed a higher genetic diversity of PkRAP1 compared to the previous study. Exon II of the gene had higher diversity (π=0.0172) than exon I (π=0.0128). The diversity of the total coding region (π=0.0167) was much higher than those of RAP1 orthologues such as PfRAP-1 (π=0.0041) and PvRAP1 (π=0.00088). Z-test results indicated that the gene was under purifying selection. Phylogenetic tree and haplotype network showed distinct clustering of Peninsular Malaysia and Malaysian Borneo PkRAP1 haplotypes. This geographical-based clustering of PkRAP1 haplotypes provides further evidence of the dimorphism of the gene and possible existence of 2 distinct P. knowlesi lineages in Malaysia.