• Development and Reproduction
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• v.25 no.4
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• pp.305-311
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• 2021

The oligonucleotides polymers (ON-polymers) were used producing a total of 110 loci unique to each clam population (LUECP) in group one and 132 in group two, respectively, varying in amount of DNA fragments (FRs) from greater than near 50 to a smaller quantity than 1,050 bp. The larger FR amounts (>1,050 bp) are not noticed in the two Scapharca subcrenata groups. The ON-polymer OPD-01 produced 33 LUECP, which were defining each group, almost 300 bp, 450 bp, and 500 bp, in the group one. The OPD-15 recognized 22 loci shared by the two clam populations (Loci shared by the two clam populations, LSTCP), a variety of FRs of sizes 300 bp that were equivalent in all specimens. The mean number of LUECP was varied and 1.2-fold greater in the shellfish group two than in the group one. Respecting mean bandsharing (BS) grade outcomes, entities in the shellfish group one (0.779±0.011) had a little higher BS grades than did entities from the group two (0.756±0.009) (p<0.05). The entities of the shellfish group one are not tightly gathered with other entities of the group two. The genetic distance (GD) (0.422) of this invertebrate (SUBCRENATA 02 and 01) is 7.41-fold hereditarily distinct to the GD (0.057) of the other invertebrate (SUBCRENATA 22 and 19). The polar dendrogram (PDG) procured by the five ON-polymers underlines two characteristic groups.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.1
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• pp.31-37
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• 2019

Objective: At least eight local duck breeds have been recognized and documented as national germplasm of Indonesia so far. It is necessary to genetically characterize the local duck breeds for aiding conservation and future improvement strategies. Thus, this study was carried out to assess genetic diversity and phylogenetic relationship of eight local duck populations of Indonesia using microsatellite markers. Methods: In total, 240 individuals (30 individuals each population) from Alabio (AL), Bayang (BY), Magelang (MG), Mojosari (MJ), Pegagan (PG), Pitalah (PT), Rambon (RM), and Turi (TR) duck populations were genotyped using 22 microsatellite markers. Results: The results showed a moderate level of genetic diversity among populations, with a total of 153 alleles detected over all loci and populations, ranging from 3 to 22 alleles per locus. Observed (Ho) and expected heterozygosity (He), as well as polymorphism information content over all loci and populations were 0.440, 0.566, and 0.513, respectively. Heterozygote deficiency in the overall populations ($F_{IT}=0.237$), was partly due to the heterozygote deficiency within populations ($F_{IS}=0.114$) and moderate level of genetic differentiation among populations ($F_{ST}=0.137$). The most diverse population was MG (He = 0.545) and the least diverse population was AL (He = 0.368). The majority of populations were relatively in heterozygote deficiency (except AL), due to inbreeding. The genetic distances, phylogenetic trees, and principal coordinates analysis concluded that the populations can be grouped into two major clusters, resulting AL, MG, and MJ in one cluster separated from the remaining populations. Conclusion: The present study revealed a considerable genetic diversity of studied populations and thus, proper management strategies should be applied to preserve genetic diversity and prevent loss of alleles.

• Journal of Life Science
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• v.21 no.3
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• pp.385-392
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• 2011

The otter (Lutra lutra) in Korea is classified as a first grade endangered species and is managed under state control. We performed a phylogenetic analysis of the otter that inhabits the Changnyeong, Jinju, and Geoje areas in Gyeongsangnamdo, Korea using mtDNA and microsatellite (MS) markers. As a result of the analysis using the 676-bp D-loop sequence of mtDNA, six haplotypes were estimated from five single nucleotide polymorphisms. The genetic distance between the Jinju and Geoje areas was greater than distances within the areas, and the distance between Jinju and Geoje was especially clear. From the phylogenetic tree estimated using the Bayesian Markov chain Monte Carlo analysis by the MrBays program, two subgroups, one containing samples from Jinju and the other containing samples from the Changnyeong and Geoje areas were clearly identified. The result of a parsimonious median-joining network analysis also showed two clear subgroups, supporting the result of the phylogenetic analysis. On the other hand, in the consensus tree estimated using the genetic distances estimated from the genotypes of 13 MS markers, there were clear two subgroups, one containing samples from the Jinju, Geoje and Changnyeong areas and the other containing samples from only the Jinju area. The samples were not identically classified into each subgroup defined by mtDNA and MS markers. It could be inferred that the differential classification of samples by the two different marker systems was because of the different characteristics of the marker systems used, that is, the mtDNA was for detecting maternal lineage and the MS markers were for estimating autosomal genetic distances. Nonetheless, the results from the two marker systems showed that there has been a progressive genetic fixation according to the habitats of the otters. Further analyses using not only newly developed MS markers that will possess more analytical power but also the whole mtDNA are needed. Expansion of the phylogenetic analysis using otter samples collected from the major habitats in Korea should be helpful in scientifically and efficiently maintaining and preserving them.

• Asian-Australasian Journal of Animal Sciences
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• v.27 no.5
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• pp.616-627
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• 2014

The Lanyu is a miniature pig breed indigenous to Lanyu Island, Taiwan. It is distantly related to Asian and European pig breeds. It has been inbred to generate two breeds and crossed with Landrace and Duroc to produce two hybrids for laboratory use. Selecting sets of informative genetic markers to track the genetic qualities of laboratory animals and stud stock is an important function of genetic databases. For more than two decades, Lanyu derived breeds of common ancestry and crossbreeds have been used to examine the effectiveness of genetic marker selection and optimal approaches for individual assignment. In this paper, these pigs and the following breeds: Berkshire, Duroc, Landrace and Yorkshire, Meishan and Taoyuan, TLRI Black Pig No. 1, and Kaohsiung Animal Propagation Station Black pig are studied to build a genetic reference database. Nineteen microsatellite markers (loci) provide information on genetic variation and differentiation among studied breeds. High differentiation index ($F_{ST}$) and Cavalli-Sforza chord distances give genetic differentiation among breeds, including Lanyu's inbred populations. Inbreeding values ($F_{IS}$) show that Lanyu and its derived inbred breeds have significant loss of heterozygosity. Individual assignment testing of 352 animals was done with different numbers of microsatellite markers in this study. The testing assigned 99% of the animals successfully into their correct reference populations based on 9 to 14 markers ranking D-scores, allelic number, expected heterozygosity ($H_E$) or $F_{ST}$, respectively. All miss-assigned individuals came from close lineage Lanyu breeds. To improve individual assignment among close lineage breeds, microsatellite markers selected from Lanyu populations with high polymorphic, heterozygosity, $F_{ST}$ and D-scores were used. Only 6 to 8 markers ranking $H_E$, $F_{ST}$ or allelic number were required to obtain 99% assignment accuracy. This result suggests empirical examination of assignment-error rates is required if discernible levels of co-ancestry exist. In the reference group, optimum assignment accuracy was achievable achieved through a combination of different markers by ranking the heterozygosity, $F_{ST}$ and allelic number of close lineage populations.

• Asian-Australasian Journal of Animal Sciences
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• v.17 no.8
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• pp.1053-1061
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• 2004

Of the 20 arbitrarily chosen primers, six oligonucleotides decamer primers were used on the basis of the number of the polymorphisms generated in catfish (Silurus asotus) from Yesan and bullhead (Pseudobagrus fulvidraco) from Dangjin in Korea. Six primers were used generating a total of 602 scorable bands in catfish and 195 in bullhead population, respectively, ranging in size of DNA fragments from less than approximately 100 to larger than 2,000 base pairs (bp). Six primers yielded 199 polymorphic fragments (33.1%) in catfish and 47 (24%) in bullhead, respectively. In the present study, a total of 328 common fragments (an average of 54.7 per primer) were observed in catfish population, whereas 84 (an average of 14.0 per primer) in bullhead. The total number of specific fragments in catfish and bullhead population were 76 and 64, respectively. In catfish population, random decamer, OPA-17 (GACCGCTTGT) generated the highest number of fragments (a total of 141) in comparison with other primers used, with an average of 11.8. The common bands in the molecular weight of 300 bp generated by random primer OPA-06 (GGTCCCTGAC) were present in every individuals in bullhead population. The major polymorphic bands in the molecular weight of 100 bp generated by OPA-17 were identified in lane 14, 15, 17, 18, 19 20 and 21, which were identifying species in bullhead population. The average bandsharing values (BS values) of all of the samples within catfish population ranged from 0.575 to 0.945, whereas 0.063-1.000 within bullhead population. The bandsharing value (index of similarity between individuals) between individual No. 5 and No. 9 showed the highest level within catfish population, whereas the bandsharing value between individual No. 1 and No. 2 showed the lowest level. The single linkage cluster analysis resulted from four primers, indicating four genetic groupings composed of group 1 (C1-C10, all of the catfish samples), group 2 (B11, B12, B13, B14, B16, B17, B18, B19), group 3 (B15) and group 4 (B20 and B21). The dendrogram reveals close relationships between individual identities within two species populations and individuals derived from the same ancestor, respectively. However, genetic distances between two species populations ranged from 0.124 to 0.333. The shortest genetic distance (0.042) displaying significant molecular differences was between individual No. 6 and No. 9 catfish population. The shortest genetic distance (0.033) displaying significant molecular differences also was between individual No. 18 and No. 19 in bullhead population. Reversely, the genetic distance of individual No. 20/21 among individuals in bullhead population was highest (0.333). This result showed that bullhead No. 20 and 21 were distinct from other individuals within bullhead population.

• Development and Reproduction
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• v.10 no.2
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• pp.141-146
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• 2006

Genotype data from seven microsatellites typed in 231 animals were used to estimate the genetic structures of eight cow population distributed by regional area in Hanwoo (Korean cattle). In total, 53 alleles were detected from the genotyping of seven microsatellite markers. The average of expected heterozygosities ranged from 0.682 to 0.734 in 8 population of Hanwoo. Even though there were also some of alleles that were found in only specific regional population, similar frequency pattern for the most of alleles appeared in various 8 population. Genetic distances between populations were obtained using STDUPGMA method to construct a phylogenetic tree. The tree illustrated that most individuals were grouped on the basis of populations, distributed by the regional area. Some of genetic parameter on the basis of microsatellite gonotyping appears to provide a useful tool for examining the regional area kindship and genetic variation in Hanwoo.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.5
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• pp.613-619
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• 2005

Indigenous Yakutian cattle' adaptation to the hardest subarctic conditions makes them a valuable genetic resource for cattle breeding in the Siberian area. Since early last century, crossbreeding between native Yakutian cattle and imported Simmental and Kholmogory breeds has been widely adopted. In this study, variations at 22 polymorphic microsatellite loci in 5 populations of Yakutian, Kholmogory, Simmental, Yakutian-Kholmogory and Yakutian-Simmental cattle were analysed to estimate the genetic contribution of Yakutian cattle to the two hybrid populations. Three statistical approaches were used: the weighted least-squares (WLS) method which considers all allele frequencies; a recently developed implementation of a Markov chain Monte Carlo (MCMC) method called likelihood-based estimation of admixture (LEA); and a model-based Bayesian admixture analysis method (STRUCTURE). At population-level admixture analyses, the estimate based on the LEA was consistent with that obtained by the WLS method. Both methods showed that the genetic contribution of the indigenous Yakutian cattle in Yakutian-Kholmogory was small (9.6% by the LEA and 14.2% by the WLS method). In the Yakutian-Simmental population, the genetic contribution of the indigenous Yakutian cattle was considerably higher (62.8% by the LEA and 56.9% by the WLS method). Individual-level admixture analyses using STRUCTURE proved to be more informative than the multidimensional scaling analysis (MDSA) based on individual-based genetic distances. Of the 9 Yakutian-Simmental animals studied, 8 showed admixed origin, whereas of the 14 studied Yakutian-Kholmogory animals only 2 showed Yakutian ancestry (>5%). The mean posterior distributions of individual admixture coefficient (q) varied greatly among the samples in both hybrid populations. This study revealed a minor existing contribution of the Yakutian cattle in the Yakutian-Kholmogory hybrid population, but in the Yakutian-Simmental hybrid population, a major genetic contribution of the Yakutian cattle was seen. The results reflect the different crossbreeding patterns used in the development of the two hybrid populations. Additionally, molecular evidence for differences among individual admixture proportions was seen in both hybrid populations, resulting from the stochastic process in crossing over generations.

• Journal of Korean Society of Forest Science
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• v.96 no.6
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• pp.667-675
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• 2007

The genetic diversity and the spatial structure in two populations of Abelia tyaihyoni in Yeongwol region were studied by employing I-SSR markers. In spite of the limited distribution and small population sizes of Abelia tyaihyoni, the amount of genetic diversity estimated at the individual level was comparable to other shrub species (S.I.=0.336, h=0.217). Genetic diversity at the genet level was very similar to that at individual level. (S.l.=0.339, h=0.219). About 18.7 percent of total variation was allocated between two populations, which was slightly higher or similar level as compared with other shrub species. Genotypic diversity estimated by the ratio of the number of genets ($N_G$) over the total number of individuals (N) and a modified Simpson's index ($D_G$) were also higher than those of other shrubs. The maximum diameter of a genet did not exceed 5.5 m. The high level of gene and genotypic diversity, and the relatively limited maximum diameter of a genet suggested that the clonal propagation is not the most dominant factor in determining the population structure of Abelia tyaihyoni. Spatial autocorrelation analysis revealed significant spatial genetic structure within 12 m and 18 m distances in two populations A and B, respectively. Autocorrelations among individuals at the both individual and genet levels in each population didn't show any considerable differences. As a sampling strategy for ex-situ conservation of populations showing continuous distribution, a minimum distance of 18 m between individuals was recommended. For the populations with many segments, it was considered very crucial to sample materials from as many segments as possible.

• Korean Journal of Poultry Science
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• v.38 no.2
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• pp.81-87
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• 2011

The study was conducted to select and optimize microsatellite (MS) markers for evaluate Korean Native Chicken (KNC) breeds in order to provide standard for the classification and breed definition of the indigenous breeds. The study also aimed to characterize and classify each KNC populations for inventory and management of avian genetic resources. A total of 462 chickens from 11 populations of chicken breeds including eight KNC breeds and three commercial chicken breeds were analyzed with 19 MS markers. KNC breeds, especially Long-Tail Chicken breeds, formed separate cluster from those commercial chicken breeds. Genetic distances between KNC populations (0.11~0.18) were relatively shorter. Genetic uniformity of KNC (except KNCR breed) (0.86~0.88) were higher than that of commercial breeds (except Cornish) (0.95~0.97). On the other hand, genetic uniformity of KNC Long Tail (KNCLT) were relatively higher (0.91~0.97). The result can be used to evaluate and manage animal genetic resources at national scale.

• Korean Journal of Medicinal Crop Science
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• v.21 no.6
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• pp.444-454
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• 2013

The development of random amplified polymorphic DNA (RAPD) and expressed sequence tag-derived simple sequence repeats (EST-SSRs) provided a useful tool for investigating Korean ginseng genetic diversity. In this study, 18 polymorphic markers (7 RAPD and 11 EST-SSR) selected to assess the genetic diversity in 31 ginseng accessions (11 Korean ginseng cultivars and 20 breeding lines). In RAPD analysis, a total of 53 unique polymorphic bands were obtained from ginseng accessions and number of amplicons ranged from 4 to 11 with a mean of 7.5 bands. Pair-wise genetic similarity coefficient (Nei) among all pairs of ginseng accessions varied from 0.01 to 0.32, with a mean of 0.11. On the basis of the resulting data, the 31 ginseng accessions were grouped into six clusters. As a result of EST-SSR analysis, 11 EST-SSR markers detected polymorphisms among the 31 ginseng accessions and revealed 49 alleles with a mean of 4.45 alleles per primer. The polymorphism information content (PIC) value ranged from 0.06 to 0.31, with an average of 0.198. The 31 ginseng accessions were classified into five groups by cluster analysis based on Nei's genetic distances. Consequently, the results of ginseng-specific RAPD and EST-SSR markers may prove useful for the evaluation of genetic diversity and discrimination of Korean ginseng cultivars and breeding lines.