• Korean Journal of Plant Taxonomy
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• v.53 no.1
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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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• v.29 no.3
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• pp.327-332
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• 2016

The genetic relationships between different populations and breeds of exotic dairy goats in Thailand were studied using 12 microsatellite markers. Blood samples were obtained from 211 goats from Department of Livestock Development breeding and research farms: 29 Anglonubian (AN), 21 Alpine (AP), 23 Jamunapari (JAM), 50 Saanen (SN), and 88 Toggenburg (TG). Five of the 12 microsatellite markers were found to be polymorphic. A mean of 7.40 alleles per locus was found, with a range from 5 (SPS115 and ETH225) to 11 (TGLA122). We found 24, 27, 19, 32, and 24 alleles in the AN, AP, JAM, SN, and TG breeds, respectively; 37 alleles were present in all breeds. The mean number of alleles in each population ranged from 3.2 (ETH225 locus) to 7.6 (TGLA122 locus). Genetic variability within the breeds was moderate as evidenced by the mean expected heterozygosity of 0.539. The average observed heterozygosity across the 5 markers in all breeds was 0.529 with the maximum observed at the BM1818 locus (0.772) and the minimum at the ETH225 locus (0.248). The observed and expected heterozygosity for all breeds for the 5 microsatellite markers ranged from 0.419 to 0.772 and 0.227 to 0.792, respectively. On the basis of their means, the TGLA122 and BM1818 loci were the most suitable markers for distinguishing genetic diversity among the goats. The estimated average $F_{is}$ value for the breeds ranged from -0.044 (ETH225) to 0.180 (SPS115), while the estimated average $F_{st}$ value ranged from 0.021 (SPS115) to 0.104 (ETH10). These results indicated that TGLA122 and BM1818 markers are suitable to be used for aiding conservation and breeding improvement strategies of dairy.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.59 no.4
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• pp.492-497
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• 2014

Soybean (Glycine max L.) is crucial legume crop as source of high quality vegetable protein and oil, and Korea is regarded as a part of center of soybean origin. To expand the information of conserved genetic diversity, we analyzed the genetic variability of soybean collection mainly introduced Korean accessions using 75 microsatellite markers. A total of 1,503 alleles with an average value of 20.0 alleles were detected among 644 accessions. Korean collection revealed average allele number of 13.4 while Chinese, Japanese and Southeast Asian accessions showed 9.0, 5.4 and 6.5 mean alleles, respectively. Especially, Korean accessions showed more number of private allele per locus as 3.4 contrary to other geographical groups. The mean expected heterozygosity and polymorphic information content was 0.654 and 0.616, respectively, and expected heterozygosity values were not significantly distinguished according to the geographical groups. The phylogenetic dendrogram and deduced population structure based on DNA profiles of 75 SSR loci showed Korean accessions formed distinct gene pool against Chinese accessions, and could be divided into five subpopulations. Korean soybean accessions have specific genetic diversity and might be serve the valuable alleles for bio-industry as a part of the center of soybean origin.

• International Journal of Industrial Entomology and Biomaterials
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• v.19 no.2
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• pp.249-253
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• 2009

Raily ecorace of Indian tasar silkworm is wild in nature and distributed abundantly in dense deciduous forest on Shorea robusta (Sal) in Bastar ($17^{\circ}4'$ and $20^{\circ}34'$ N, $80^{\circ}15'$ and $82^{\circ}15'$ E and altitude ranging from 150 to 1200 mMSL) forest ranges of Chhattisgarh, India. It is represented by about 20 populations. Out of those, eleven populations showed intra- as well as inter- population variability based on phenotypic expression and also in major economic traits viz. cocoon weight, shell weight, filament length and denier. Genetic diversity in these eleven populations was studied using Inter-Simple Sequence Repeat (ISSR) markers. The band profiles generated with eight ISSR primers have depicted variation in band size. All the primers exhibited polymorphism which is an indicative of the genetic variation in individual Raily silkworm. Among the populations, total polymorphism recorded was 76%. The population genetic aspects assessed through POPGENE software package are discussed in the paper. Nei's gene diversity (h) ranged from 0.194 to 0.337 exhibiting high heterozygosity. Relevance of the present study is of high significance in formulating conservation strategies and sustainable utilization of the economically important Raily ecorace of Antheraea mylitta.

• Korean Journal of Agricultural Science
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• v.45 no.4
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• pp.575-582
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• 2018

Bacterial fruit blotch (BFB) caused by Acidovorax citrulli is a devastating disease found in many cucurbits cultivation fields. The genetic diversity for 29 strains of A. citrulli collected from various cucurbits in South Korea was determined by DNA fingerprinting with a pathogenicity test, multi locus analysis, Rep-PCR (repetitive sequence polymerase chain reaction), and URP (universal rice primers) PCR bands. Two distinct groups (Korean Clonal Complex, KCC1 and KCC2) in the population were identified based on group specific genetic variation in the multi locus phylogeny using six conserved loci and showed a very high similarity with DNA sequences for representative foreign groups [the group I (CC1-1 type) and the group II (CC2-5 type)] widely distributed worldwide, respectively. Additionally, in the case of phaC, a new genotype was found within each Korean group. The KCC1 was more heterogeneous compared to the KCC2. The KCC1 recovered mainly from melons and watermelons (ratio of 6 : 3) and 15 of the 20 KCC2 strains recovered from watermelons were dominant in the pathogen population. Accordingly, this study found that two distinct groups of differentiated A. citrulli exist in South Korea, genetically very similar to representative foreign groups, with a new genotype in each group resulting in their genetic diversity.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.212-212
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• 2022

Soluble starch synthase (SS) IV-2 is one of the starch synthase gene family members and responsible for starch chain elongation interacting with other rice eating and cooking quality controlling genes (e.g., AGPlar and PUL). SSIV-2 is mainly expressed in leaves, especially at grain-filling stage and its alleles can significantly affect rice quality. Here, we investigated the genetic diversity and population structure analyses of SSIV-2 gene by using 374 rice accessions. This rice set was grouped into 320 cultivated bred (subsequently classified into temperate japonica, indica, tropical japonica, aus, aromatic and admixture) and 54 wild rice. Haplotyping of cultivated rice accessions provided a total of 7 haplotypes, and only three haplotypes are functional indicating four substituted SNPs in two exons of chromosome 5: T/A and G/T in exon 4, and C/G and G/A in exon 13. Including the wild, a highest diverse group (0.0041), nucleotide diversity analysis showed temperate japonica (0.0001) had a lowest diversity value indicating the origin information of this gene evolution. Higher and positive Tajima5s D value of indica (1.9755) indicate a selective signature under balancing selection while temperate japonica (-0.9018) was in lowest Tajima's D value due to a recent selective sweep by positive selection. We found the most diverse genetic components of the wild in PCA but shared in some portion with other cultivated groups. Fixation index (F_ST-values) and phylogenetic analysis indicate a closer relationship of the wild with indica (F_ST=0.256) than to its association to both of temperate japonica (F_ST=0.589). Structure analysis shows a clear separation of cultivated subpopulations at every K value, but genetic components were admixed within the wild illustrating the same genetic background with japonica and indica in some proportion.

• Animal Systematics, Evolution and Diversity
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• v.32 no.2
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• pp.105-111
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• 2016

The genetic structure of marine animals that inhabit the seashore is affected by numerous factors. Of these, gene flow and natural selection during recruitment have strong influences on the genetic structure of seashore-dwelling species that have larval periods. Relative contributions of these two factors to the genetic structure of marine species would be determined mainly by the duration of larval stage. The relationship between larval period and genetic structure of population has been rarely studied in Korea. In this study, genetic variations of cytochrome oxidase subunit I (COI) were analyzed in two dominant species on rocky shore habitats in the Korean peninsula: periwinkle Littorina brevicula and acorn barnacle Fistulobalanus albicostatus. Both species are not strongly structured and may have experienced recent population expansion. Unlike periwinkle, however, barnacle populations have considerable genetic variation, and show a bimodal pattern of mismatch distribution. These results suggest that barnacle populations are more affected by local adaptation rather than gene flow via larval migration. The bimodal patterns of barnacle populations observed in mismatch distribution plots imply that they may have experienced secondary contact. Further studies on seashore-dwelling species are expected to be useful in understanding the evolution of the coastal ecosystem around Korean waters.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.1
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• pp.14-19
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• 2015

The genetic diversity of native chicken populations from Myanmar, Thailand, and Laos was examined by using 102 insertion and/or deletion (indels) markers. Most of the indels loci were polymorphic (71% to 96%), and the genetic variability was similar in all populations. The average observed heterozygosities ($H_O$) and expected heterozygosities ($H_E$) ranged from 0.205 to 0.263 and 0.239 to 0.381, respectively. The coefficients of genetic differentiation (Gst) for all cumulated populations was 0.125, and the Thai native chickens showed higher Gst (0.088) than Myanmar (0.041) and Laotian (0.024) populations. The pairwise Fst distances ranged from 0.144 to 0.308 among populations. A neighbor-joining (NJ) tree, using Nei's genetic distance, revealed that Thai and Laotian native chicken populations were genetically close, while Myanmar native chickens were distant from the others. The native chickens from these three countries were thought to be descended from three different origins (K = 3) from STRUCTURE analysis. Genetic admixture was observed in Thai and Laotian native chickens, while admixture was absent in Myanmar native chickens.

• Animal Bioscience
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• v.34 no.11
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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.

• Animal Bioscience
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• v.37 no.5
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• pp.795-806
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• 2024

Objective: Karan Fries (KF), a high-producing composite cattle was developed through crossing indicine Tharparkar cows with taurine bulls (Holstein Friesian, Brown Swiss, and Jersey), to increase the milk yield across India. This composite cattle population must maintain sufficient genetic diversity for long-term development and breed improvement in the coming years. The level of linkage disequilibrium (LD) measures the influence of population genetic forces on the genomic structure and provides insights into the evolutionary history of populations, while the decay of LD is important in understanding the limits of genome-wide association studies for a population. Effective population size (N_e) which is genomically based on LD accumulated over the course of previous generations, is a valuable tool for e valuation of the genetic diversity and level of inbreeding. The present study was undertaken to understand KF population dynamics through the estimation of N_e and LD for the long-term sustainability of these breeds. Methods: The present study included 96 KF samples genotyped using Illumina HDBovine array to estimate the effective population and examine the LD pattern. The genotype data were also obtained for other crossbreds (Santa Gertrudis, Brangus, and Beefmaster) and Holstein Friesian cattle for comparison purposes. Results: The average LD between single nucleotide polymorphisms (SNPs) was r² = 0.13 in the present study. LD decay (r² = 0.2) was observed at 40 kb inter-marker distance, indicating a panel with 62,765 SNPs was sufficient for genomic breeding value estimation in KF cattle. The pedigree-based N_e of KF was determined to be 78, while the N_e estimates obtained using LD-based methods were 52 (SNeP) and 219 (genetic optimization for N_e estimation), respectively. Conclusion: KF cattle have an N_e exceeding the FAO's minimum recommended level of 50, which was desirable. The study also revealed significant population dynamics of KF cattle and increased our understanding of devising suitable breeding strategies for long-term sustainable development.