• Asian Pacific Journal of Cancer Prevention
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• v.15 no.3
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• pp.1255-1262
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• 2014

Background: The aim of the study was to investigate any associations between benign prostate hyperplasia (BPH) and single nucleotide polymorphisms (SNPs) in the VDR gene (FokI, BsmI, ApaI and Taq${\alpha}$I loci) and the CYP17 gene (MspA1I locus), as well as TA repeat polymorphism in SRD5A2 gene among Lebanese men. Materials and Methods: DNA extracted from blood of 68 subjects with confirmed BPH and 79 age-matched controls was subjected to PCR/PCR-restriction fragment length polymorphism analysis. The odds ra=tio (OR) of having a genotype and the relative risk (RR) of developing BPH for having the genotype were calculated and the alleles were designated risk-bearing or protective. Results: Our data indicated that the A and B alleles of the VDR ApaI and BsmI SNPs were highly associated with increased risk of BPH (p=0.0168 and 0.0002, respectively). Moreover, 63% of the controls compared to 43% of the subjects with BPH were homozygous for none of the risk-bearing alleles (p=0.0123) whereas 60% of the controls and 28% of the subjects with BPH were homozygous for two or more protective alleles (p<0.0001). Conclusions: For the first time, our study demonstrated that ApaI and BsmI of the VDR gene are associated with risk of BPH among Lebanese men. Our study also indicated that overall polymorphism profile of all the genes involved in prostate physiology could be a better predictor of BPH risk.

• Asian-Australasian Journal of Animal Sciences
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• v.23 no.2
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• pp.154-161
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• 2010

The level of genetic differentiation and genetic structure in a Chinese native chicken breed, Bian chicken, and two controlled chicken populations (Jinghai chicken and Youxi chicken in China) were analysed based on 29 microsatellite markers. A total of 166 distinct alleles were observed across the 3 breeds, and 32 of these alleles (19.3%) were unique to only 1 breed. Bian chicken carried the largest number of private alleles at 15 (46.9%), followed by the Jinghai chicken with 12 private alleles (37.5%). The average polymorphism information content (0.5168) and the average expected heterozygote frequency (0.5750) of the Bian chicken were the highest, and those of the Jinghai chicken were 0.4915 and 0.5505, respectively, which were the lowest. Among 29 microsatellite loci, there were 15 highly informative loci in Bian chicken, and the other 14 were reasonably informative loci. The highly informative loci in Jinghai chicken and Youxi chicken were 17 and 14 respectively. Significant deviations from the Hardy-Weinberg equilibrium were observed at several locus-breed combinations, showing a deficit of heterozygotes in many cases. As a whole, genetic differentiation among the breeds estimated by the fixation index (Fst) were at 6.7% (p<0.001). The heterozygote deficit within population (Fis) was 22.2% (p<0.001), with the highest (0.249) in Bian chicken and lowest (0.159) in Youxi chicken. These results serve as an initial step in the plan for genetic characterization and conservation of the Chinese chicken genetic resource of Bian, as well as Jinghai and Youxi chickens.

• 한국균학회소식:학술대회논문집
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• 2018.05a
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• pp.37-37
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• 2018

Mating type of Lentinula edodes is determined by two unlinked genetic loci, A and B. To better understand mating behavior of L. edodes, we investigated variations in mating type genes in129 dikaryotic strains collected from East Asia. Through sequence analysis of A locus, we discovered that hypervariable region spanning N-term of HD2-intergenic region-N-term of HD1 could represent A mating type. Mating and hypervariable region analyses revealed 70 unique A mating types: 27 from 98 cultivated strains, 53 from 31 wild strains, and 10 commonly found. It was also revealed that only a few A mating type alleles such as A1, A4, A5, and A7 were prevalent in cultivated strains. Contrarily, A mating type in wild strains was highly diverse: 23 unique A alleles were discovered in small mountainous area in Korean peninsula, suggesting rapid evolution of A mating type in nature. The B locus was assessed by allelic variations in pheromone (PHB) and pheromone receptor (RCB) pairs which constituted subloci Ba and Bb. Sequence analyses and mating assay revealed 5 alleles of RCB1 with 9 associated PHBs in Ba sublocus and 3 alleles of RCB2 with 5 associated PHBs in Bb sublocus. Each RCB was primarily associated with two PHBs. Each PHB-RCB pair was always discovered as a distinct unit. This allowed us to propose 15 B mating types via combinations of five Ba and three Bb subloci. Further investigation on 129 strains confirmed that the B locus, unlike the A locus, was indeed restricted to 15 mating types. Thus, the total number of mating types became 1,050 in L. edodes through a combination of 70 A and 15 B. This number will further increase because of rapid diversification of A mating type. Our findings provide a comprehensive and practical knowledge on mating behaviors of L. edodes.

• International Journal of Industrial Entomology and Biomaterials
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• v.25 no.1
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• pp.81-92
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• 2012

A total of 85 Chinese-origin silkworm strains preserved in Korea were genotyped for eight polymorphic micro-satellite loci. We obtained per-locus number of alleles, ranging from 5 to 14 with an average value of 9.5, perlocus observed heterozygosity, ranging from 0.07 to 0.99, and per-locus polymorphic information content (PIC), ranging from 0.34 to 0.82, indicating that some loci are highly variable. Phylogenetic analysis with the eight concatenated microsatellite loci showed no clustering on the basis of known strain characteristics. A total of 22 strain-specific apomorphic alleles, which discriminate 19 among 85 silkworm strains were obtained from eight loci. These strain-specific alleles, thus, can casually be utilized for the discrimination of applicable strains without any further typing of other loci. Furthermore, a substantial number of homozygote strains, represented by 27 among 76 alleles in eight loci were found. These results collectively suggest that the silkworm microsatellite DNA is actually and potentially important molecular markers for the eventual discrimination of silkworm strains that are preserved as hundreds in Korea.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.2
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• pp.176-182
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• 2019

Objective: This study was conducted to investigate basic information on genetic structure and characteristics of Limousin population in Hungary. Obtained results will be taken into consideration when adopting the new breeding strategy by the Association of Hungarian Limousin and Blonde d'Aquitaine Breeders (AHLBB). Methods: Genetic diversity and phylogenetic relationship of 3,443 Limousin cattle from 16 different herds were investigated by performing genotyping using 18 microsatellite markers. Amplified DNA was genotyped using an automated genetic analyzer. Results: Mean of effective alleles ($n_e$) of the populations was 3.77. Population C had the lowest number of effective alleles (3.01) and the lowest inbreeding coefficient ($F_{IS}$) value (-0.15). Principal component analysis of estimated genetic distance ($F_{ST}$) values (p<0.000) revealed two herds (C and E) distinct from the majority of other Limousin herds. The pairwise $F_{ST}$ values of population C compared to the others (0.066 to 0.120) fell into the range of moderate genetic distance: 0.050 to 0.150, while population E displayed also moderate genetic distance ($F_{ST}$ values in range 0.052 to 0.064) but only to six populations (G, H, J, L, N, and P). $F_{ST(C-E)}$ was 0.148, all other pairs -excluding C and E herds- displayed low genetic distance ($F_{ST}$<0.049). Population D, F, I, J, K, L, N, O, and P carried private alleles, which alleles belonged to 1.1% of the individuals. Most probable number of clusters (K) were 2 and 7 determined by Structure and BAPS software. Conclusion: This study showed useful genetic diversity and phylogenetic relationship data that can be utilized for the development of a new breeding strategy by AHLBB. The results presented could also contribute to the proper selection of animals for further whole genome scan studies of Limousins.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.4
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• pp.467-476
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• 2019

Objective: This research was conducted to study the genetic diversity in several Indonesian cattle breeds using microsatellite markers to classify the Indonesian cattle breeds. Methods: A total of 229 DNA samples from of 10 cattle breeds were used in this study. The polymerase chain reaction process was conducted using 12 labeled primers. The size of allele was generated using the multiplex DNA fragment analysis. The POPGEN and CERVUS programs were used to obtain the observed number of alleles, effective number of alleles, observed heterozygosity value, expected heterozygosity value, allele frequency, genetic differentiation, the global heterozygote deficit among breeds, and the heterozygote deficit within the breed, gene flow, Hardy-Weinberg equilibrium, and polymorphism information content values. The MEGA program was used to generate a dendrogram that illustrates the relationship among cattle population. Bayesian clustering assignments were analyzed using STRUCTURE program. The GENETIX program was used to perform the correspondence factorial analysis (CFA). The GENALEX program was used to perform the principal coordinates analysis (PCoA) and analysis of molecular variance. The principal component analysis (PCA) was performed using adegenet package of R program. Results: A total of 862 alleles were detected in this study. The INRA23 allele 205 is a specific allele candidate for the Sumba Ongole cattle, while the allele 219 is a specific allele candidate for Ongole Grade. This study revealed a very close genetic relationship between the Ongole Grade and Sumba Ongole cattle and between the Madura and Pasundan cattle. The results from the CFA, PCoA, and PCA analysis in this study provide scientific evidence regarding the genetic relationship between Banteng and Bali cattle. According to the genetic relationship, the Pesisir cattle were classified as Bos indicus cattle. Conclusion: All identified alleles in this study were able to classify the cattle population into three clusters i.e. Bos taurus cluster (Simmental Purebred, Simmental Crossbred, and Holstein Friesian cattle); Bos indicus cluster (Sumba Ongole, Ongole Grade, Madura, Pasundan, and Pesisir cattle); and Bos javanicus cluster (Banteng and Bali cattle).

• Nutrition Research and Practice
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• v.17 no.1
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• pp.62-72
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• 2023

BACKGROUND/OBJECTIVES: Many studies have revealed an association between fat mass and the obesity-related gene (FTO) and obesity. On the other hand, no meta-analysis was conducted with data from only Koreans. Therefore, this study performed a meta-analysis using Korean data to provide evidence for the association between FTO single nucleotide polymorphisms (SNPs) and the risk of obesity among Korean adults. SUBJECT/METHODS: Meta-analysis was finally conducted with data extracted from seven datasets of four studies performed on Korean adults after the screening passed. Five kinds of FTO SNPs (rs9939609, rs7193144, rs9940128, rs8050136, and rs9926289) were included, and the relationship between FTO SNPs and body mass index (BMI) was investigated using linear regression with an additive model adjusted for covariants, such as age, sex, and area. RESULTS: The minor alleles of FTO SNPs were associated with increased BMI (odds ratio [OR], 1.31; 95% confidence interval [CI], 1.21-1.42). In sub-group analysis, FTO rs9939609 T>A was significantly associated with BMI (OR, 1.23; 95% CI, 1.06-1.42). The other FTO SNPs together were significantly associated with BMI (OR, 1.37; 95% CI, 1.25-1.49). The publication bias was not observed based on Egger's test. CONCLUSIONS: This meta-analysis showed that minor alleles in the FTO SNPs were significantly associated with an increased BMI among Korean adults. This meta-analysis is the first to demonstrate that minor alleles in the FTO SNPs contribute significantly to the increased risk of obesity among Korean adults using data from a Korean population.

• Journal of Korean Society of Forest Science
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• v.43 no.1
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• pp.39-50
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• 1979

Twelve Pinus taeda were used as mother trees and one P. rigida plus tree was used as pollen tree for 12 cross combinations. Nine P. densiflora plus trees(4 mother and 7 pollen trees) were used as parents for 11 cross combinations. Those parents and 10 progenies were analyzed for LAP of ${\times}$P. taeda rigida hybrid and P. densiflora and for peroxidase of ${\times}$P. taeda rigida. The analysis, based on the banding patterns, indicate three alleles for LAP-A locus(A1, A2, A3) and two alleles for LAP-B locus (B1, B2) in ${\times}$P. taeda rigida hybrids. Chi-square test on the segregation for progenies did not show significant differences. The results indicated good agreement with monohybrid Mendelian inheritance. Independence test for occurrence frequency of 2 alleles(LAP-A3, LAP-B2) illustrated that there is neither linkage nor repulsion relationship between LAP-A3 and LAP-B2 alleles. Three band at LAP-A locus were always exhibited from all parents and their progenies of P. densiflora. However, the occurrence of two bands at LAP-B locus was variable, one bands assumed as homozygous alleles(B2/B2) and two bands as heterozygous alleles(B1/B2). The segregation ratio for progenies of P. densiflora suggested that LAP-B locus may be controlled by two alleles(B1 and B2). Three Peroxidase loci(Px-A, Px-B, Px-C) assumed to be controlled by allozyme in ${\times}$P. taeda rigida hybrid. The Px-B and Px-C loci could not find out the variations from banding patterns of parents and their progenies, while the Px-A locus showed the variations of occurrence frequency by two bands. The segregation ratio for A1/A2 at LAP-A locus suggest that the peroxidase allozymes of ${\times}$P. taeda rigida hybrid appeare to be monomeric products; that is, Px-A locus may be controlled by two alleles (A1 and A2).

• Asian-Australasian Journal of Animal Sciences
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• v.22 no.1
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• pp.1-6
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• 2009

Genetic variability is an important component in the ability of populations to adapt in the face of environmental change. Severe human impacts reduced Muzzafarnagri sheep of India from 500,000 in 1972 to 10,989 in 1973-74. Here we report for the first time the effect of this population decline on levels of genetic variability at 13 FAO recommended ovine microsatellite loci and contrast levels of variability to that in a breed from the same geographical region, which differed in numbers, by an order of magnitude (Marwari sheep). Of the 13 loci, 100% were polymorphic in both breeds. A high degree of genetic variation was observed within populations in terms of both allele diversity (number of alleles per locus, >4) and gene diversity (expected heterozygosity, >0.5), which implied that there is still a substantial amount of genetic diversity at the nuclear loci in a declining population. Nevertheless, overall low number of alleles per locus and relatively less abundance of low frequency alleles in Muzzafarnagri sheep suggested that genetic variability has been comparatively reduced in this population. Bottleneck analysis indicated that a genetic bottleneck did not occur during the most recent decline. In addition, we found that the differentiation among populations was moderate ($F_{ST}$= 11.8%). This study on assessment of genetic effects of the population declines in ovines is a step towards identification of genetically impoverished or healthy populations, which could prove to be a useful tool to facilitate conservation planning in this important species of small ruminants.

• BMB Reports
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• v.28 no.4
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• pp.359-362
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• 1995

The highly polymorphic variable number of tandem repeat (VNTR) loci in the human genome are informative markers for the genetic characterization of individuals in the paternity test and forensic science as well as for the study of human disease. In this study, VNTR loci D1S80 and D2S123 have been amplified by PCR and the amplified length polymorphic alleles were detected with a discontinuous vertical PAGE system and silver staining. For explicit DNA typing, PCR optimization, in which amplification efficiencies are similar over a wide range of allele sizes, non-specific amplifications are minimal, and new longer alleles have high amplification efficiency, has been performed by changing the PCR reaction buffer composition and thermal cycling conditions. It turned out that adding an appropriate amount of Tween 20 and NP40 to the PCR reaction buffer and raising the annealing temperature to $68^{\circ}C$ in thermal cycling made it possible for optimal VNTR loci amplification. A modified PAGE system for VNTR separation was established. Under these conditions, new longer alleles in the 01580 locus were discovered and 025123 pattern changes in colorectal tumors were observed. These technical tips are valuable for detecting various amplified fragment length polymorphisms.