• Animal Bioscience
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• v.37 no.8
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• pp.1355-1366
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• 2024

Objective: The analysis of runs of homozygosity (ROH) has been applied to assess the level of inbreeding and identify selection signatures in various livestock species. The objectives of this study were to characterize the ROH pattern, estimate the rate of inbreeding, and identify signatures of selection in the red-brown Korean native chickens. Methods: The Illumina 60K single nucleotide polymorphism chip data of 651 chickens was used in the analysis. Runs of homozygosity were analysed using the PLINK v1.9 software. Inbreeding coefficients were estimated using the GCTA software and their correlations were examined. Genomic regions with high levels of ROH were explored to identify selection signatures. Results: A total of 32,176 ROH segments were detected in this study. The majority of the ROH segments were shorter than 4 Mb. The average ROH inbreeding coefficients (F_ROH) varied with the length of ROH segments. The means of inbreeding coefficients calculated from different methods were also variable. The correlations between different inbreeding coefficients were positive and highly variable (r = 0.18-1). Five ROH islands harbouring important quantitative trait loci were identified. Conclusion: This study assessed the level of inbreeding and patterns of homozygosity in Red-brown native Korean chickens. The results of this study suggest that the level of recent inbreeding is low which indicates substantial progress in the conservation of red-brown Korean native chickens. Additionally, Candidate genomic regions associated with important production traits were detected in homozygous regions.

• Clinical and Experimental Reproductive Medicine
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• v.29 no.3
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• pp.187-193
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• 2002

Objective : To analyze the interrelationship between homocysteine and methylenetetrahydrofolate reductase (MTHFR) mutation in patients with recurrent spontaneous abortion. Material and Method: Homocysteine and MTHFR mutation were tested by fluorescent polarizing immunoassay and PCR-RFLP method, respectively. Results: In patients with homocysteine level less than 5 ?mol/L, there was no case of normal group but there were four cases of heterozygosity and one case of homozygosity. In patients with homocysteine level 5$\sim$10 ? mol/L, the number of normal, heterozygosity and homozygosity group were eleven, eighteen and eight, respectively. In patients with homocysteine level $10{\sim}15$ ? mol/L, the number of normal, heterozygosity and homozygosity group were four, one and one, respectively. In patients with homocysteine level more than 15 ? mol/L, there was no case of normal and heterozygosity group but there were two cases of homozygosity. Conclusions: Hyperhomocysteinemia due to MTHFR mutation is a cause of recurrent spontaneous abortion. And there was a significant relationship between homocysteine and MTHFR mutation.

• Animal Bioscience
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• v.34 no.12
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• pp.1895-1902
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• 2021

Objective: Runs of homozygosity (ROH) are contiguous lengths of homozygous genotypes that can reveal inbreeding levels, selection pressure, and mating schemes. In this study, ROHs were evaluated in Wannan Black pigs to assess the inbreeding levels and the genome regions with high ROH frequency. Methods: In a previous study, we obtained 501.52 GB of raw data from resequencing (10×) of the genome and identified 21,316,754 single-nucleotide variants in 20 Wannan Black pig samples. We investigated the number, length, and frequency of ROH using resequencing data to characterize the homozygosity in Wannan Black pigs and identified genomic regions with high ROH frequencies. Results: In this work, 1,813 ROHs (837 ROHs in 100 to 500 kb, 449 ROHs in 500 to 1,000 kb, 527 ROHs in >1,000 kb) were identified in all samples, and the average genomic inbreeding coefficient (F_ROH) in Wannan Black pigs was 0.5234. Sixty-one regions on chromosomes 2, 3, 7, 8, 13, 15, and 16 harbored ROH islands. In total, 105 genes were identified in 42 ROH islands, among which some genes were related to production traits. Conclusion: This is the first study to identify ROH across the genome of Wannan Black pigs, the Chinese native breed of the Anhui province. Overall, Wannan Black pigs have high levels of inbreeding due to the influence of ancient and recent inbreeding due to the genome. These findings are a reliable resource for future studies and contribute to save and use the germplasm resources of Wannan Black pigs.

• Asian-Australasian Journal of Animal Sciences
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• v.27 no.12
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• pp.1691-1694
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• 2014

Copy number variation (CNV) or single nucleotide phlyorphism (SNP) is useful genetic resource to aid in understanding complex phenotypes or deseases susceptibility. Although thousands of CNVs and SNPs are currently avaliable in the public databases, they are somewhat difficult to use for analyses without visualization tools. We developed a web-based tool called the VCS (visualization of CNV or SNP) to visualize the CNV or SNP detected. The VCS tool can assist to easily interpret a biological meaning from the numerical value of CNV and SNP. The VCS provides six visualization tools: i) the enrichment of genome contents in CNV; ii) the physical distribution of CNV or SNP on chromosomes; iii) the distribution of log2 ratio of CNVs with criteria of interested; iv) the number of CNV or SNP per binning unit; v) the distribution of homozygosity of SNP genotype; and vi) cytomap of genes within CNV or SNP region.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.25 no.3
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• pp.21-30
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• 1980

This is the fourth report in serial studies on the botanical characters of Korean maize lines collected. Several plant characters and genetical nature of lines were investigated and compared among selfed, sibbed and test crossed lines. Inbreeding depression and heterosis, and homozygosity expressed in percent were calculated. Throughout the study a great extent of variation of plant characters and genetical variation expressed in terms of inbreeding depression and heterosis were observed. The observed plant and genetic variation of plant characters were assumed to be enough for providing new breeding materials for future maize breeding program. The degree of homozygosity of Korean local maize lines suggested that a great portion of maize grown by Korean farmers presently are near or close to inbred and presumed to show a great heterosis when crossed to divergent lines.

• The Korean Journal of Zoology
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• v.30 no.1
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• pp.44-52
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• 1987

The spontaneous bilateral asymmetry was analyzed in the hermaphroditic fish Rivulus marmoratus to obtain base line data on the developmental stability of this fish. The results obtained were as follows; 1. Eight kinds of countable anatomical characters except numbers of otolith and radii branchiostegi showed bilateral asymmetry at the frequency ranging from 9.8% to 64.7%. 2. Asymmetry index was not significantly different from that of gonochoristic fish species previously reported. Genetical implication of the results was discussed in relation to developmental stability and homozygosity of this species.

• Journal of applied mathematics & informatics
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• v.29 no.3_4
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• pp.1043-1048
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• 2011

W. Choi([1]) identified and characterized the limiting diffusion of this diploid model by defining discrete generator for the rescaled Markov chain. We denote by F the homozygosity and by S the average selection intensity. In this note, we define the Fleming-Viot process with generator of limiting diffusion and provide exact result for the relations of F and S.

• Clinical and Experimental Reproductive Medicine
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• v.28 no.3
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• pp.247-253
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• 2001

Objective: To analyze the methylenetetrahydrofolate reductase (MTHFR) mutation in patients with recurrent spontaneous abortion. Material and Method: The blood samples of patients with recurrent spontaneous abortion were tested by PCR-RFLP method. Results: Of 51 cases of study group, 14 (27.5%) were normal, 25 (49.0%) were heterozygosity, and 12 (23.5%) were homozygosity. Of 58 cases of control group, 20 (34.5%) were normal, 30 (51.7%) were heterozygosity, and 8 (13.8%) were homozygosity. But the difference between two groups was not significant (p=0.190). Conclusion: Hyperhomocysteinemia due to MTHFR mutation is a cause of recurrent spontaneous abortion. Therefore, the study for MTHFR mutation should be included in the workup of recurrent spontaneous abortion.

• Clinical and Experimental Reproductive Medicine
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• v.47 no.2
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• pp.122-129
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• 2020

Objective: The survival of a semi-allogeneic fetus depends on several immunological mechanisms, and it has been suggested that recurrent pregnancy loss (RPL) could develop as a result of one or more immunological abnormalities. Methods: Compatibility between partners for human leukocyte antigen (HLA) genotypes and the relationships between maternal killer-cell immunoglobulin-like receptor (KIR) and paternal HLA-Bw4/Bw6 and HLA-C1/C2 supra-groups were investigated in 25 couples with RPL in comparison to healthy couples with children. HLA and KIR genotyping was performed using polymerase chain reaction with sequence-specific primers and/or sequence-specific oligonucleotides. Results: HLA class I incompatibility between partners, especially in HLA-B alleles, was more common in the RPL group (p= 0.01). HLA-C2 homozygosity was more frequent in the male partners of RPL couples than in other groups (p= 0.03). The KIR2DL5 gene frequency was significantly higher in both the female and male partners of RPL couples, whereas the KIR2DS3 gene frequency in male partners of RPL couples was significantly reduced (p= 0.03). The presence of KIR2DL3 in women with RPL was correlated with the presence of HLA-C2 alleles in their spouses (p= 0.03). Conclusion: Our data from a Turkish population suggest that male HLA-C2 homozygosity may play an important role in RPL. Additionally, an incidental match between male HLA-C2 and female HLA-C1 ligand KIR receptors might perturb the balance between activatory and inhibitory KIR-ligand interactions during pregnancy in couples affected by RPL. The roles of orphan KIR2DL5 and orphan KIR2DS3 in RPL remain obscure.

• Clinical and Experimental Reproductive Medicine
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• v.26 no.3
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• pp.441-445
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• 1999

Objective: To analyze the methylenetetrahydrofolate reductase (MTHFR) mutation in recurrent spontaneous abortion associated with hyperhomocysteinemia. Material and Method: The blood sample of habitual aborter with high fasting homocysteine level was tested by PCR - RFLP method. Results: The patient was found to be a homozygosity for MTHFR gene mutation that was confirmed by the finding which is consistent with the mutation at the nucleotide 677 C to T, corresponding to Ala to Val. Conclusions: Hyperhomocysteinemia due to MTHFR mutation is a cause of recurrent spontaneous abortion. Therefore, the MTHFR mutation should be examined in the workup of recurrent spontaneous abortion showing hyperhomocysteinemia.