• Asian-Australasian Journal of Animal Sciences
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• v.29 no.1
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• pp.36-42
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• 2016

Milk-related traits (milk yield, fat and protein) have been crucial to selection of Holstein. It is essential to find the current selection trends of Holstein. Despite this, uncovering the current trends of selection have been ignored in previous studies. We suggest a new formula to detect the current selection trends based on single nucleotide polymorphisms (SNP). This suggestion is based on the best linear unbiased prediction (BLUP) and the Fisher's fundamental theorem of natural selection both of which are trait-dependent. Fisher's theorem links the additive genetic variance to the selection coefficient. For Holstein milk production traits, we estimated the additive genetic variance using SNP effect from BLUP and selection coefficients based on genetic variance to search highly selective SNPs. Through these processes, we identified significantly selective SNPs. The number of genes containing highly selective SNPs with p-value <0.01 (nearly top 1% SNPs) in all traits and p-value <0.001 (nearly top 0.1%) in any traits was 14. They are phosphodiesterase 4B (PDE4B), serine/threonine kinase 40 (STK40), collagen, type XI, alpha 1 (COL11A1), ephrin-A1 (EFNA1), netrin 4 (NTN4), neuron specific gene family member 1 (NSG1), estrogen receptor 1 (ESR1), neurexin 3 (NRXN3), spectrin, beta, non-erythrocytic 1 (SPTBN1), ADP-ribosylation factor interacting protein 1 (ARFIP1), mutL homolog 1 (MLH1), transmembrane channel-like 7 (TMC7), carboxypeptidase X, member 2 (CPXM2) and ADAM metallopeptidase domain 12 (ADAM12). These genes may be important for future artificial selection trends. Also, we found that the SNP effect predicted from BLUP was the key factor to determine the expected current selection coefficient of SNP. Under Hardy-Weinberg equilibrium of SNP markers in current generation, the selection coefficient is equivalent to $2^*SNP$ effect.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.6
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• pp.804-811
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• 2018

Objective: Complete mtDNA D-loop sequences of four Thai indigenous chicken varieties, including Pra-dhu-hang-dam (PD), Leung-hang-khao (LK), Chee (CH), and Dang (DA) were explored for genetic diversity and relationships with their potential ancestor and possible associates to address chicken domestication in Thailand. Methods: A total of 220 complete mtDNA D-loop sequences of the four Thai indigenous chicken varieties were obtained by Sanger direct sequencing of polymerase chain reaction amplicons of 1,231 to 1,232 base pair in size. A neighbor-joining dendrogram was constructed with reference complete mtDNA D-loop sequences of Red Junglefowl (RJF) and those different chicken breeds available on National Center for Biotechnology Information database. Genetic diversity indices and neutrality test by Tajima's D test were performed. Genetic differences both within and among populations were estimated using analysis of molecular variance (AMOVA). Pairwise fixation index ($F_{ST}$) was conducted to evaluated genetic relationships between these varieties. Results: Twenty-three identified haplotypes were classified in six haplogroups (A-E and H) with the majority clustered in haplogroup A and B. Each variety was in multiple haplogroups with haplogroups A, B, D, and E being shared by all studied varieties. The averaged haplotype and nucleotide diversities were, respectively 0.8607 and 0.00579 with non-significant Tajima's D values being observed in all populations. Haplogroup distribution was closely related to that of RJF particularly Gallus gallus gallus (G. g. gallus) and G. g. spadiceus. As denoted by AMOVA, the mean diversity was mostly due to within-population variation (90.53%) while between-population variation (9.47%) accounted for much less. By pairwise $F_{ST}$, LK was most closely related to DA ($F_{ST}=0.00879$) while DA was farthest from CH ($F_{ST}=0.24882$). Conclusion: All 4 Thai indigenous chickens are in close relationship with their potential ancestor, the RJF. A contribution of shared, multiple maternal lineages was in the nature of these varieties, which have been domesticated under neutral selection.

• Asian-Australasian Journal of Animal Sciences
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• v.24 no.6
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• pp.739-743
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• 2011

The aim of this paper was to estimate genetic parameters for body weight and five body measurements for an experimental population of Iranian Makooei sheep maintained at the Makooei Sheep Breeding Station at Makoo, Iran. To do this, yearling live weight (YW), and five body measurements, i.e., body length (BL), heart girth (HG), height at withers (HW), height at back (HB) and scrotal circumference (SC), were analyzed in a multi-trait animal model using the DXMUX program of DFREML software package. Heritability estimates were $0.22{\pm}0.08$, $0.11{\pm}0.06$, $0.21{\pm}0.07$, $0.17{\pm}0.06$, $0.17{\pm}0.06$ and $0.32{\pm}0.10$ for YW, BL, HG, HW, HB and SC, respectively. These estimates indicate that selection in Makooei sheep would generate moderate genetic progress in body weight and body measurements. Scrotal circumference, as an indicator of reproductive potential, exhibited the highest heritability. This trait, therefore, could successfully be used to increase productivity of males and, indirectly, female fertility. Genetic correlations between traits studied were all positive and ranged from 0.15 (YW/HB) to 0.99 (HW/HB). Phenotypic correlations were also positive and ranged from moderate (0.32, HW/SC) to high (0.94, HW/HB). Positive genetic and phenotypic correlations indicate that improvement in body measurements both at the genetic and phenotypic levels is expected through selection on body weight and vice versa.

• Journal of Crop Science and Biotechnology
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• v.11 no.2
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• pp.83-90
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• 2008

Two hundred and sixty Korean soybean landrace accessions were analyzed for polymorphism at 92 simple sequence repeat(SSR) loci. The 995 identified alleles served as raw data for estimating genetic diversity and population structure. The number of alleles at a locus ranged from three to 27 with a mean of 10.4 alleles per locus. $F_{ST}$ values estimated by analysis of molecular variance(AMOVA) using SSR data set were 0.018, 0.027, and 0.016 for usage, collection site and maturity groups, respectively, indicating little genetic differentiation. The model-based clustering analysis placed the accessions into three clusters(K=3) with 0.0503 of $F_{ST}$, indicating moderate genetic differentiation. Duncan's Multiple Range Test at K = 3 on the basis of 18 quantitative traits revealed that one cluster was mainly differentiated from the other two clusters by seed related traits and the other two clusters were differentiated from each other by biochemical traits. Genetic structure of Korean soybean landraces was differentiated by model-based clustering and supported by their phenotypic traits in part. This preliminary study could be the first step towards more efficient germplasm management and utilization of soybean landraces and helpful in association studies between genotypic and phenotypic traits in Korean soybean landraces.

• Journal of Genetic Medicine
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• v.2 no.1
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• pp.27-30
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• 1998

Previously, we made a study report on the genotype distribution and the gene frequency of angiotesin I-converting enzyme (ACE) in Korean population, and on the association between hypertension and genetic variance of ACE. This time, we have investigated a rapid mismatch-PCR/RFLP assays for the variant of the angiotesin II type 1 receptor ($AT_1R$) gene (an $A{\rightarrow}C$ transversion at position 1166 of $AT_1R$ gene), a mutation which may interact with the ACE polymorphism in the determining of risk of myocardial infarction. The genotype distributions of Koreans' angiotensin II type 1 receptor gene were AA (66.3%):AC (28.1%):CC (5.6%), thus the AA genotype was most numerous, and the allele frequency was A:C = 0.803:0.197. Genotype distributions were shown as AA (76.8%):AC (20.9%):CC (2.3%), the allele frequency was A:C = 0.872:0.128 in the male group, and AA (47.4%):AC (41.0%):CC (11.6%), A:C = 0.679:0.321 in the female group. Differences were highly significant between the male and female groups (p<0.0001). Genotype distributions between angiotensin II type 1 receptor gene and angiotensin converting enzyme gene showed that there is no significance between $AT_1R$ genotypes and ACE genotypes in total subjects (p>0.05).

• Tunnel and Underground Space
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• v.15 no.1 s.54
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• pp.47-54
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• 2005

One of the standard procedures of discontinuity survey is the joint set identification from the population of field orientation data. Discontinuity set identification is fundamental to rock engineering tasks such as rock mass classification, discrete element analysis, key block analysis. and discrete fracture network modeling. Conventionally, manual method using contour plot had been widely used for this task, but this method has some short-comings such as yielding subjective identification results, manual operations, and so on. In this study, the method of discontinuity set identification using genetic algorithm was introduced, but slightly modified to handle the orientation data. Finally, based on the genetic algorithm, we developed a FORTRAN program, Genetic Algorithm based Clustering(GAC) and applied it to two different discontinuity data sets. Genetic Algorithm based Clustering(GAC) was proved to be a fast and efficient method for the discontinuity set identification task. In addition, fitness function based on variance showed more efficient performance in finding the optimal number of clusters when compared with Davis - Bouldin index.

• Animal cells and systems
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• v.8 no.4
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• pp.289-294
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• 2004

Bupleurum latissimum is a narrowly endemic and endangered plant, restricted to only two small populations on steep cliffs of a small island, Ulleung Island, in Korea. The genetic diversity and population differentiation in the two remnant populations of the species were investigated using RAPD (random amplified polymorphic DNA) analysis. The Neis gene diversities were 0.146 in the smaller population of 45 individuals, and 0.151 in the larger population of 61 individuals. The genetic variation was not significantly different between these two populations. Genetic diversity within populations was not low considering the very small size of populations. Analysis of molecular variance (AMOVA) revealed higher variation within populations (65.9%) than genetic differentiation between them (34.1%). B. latissimum revealed higher population differentiation than other outbreeding species. The differentiation of the populations corresponded to low gene flow (Nem = 0.482). The cluster and principal coordination analyses provide strong support for high population differentiation, showing that all individuals of the two populations have built up population-specific clusters. Although gene flow between the two populations of B. latissimum was limited, they have preserved relatively high levels of genetic variation.

• Journal of Korean Society of Forest Science
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• v.88 no.3
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• pp.408-418
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• 1999

On the basin of RAPD analysis, genetic diversity and structure of the natural populations of Abies holophylla was estimated by AMOVA procedure. The average value of percent of polymorphic markers was 71.9%. Most variation existed among individuals within population(80.2%). Genetic differentiation among populations(${\Phi}_{ST}$) was 0.198. When the populations were grouped as two region(i.e., Taebaek and Sobaek Mountain Regions), 8.5% of the total genetic variation was explained as regional differences. The heterogeneity of molecular variance among populations was investigated with Bartlett's test, which revealed that populations of Mt. Taebaek and Mt. Gariwang were more heterogeneous. Generally, the populations of Taebaek Mountain Reion were more heterogeneous than those of Sobaek Mountain Reion. Finally, the applicability of AMOVA to the populations frenetic study was discussed in comparison with other measures of genetic differentiation which were widely used.

• Women's Health Nursing
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• v.25 no.4
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• pp.365-378
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• 2019

Purpose: The awareness of hereditary breast and ovarian cancer (HBOC) and BRCA testing is increasing in Korea. Compared to the sizable research on HBOC knowledge among breast cancer women, studies in the ovarian cancer population are limited. This paper aimed to investigate the level of knowledge of hereditary ovarian cancer and anxiety in women diagnosed with serous ovarian cancer in Korea and determine differences in the knowledge and anxiety according to whether genetic testing was undertaken and whether BRCA1 or BRCA2 mutations were present. Methods: Using a descriptive research design, a cross-sectional survey was conducted on 100 women diagnosed with serous ovarian cancer at N hospital in Gyeonggi-do, Korea, from July to November 2018. The collected data were analyzed by descriptive statistics, independent t-tests, one-way analysis of variance, and Pearson's correlation coefficient using the SPSS 21.0 program. Results: The hereditary ovarian cancer-related knowledge score was mid-level (mean score 8.90±3.29 out of a total of 17), as was the state anxiety level was mid-level (mean score 47.96±3.26 out of possible score range of 20-80). Genetic knowledge of hereditary ovarian cancer was associated with age, education, occupation, genetic counseling, and BRCA mutations. There were no statistically significant factors related to anxiety and there were no statistically significant correlations between knowledge level and anxiety. Conclusion: More comprehensive education on gene-related cancer is needed for ovarian cancer patients, especially for items with low knowledge scores. A genetic counseling protocol should be developed to allow more patients to alleviate their anxiety through genetic counseling.

• Animal Bioscience
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• v.34 no.4
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• pp.516-524
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• 2021

Objective: The genetic evaluation of Santa Inês sheep was performed for resistance to gastrointestinal nematode infection (RGNI) and body size using different relationship matrices to assess the efficiency of including genomic information in the analyses. Methods: There were 1,637 animals in the pedigree and 500, 980, and 980 records of RGNI, thoracic depth (TD), and rump height (RH), respectively. The genomic data consisted of 42,748 SNPs and 388 samples genotyped with the OvineSNP50 BeadChip. The (co)variance components were estimated in single- and multi-trait analyses using the numerator relationship matrix (A) and the hybrid matrix H, which blends A with the genomic relationship matrix (G). The BLUP and single-step genomic BLUP methods were used. The accuracies of estimated breeding values and Spearman rank correlation were also used to assess the feasibility of incorporating genomic information in the analyses. Results: The heritability estimates ranged from 0.11±0.07, for TD (in single-trait analysis using the A matrix), to 0.38±0.08, for RH (using the H matrix in multi-trait analysis). The estimates of genetic correlation ranged from -0.65±0.31 to 0.59±0.19, using A, and from -0.42±0.30 to 0.57±0.16 using H. The gains in accuracy of estimated breeding values ranged from 2.22% to 75.00% with the inclusion of genomic information in the analyses. Conclusion: The inclusion of genomic information will benefit the direct selection for the traits in this study, especially RGNI and TD. More information is necessary to improve the understanding on the genetic relationship between resistance to nematode infection and body size in Santa Inês sheep. The genetic evaluation for the evaluated traits was more efficient when genomic information was included in the analyses.