• Asian Pacific Journal of Cancer Prevention
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• v.16 no.6
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• pp.2231-2235
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• 2015

Genome-wide association studies (GWASs) of the entire genome provide a systematic approach for revealing novel genetic susceptibility loci for breast cancer. However, genetic association studies have hitherto been primarily conducted in women of European ancestry. Therefofre we here performed a pilot GWAS with a single nucleotide polymorphism (SNP) array 5.0 platform from $Affymetrix^{(R)}$ that contains 443,813 SNPs to search for new genetic risk factors in 89 breast cancer cases and 46 healthy women of Indonesian ancestry. The case-control association of the GWAS finding set was evaluated using PLINK. The strengths of allelic and genotypic associations were assessed using logistic regression analysis and reported as odds ratios (ORs) and P values; P values less than $1.00{\times}10^{-8}$ and $5.00{\times}10^{-5}$ were required for significant association and suggestive association, respectively. After analyzing 292,887 SNPs, we recognized 11 chromosome loci that possessed suggestive associations with breast cancer risk. Of these, however, there were only four chromosome loci with identified genes: chromosome 2p.12 with the CTNNA2 gene [Odds ratio (OR)=1.20, 95% confidence interval (CI)=1.13-1.33, $P=1.08{\times}10^{-7}$]; chromosome 18p11.2 with the SOGA2 gene (OR=1.32, 95%CI=1.17-1.44, $P=6.88{\times}10^{-6}$); chromosome 5q14.1 with the SSBP2 gene (OR=1.22, 95%CI=1.11-1.34, $P=4.00{\times}10^{-5}$); and chromosome 9q31.1 with the TEX10 gene (OR=1.24, 95%CI=1.12-1.35, $P=4.68{\times}10^{-5}$). This study identified 11 chromosome loci which exhibited suggestive associations with the risk of breast cancer among Indonesian women.

• Animal Bioscience
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• v.36 no.2
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• pp.191-199
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• 2023

Objective: This study aimed to investigate the significant single nucleotide polymorphisms (SNPs) and genes associated with nine reproduction and morphological traits in three breed populations of Chinese goats. Methods: The genome-wide association of nine reproduction and morphological traits (litter size, nipple number, wattle, skin color, coat color, black dorsal line, beard, beard length, and hind leg hair) were analyzed in three Chinese native goat breeds (n = 336) using an Illumina Goat SNP50 Beadchip. Results: A total of 17 genome-wide or chromosome-wide significant SNPs associated with one reproduction trait (litter size) and six morphological traits (wattle, coat color, black dorsal line, beard, beard length, and hind leg hair) were identified in three Chinese native goat breeds, and the candidate genes were annotated. The significant SNPs and corresponding putative candidate genes for each trait are as follows: two SNPs located on chromosomes 6 (CSN3) and 24 (TCF4) for litter size trait; two SNPs located on chromosome 9 (KATNA1) and 1 (UBASH3A) for wattle trait; three SNPs located on chromosome 26 (SORCS3), 24 (DYM), and 20 (PDE4D) for coat color trait; two SNPs located on chromosome 18 (TCF25) and 15 (CLMP) for black dorsal line trait; four SNPs located on chromosome 8, 2 (PAX3), 5 (PIK3C2G), and 28 (PLA2G12B and OIT3) for beard trait; one SNP located on chromosome 18 (KCNG4) for beard length trait; three SNPs located on chromosome 17 (GLRB and GRIA2), 28 (PGBD5), and 4 for hind leg hair trait. In contrast, there were no SNPs identified for nipple number and skin color. Conclusion: The significant SNPs or genes identified in this study provided novel insights into the genetic mechanism underlying important reproduction and morphological traits of three local goat breeds in Southern China as well as further potential applications for breeding goats.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.66 no.4
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• pp.318-325
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• 2021

The objective of this study was to identify the effect of zebularine, a DNA methylation inhibitor, on the chromosomal association between homoeologous chromosomes in the wheat genetic background. Zebularine at a final concentration of 10 µM was used to treat the spikes of the double monosomic wheat addition line (DMA) with one Leymus mollis chromosome and one Leymus racemosus chromosome, both of which were in a homoeologous relationship. In late prophase, zebularine led to chromosome breakage in the Leymus homoeologous chromosomes. Chromosome breakage caused an increase in the frequency of chromosomal associations between the Leymus homoeologous chromosomes. Ordinary DMA showed 65 cells (35.3%) with chromosomal associations and 119 cells (64.7%) with no association, whereas treated DMA showed 102 cells (60.0%) with chromosomal associations and 67 cells (39.4%) with no association. In diakinesis, the Leymus bivalent showed a chromosomal association in the whole euchromatic region. In metaphase, the Leymus bivalent showed association in the whole chromosomal region, unlike other Leymus bivalents with partial chromosomal association. Chromosomal association by chromosome breakage occurred not only between Leymus chromosomes but also between Leymus and wheat chromosomes. The frequency of other chromosomal association (such as fusion and insert) was increased. Chromosome breakage by zebularine treatment is a useful method at the chromosome level as the spores with others are hereditary stable, although the homologous index (h) was not significantly different between ordinary DMA and treated DMA. It is necessary to study how to control zebularine treatment with a more stable concentration for chromosome breakage during meiosis.

• Korean Journal of Plant Taxonomy
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• v.41 no.3
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• pp.215-222
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• 2011

Various aneuploidy and polyploidy have been reported in the genus Aconitum L. (ca. 300 species worldwide, Ranunculaceae), and there is a demonstrated association between major lineage diversification and polyploidy. This study reports chromosome counts of eight Aconitum from Korea, including the first counts for A. japonicum Thunb. subsp. napiforme ($H. L{\acute{e}}v.$ & Vaniot) Kadota (2n = 32) and A. longecassidatum Nakai (2n = 16). The study also includes chromosome numbers for two taxa on the Critically Endangered species list in Korea. Among Korean native species, chromosome numbers in Aconitum subgenus Aconitum range from 2n = 16 to 2n = 64 with diverse levels of polyploidy (2x, 4x, and 8x), whereas Aconitum subg. Lycoctonum exhibits only diploids (2n = 16). Greater chromosome number diversity in subg. Aconitum than subg. Lycoctonum might explain higher species diversity within the former subgenus (more than 250 species worldwide). Investigating chromosome number diversity of Aconitum in a phylogenetic framework will be a critical step to understand species richness of the genus.

• Journal of Yeungnam Medical Science
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• v.40 no.4
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• pp.419-422
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• 2023

Septo-optic dysplasia (SOD) is a rare congenital anomaly that is clinically defined by developmental delay and characteristic brain magnetic resonance imaging findings, including optic nerve hypoplasia, pituitary hormone abnormalities, and midline brain defects. The occurrence of SOD is generally sporadic; however, it can be inherited rarely. Although an association with HESX1, SOX2, and SOX3 mutations has been identified, the detailed etiology is multifactorial and unclear. Here, we present the case of a 7-year-old girl who was clinically diagnosed with SOD and 15q13.3 duplication. Patients with duplication at chromosome 15q13.3 were reported to be diagnosed with autism spectrum disorder, epilepsy, and schizophrenia in previous studies. The relationship between SOD and the microduplication of 15q13.3 has not yet been explored. In this study, we suggest that there may be an association between chromosome 15q13.3 microduplication and SOD.

• Toxicological Research
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• v.19 no.1
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• pp.29-31
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• 2003

It has been reported that the genetic variations in the Y chromosome has influence the blood pressure in some Caucasian male populations, but the effect in non-Caucasian population is unclear. In the present study, we examined the relationship between blood pressure and a HindIII RFLP of Y chromosome in 152 unrelated male individuals of ethnically homogeneous Korean origin. There were no significant differences in systolic and diastolic blood pressures between genotype groups, respectively. However, the frequency of A genotype in Korean population was much higher than those of Caucasian populations (P＜0.05). Therefore, the results of this study will con-tribute the better understanding the genetic characteristics of Y chromosome in Korean population.

• Molecules and Cells
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• v.24 no.2
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• pp.288-293
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• 2007

The conversion of mitotic chromosome into interphase chromatin consists of at least two separate processes, the decondensation of the mitotic chromosome and the formation of the higher-order structure of interphase chromatin. Previously, we showed that depletion of BAF53 led to the expansion of chromosome territories and decompaction of the chromatin, suggesting that BAF53 plays an essential role in the formation of higher-order chromatin structure. We report here that BAF53 is associated with mitotic chromosomes during mitosis. Immunostaining with two different anti-BAF53 antibodies gave strong signals around the DNA of mitotic preparations of NIH3T3 cells and mouse embryo fibroblasts (MEFs). The immunofluorescent signals were located on the surface of mitotic chromosomes prepared by metaphase spread. BAF53 was also found in the mitotic chromosome fraction of sucrose gradients. Association of BAF53 with mitotic chromosomes would allow its rapid activation on the chromatin upon exit from mitosis.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.2
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• pp.155-160
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• 2008

Several studies have reported quantitative trait loci (QTL) for meat quality on porcine chromosome 2 (http://www.animalgenome.org/QTLdb/pig.html). For application of the molecular genetic information to the pig industry through marker-assisted selection, single nucleotide polymorphism (SNP) markers were analyzed by comparative re-sequencing of polymerase chain reaction (PCR) products of 13 candidate genes with DNA from commercial pig breeds such as Berkshire, Yorkshire, Landrace, Duroc and Korean Native pig. A total of 34 SNPs were identified in 15 PCR products producing an average of one SNP in every 253 bp. PCR restriction fragment length polymorphism (RFLP) assays were developed for 11 SNPs and used to investigate allele frequencies in five commercial pig breeds in Korea. Eight of the SNPs appear to be fixed in at least one of the five pig breeds, which indicates that different selection among pig breeds might be applied to these SNPs. Polymorphisms detected in the PTH, CSF2 and FOLR genes were chosen to genotype a Berkshire-Yorkshire pig breed reference family for linkage and association analyses. Using linkage analysis, PTH and CSF2 loci were mapped to pig chromosome 2, while FOLR was mapped to pig chromosome 9. Association analyses between SNPs in the PTH, CSF2 and FOLR suggested that the CSF2 MboII polymorphism was significantly associated with several pork quality traits in the Berkshire and Yorkshire crossed F2 pigs. Our current findings provide useful SNP marker information to fine map QTL regions on pig chromosome 2 and to clarify the relevance of SNP and quantitative traits in commercial pig populations.

• Korean Journal of Plant Resources
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• v.35 no.5
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• pp.659-666
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• 2022

The effect of rye B chromosome (rye B) on chromosome association was investigated in meiosis of wheat addition line. The wheat addition line was with one Leymus mollis chromosome and one L. racemosus chromosome which are under homoeologous relationship. Chromosome behavior of the two Leymus chromosomes in wheat genetic background was revealed by genomic in situ hybridization. In the first metaphase, most of the two Leymus chromosomes showed univalent in the wheat addition line without rye B (98.1 ± 0.5%). On the other hand, the wheat addition line with rye B showed higher frequency of bivalent (10.3 ± 0.2%) than wheat addition line without rye B (1.9 ± 0.5%). The wheat addition line without rye B showed abnormal bivalents with abnormal structure while the wheat addition line with rye B showed normal bivalent in low frequency. By rye B, some bivalent was composed of wheat and L. racemosus, and some trivalent was composed of wheat bivalents with L. mollis chromosome. Also, some wheat bivalents showed hyper-crossover, so those wheat bivalents showed abnormal structure compared to other wheat bivalents with normal structure such as ring, rod, and pan.

• Asian-Australasian Journal of Animal Sciences
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• v.12 no.1
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• pp.15-21
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• 1999

The aim of the present study was to determine the effect of paternal sex chromosome on early development of buffalo embryos fertilized and cultured in vitro. Embryos were produced in vitro from abattoir derived buffalo oocytes. The cleaved embryos were cocultured with buffalo oviductal epithelial cells and evaluated on day 7 under the phase contrast microscope to classify development. The embryos which reached the morula/blastocyst stage were fast developing, the embryos which were at 16-32 cell stage were medium developing and the embryos below 16 cell stage were slow developing. The embryos which showed some fragmentation in the blastomeres or degenerated blastomeres, were degenerating. Sex of emberyos (n=159) was determined using PCR for amplification of a male specific BRY. 1 (301 bp) and a buffalo specific satellite DNA (216 bp) fragments. The results thus obtained show that 1) X and Y chromosome bearing sperms fertilize oocytes to give almost equal numbers of cleaved XX and XY embryos, 2) male embryos develop faster than female embryos to reach advanced stage and 3) degeneration of buffalo embryos is not linked with the paternal sex chromosome. We suggest that faster development of males is due to differential processing of X and Y chromosome within the zygote for its activation and / or differential expression of genes on paternal sex chromosome sex chromosome during development of buffalo embryos fertilized and cultured in vitro which may be attributed to a combination of genetic and environmental factors.