• Korean Journal of Agricultural Science
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• v.45 no.1
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• pp.1-8
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• 2018

Glucosinolates are one of the important plant secondary metabolites that are produced mainly in Brassicaceae plants. The compounds are primarily involved in defense responses to biotic and abiotic resistance in plants and play important biological roles during plant growth and development. In this study, the glucosinolate profiles in leaves of two different Brassica oleracea populations were compared using high-performance liquid chromatography (HPLC). The nine major glucosinolates compounds in cabbage leaves were identified as belonging to the aliphatic and indolic groups. Among them, sinigrin, which belongs to the aliphatic group, was recorded to be 41% whereas glucobrassicin and 4-methoxyglucobrassicin, which belong to the indolic group, were recorded to be 53.8%. In addition, we performed a genetic analysis to identify regions of the genome regulating glucosinolates biosynthesis in the $F_3$ population of Brassica oleracea. A total of 9 glucosinolates were used for the quantitative trait locus (QTL) analysis. Out of 9, a total of 3 QTLs were identified and they were associated with sinigrin, glucobrassicin, and 4-methoxyglucobrassicin synthesis located in Chromosome 1 and Chromosome 8, respectively. The results of this study will provide valuable information for the breeding of cabbage containing high glucosinolate content, and our next target is to develop component-specific and tightly linked markers for various glucosinolates.

• Clinical and Experimental Reproductive Medicine
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• v.44 no.4
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• pp.201-206
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• 2017

Objective: The aim of this study was to compare the efficacy of swim-up and density gradient centrifugation (DGC) for reducing the amount of sperm with fragmented DNA, sex chromosome aneuploidy, and abnormal chromatin structure. Methods: Semen samples were obtained from 18 healthy male partners who attended infertility clinics for infertility investigations and were processed with swim-up and DGC. The percentages of sperm cells with fragmented DNA measured by the sperm chromatin dispersion test, normal sex chromosomes assessed by fluorescence in situ hybridization, and abnormal chromatin structure identified by toluidine blue staining were examined. Results: The percentage of sperm cells with fragmented DNA was significantly lower in the swim-up fraction (9.7%, p= 0.001) than in the unprocessed fraction (27.0%), but not in the DGC fraction (27.8%, p= 0.098). The percentage of sperm cells with normal X or Y chromosomes was comparable in the three fractions. The percentage of sperm cells with abnormal chromatin structure significantly decreased after DGC (from 15.7% to 10.3%, p= 0.002). The swim-up method also tended to reduce the percentage of sperm cells with abnormal chromatin structure, but the difference was not significant (from 15.7% to 11.6%, p= 0.316). Conclusion: The swim-up method is superior for enriching genetically competent sperm.

• Reproductive and Developmental Biology
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• v.35 no.1
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• pp.105-113
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• 2011

The present study investigated the nuclear remodeling, development potential with telomerase activity and transcription level of X-linked genes (ANT3, HPRT, MeCP2, RPS4X, XIAP, XIST and ZFX) in the bovine somatic cell nuclear transfer (SCNT) embryos using two different fusion and activation methods. Female adult fibroblasts were injected into perivitelline space of in vitro matured oocytes. The oocyte-nucleus complexes were fused and followed by immediately either activated (Group 1), or activated at 1 h post-fusion (hpf) (Group 2), respectively. The incidence of normal premature chromosome condensation (PCC) at 1 hpf was slightly increased in the Group 2, compared to those of Group 1, but there was no significant (p<0.05) difference. The incidence of normal pronucleus (PN) and chromosome spread at 5 and 18 hpf were significantly (p<0.05) higher in the Group 2 than those of Group 1. The cleavage rate to 2-cell stage, developmental rate to blastocyst stage, and the mean number of total and ICM cell numbers were significantly (p<0.05) higher in the Group 2, compared to those of Group 1. Level of telomerase activity was significantly (p<0.05) higher in the SCNT blastocysts of Group 2, compared to those of Group 1. Transcript levels of HPRT, MeCP2 and XIST were not significantly (p<0.05) different between blastocysts of Group 1 and 2. However, transcript level of ANT3, RPS4X, XIAP and ZFX were significantly (p<0.05) up-regulated in the SCNT blastocysts of Group 2, compared to those of Group 1. Taken together, it is concluded that oocyte activation at 1 hpf induces the enhanced developmental potential by efficient nuclear remodeling and subsequent facilitation of the nuclear reprogramming of bovine SCNT embryos.

• BMB Reports
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• v.39 no.4
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• pp.418-425
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• 2006

A human bacterial artificial chromosome (BAC) library was constructed with high molecular weight DNA extracted from the blood of a male Korean. This Korean BAC library contains 100,224 clones of insert size ranging from 70 to 150 kb, with an average size of 86 kb, corresponding to a 2.9-fold redundancy of the genome. The average insert size was determined from 288 randomly selected BAC clones that were well distributed among all the chromosomes. We developed a pooling system and three-step PCR screen for the Korean BAC library to isolate desired BAC clones, and we confirmed its utility using primer pairs designed for one of the clones. The Korean BAC library and screening pools will allow PCR-based screening of the Korean genome for any gene of interest. We also determined the allele types of HLA-DRA and HLA-DRB3 of clone KB55453, located in the HLA class II region on chromosome 6p21.3. The HLA-DRA and DRB3 genes in this clone were identified as the DRA*010202 and DRB3*01010201 types, respectively. The haplotype found in this library will provide useful information in future human disease studies.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.56 no.4
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• pp.329-341
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• 2011

The objective of this study was to determine the genetic diversities of major rice blast resistance genes among 84 accessions of aromatic rice germplasm. Eighty four accessions were characterized by a dominant 11 set of PCR-based SNP and CAPS marker, which showed the broad spectrum resistance and closest linkage to seven major rice blast resistance (R) genes, Pia, Pib, Pii, Pi5 (Pi3), Pita (Pita-2), and Pi9 (t). The allele specific PCR markers assay genotype of SCAR and STS markers was applied to estimate the presence or absence of PCR amplicons detected with a pair of PCR markers. One indica accession, Basmati (IT211194), showed the positive amplicons of five major rice blast resistance genes, Pia, Pi5 (Pi3), Pib, Pi-ta (Pi-ta2), and Pik-5 (Pish). Among 48 accessions of the PCR amplicons detected with yca72 marker, only five accessions were identified to Pia gene on chromosome 11. The Pib gene was estimated with the NSb marker and was detected in 65 of 84 accessions. This study showed that nine of 84 accessions contained the Pii gene and owned Pi5 (Pi3) in 42 of 84 accessions by JJ817 and JJ113-T markers, which is coclosest with Pii on chromosome 9. Only six accessions were detected two alleles of the Pita or Pita-2 genes. Three of accessions were identified as the Pi9 (t) gene locus.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.7
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• pp.926-935
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• 2015

The efficiency of genome-wide association analysis (GWAS) depends on power of detection for quantitative trait loci (QTL) and precision for QTL mapping. In this study, three different strategies for GWAS were applied to detect QTL for carcass quality traits in the Korean cattle, Hanwoo; a linkage disequilibrium single locus regression method (LDRM), a combined linkage and linkage disequilibrium analysis (LDLA) and a $BayesC{\pi}$ approach. The phenotypes of 486 steers were collected for weaning weight (WWT), yearling weight (YWT), carcass weight (CWT), backfat thickness (BFT), longissimus dorsi muscle area, and marbling score (Marb). Also the genotype data for the steers and their sires were scored with the Illumina bovine 50K single nucleotide polymorphism (SNP) chips. For the two former GWAS methods, threshold values were set at false discovery rate <0.01 on a chromosome-wide level, while a cut-off threshold value was set in the latter model, such that the top five windows, each of which comprised 10 adjacent SNPs, were chosen with significant variation for the phenotype. Four major additive QTL from these three methods had high concordance found in 64.1 to 64.9Mb for Bos taurus autosome (BTA) 7 for WWT, 24.3 to 25.4Mb for BTA14 for CWT, 0.5 to 1.5Mb for BTA6 for BFT and 26.3 to 33.4Mb for BTA29 for BFT. Several candidate genes (i.e. glutamate receptor, ionotropic, ampa 1 [GRIA1], family with sequence similarity 110, member B [FAM110B], and thymocyte selection-associated high mobility group box [TOX]) may be identified close to these QTL. Our result suggests that the use of different linkage disequilibrium mapping approaches can provide more reliable chromosome regions to further pinpoint DNA makers or causative genes in these regions.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.21
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• pp.9495-9498
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• 2014

Background: The difference in prognosis of adult and childhood acute lymphoblastic leukemia (ALL) can be attributed largely to variation in cytogenetic abnormalities with age groups. Cytogenetic analysis in acute leukemia is now routinely used to assist patient management, particularly in terms of diagnosis, disease monitoring, prognosis and risk stratification. Knowing about cytogenetic profile at the time of diagnosis is important in order to take critical decisions in management of the patients. Aim and Objectives: To determine the frequency of cytogenetic abnormalities in Pakistani adult patients with ALL in order to have insights regarding behavior of the disease. Materials and Methods: A retrospective analysis of all the cases of ALL (${\geq}15$years old) diagnosed at Aga Khan University from January 2006 to June 2014 was performed. Phenotype (B/T lineage) was confirmed in all cases by flow cytometry. Cytogenetic analysis was made for all cases using the trypsin-Giemsa banding technique. Karyotypes were interpreted using the International System for Human Cytogenetic Nomenclature (ISCN) criteria. Results: A total of 166 patients were diagnosed as ALL during the study period, of which 151 samples successfully yielded metaphase chromosomes. The male to female ratio was 3.4:1. The majority (n=120, 72.3%) had a B-cell phenotype. A normal karyotype was present in 51% (n=77) of the cases whereas 49% (n=74) had an abnormal karyotype. Of the abnormal cases, 10% showed Philadelphia chromosome; t(9;22)(q34;q11.2). Other poor prognostic cytogenetic subgroups were t(4;11)(q21;q23), hypodiploidy (35-45 chromosomes) and complex karyotype. Hyperdiploidy (47-57 chromosomes) occurred in 6.6%; all of whom were younger than 30 years. Conclusions: This study showed a relatively low prevalence of Philadelphia chromosome in Pakistani adults with ALL with an increase in frequency with age (p=0.003). The cumulative prevalence of Philadelphianegative poor cytogenetic aberrations in different age groups was not significant (p=0.6).

• Journal of Genetic Medicine
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• v.6 no.1
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• pp.62-66
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• 2009

Purpose: Chromosomal abnormalities of abortuses have been used to investigate common etiologies of spontaneous abortion, but the frequencies and types of spontaneous abortions have demonstrated considerable variation among different countries and races. Materials and Methods: A cytogenetic analysis of 75 abortuses was performed at GenDix, Inc. from January 2006 to December 2007. Results: The frequency of chromosome abnormalities in abortuses was 32.0% (24/75 cases). Among the chromosomal abnormalities, trisomy was present in 62.5% (15/24 cases) of cases and the most frequent trisomy was trisomy 21 with an occurrence rate of 26.6% (4/15 cases). The following was trisomy 22 (3/15 cases) and trisomy 20 (2/15 cases). The average maternal age for abnormal karyotypes was $34.3{\pm}3.3$. Conclusion: Cytogenetic analysis of abortus is important for diagnosis and genetic counseling of patients with spontaneous abortion.

• Journal of the Korean Academy of Child and Adolescent Psychiatry
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• v.2 no.1
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• pp.66-75
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• 1991

The authors studied chromosomal abnormalities in 38 autistic children meeting the diagnostic criteria of DSM-III-R in order to investigate genere factor in autistic disorder There were 28 males and 10 females, with the mean age being $108.8{\pm}28.5months(70-156months).$ All samples were analyzed on short-term lymphocyre cultures in Medium 199 that contained FUdR. The fragile X chromosome was not found in any of the patients. There were other chromosomal abnormalities in 14(36.8%) of 38 patients, such as breakage, 11cases ; gap, 2case ; breakage and gap, 1 case. In grouping of chromosomal abnormalities, group A patients were 4 cases ; group C were 3 cases ; group A and B was 1 case ; group A and E was 1 case ; group C and E was 1 case ; group A, B and C was 1 case. There were no statistical significance in the 16 symptoms of autistic disorder of DSM-III-R between patients with chromosomal abnormalities and patients without chromosomal abnormalites. These results do not support the hypothesis that fragile X chromosome is an etiological factor in autistic disorder.

• Horticultural Science & Technology
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• v.32 no.4
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• pp.535-543
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• 2014

Backcross breeding is the method most commonly used to introgress new traits into elite lines. Conventional backcross breeding requires at least 4-5 generations to recover the genomic background of the recurrent parent. Marker-assisted backcrossing (MABC) represents a new breeding approach that can substantially reduce breeding time and cost. For successful MABC, highly polymorphic markers with known positions in each chromosome are essential. Single nucleotide polymorphism (SNP) markers have many advantages over other marker systems for MABC due to their high abundance and amenability to genotyping automation. To facilitate MABC in hot pepper (Capsicum annuum), we utilized expressed sequence tags (ESTs) to develop SNP markers in this study. For SNP identification, we used Bukang $F_1$-hybrid pepper ESTs to prepare a reference sequence through de novo assembly. We performed large-scale transcriptome sequencing of eight accessions using the Illumina Genome Analyzer (IGA) IIx platform by Solexa, which generated small sequence fragments of about 90-100 bp. By aligning each contig to the reference sequence, 58,151 SNPs were identified. After filtering for polymorphism, segregation ratio, and lack of proximity to other SNPS or exon/intron boundaries, a total of 1,910 putative SNPs were chosen and positioned to a pepper linkage map. We further selected 412 SNPs evenly distributed on each chromosome and primers were designed for high throughput SNP assays and tested using a genetic diversity panel of 27 Capsicum accessions. The SNP markers clearly distinguished each accession. These results suggest that the SNP marker set developed in this study will be valuable for MABC, genetic mapping, and comparative genome analysis.