• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2019년도 춘계학술대회
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• pp.62-62
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• 2019

Bacterial leaf blight(BLB), caused by X. oryzae pv. oryzae(Xoo), is one of the most destructive diseases of rice due to its high epidemic potential. Understanding BLB resistance at a genetic level is important to further improve the rice breeding that provides one of the best approaches to control BLB disease. In the present investigation, a collection of 192 accessions was used in the genome-wide association study (GWAS) for BLB resistance loci against four Korean races of Xoo that were represented by the prevailing BLB isolates under Xoo differential system. A total of 192 accessions of rice germplasm were selected on the basis of the bioassay using four isolated races of Xoo such as K1 and K2. The selected accessions was used to prepare 384-plex genotyping by sequencing (GBS) libraries and Illumina HiSeq 2000 pairedend read was used for GBS sequencing. GWAS was conducted using TASSEL 5.0. The TASSEL program uses a mixed linear model (MLM). The results of the bioassay using a selected set of 192 accessions showed that a large number of accessions (93.75%) were resistant to K1 race and K2 resistant germplasm proportion remained between 66.67. The genotypic data produced SNP matrix for a total of 293,379 SNPs. After imputation the missing data was removed, which exhibited 34,724 SNPs for association analysis. GWAS results showed strong signals of association at a threshold of [-log10(P-value)] more than 5 (K1 and K2) for nine of the 39 SNPs, which are plausible candidate loci of resistance genes. These SNP loci were positioned on rice chromosome 2, 9, and 11 for K1 and K2 races. The significant loci detected have also been illustrated and make the CPAS markers for NBS-LRR type disease resistance protein, SNARE domain containing protein, Histone deacetylase 19, NADP-dependent oxidoreductase, and other expressed and unknown proteins. Our results provide a better understanding of the distribution of genetic variation of BLB resistance to Korean pathogen races and breeding of resistant rice.

• Animal Bioscience
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• 제34권12호
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• pp.1879-1885
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• 2021

Objective: Owing to the lack of a breeding index for efficient and quick fertility evaluations of Holstein bulls when using traditional or genome-wide detection methods, this study aimed to determine whether in vitro fertilization (IVF) could be used as an indicator of conception rate of artificial insemination (AI). Methods: Conventional and sexed frozen semen from nine bulls were used for IVF and AI. Results: The IVF and AI conception rates of each bull were confirmed to be positively correlated between the conventional frozen and sexed frozen semen. The correlation coefficient R values of nine bulls between IVF and AI methods were 0.73 and 0.97 for the conventional frozen and sexed frozen semen, respectively. The average conception rate of three bulls undergoing AI was 69.5% and 64.2%, 61.8% and 58.8%, and 48.2% and 46.2% in first-, second-, and third-born cows when conventional frozen and sexed frozen semen were used, respectively, which showed a positive correlation with the fertilization rate in the same parity. We propose an evaluation standard to assess the fertilization ability of bulls based on their IVF test results, which is categorized into three grades: grade one, normal fertility bull with an AI conception rate of 40%±5% and IVF rate of 45% to 60%; grade two, higher fertility bull with an AI conception rate of 50%±5% and IVF rate of 61% to 80%; and grade three, highest fertility bull with an AI conception rate of 60%±5% and IVF rate of >80%. Conclusion: These findings reveal that IVF results can be used as a breeding index for bulls to evaluate their AI conception ability, which may shorten the time required to select bulls for breeding.

• Animal Bioscience
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• 제34권11호
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• pp.1739-1748
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• 2021

Objective: In recent years, long noncoding RNAs (lncRNAs) have been identified in many species, and some of them have been shown to play important roles in muscle development and myogenesis. However, the differences in lncRNAs between Kazakh cattle and Xinjiang brown cattle remain undefined; therefore, we aimed to confirm whether lncRNAs are differentially expressed in the longissimus dorsi between these two types of cattle and whether differentially expressed lncRNAs regulate muscle differentiation. Methods: We used RNA-seq technology to identify lncRNAs in longissimus muscles from these cattle. The expression of lncRNAs were analyzed using StringTie (1.3.1) in terms of the fragments per kilobase of transcript per million mapped reads values of the encoding genes. The differential expression of the transcripts in the two samples were analyzed using the DESeq R software package. The resulting false discovery rate was controlled by the Benjamini and Hochberg's approach. KOBAS software was utilized to measure the expression of different genes in Kyoto encyclopedia of genes and genomes pathways. We randomly selected eight lncRNA genes and validated them by quantitative reverse transcription polymerase chain reaction (RT-qPCR). Results: We found that 182 lncRNA transcripts, including 102 upregulated and 80 downregulated transcripts, were differentially expressed between Kazakh cattle and Xinjiang brown cattle. The results of RT-qPCR were consistent with the sequencing results. Enrichment analysis and functional annotation of the target genes revealed that the differentially expressed lncRNAs were associated with the mitogen-activated protein kinase, Ras, and phosphatidylinositol 3-kinase (PI3k)/Akt signaling pathways. We also constructed a lncRNA/mRNA coexpression network for the PI3k/Akt signaling pathway. Conclusion: Our study provides insights into cattle muscle-associated lncRNAs and will contribute to a more thorough understanding of the molecular mechanism underlying muscle growth and development in cattle.

• Biomolecules & Therapeutics
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• 제29권2호
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• pp.234-247
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• 2021

We used a heterozygous gene deletion library of fission yeasts comprising all essential and non-essential genes for a microarray screening of target genes of the antifungal terbinafine, which inhibits ergosterol synthesis via the Erg1 enzyme. We identified 14 heterozygous strains corresponding to 10 non-essential [7 ribosomal-protein (RP) coding genes, spt7, spt20, and elp2] and 4 essential genes (tif302, rpl2501, rpl31, and erg1). Expectedly, their erg1 mRNA and protein levels had decreased compared to the control strain SP286. When we studied the action mechanism of the non-essential target genes using cognate haploid deletion strains, knockout of SAGA-subunit genes caused a down-regulation in erg1 transcription compared to the control strain ED668. However, knockout of RP genes conferred no susceptibility to ergosterol-targeting antifungals. Surprisingly, the RP genes participated in the erg1 transcription as components of repressor complexes as observed in a comparison analysis of the experimental ratio of erg1 mRNA. To understand the action mechanism of the interaction between the drug and the novel essential target genes, we performed isobologram assays with terbinafine and econazole (or cycloheximide). Terbinafine susceptibility of the tif302 heterozygous strain was attributed to both decreased erg1 mRNA levels and inhibition of translation. Moreover, Tif302 was required for efficacy of both terbinafine and cycloheximide. Based on a molecular modeling analysis, terbinafine could directly bind to Tif302 in yeasts, suggesting Tif302 as a potential off-target of terbinafine. In conclusion, this genome-wide screening system can be harnessed for the identification and characterization of target genes under any condition of interest.

• Animal Bioscience
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• 제36권1호
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• pp.10-18
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• 2023

Objective: In this study, we aimed to position the Hungarian Merino among other Merinoderived sheep breeds, explore the characteristics of our sampled animals' genetic similarity network within the breed, and highlight single nucleotide polymorphisms (SNPs) associated with daily weight-gain. Methods: Hungarian Merino (n = 138) was genotyped on Ovine SNP50 Bead Chip (Illumina, San Diego, CA, USA) and positioned among 30 Merino and Merino-derived breeds (n = 555). Population characteristics were obtained via PLINK, SVS, Admixture, and Treemix software, within-breed network was analysed with python networkx 2.3 library. Daily weight gain of Hungarian Merino was standardised to 60 days and was collected from the database of the Association of Hungarian Sheep and Goat Breeders. For the identification of loci associated with daily weight gain, a multi-locus mixed-model was used. Results: Supporting the breed's written history, the closest breeds to Hungarian Merino were Estremadura and Rambouillet (pairwise F_ST values are 0.035 and 0.036, respectively). Among Hungarian Merino, a highly centralised connectedness has been revealed by network analysis of pairwise values of identity-by-state, where the animal in the central node had a betweenness centrality value equal to 0.936. Probing of daily weight gain against the SNP data of Hungarian Merinos revealed five associated loci. Two of them, OAR8_17854216.1 and s42441.1 on chromosome 8 and 9 (-log₁₀P>22, false discovery rate<5.5e-20) and one locus on chromosome 20, s28948.1 (-log₁₀P = 13.46, false discovery rate = 4.1e-11), were close to the markers reported in other breeds concerning daily weight gain, six-month weight, and post-weaning gain. Conclusion: The position of Hungarian Merino among other Merino breeds has been determined. We have described the similarity network of the individuals to be applied in breeding practices and highlighted several markers useful for elevating the daily weight gain of Hungarian Merino.

• 대한조현병학회지
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• 제21권2호
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• pp.43-50
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• 2018

Objectives : Genome-wide association studies (GWASs) and meta-analyses indicate that single-nucleotide polymorphisms (SNPs) in the a-1C subunit of the L-type voltage-dependent calcium channel (CACNA1C) gene increase the risk for schizophrenia and bipolar disorders (BDs). We investigated the association between the genetic variants on CACNA1C and schizophrenia and/or BDs in the Korean population. Methods : A total of 582 patients with schizophrenia, 336 patients with BDs consisting of 179 bipolar I disorder (BD-I) and 157 bipolar II disorder (BD-II), and 502 healthy controls were recruited. Based on previous results from other populations, three SNPs (rs10848635, rs1006737, and rs4765905) were selected and genotype-wise association was evaluated using logistic regression analysis under additive, dominant and recessive genetic models. Results : rs10848635 showed a significant association with schizophrenia (p=0.010), the combined schizophrenia and BD group (p=0.018), and the combined schizophrenia and BD-I group (p=0.011). The best fit model was dominant model for all of these phenotypes. The association remained significant after correction for multiple testing in schizophrenia and the combined schizophrenia and BD-I group. Conclusion : We identified a possible role of CACNA1C in the common susceptibility of schizophrenia and BD-I. However no association trend was observed for BD-II. Further efforts are needed to identify a specific phenotype associated with this gene crossing the current diagnostic categories.

• Animal Bioscience
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• 제37권5호
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• pp.795-806
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• 2024

Objective: Karan Fries (KF), a high-producing composite cattle was developed through crossing indicine Tharparkar cows with taurine bulls (Holstein Friesian, Brown Swiss, and Jersey), to increase the milk yield across India. This composite cattle population must maintain sufficient genetic diversity for long-term development and breed improvement in the coming years. The level of linkage disequilibrium (LD) measures the influence of population genetic forces on the genomic structure and provides insights into the evolutionary history of populations, while the decay of LD is important in understanding the limits of genome-wide association studies for a population. Effective population size (N_e) which is genomically based on LD accumulated over the course of previous generations, is a valuable tool for e valuation of the genetic diversity and level of inbreeding. The present study was undertaken to understand KF population dynamics through the estimation of N_e and LD for the long-term sustainability of these breeds. Methods: The present study included 96 KF samples genotyped using Illumina HDBovine array to estimate the effective population and examine the LD pattern. The genotype data were also obtained for other crossbreds (Santa Gertrudis, Brangus, and Beefmaster) and Holstein Friesian cattle for comparison purposes. Results: The average LD between single nucleotide polymorphisms (SNPs) was r² = 0.13 in the present study. LD decay (r² = 0.2) was observed at 40 kb inter-marker distance, indicating a panel with 62,765 SNPs was sufficient for genomic breeding value estimation in KF cattle. The pedigree-based N_e of KF was determined to be 78, while the N_e estimates obtained using LD-based methods were 52 (SNeP) and 219 (genetic optimization for N_e estimation), respectively. Conclusion: KF cattle have an N_e exceeding the FAO's minimum recommended level of 50, which was desirable. The study also revealed significant population dynamics of KF cattle and increased our understanding of devising suitable breeding strategies for long-term sustainable development.

• IMMUNE NETWORK
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• 제20권5호
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• pp.41.1-41.11
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• 2020

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) is a positive-sense single-stranded RNA (+ssRNA) that causes coronavirus disease 2019 (COVID-19). The viral genome encodes twelve genes for viral replication and infection. The third open reading frame is the spike (S) gene that encodes for the spike glycoprotein interacting with specific cell surface receptor - angiotensin converting enzyme 2 (ACE2) - on the host cell membrane. Most recent studies identified a single point mutation in S gene. A single point mutation in S gene leading to an amino acid substitution at codon 614 from an aspartic acid 614 into glycine (D614G) resulted in greater infectivity compared to the wild type SARS-CoV2. We were interested in investigating the mutation region of S gene of SARS-CoV2 from Korean COVID-19 patients. New mutation sites were found in the critical receptor binding domain (RBD) of S gene, which is adjacent to the aforementioned D614G mutation residue. This specific sequence data demonstrated the active progression of SARS-CoV2 by mutations in the RBD of S gene. The sequence information of new mutations is critical to the development of recombinant SARS-CoV2 spike antigens, which may be required to improve and advance the strategy against a wide range of possible SARS-CoV2 mutations.

• Asian Pacific Journal of Cancer Prevention
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• 제13권12호
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• pp.6273-6276
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• 2012

Background/Aim: Six prostate cancer (PCa) susceptibility loci were identified in a genome-wide association study (GWAS) in populations of European decent. However, the associations of these 6 single-nucleotide polymorphisms (SNPs) with PCa has remained tobe clarified in men in Northern China. This study aimed to explore the loci associated with PCa risk in a Northern Chinese population. Methods: Blood samples and clinical information of 289 PCa patients and 288 controls from Beijing and Tianjin were collected. All risk SNPs were genotyped using polymerase chain reaction (PCR)-high resolution melting curve technology and gene sequencing. Associations between PCa and clinical covariates (age at diagnosis, prostate-specific antigen [PSA], Gleason score, tumor stage, and level of aggressiveness) and frequencies of alleles and genotypes of these SNPs were analyzed using genetic statistics. Results: Among the candidate SNPs, 11p15 (rs7127900, A) was associated with PCa risk (P = 0.02, odds ratio [OR] = 1.64, 95% confidence interval [CI] = 1.09-2.46). Genotypes showed differences between cases and controls on 11p15 (rs7127900, A), 11q13 (rs7931342, T), and HNF1B (rs4430796, A) (P = 0.03, P = 0.01, and P = 0.04, respectively). The genotype TG on 11q13 (rs7931342, T) was positively associated with an increased Gleason score (P = 0.04, OR = 2.15, 95% CI = 1.02-4.55). Patients carrying TG on 17q24 (rs1859962, G) were negatively associated with an increased body mass index (BMI) (P = 0.03, OR = 0.44, 95% CI = 0.21-0.92) while those with AG on HNF1B (rs4430796, A) were more likely to have PSA increase (P = 0.002). Conclusion: Our study suggests that 11p15 (rs7127900, A) could be a susceptibility locus associated with PCa in Northern Chinese. Genotype TG on 11q13 (rs7931342, T) could be related to an increased Gleason score, AG on HNF1B (rs4430796, A) could be associated with PSA increase, and TG on 17q24 (rs1859962, G) could be negatively associated with an increased BMI in Chinese men with PCa.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.10-10
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• 2017

Rice consumption has been continuously decreasing as the eating habits of Koreans have become westernized and diversified. The per capita annual rice consumption in Korea has dropped sharply from 136.4 kg in 1970 to 61.9 kg in 2016. The Korean government, therefore, has been trying to promote rice consumption by invigorating the processed food industry using rice flour. To facilitate the market for processed rice foods, it is essential to develop proper milling technology in terms of flour particle size and damaged starch content to produce high quality rice flour at competitive cost. Dry milling and wet milling are the two major processes used to produce rice flour. Although the dry milling process is relatively simple with a lower production cost, damaged starch content increases because of the high grain hardness of rice. In wet milling, the quality of rice flour is improved by reducing flour particle size as well as damaged starch content through soaking procedures. However, the production costs are high because of the additional expenses associated with the disposal of waste water, sterilization and drying of the wet flour. Recently developed technologies such as jet milling and cryogenic milling also require expensive investment and production. Therefore, developing new rice cultivars with dry milling adaptability as well as good processing properties is an important goal of rice breeding in Korea. 'Suweon 542' is a floury endosperm mutant line derived from sodium azide treatment on a high-yield, early maturing, and non-glutinous japonica rice cultivar, 'Namil'. Compared with the wild type, after dry milling process, the grain hardness of 'Suweon 542' was significantly lower because of its round and loosely packed starch granules. Also, the flour of 'Suweon 542' had significantly smaller particles and less damaged starch than 'Namil' and other rice cultivars and its particle size distribution was similar to a commercial wheat cultivar. Recently, through collaborations with nine universities and food companies, a total of 21 kinds of processed prototypes, using the dry milling flour of 'Suweon 542', were evaluated. In the production of major rice processing products, there was no significant quality difference between the flours prepared by wet milling and dry milling. Although the amount of water added to the dough was slightly increased, it was confirmed that the recipe applying the wet flour could be used without significant change. To efficiently transfer the floury endosperm characteristics of 'Suweon 542' to other commercial rice cultivars, it is essential to develop DNA marker tightly linked to the target gene. Association analysis using 70 genome-wide SSR markers and 94 F2 plants derived from 'Suweon 542'/'Milyang 23' showed that markers on chromosome 5 explained a large portion of the variation in floury grains percentage (FGP). Further analysis with an increased number of SSR markers revealed that the floury endosperm of 'Suweon 542' was directed by a major recessive locus, flo7(t), located in the 19.33-19.86 Mbp region of chromosome 5, with RM18639 explaining 92.2% of FGP variation in the F2 population. Through further physical mapping, a co-segregate and co-dominant DNA marker with the locus, flo7(t) was successfully developed, by which, thereby, breeding efficiency of rice cultivars having proper dry milling adaptability with high yield potential or useful functional materials would be improved. 'Suweon 542' maintained the early maturity of the wild type, Namil, which can be used in rice-wheat double cropping systems in Korea not only for improved arable land but also for sharing flour production facilities. In addition to the high susceptibility against major rice diseases, nevertheless, another possible drawback of 'Suweon 542' is the high rate of viviparous under prolonged rainfall during the harvesting season. To overcome susceptibility and vivipary of 'Suweon 542', the progeny lines, derived from the crosses 'Suweon 542' and 'Jopyeong', an early maturing rice cultivar with multiple resistance against rice blast, bacterial blight, and rice strip virus, and 'Heugjinju', a anthocyanin pigment containing black rice cultivar, were intensively evaluated. As the outputs, three dry milling suitable rice elite lines, 'Jeonju614', 'Jeonju615', and 'Jeonju616' were developed.