• Korean Journal of Agricultural Science
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• v.45 no.4
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• pp.707-713
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• 2018

This study was done to search for positional candidate genes associated with the back fat thickness trait using a Genome-Wide Association Study (GWAS) in purebred Yorkshires (N = 1755). Genotype and phenotype analyses were done for 1,642 samples. As a result of the associations with back fat thickness using the Gemma program (ver. 0.93), when the genome-wide suggestive threshold was determined using the Bonferroni method ($p=1.61{\times}10^{-5}$), the single nucleotide polymorphism (SNP) markers with suggestive significance were identified in 1 SNP marker on chromosome 2 (MARC0053928; $p=3.65{\times}10^{-6}$), 2 SNP markers on chromosome 14 (ALGA0083078; $p=7.85{\times}10^{-6}$, INRA0048453; $p=1.27{\times}10^{-5}$), and 1 SNP marker on chromosome 18 (ALGA0120564; $p=1.44{\times}10^{-5}$). We could select positional candidate genes (KCNQ1, DOCK1, LOC106506151, and LOC110257583), located close to the SNP markers. Among these, we identified a potassium voltage-gated channel subfamily Q member gene (KCNQ1) and the dedicator of cytokinesis 1 (DOCK1) gene associated with obesity and Type-2 diabetes. The SNPs and haplotypes of the KCNQ1 and DOCK1 genes can contribute to understanding the genetic structure of back fat thickness. Additionally, it may provide basic data regarding marker assisted selection for a meat quality trait in pigs.

• Proceedings of The Korean Society of Agricultural and Forest Meteorology Conference
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• 2015.08a
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• pp.18-28
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• 2015

Apple is cultivated under various climatic conditions in many parts of the world. Better understanding of how climate, genotype, soil, and management factors interact to determine crop productivity will improve our ability to optimize crop selection, management strategies, and resource use efficiencies. We developed and applied a physiology-based apple canopy model to evaluate how climatic factors and crop phenotypes interact to determine biomass accumulation, radiation use efficiency (RUE), and water use efficiency (WUE) at multiple production sites between western and eastern states of the US including WA, CA, NY, WV, and PA. Our results indicate that solar radiation is a dominant factor limiting biomass production in the eastern states while VPD is the primary factor governing crop water use across eastern and western states during the peak growing season. Crop RUE and WUE were strongly correlated in the western states but not in the eastern states while VPD showed highly negative correlation with both RUE and WUE across all locations. The RUE improved with increasing fraction of diffuse radiation ($f_{df}$) and the $RUE-f_{df}$ relationships revealed distinctive responses between western and eastern states. Overall, the eastern locations exhibited slightly higher RUE and WUE than the western locations. However, overall productivity and total water use were greater in the western states. A clear decline of productivity with increasing temperature and afternoon VPD past an optimum was predicted in the western locations but this pattern was less clear in the eastern locations. We also discuss potential phenotypes with specific physiological and morphological traits that are differentially suitable for western and eastern locations. Our results provide plausible, spatially explicit explanations and insights to disentangle the complex relationships between crop productivity, resource use efficiencies, phenotype, and climate drivers in apple grown in the US.

• Journal of IKEEE
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• v.26 no.3
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• pp.494-499
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• 2022

It is reported that genome-wide RNA-seq profiles has potential as biomarkers of aging. A number of researches achieved promising prediction performance based on gene expression profiles. We develop an age prediction method based on the transcriptome of human dermal fibroblasts by selecting a proper age interval. The proposed method executes multiple rules in a sequential manner and a rule utilizes a classifier and a regression model to determine whether a given test sample belongs to the target age interval of the rule. If a given test sample satisfies the selection condition of a rule, age is predicted from the associated target age interval. Our method predicts age to a mean absolute error of 5.7 years. Our method outperforms prior best performance of mean absolute error of 7.7 years achieved by an ensemble based prediction method. We observe that it is possible to predict age based on genome-wide RNA-seq profiles but prediction performance is not stable but varying with age.

• Journal of Practical Agriculture & Fisheries Research
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• v.24 no.3
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• pp.25-31
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• 2022

Low-temperature germinability (LTG) is an important trait for the direct seeding of rice in temperate and high altitudes regions. Water temperature of rice fields at sowing season is frequently under 15℃ in Korea, resulting in poor seedlings establishment. The objective of this study was to phenotypically and genetically evaluate 600 rice germplasm composed of six rice subpopulations. In the phenotypic evaluation, aus (AUS) showed the highest visual rating (VR) and germination rate (GR) of 5 and 83.1%, respectively, than other subpopulations. The lowest value of VR (7.1) and GR (53.1%) was observed in aromatic (ARO) subpopulation. Association of the phenotype for LTG with the genotype for qLTG3-1, a major QTL for LTG, and other three SNP markers (LTG_8, qLTG4b-1, qLTG2-6) was conducted. The results suggested that the allele distribution of two markers, qLTG3-1 and qLTG2-6, affects the difference in VR and GR between subpopulations. qLTG4b-1 and LTG_8 were also highly significant with LTG in all subpopulations except that qLTG4b-1 did now show significance in AUS. Therefore, the combination use of these four markers might be effective for evaluation of LTG in rice germplasm.

• Journal of Genetic Medicine
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• v.19 no.2
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• pp.76-84
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• 2022

Purpose: Whole-exome sequencing (WES) has been a useful tool for novel gene discovery of various disease categories, further increasing the diagnostic yield. This study aimed to investigate the clinical utility of WES prospectively in undiagnosed genetic diseases. Materials and Methods: WES tests were performed on 110 patients (age range, 0-28 years) with suspected rare genetic diseases. WES tests were performed at a single reference laboratory and the variants reported were reviewed by clinical geneticists, pediatricians, neurologists, and laboratory physicians. Results: The patients' symptoms varied with abnormalities in the head or neck, including facial dysmorphism, being the most common, identified in 85.4% of patients, followed by abnormalities in the nervous system (83.6%). The average number of systems manifesting phenotypic abnormalities per patient was 3.9±1.7. The age at presentation was 2.1±2.7 years old (range, 0-15 years), and the age at WES testing was 6.7±5.3 years (range, 0-28 years). In total, WES test reported 100 pathogenic/likely pathogenic variants or variants of uncertain significance for 79 out of 110 probands (71.8%). Of the 79 patients with positive or inconclusive calls, 55 (50.0%) patients were determined to have good genotype-phenotype correlations after careful review. Further clinical reassessment and family member testing determined 45 (40.9%) patients to have been identified with a molecular diagnosis. Conclusion: This study showed a 40.9% diagnostic yield for WES test for a heterogeneous patient cohort with suspected rare genetic diseases. WES could be the feasible genetic test modality to overcome the diversity and complexity of rare disease diagnostics.

• Journal of Nutrition and Health
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• v.55 no.6
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• pp.601-616
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• 2022

In the era of the fourth industrial revolution technology, the inclusion of personalized nutrition for healthcare (PNH), when establishing a healthcare platform to prevent chronic diseases such as obesity, diabetes, cerebrovascular and cardiovascular disease, pulmonary disease, and inflammatory diseases, enhances the national competitiveness of global healthcare markets. Furthermore, since the government experienced COVID-19 and the population dead cross in 2020, as well as numerous health problems due to an increasing super-aged Korean society, there is an urgent need to secure, develop, and utilize PNH-related technologies. Three conditions are essential for the development of PNH technologies. These include the establishment of causality between obesity genome (genotype) and prevalence (phenotype) in Koreans, validation of clinical intervention research, and securing PNH-utilization technology (i.e., algorithm development, artificial intelligence-based platform, direct-to-customer [DTC]-based PNH, etc.). Therefore, a national control tower is required to establish appropriate PNH infrastructure (basic and clinical research, cultivation of PNH-related experts, etc.). The post-corona era will be aggressive in sharing data knowledge and developing related technologies, and Korea needs to actively participate in the large-scale global healthcare markets. This review provides the importance of scientific evidence based on a huge dataset, which is the primary prerequisite for the DTC obesity gene-based PNH technologies to be competitive in the healthcare market. Furthermore, based on comparing domestic and internationally approved DTC obese genes and the current status of Korean obesity genome-based PNH research, we intend to provide a direction to PNH planners (individuals and industries) for establishing scientific PNH guidelines for the prevention of obesity.

• Fisheries and Aquatic Sciences
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• v.26 no.1
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• pp.48-57
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• 2023

One of the ways to increase the production for aquaculture is through the cultivation of monosexuals by ensuring genital reversal from which energy for reproduction is diverted towards growth. Masculinization has been identified as one of the most prominent techniques, where sex development was directed from female to male. This approach only altered the phenotype and not the genotype. The red claw crayfish (Cherax quadricarinatus) was a relatively new commercial commodity, and the males were known to grow faster than females. Hence, it was proposed to use monocultures comprising an all-male population to increase yield using steroid hormone, synthetic 17α-methyltestosterone. However, this technique generated residues that detrimentally affect human health, the environment, and cultivated organisms. Therefore, finding new safe natural steroid sources was essential, and one of which is exploring of natural hormones extracted from the viscera of sea cucumbers (Holothuria scabra Jaeger). This study focused on the determination of male formation and testosterone levels among juvenile crayfish, after immersing in sea cucumber steroid extract (SCSE). A completely random design with factorial was used with two variables, encompassing the varied doses (0, 2, 4 mg/L, 2 mg/L 17α-methyl testosterone as control group) and immersion times of 18 and 30 h. The result showed the dose-dependent ability of SCSE increase the male genital formation and promote the testosterone level of juvenile crayfish. In addition, the testosterone was influenced by dose and immersion duration time, with the highest level of testosterone observed in treatments of 4 mg/L SCSE with 30 h immersion was 0.248 ng/mL, while the male percentage was 77%. In conclusion, the combination of dose and immersion time significantly affected growth and testosterone levels.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.277-277
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• 2022

Lignin modification has been a breeding target for the improvements of forage digestibility and fermentation in whole crop silage(WCS) rice. In rice, gold hull and internode 2 (gh2) was identified as a lignin-deficient mutant. gh2 exhibits a reddish-brown pigmentation in the hull and the internode is located on the short arm of chromosome 2 and codes for cinnamyl-alcohol dehydrogenase (CAD). To develop WCS rice variety improved digestibility and fermentation, we measured acid detergent fiber (ADF), lignin and total digestible nutrient (TDN) calculated from ADF (TDN=88.9-(0.79% × ADF) and performed marker-assisted selection using CAD(Os2g0187800) gene first intron region specific marker with 55 Jungmo1038/J.collection lines. Those lines had lignin content range from 0.82 to 6.61%, ADF from 15.8 to 45.8%, TDN from 52.7 to 78.8 compared to 'Jungmo1038'(1.53,20.7,72.6), 'J.collection'(0.98,12.8,78.8%) and gh2 were introgressed into 44 lines. Considering on these genotype and low-lignin phenotype, we finally selected 2 elite lines(Suweon668, Suweon669). Suweon668 and Suweon669 line are high biomass-low lignin lines that the ADF content is relatively low, even though the dry matter weight is high. Also they have lodging and shattering resistance and glabrous leaf and hull important to improve cattle palatability. Our results will provide that rice can be improved for forage digestibility and fermentation with low lignin concentration.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.235-235
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• 2022

Genome selection is a promising tool for plant and animal breeding, which uses genome-wide molecular marker data to capture large and small effect quantitative trait loci and predict the genetic value of selection candidates. Genomic selection has been shown previously to have higher prediction accuracies than conventional marker-assisted selection (MAS) for quantitative traits. In this study, the prediction accuracy of 10 agricultural traits in the wheat core group with 567 points was compared. We used a cross-validation approach to train and validate prediction accuracy to evaluate the effects of training population size and training model.As for the prediction accuracy according to the model, the prediction accuracy of 0.4 or more was evaluated except for the SVN model among the 6 models (GBLUP, LASSO, BayseA, RKHS, SVN, RF) used in most all traits. For traits such as days to heading and days to maturity, the prediction accuracy was very high, over 0.8. As for the prediction accuracy according to the training group, the prediction accuracy increased as the number of training groups increased in all traits. It was confirmed that the prediction accuracy was different in the training population according to the genetic composition regardless of the number. All training models were verified through 5-fold cross-validation. To verify the prediction ability of the training population of the wheat core collection, we compared the actual phenotype and genomic estimated breeding value using 35 breeding population. In fact, out of 10 individuals with the fastest days to heading, 5 individuals were selected through genomic selection, and 6 individuals were selected through genomic selection out of the 10 individuals with the slowest days to heading. Therefore, we confirmed the possibility of selecting individuals according to traits with only the genotype for a shorter period of time through genomic selection.

• Journal of Microbiology and Biotechnology
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• v.33 no.8
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• pp.1084-1090
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• 2023

The strain KIST612, initially identified as E. limosum, was a suspected member of E. callanderi due to differences in phenotype, genotype, and average nucleotide identity (ANI). Here, we found that E. limosum ATCC 8486^T and KIST612 are genetically different in their central metabolic pathways, such as that of carbon metabolism. Although 16S rDNA sequencing of KIST612 revealed high identity with E. limosum ATCC 8486^T (99.2%) and E. callanderi DSM 3662^T (99.8%), phylogenetic analysis of housekeeping genes and genome metrics clearly indicated that KIST612 belongs to E. callanderi. The phylogenies showed that KIST612 is closer to E. callanderi DSM 3662^T than to E. limosum ATCC 8486^T. The ANI between KIST612 and E. callanderi DSM 3662^T was 99.8%, which was above the species cut-off of 96%, Meanwhile, the ANI value with E. limosum ATCC 8486^T was not significant, showing only 94.6%. The digital DNA-DNA hybridization (dDDH) results also supported the ANI values. The dDDH between KIST612 and E. callanderi DSM 3662^T was 98.4%, whereas between KIST612 and E. limosum ATCC 8486^T , it was 57.8%, which is lower than the species cut-off of 70%. Based on these findings, we propose the reclassification of E. limosum KIST612 as E. callanderi KIST612.