• Animal Bioscience
• /
• v.35 no.9
• /
• pp.1303-1313
• /
• 2022

Objective: The current study aimed to perform whole-genome resequencing of Chinese indigenous Mongolian sheep breeds including Ujimqin, Sunit, and Wu Ranke sheep breeds (UJMQ, SNT, WRK) and deeply analyze genetic variation, population structure, domestication, and selection for domestication traits among these Mongolian sheep breeds. Methods: Blood samples were collected from a total of 60 individuals comprising 20 WRK, 20 UJMQ, and 20 SNT. For genome sequencing, about 1.5 ㎍ of genomic DNA was used for library construction with an insert size of about 350 bp. Pair-end sequencing were performed on Illumina NovaSeq platform, with the read length of 150 bp at each end. We then investigated the domestication and signatures of selection in these sheep breeds. Results: According to the population and demographic analyses, WRK and SNT populations were very similar, which were different from UJMQ populations. Genome wide association study identified 468 and 779 significant loci from SNT vs UJMQ, and UJMQ vs WRK, respectively. However, only 3 loci were identified from SNT vs WRK. Genomic comparison and selective sweep analysis among these sheep breeds suggested that genes associated with regulation of secretion, metabolic pathways including estrogen metabolism and amino acid metabolism, and neuron development have undergone strong selection during domestication. Conclusion: Our findings will facilitate the understanding of Chinese indigenous Mongolian sheep breeds domestication and selection for complex traits and provide a valuable genomic resource for future studies of sheep and other domestic animal breeding.

• Proceedings of the Korean Society of Crop Science Conference
• /
• 2022.10a
• /
• pp.207-207
• /
• 2022

Eating and cooking quality (ECQ) is one of the most complex quantitative traits in rice. The understanding of genetic regulation of transcript expression levels attributing to phenotypic variation in ECQ traits is limited. We integrated whole-genome resequencing, transcriptome, and phenotypic variation data from 84 Japonica accessions to build a transcriptome-wide association study (TWAS) based regulatory network. All ECQ traits showed a large phenotypic variation and significant phenotypic correlations among the traits. TWAS analysis identified a total of 285 transcripts significantly associated with six ECQ traits. Genome-wide mapping of ECQ-associated transcripts revealed 66,905 quantitative expression traits (eQTLs), including 21,747 local eQTLs, and 45,158 trans-eQTLs, regulating the expression of 43 genes. The starch synthesis-related genes (SSRGs), starch synthase IV-1 (SSIV-1), starch branching enzyme 1 (SBE1), granule-bound starch synthase 2 (GBSS2), and ADP-glucose pyrophosphorylase small subunit 2a (OsAGPS2a) were found to have eQTLs regulating the expression of ECQ associated transcripts. Further, in co-expression analysis, 130 genes produced at least one network with 22 master regulators. In addition, we developed CRISPR/Cas9-edited glbl mutant lines that confirmed the role of alpha-globulin (glbl) in starch synthesis to validate the co-expression analysis. This study provided novel insights into the genetic regulation of ECQ traits, and transcripts associated with these traits were discovered that could be used in further rice breeding.

• Biomedical Science Letters
• /
• v.20 no.4
• /
• pp.221-226
• /
• 2014

High-density lipoprotein (HDL) cholesterol levels are associated with decreased risk of coronary artery disease. Several genome-wide association studies (GWAS) for HDL cholesterol levels have implicated Lipoprotein lipase (LPL) as possibly being causal. Herein, the association between single nucleotide polymorphism (SNP) rs10503669 in the LPL gene and HDL cholesterol levels and triglyceride levels was tested in the Korean population. A total of 994 subjects from Seoul City were included in a replication study with LPL SNP rs10503669. SNP rs10503669 in the LPL gene was associated with mean HDL cholesterol levels (effect per allele 3.13 mg/dL, P<0.0001) and triglyceride levels (effect per allele -18.0 mg/dL, P=0.0026). Subjects with the CA/AA genotype had a 0.42-fold (range 0.23~0.77-fold) lower risk of having abnormal HDL cholesterol levels (<40 mg/dL) than subjects with the CC genotype. When analyzed by gender, the association of LPL was stronger in men than in women. This study clearly demonstrates that genetic variants in LPL influence HDL cholesterol levels and triglyceride levels in Korean adults.

• Journal of Gastric Cancer
• /
• v.20 no.2
• /
• pp.127-138
• /
• 2020

Purpose: Mucin 1 (MUC1) was identified as a gastric cancer (GC) susceptibility gene by genome-wide association studies in Asians and candidate gene studies in Europeans. This study aimed to investigate the association between the MUC1 rs4072037 polymorphism and GC in terms of the Lauren classification and long-term clinical outcomes. Materials and Methods: A total of 803 patients with GC and 816 unrelated healthy controls were enrolled in the study. The association between the MUC1 rs4072037 variant and GC histological types and clinical outcomes, including tumor recurrence and prognosis was investigated. Results: The major A allele of rs4072037 was associated with increased GC risk (P<0.05). In subtype analysis, the association was most significant for diffuse-type GC (P<0.05) and in a dominant model (P<0.05), whereas there was no association with intestinal-type GC (P>0.05). Cox proportional hazards analysis revealed the heterozygote AG rs4072037 allele as an independent risk factor influencing tumor recurrence and disease-related death in diffusetype GC (P<0.05). but not in intestinal-type GC (P>0.05). Conclusions: The exonic single nucleotide polymorphism rs4072037 in MUC1 was associated with diffuse-type GC and was an independent risk factor influencing tumor recurrence and disease-related death in diffuse-type GC.

• Asian-Australasian Journal of Animal Sciences
• /
• v.28 no.9
• /
• pp.1235-1243
• /
• 2015

The goat Capra hircus is one of several economically important livestock in China. Advances in molecular genetics have led to the identification of several single nucleotide variation markers associated with genes affecting economic traits. Validation of single nucleotide variations in a whole-transcriptome sequencing is critical for understanding the information of molecular genetics. In this paper, we aim to develop a large amount of convinced single nucleotide polymorphisms (SNPs) for Cashmere goat through transcriptome sequencing. In this study, the transcriptomes of Cashmere goat skin at four stages were measured using RNA-sequencing and 90% to 92% unique-mapped-reads were obtained from total-mapped-reads. A total of 56,231 putative SNPs distributed among 10,057 genes were identified. The average minor allele frequency of total SNPs was 18%. GO and KEGG pathway analysis were conducted to analyze the genes containing SNPs. Our follow up biological validation revealed that 64% of SNPs were true SNPs. Our results show that RNA-sequencing is a fast and efficient method for identification of a large number of SNPs. This work provides significant genetic resources for further research on Cashmere goats, especially for the high density linkage map construction and genome-wide association studies.

• Journal of Sasang Constitutional Medicine
• /
• v.32 no.2
• /
• pp.10-21
• /
• 2020

Objectives Genome-wide association studies(GWAS) is a useful method to identify genetic associations for various phenotypes. The purpose of this study was to develop predictive models for Sasang constitution types using genetic factors. Methods The genotypes of the 1,999 subjects was performed using Axiom Precision Medicine Research Array (PMRA) by Life Technologies. All participants were prescribed Sasang Constitution-specific herbal remedies for the treatment, and showed improvement of original symptoms as confirmed by Korean medicine doctor. The genotypes were imputed by using the IMPUTE program. Association analysis was conducted using a logistic regression model to discover Single Nucleotide Polymorphism (SNP), adjusting for age, sex, and BMI. Results & Conclusions We developed models to predict Korean medicine constitution types using identified genectic factors and sex, age, BMI using Random Forest (RF), Support Vector Machine (SVM), and Neural Network (NN). Each maximum Area Under the Curve (AUC) of Teaeum, Soeum, Soyang is 0.894, 0.868, 0.767, respectively. Each AUC of the models increased by 6~17% more than that of models except for genetic factors. By developing the predictive models, we confirmed usefulness of genetic factors related with types. It demonstrates a mechanism for more accurate prediction through genetic factors related with type.

• Asian Pacific Journal of Cancer Prevention
• /
• v.13 no.12
• /
• pp.6005-6010
• /
• 2012

Background: Nasopharyngeal carcinoma (NPC) is endemic in Southern Chinese and Southeast Asian populations. Geographical and ethnic clustering of the cancer is due to genetic, environmental, and lifestyle risk factors. This case-control study aimed to identify or confirm both genetic and non-genetic risk factors for NPC in one of the endemic countries, Malaysia. Materials and Methods: A panel of 768 single-nucleotide polymorphisms (SNPs) previously associated with various cancers and known non-genetic risk factors for NPC were selected and analyzed for their associations with NPC in a case-control study. Results: Statistical analysis identified 40 SNPs associated with NPC risk in our population, including 5 documented previously by genome-wide association studies (GWAS) and other case-control studies; the associations of the remaining 35 SNPs with NPC were novel. In addition, consistent with previous studies, exposure to occupational hazards, overconsumption of salt-cured foods, red meat, as well as low intake of fruits and vegetables were also associated with NPC risk. Conclusions: In short, this study confirmed and/or identified genetic, environmental and dietary risk factors associated with NPC susceptibility in a Southeast Asian population.

• Biomedical Science Letters
• /
• v.25 no.2
• /
• pp.190-195
• /
• 2019

Hemoglobin (Hb) concentrations and hematocrit (Hct) values can be changed by factors such as erythrocyte production, destruction, and bleeding. In addition, variants in the protein expression involved in the amount of red blood cells that determine Hb metabolism or Hct value can increase susceptibility to complex blood diseases. Previous studies have reported significant single nucleotide polymorphisms (SNPs) by applying a genome-wide association study (GWAS) on Hb levels and Hct values in European population. In this study, we confirmed whether the significant SNPs are replicated in Koreans. In previous studies, 26 and 18 SNPs with a significant correlation Hb and Hct were identified in Korean genotype data, and 21 and 12 SNPs were selected, respectively. The SNPs of PRKCE (rs10495928), TMPRSS6 (rs2235321, rs5756505, rs855791) were significantly associated with Hb (P<0.05). In the association analysis of Hct, the SNPs of HBS1L (rs6920211, rs9389268, rs9483788), PRKCE (rs4953318), SCGN (rs9348689) and TMPRSS6 (rs2413450) genes showed a significant correlation (P<0.05). Replicated SNPs and not replicated SNPs showed the difference of genetic distance calculated by Fst. The replicated SNPs with a significant correlation showed similar allele frequencies, whereas the not replicated SNPs showed a large difference in allele frequency. All replicated SNPs with significant correlations had Fst values less than 0.05, indicating that the genetic distance between the groups was close. On the other hand, the not replicated SNPs showed that the Fst value was 0.05 or more and the genetic distance was relatively large.

• Interdisciplinary Bio Central
• /
• v.6 no.4
• /
• pp.2.1-2.7
• /
• 2014

Sexual dimorphism in intelligence suggests that this phenotype is a sexually selected trait. This view is supported by an overrepresentation (compared to the autosomal genome) of genes affecting cognition on the X chromosome. The aim of this study is to test the hypothesis that sexual selection can explain sex and country-level differences in performance on tests of fluid intelligence. Nationally representative samples from N = 44 countries were obtained from the Programme for International Student Assessment (PISA) Creative Problem Solving (CPS), which evaluates the core of intelligence, that is novel problem solving ability. Sexual selection has the double effect of increasing the prevalence of a favored phenotype and reducing genetic variation in sexually selected traits. Matching these predictions from evolutionary theory, the average country fluid intelligence is positively correlated to sexual dimorphism after partialling out per capita GDP and the latter in turn is inversely correlated to variance in intelligence scores within populations. Males have a higher variance than females but there is a negative correlation between male-female difference in variance and sexual dimorphism in intelligence, suggesting that selection reduces variance more in the selected sex. Average country male height is negatively correlated to sexual dimorphism in intelligence, a fact that supports the notion of a trade-off between physical and intellectual competition in the context of access to females. The results of this study, if replicated, imply that genome-wide association studies of cognition may benefit from a focus on sex chromosomes, which so far have been neglected. Another implication of this study is that intelligence has continued to evolve after different human populations migrated out of Africa and possibly up to the 19th century, as suggested by the substantial variability in sex differences even between neighbouring countries.

• Proceedings of the Korean Society of Crop Science Conference
• /
• 2017.06a
• /
• pp.106-106
• /
• 2017

The soybean [Glycine max (L.) Merr.] is one of the most important crop resources worldwide as food and forage. It is also important and valuable that to hold crop resources to have high genetic diversities. Recently, a core collection has been constructed in many plants to preserve the genetic resources of various plants. A core collection is small population to represent the genetic diversity of the total collection, and is of strategic importance as they allow the use of a small part of a germplasm collection that is representative of the total collection. Here, we developed the core collection consisting of 816 accessions by using approximately 180,000 (180K) single nucleotide polymorphisms (SNPs) developed in previous study. In addition, we performed genetic diversity and population structure analysis to construct the core collection from entire 4,392 collections. there were excluded sample call rates less than 93% and duplicated samples more than 99.9% according to genotype analysis using 180K SNPs from entire collections. Furthermore, we were also excluded natural hybrid resources which Glycine max and Glycine soja are mixed in half through population structure analysis. As a result, we are constructed the core collection of genetic diversity that reflects 99% of the entire collections, including 430 cultivated soybeans (Glycine max) and 386 wild soybeans (Glycine soja). The core collection developed in this study should be to provide useful materials for both soybean breeding programs and genome-wide association studies.