Excavating the quantitative trait locus (QTL) associated with rice cooking quality, analyzing candidate genes, and improving cooking quality-associated traits of rice varieties by genetic breeding can effectively improve the taste of rice. In this study, we used the indica rice HZ, the japonica rice Nekken2 and 120 recombinant inbred lines (RILs) populations constructed from them as experimental materials to measure the gelatinization temperature (GT), gel consistency (GC) and amylose content (AC) of rice at the maturity stage. We combined the high-density genetic map for QTL mapping. A total of 26 QTLs associated with rice cooking quality (1 QTL associated with GT, 13 QTLs associated with GC, and 12 QTLs associated with AC) were detected, among which the highest likelihood of odd (LOD) value reached 30.24. The expression levels of candidate genes in the localization interval were analyzed by quantitative real-time polymerase chain reaction (qRT-PCR), and it was found that the expression levels of six genes were significantly different from that in parents. It was speculated that the high expression of LOC_Os04g20270 and LOC_Os11g40100 may greatly increase the GC of rice, while the high expression of LOC_Os01g04920 and LOC_Os02g17500 and the low expression of LOC_Os03g02650 and LOC_Os05g25840 may reduce the AC. The results lay a molecular foundation for the cultivation of new high-quality rice varieties, and provide important genetic resources for revealing the molecular regulation mechanism of rice cooking quality.
Quantitative Trait Loci ; Oryza/genetics* ; Plant Breeding ; Cooking ; Genetic Association Studies

OBJECTIVES: The molecular mechanisms underlying attention-deficit hyperactivity disorder (ADHD) remain unclear. Therefore, this study aimed to identify the genetic susceptibility loci for ADHD in Korean children with ADHD. We performed a case-control and a family-based genome-wide association study (GWAS), as well as genome-wide quantitative trait locus (QTL) analyses, for two symptom traits. METHODS: A total of 135 subjects (71 cases and 64 controls), for the case-control analysis, and 54 subjects (27 probands and 27 unaffected siblings), for the family-based analysis, were included. RESULTS: The genome-wide QTL analysis identified four single nucleotide polymorphisms (SNPs) (rs7684645 near APELA, rs12538843 near YAE1D1 and POU6F2, rs11074258 near MCTP2, and rs34396552 near CIDEA) that were significantly associated with the number of inattention symptoms in ADHD. These SNPs showed possible association with ADHD in the family-based GWAS, and with hyperactivity-impulsivity in genome-wide QTL analyses. Moreover, association signals in the family-based QTL analysis for the number of inattention symptoms were clustered near genes IL10, IL19, SCL5A9, and SKINTL. CONCLUSION: We have identified four QTLs with genome-wide significance and several promising candidates that could potentially be associated with ADHD (CXCR4, UPF1, SETD5, NALCN-AS1, ERC1, SOX2-OT, FGFR2, ANO4, and TBL1XR1). Further replication studies with larger sample sizes are needed.
Adolescent* ; Case-Control Studies ; Child ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Humans ; Interleukin-10 ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; Sample Size

Although pork quality traits are important commercially, genome-wide association studies (GWASs) have not well considered Landrace and Yorkshire pigs worldwide. Landrace and Yorkshire pigs are important pork-providing breeds. Although quantitative trait loci of pigs are well-developed, significant genes in GWASs of pigs in Korea must be studied. Through a GWAS using the PLINK program, study of the significant genes in Korean pigs was performed. We conducted a GWAS and surveyed the gene ontology (GO) terms associated with the backfat thickness (BF) trait of these pigs. We included the breed information (Yorkshire and Landrace pigs) as a covariate. The significant genes after false discovery rate (<0.01) correction were AFG1L, SCAI, RIMS1, and SPDEF. The major GO terms for the top 5% of genes were related to neuronal genes, cell morphogenesis and actin cytoskeleton organization. The neuronal genes were previously reported as being associated with backfat thickness. However, the genes in our results were novel, and they included ZNF280D, BAIAP2, LRTM2, GABRA5, PCDH15, HERC1, DTNBP1, SLIT2, TRAPPC9, NGFR, APBB2, RBPJ, and ABL2. These novel genes might have roles in important cellular and physiological functions related to BF accumulation. The genes related to cell morphogenesis were NOX4, MKLN1, ZNF280D, BAIAP2, DNAAF1, LRTM2, PCDH15, NGFR, RBPJ, MYH9, APBB2, DTNBP1, TRIM62, and SLIT2. The genes that belonged to actin cytoskeleton organization were MKLN1, BAIAP2, PCDH15, BCAS3, MYH9, DTNBP1, ABL2, ADD2, and SLIT2.
Actin Cytoskeleton ; Gene Ontology ; Genome-Wide Association Study* ; Korea ; Morphogenesis ; Neurons ; Quantitative Trait Loci ; Red Meat ; Swine*

The alteration of alternative splicing patterns has an effect on the quantification of functional proteins, leading to phenotype variation. The splicing quantitative trait locus (sQTL) is one of the main genetic elements affecting splicing patterns. Here, we report the results of genome-wide sQTLs across 141 strains of Arabidopsis thaliana with publicly available next generation sequencing datasets. As a result, we found 1,694 candidate sQTLs in Arabidopsis thaliana at a false discovery rate of 0.01. Furthermore, among the candidate sQTLs, we found 25 sQTLs that overlapped with the list of previously examined trait-associated single nucleotide polymorphisms (SNPs). In summary, this sQTL analysis provides new insight into genetic elements affecting alternative splicing patterns in Arabidopsis thaliana and the mechanism of previously reported trait-associated SNPs.
Alternative Splicing ; Arabidopsis* ; Dataset ; Phenotype ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci*

Genome-wide association studies (GWAS) have identified thousands of genetic loci associated with complex diseases or traits. However, the exact biological functions of these loci are largely unknown. Recent functional annotation indicates that the majority of disease/trait associated loci are concentrated in regulatory DNA of human genome. Expression quantitative trait loci (eQTL) analyses, chromosome conformation capture related methods and genome editing methods (such as CRISPR/Cas9) may facilitate the functional study of these loci. Research on noncoding RNAs and rare variants may improve the functional understanding. These efforts may promise translation of GWAS findings to clinical practices.
Genetic Predisposition to Disease ; Genome-Wide Association Study ; Humans ; Quantitative Trait Loci

DNA microarray and next-generation sequencing provide data that can be used for the genetic analysis of multiple quantitative traits such as gene expression levels, transcription factor binding profiles, and epigenetic signatures. In particular, chromatin opening is tightly coupled with gene transcription. To understand how these two processes are genetically regulated and associated with each other, we examined the changes of chromatin accessibility and gene expression in response to genetic variation by means of quantitative trait loci mapping. Regulatory patterns commonly observed in yeast and human across different technical platforms and experimental designs suggest a higher genetic complexity of transcription regulation in contrast to a more robust genetic architecture of chromatin regulation.
Chromatin* ; Epigenesis, Genetic ; Epigenomics ; Gene Expression ; Genetic Variation ; Humans ; Oligonucleotide Array Sequence Analysis ; Quantitative Trait Loci ; Regulatory Sequences, Nucleic Acid ; Research Design ; Transcription Factors ; Yeasts

Metabolic syndrome (METS) is a disorder of energy utilization and storage and increases the risk of developing cardiovascular disease and diabetes. To identify the genetic risk factors of METS, we carried out a genome-wide association study (GWAS) for 2,657 cases and 5,917 controls in Korean populations. As a result, we could identify 2 single nucleotide polymorphisms (SNPs) with genome-wide significance level p-values (<5 x 10(-8)), 8 SNPs with genome-wide suggestive p-values (5 x 10(-8) < or = p < 1 x 10(-5)), and 2 SNPs of more functional variants with borderline p-values (5 x 10(-5) < or = p < 1 x 10(-4)). On the other hand, the multiple correction criteria of conventional GWASs exclude false-positive loci, but simultaneously, they discard many true-positive loci. To reconsider the discarded true-positive loci, we attempted to include the functional variants (nonsynonymous SNPs [nsSNPs] and expression quantitative trait loci [eQTL]) among the top 5,000 SNPs based on the proportion of phenotypic variance explained by genotypic variance. In total, 159 eQTLs and 18 nsSNPs were presented in the top 5,000 SNPs. Although they should be replicated in other independent populations, 6 eQTLs and 2 nsSNP loci were located in the molecular pathways of LPL, APOA5, and CHRM2, which were the significant or suggestive loci in the METS GWAS. Conclusively, our approach using the conventional GWAS, reconsidering functional variants and pathway-based interpretation, suggests a useful method to understand the GWAS results of complex traits and can be expanded in other genomewide association studies.
Cardiovascular Diseases ; Genome-Wide Association Study* ; Hand ; Metabolic Networks and Pathways ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; Risk Factors

Sixty-three morphological traits from 743 specimens of the 41 taxa within the cultivated Lonicera japonica were observed and measured, such as the height of plants, the length of leaf, the width of leaf, the length of anther, the alabastrum's number of one branch, the color of alabastrum and so on. A numerical taxonomy is presented by using the cluster analysis, principal components analysis (PCA) and factor analysis. Sixteen of 63 characters were screened by means of PCA and used for cluster analysis of 41 taxa with the method of Ward linkage and average euclidean distance. The cluster analysis showed that the 41 taxa could be divided into 5 groups when the Euclidean distance coefficient was 11.84. The factor analysis indicated that the shape of leaf, color of alabastrum, the pilosity and color of twiggery were of significance for the cultivated L. japonica classification. The results of this study will be a base for the core collection and breeding of L. japonica.
Breeding ; China ; Flowers ; chemistry ; classification ; genetics ; Lonicera ; chemistry ; classification ; genetics ; growth & development ; Plant Leaves ; chemistry ; classification ; genetics ; Quantitative Trait Loci

OBJECTIVEIn order to provide scientific basis for introduction breeding and production regionalization of Panax notoginseng, the environment of producing area, agronomic traits and medicinal material output were investigated.

METHODUsing field survey sampling at harvest time, agronomic traits indicators of leaf segment, stem segment and roots segment etc. of commodity P. notoginseng, longitude and latitude, elevation, soil type, landform of producing area were measured and observed.

RESULTThe P. notogiseng cultivation was expanding from traditional area like Wenshang to new areas as Honghe, Kunming, Qujing at large scale. Comparing with traditional cultivated fields, the elevation of new fields, which are red soil of moderate or low mountain slopes and gentle hills between 1 800-2 130 m, increases markedly. The agronomic traits of new cultivated fields such as plant height, stem diameter, the ground and underground biomass were better than those of traditional cultivated fields in varying degree. Furthermore, the root weight, taproot weight, taproot length and other agronomic index augmented more than 20%. Comparison among different cultivated fields showed P. notoginseng of Honghe Shiping Niujie, Kunming Shilin Guishan, Honghe Jiangshui Guanting etc. had better agronomic traits, the plant were thick and tall, the taproot and the top of reed were large, the number of root was more. Inversely, P. notoginseng of Kunming Guandu Xiaoshao, Guangxi Jingxi Lutong, Wenshang Yanshan Jiangna were thin and small. Cluster analysis showed that cultivated fields of P. notoginseng which was across clustered by traditional and new cultivated fields can be divided into three groups, including a high-yielding region insist of three new cultivated fields Honghe Shiping Niujie, Kunming Shilin Guishan, Honghe Jiangshui Guanting and one traditional cultivated field Wenshan Yanshan Jiangna. Correlation analysis indicated that the size and weight of taproot and top of reed were significantly positive correlated with plant height, stem diameter, leaf size, leaf weight and stem weight. Regression analysis pointed out that stem diameter, leaf width, leaf length/width, leaf weight were the main factors affecting the dry weight of taproot, and the main factors influencing the dry weight of top of reed were plant height, petiole, leaf length, leaf width and other agronomic traits.

CONCLUSIONFrom agronomic traits, P. notoginseng in new cultivated fields were more robust than that in traditional fields, but besides the length of taproot, the difference of rest agronomic traits didn't reach the significant level. It is suggested that, in the west and the north of traditional area, the red soil land of moderate or low mountain slopes and gentle hills where the elevation is between 1 800-2 130 m is suitable for cultivating P. notoginseng. Honghe Shiping Niujie, Honghe Jianshui Guanting, Kuming Shilin Gongshan can be used as vital development area for commodity P. notoginseng.

Agriculture ; methods ; Breeding ; China ; Drugs, Chinese Herbal ; analysis ; Panax notoginseng ; chemistry ; classification ; genetics ; growth & development ; Quality Control ; Quantitative Trait Loci ; Soil ; chemistry

This study was undertaken to identify genetic polymorphisms that are associated with the risk of an elevated fasting glucose (FG) level using genome-wide analyses. We explored a quantitative trait locus (QTL) for FG level in a genome-wide study from a Korean twin-family cohort (the Healthy Twin Study) using a combined linkage and family-based association analysis approach. We investigated 1,754 individuals, which included 432 families and 219 pairs of monozygotic twins. Regions of chromosomes 2q23.3-2q31.1, 15q26.1-15q26.3, 16p12.1, and 20p13-20p12.2, were found to show evidence of linkage with FG level, and several markers in these regions were found to be significantly associated with FG level using family-based or general association tests. In particular, a single-nucleotide polymorphism (rs6138953) on the PTPRA gene in the 20p13 region (combined P = 1.8 x 10(-6)) was found to be associated with FG level, and the PRKCB1 gene (in 16p12.1) to be possibly associated with FG level. In conclusion, multiple regions of chromosomes 2q23.3-2q31.1, 15q26.1-15q26.3, 16p12.1, and 20p13-20p12.2 are associated with FG level in our Korean twin-family cohort. The combined approach of genome-wide linkage and family-based association analysis is useful to identify novel or known genetic regions concerning FG level in a family cohort study.
Adult ; Aged ; Asian Continental Ancestry Group/*genetics ; Blood Glucose/*genetics ; Chromosomes, Human, Pair 15/genetics ; Chromosomes, Human, Pair 16/genetics ; Chromosomes, Human, Pair 2/genetics ; Chromosomes, Human, Pair 20/genetics ; Cohort Studies ; Family ; Female ; *Genetic Linkage ; *Genome-Wide Association Study ; Genotype ; Humans ; Male ; Middle Aged ; Polymorphism, Single Nucleotide ; Protein Kinase C/genetics ; Quantitative Trait Loci ; Receptor-Like Protein Tyrosine Phosphatases, Class 4/*genetics ; Republic of Korea ; Twins, Monozygotic/*genetics