OBJECTIVETo evaluate the effect and profitability of using the quantitative trait loci (QTL)-linked direct marker (DR marker) in gene-assisted selection (GAS).

METHODSThree populations (100, 200, or 300 sows plus 10 boars within each group) with segregating QTL were simulated stochastically. Five economic traits were investigated, including number of born alive (NBA), average daily gain to 100 kg body weight (ADG), feed conversion ratio (FCR), back fat at 100 kg body weight (BF) and intramuscular fat (IMF). Selection was based on the estimated breeding value (EBV) of each trait. The starting frequencies of the QTL's favorable allele were 0.1, 0.3 and 0.5, respectively. The economic return was calculated by gene flow method.

RESULTSThe selection efficiency was higher than 100% when DR markers were used in GAS for 5 traits. The selection efficiency for NBA was the highest, and the lowest was for ADG whose QTL had the lowest variance. The mixed model applied DR markers and obtained higher extra genetic gain and extra economic returns. We also found that the lower the frequency of the favorable allele of the QTL, the higher the extra return obtained.

CONCLUSIONGAS is an effective selection scheme to increase the genetic gain and the economic returns in pig breeding.

Animals ; Breeding ; economics ; methods ; Genetic Markers ; Models, Genetic ; Quantitative Trait Loci ; Selection, Genetic ; Swine

Quantitative trait loci (QTL) and their additive, dominance and epistatic effects play a critical role in complex trait variation. It is often infeasible to detect multiple interacting QTL due to main effects often being confounded by interaction effects. Positioning interacting QTL within a small region is even more difficult. We present a variance component approach nested in an empirical Bayesian method, which simultaneously takes into account additive, dominance and epistatic effects due to multiple interacting QTL. The covariance structure used in the variance component approach is based on combined linkage disequilibrium and linkage (LDL) information. In a simulation study where there are complex epistatic interactions between QTL, it is possible to simultaneously fine map interacting QTL using the proposed approach. The present method combined with LDL information can efficiently detect QTL and their dominance and epistatic effects, making it possible to simultaneously fine map main and epistatic QTL.
Chromosome Mapping ; Epistasis, Genetic ; Genetic Linkage ; Humans ; Linkage Disequilibrium ; Monte Carlo Method ; Quantitative Trait Loci ; genetics

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

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 <i>LOC_Os04g20270i> and <i>LOC_Os11g40100i> may greatly increase the GC of rice, while the high expression of <i>LOC_Os01g04920i> and <i>LOC_Os02g17500i> and the low expression of <i>LOC_Os03g02650i> and <i>LOC_Os05g25840i> 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

Based on randomized block design of experiment, agronomic traits and yields of 14 F1 generations of Dendrobium officinale were determined. The results showed that the differences in agronomic traits and yields among families were significant, and the hybrid vigor was obvious. Families of 6b x 2a, 9 x 66 and 78 x 69 were selected with the remarkable superiority of yields, agronomic traits and product customization. Correlation analysis between agronomic traits and yields showed that plant height, stem diameter, leaf number, blade length and blade width were all significantly correlated with biological yields and economic yields. Among which, stem diameter, leaf number and blade length were the most significant, and an optimal linear regression model could be established. When the number of shoots was fewer than 4.5, both biological yields and economic yields increased with the increasing number of shoots, but it could not much affect yields when the number of shoots was larger than 4.5. Shoots number, stem diameter and leaf index were basic stability when compared biennial traits to annual, which could be used for early selection.
Biomass ; Dendrobium ; genetics ; growth & development ; Hybridization, Genetic ; Plant Leaves ; genetics ; growth & development ; Plant Stems ; genetics ; growth & development ; 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

Several reports have described aberrant methylation in various types of human cancers. However, the interpretation of methylation frequency in various human cancers has some limitations because of the different materials and methods used for methylation analysis. To gain an insight into the role of DNA hypermethylation in human cancers and allow direct comparison of tissue specific methylation, we generated methylation profiles in 328 human cancers, including 24 breast, 48 colon, 61 stomach, 48 liver, 37 larynx, 24 lung, 40 prostate, and 46 uterine cervical cancer samples by analyzing CpG island hypermethylation of 13 genes using methylation-specific PCR. The mean numbers of methylated genes were 6.5, 4.4, 3.6, 3.4, 3.1, 3.1, 3.1, and 2.1 in gastric, liver, prostate, larynx, colon, lung, uterine cervix, and in breast cancer samples, respectively. The number of genes that were methylated at a frequency of more than 40% in each tumor type ranged from nine (stomach) to one (breast). Generally genes frequently methylated in a specific cancer type differed from those methylated in other cancer types. The findings indicate that aberrant CpG island hypermethylation is a frequent finding in human cancers of various tissue types, and each tissue type has its own distinct methylation pattern.
Quantitative Trait Loci/*genetics ; Polymerase Chain Reaction ; Neoplasms/*genetics ; Humans ; Genetic Predisposition to Disease/genetics ; Gene Frequency/genetics ; DNA, Neoplasm/*genetics ; *DNA Methylation ; CpG Islands/*genetics ; Chromosome Mapping/*methods

Anthropometric traits for eyes and nose are complex quantitative traits influenced by genetic and environmental factors. To date, there have been few reports on the contribution of genetic influence to these traits in Asian populations. The aim of this study was to determine the genetic effect and quantitative trait locus (QTL) of seven traits eyes- and nose-related anthropometric measurements in an isolated Mongolian population. Frontal and lateral photographs were obtained from 1,014 individuals (434 males and 580 females) of Mongolian origin. A total of 349 short tandem repeat markers on 22 autosomes were genotyped for each individual. Heritability estimates of the seven ocular and nasal traits, adjusted for significant covariates, ranged from 0.48 to 0.90, providing evidence for a genetic influence. Variance-component linkage analyses revealed 10 suggestive linkage signals on 5q34 (LOD = 3.2), 18q12.2 (LOD = 2.7), 5q15 (LOD = 2.0), 9q34.2 (LOD = 1.9), 5q34 (LOD = 1.9), 17q22 (LOD = 1.9), 13q33.3 (LOD = 2.7), 1q36.22 (LOD = 1.9), 4q32.1 (LOD = 2.1) and 15q22.31 (LOD = 2.9). Our study provides the first evidence that genetics influences nasal and ocular traits in a Mongolian population. Additional collaborative efforts will further extend our understanding of the link between genetic factors and human anthropometric traits.
Anthropometry ; *Asian Continental Ancestry Group ; Eye ; Facial Bones/*anatomy & histology ; Female ; *Genetic Linkage ; *Genome, Human ; Humans ; Lod Score ; Male ; Mongolia ; Nose ; Quantitative Trait Loci

OBJECTIVETo assess the association between gene polymorphisms and memory function through a genome-wide association study (GWAS) of schizophrenia and control group. Memory cognition was used as a quantitative trait (QT).

METHODSNinty-eight subjects with chronic schizophrenia and 60 matched controls were genotyped with HumanHap660 Bead Array. The results were correlated with quantitative traits including memory and memory delay.

RESULTSFive candidate genes, including RASGRF2 (rs401758, P = 8.03×10(-5)), PLCG2 (rs7185362, P= 4.54×10(-5)), LMO1 (rs484161, P=9.80×10(-7), CSMD1 (rs2469383, P= 2.77×10(-6)) and PRKG1 (rs7898516, P=6.94×10(-5)) were associated with memory cognition deficits.

CONCLUSIONUsing memory cognition as a quantitative trait, this Genome- wide association study has identified 5 susceptibility loci. With their association with nervous system development, neuronal growth, axon guidance and plasticity, brain development, above loci may play a role in the development of memory dysfunction in schizophrenia.

Adult ; Female ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; methods ; Humans ; Male ; Memory ; physiology ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; Schizophrenia ; genetics ; Young Adult

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