scholarly journals Candidate genes for productivity identified by genome-wide association study with indicators of class in the Russian meat merino sheep breed

2020 ◽  
Vol 24 (8) ◽  
pp. 836-843
Author(s):  
A. Y. Krivoruchko ◽  
O. A. Yatsyk ◽  
E. Y. Safaryan
Keyword(s):  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Association Studies ◽  
Genome Wide Association ◽  
Phenotypic Traits ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
High Association ◽  
Genome Wide ◽  
Individual Snps

Genome-wide association studies allow identification of loci and polymorphisms associated with the formation of relevant phenotypes. When conducting a full genome analysis of sheep, particularly promising is the study of individuals with outstanding productivity indicators – exhibition animals, representatives of the super-elite class. The aim of this study was to identify new candidate genes for economically valuable traits based on the search for single nucleotide polymorphisms (SNPs) associated with belonging to different evaluation classes in rams of the Russian meat merino breed. Animal genotyping was performed using Ovine Infinium HD BeadChip 600K DNA, association search was performed using PLINK v. 1.07 software. Highly reliable associations were found between animals belonging to different evaluation classes and the frequency of occurrence of individual SNPs on chromosomes 2, 6, 10, 13, and 20. Most of the substitutions with high association reliability are concentrated on chromosome 10 in the region 10: 30859297–31873769. To search for candidate genes, 15 polymorphisms with the highest association reliability were selected (–log10(р) > 9). Determining the location of the analyzed SNPs relative to the latest annotation Oar_rambouillet_v1.0 allowed to identify 11 candidate genes presumably associated with the formation of a complex of phenotypic traits of animals in the exhibition group: RXFP2, ALOX5AP, MEDAG, OPN5, PRDM5, PTPRT, TRNAS-GGA, EEF1A1, FRY, ZBTB21-like, and B3GLCT-like. The listed genes encode proteins involved in the control of the cell cycle and DNA replication, regulation of cell proliferation and apoptosis, lipid and carbohydrate metabolism, the development of the inflammatory process and the work of circadian rhythms. Thus, the candidate genes under consideration can influence the formation of exterior features and productive qualities of sheep. However, further research is needed to confirm the influence of genes and determine the exact mechanisms for implementing this influence on the phenotype.

scholarly journals Genome-wide association study of clinically defined gout identifies multiple risk loci and its association with clinical subtypes

2015 ◽  
Vol 75 (4) ◽  
pp. 652-659 ◽  
Author(s):  
Hirotaka Matsuo ◽  
Ken Yamamoto ◽  
Hirofumi Nakaoka ◽  
Akiyoshi Nakayama ◽  
Masayuki Sakiyama ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Association Studies ◽  
Clinical Information ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Clinical Parameters ◽  
Nucleotide Polymorphisms ◽  
Male Population ◽  
Significance Level ◽  
Genome Wide

ObjectiveGout, caused by hyperuricaemia, is a multifactorial disease. Although genome-wide association studies (GWASs) of gout have been reported, they included self-reported gout cases in which clinical information was insufficient. Therefore, the relationship between genetic variation and clinical subtypes of gout remains unclear. Here, we first performed a GWAS of clinically defined gout cases only.MethodsA GWAS was conducted with 945 patients with clinically defined gout and 1213 controls in a Japanese male population, followed by replication study of 1048 clinically defined cases and 1334 controls.ResultsFive gout susceptibility loci were identified at the genome-wide significance level (p<5.0×10−8), which contained well-known urate transporter genes (ABCG2 and SLC2A9) and additional genes: rs1260326 (p=1.9×10−12; OR=1.36) of GCKR (a gene for glucose and lipid metabolism), rs2188380 (p=1.6×10−23; OR=1.75) of MYL2-CUX2 (genes associated with cholesterol and diabetes mellitus) and rs4073582 (p=6.4×10−9; OR=1.66) of CNIH-2 (a gene for regulation of glutamate signalling). The latter two are identified as novel gout loci. Furthermore, among the identified single-nucleotide polymorphisms (SNPs), we demonstrated that the SNPs of ABCG2 and SLC2A9 were differentially associated with types of gout and clinical parameters underlying specific subtypes (renal underexcretion type and renal overload type). The effect of the risk allele of each SNP on clinical parameters showed significant linear relationships with the ratio of the case–control ORs for two distinct types of gout (r=0.96 [p=4.8×10−4] for urate clearance and r=0.96 [p=5.0×10−4] for urinary urate excretion).ConclusionsOur findings provide clues to better understand the pathogenesis of gout and will be useful for development of companion diagnostics.

scholarly journals Genome-Wide Association Study towards Genomic Predictive Power for High Production and Quality of Milk in American Alpine Goats

2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Y. Tilahun ◽  
T. A. Gipson ◽  
T. Alexander ◽  
M. L. McCallum ◽  
P. R. Hoyt
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Predictive Power ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Breeding Value ◽  
Phenotypic Traits ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
Dairy Traits

This paper reports an exploratory study based on quantitative genomic analysis in dairy traits of American Alpine goats. The dairy traits are quality-determining components in goat milk, cheese, ice cream, etc. Alpine goat phenotypes for quality components have been routinely recorded for many years and deposited in the Council on Dairy Cattle Breeding (CDCB) repository. The data collected were used to conduct an exploratory genome-wide association study (GWAS) from 72 female Alpine goats originating from locations throughout the U.S. Genotypes were identified with the Illumina Goat 50K single-nucleotide polymorphisms (SNP) BeadChip. The analysis used a polygenic model where the dropping criterion was a call rate≥0.95. The initial dataset was composed of ~60,000 rows of SNPs and 21 columns of phenotypic traits and composed of 53,384 scaffolds containing other informative data points used for genomic predictive power. Phenotypic association with the 50K BeadChip revealed 26,074 reads of candidate genes. These candidate genes segregated as separate novel SNPs and were identified as statistically significant regions for genome and chromosome level trait associations. Candidate genes associated differently for each of the following phenotypic traits: test day milk yield (13,469 candidate genes), test day protein yield (25,690 candidate genes), test day fat yield (25,690 candidate genes), percentage protein (25,690 candidate genes), percentage fat (25,690 candidate genes), and percentage lactose content (25,690 candidate genes). The outcome of this study supports elucidation of novel genes that are important for livestock species in association to key phenotypic traits. Validation towards the development of marker-based selection that provides precision breeding methods will thereby increase the breeding value.

scholarly journals Identification of QTNs and Their Candidate Genes for 100-Seed Weight in Soybean (Glycine max L.) Using Multi-Locus Genome-Wide Association Studies

Genes ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 714 ◽  
Author(s):  
Muhammad Ikram ◽  
Xu Han ◽  
Jian-Fang Zuo ◽  
Jian Song ◽  
Chun-Yu Han ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Marker Assisted Selection ◽  
Seed Weight ◽  
Genome Wide Association Study ◽  
Association Studies ◽  
Single Locus ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
100 Seed Weight

100-seed weight (100-SW) in soybeans is a yield component trait and controlled by multiple genes with different effects, but limited information is available for its quantitative trait nucleotides (QTNs) and candidate genes. To better understand the genetic architecture underlying the trait and improve the precision of marker-assisted selection, a total of 43,834 single nucleotide polymorphisms (SNPs) in 250 soybean accessions were used to identify significant QTNs for 100-SW in four environments and their BLUP values using six multi-locus and one single-locus genome-wide association study methods. As a result, a total of 218 significant QTNs were detected using multi-locus methods, whereas eight QTNs were identified by a single-locus method. Among 43 QTNs or QTN clusters identified repeatedly across various environments and/or approaches, all of them exhibited significant trait differences between their corresponding alleles, 33 were found in the genomic region of previously reported QTLs, 10 were identified as new QTNs, and three (qHSW-4-1, qcHSW-7-3, and qcHSW-10-4) were detected in all the four environments. The number of seed weight (SW) increasing alleles for each accession ranged from 8 (18.6%) to 36 (83.72%), and three accessions (Yixingwuhuangdou, Nannong 95C-5, and Yafanzaodou) had more than 35 SW increasing alleles. Among 36 homologous seed-weight genes in Arabidopsis underlying the above 43 stable QTNs, more importantly, Glyma05g34120, GmCRY1, and GmCPK11 had known seed-size/weight-related genes in soybean, and Glyma07g07850, Glyma10g03440, and Glyma10g36070 were candidate genes identified in this study. These results provide useful information for genetic foundation, marker-assisted selection, genomic prediction, and functional genomics of 100-SW.

scholarly journals Comparison of the Performance of Two Commercial Genome-Wide Association Study Genotyping Platforms in Han Chinese Samples

2013 ◽  
Vol 3 (1) ◽  
pp. 23-29 ◽  
Author(s):  
Lei Jiang ◽  
Dana Willner ◽  
Patrick Danoy ◽  
Huji Xu ◽  
Matthew A Brown
Keyword(s):  
Allele Frequency ◽  
Minor Allele Frequency ◽  
Genome Wide Association Study ◽  
Association Studies ◽  
Han Chinese ◽  
Minor Allele ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Genome Wide

Abstract Most genome-wide association studies to date have been performed in populations of European descent, but there is increasing interest in expanding these studies to other populations. The performance of genotyping chips in Asian populations is not well established. Therefore, we sought to test the performance of widely used fixed-marker, genome-wide association studies chips in the Han Chinese population. Non-HapMap Chinese samples (n = 396) were genotyped using the Illumina OmniExpress and Affymetrix 6.0 platforms, whereas a subset also were genotyped using the Immunochip. Genotyped markers from the Affymetrix 6.0 and Illumina OmniExpress were used for full genome imputation based on the HapMap 2 JPT+CHB (Japanese from Tokyo, Japan and Chinese from Beijing, China) reference panel. The concordance between markers genotypes for the three platforms was very high whether directly genotyped or genotyped and imputed single nucleotide polymorphisms (SNPs; &gt;99.8% for directly genotyped and &gt;99.5% for genotyped and imputed SNPs, respectively) were compared. The OmniExpress chip data enabled more SNPs to be imputed, particularly SNPs with minor allele frequency &gt;5%. The OmniExpress chip achieved better coverage of HapMap SNPs than the Affymetrix 6.0 chip (73.6% vs. 65.9%, respectively, for minor allele frequency &gt;5%). The Affymetrix 6.0 and Illumina OmniExpress chip have similar genotyping accuracy and provide similar accuracy of imputed SNPs. The OmniExpress chip however provides better coverage of Asian HapMap SNPs, although its coverage of HapMap SNPs is moderate.

Replication study of previous migraine genome-wide association study findings in a Spanish sample of migraine with aura

Cephalalgia ◽  
2014 ◽  
Vol 35 (9) ◽  
pp. 776-782 ◽  
Author(s):  
Cèlia Sintas ◽  
Jèssica Fernández-Morales ◽  
Marta Vila-Pueyo ◽  
Bernat Narberhaus ◽  
Concepció Arenas ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Association Study ◽  
Migraine With Aura ◽  
Genome Wide Association Study ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide

Background Migraine is a common disabling condition that affects approximately 15% of the population. Several genome-wide association studies have attempted to identify susceptibility variants involved in migraine, reporting several candidate loci for the disorder. Methods In order to replicate findings from previous genome-wide association studies, a case–control association study was performed. Twelve single nucleotide polymorphisms were genotyped in a Spanish sample of 512 migraine with aura patients and 535 migraine-free controls. Results Nominal associations were found for single nucleotide polymorphisms rs2651899 (within the PRDM16 gene), rs10166942 (near TRPM8), rs12134493 (close to TSPAN2) and rs10504861 (near MMP16) in our migraine with aura sample. Conclusions Our study provides suggestive replication, in a Spanish migraine with aura sample, of four genome-wide association study findings previously reported in common migraine. However, larger sample sets should be explored to confirm our results.

Genome-wide association studies reveal the coordinated regulatory networks underlying photosynthesis and wood formation in Populus

2021 ◽  
Author(s):  
Mingyang Quan ◽  
Xin Liu ◽  
Qingzhang Du ◽  
Liang Xiao ◽  
Wenjie Lu ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Regulatory Networks ◽  
Genome Wide Association Study ◽  
Association Studies ◽  
Wood Properties ◽  
Wood Formation ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Regulatory Pathways ◽  
Genome Wide

Abstract Photosynthesis and wood formation underlie the ability of trees to provide renewable resources and perform ecosystem services; however, the genetic basis and regulatory pathways coordinating these two linked processes remain unclear. Here, we used a systems genetics strategy, integrating genome-wide association study, transcriptomic analyses, and transgenic experiments, to investigate the genetic architecture of photosynthesis and wood properties among 435 unrelated individuals of Populus tomentosa and unravel the coordinated regulatory networks causative of two trait categories. We totally detected 222 significant single-nucleotide polymorphisms, annotated to 177 candidate genes, for 10 traits of photosynthesis and wood properties. Epistasis uncovered 74 epistatic interactions for phenotypes. Strikingly, we deciphered the coordinated regulation patterns of pleiotropic genes underlying phenotypic variations for two trait categories. Furthermore, expression quantitative trait nucleotide mapping and coexpression analysis were integrated to unravel the potential transcriptional regulatory networks of candidate genes coordinating photosynthesis and wood properties. Finally, we heterologously expressed two pleiotropic genes, PtoMYB62 and PtoMYB80, in Arabidopsis thaliana, and demonstrated that they coordinate regulatory networks balancing photosynthesis and stem secondary cell wall components, respectively. Our study provides insight into the regulatory mechanisms coordinating photosynthesis and wood formation in poplar, which will accelerate the genetic breeding in trees via molecular design.

scholarly journals Genome-Wide Association Studies Reveal Neurological Genes for Dog Herding, Predation, Temperament, and Trainability Traits

2021 ◽  
Vol 8 ◽  
Author(s):  
Shuwen Shan ◽  
Fangzheng Xu ◽  
Bertram Brenig
Keyword(s):  
Body Size ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Association Studies ◽  
Nervous System Development ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Behavioral Traits ◽  
Genome Wide ◽  
Dog Breed

Genome-wide association study (GWAS) using dog breed standard values as phenotypic measurements is an efficient way to identify genes associated with morphological and behavioral traits. As a result of strong human purposeful selections, several specialized behavioral traits such as herding and hunting have been formed in different modern dog breeds. However, genetic analyses on this topic are rather limited due to the accurate phenotyping difficulty for these complex behavioral traits. Here, 268 dog whole-genome sequences from 130 modern breeds were used to investigate candidate genes underlying dog herding, predation, temperament, and trainability by GWAS. Behavioral phenotypes were obtained from the American Kennel Club based on dog breed standard descriptions or groups (conventional categorization of dog historical roles). The GWAS results of herding behavior (without body size as a covariate) revealed 44 significantly associated sites within five chromosomes. Significantly associated sites on CFA7, 9, 10, and 20 were located either in or near neuropathological or neuronal genes including THOC1, ASIC2, MSRB3, LLPH, RFX8, and CHL1. MSRB3 and CHL1 genes were reported to be associated with dog fear. Since herding is a restricted hunting behavior by removing killing instinct, 36 hounds and 55 herding dogs were used to analyze predation behavior. Three neuronal-related genes (JAK2, MEIS1, and LRRTM4) were revealed as candidates for predation behavior. The significantly associated variant of temperament GWAS was located within ACSS3 gene. The highest associated variant in trainability GWAS is located on CFA22, with no variants detected above the Bonferroni threshold. Since dog behaviors are correlated with body size, we next incorporate body mass as covariates into GWAS; and significant signals around THOC1, MSRB3, LLPH, RFX8, CHL1, LRRTM4, and ACSS3 genes were still detected for dog herding, predation, and temperament behaviors. In humans, these candidate genes are either involved in nervous system development or associated with mental disorders. In conclusion, our results imply that these neuronal or psychiatric genes might be involved in biological processes underlying dog herding, predation, and temperament behavioral traits.

scholarly journals Genome-Wide Association Study of Maize Aboveground Dry Matter Accumulation at Seedling Stage

2021 ◽  
Vol 11 ◽  
Author(s):  
Xianju Lu ◽  
Jinglu Wang ◽  
Yongjian Wang ◽  
Weiliang Wen ◽  
Ying Zhang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Dry Matter ◽  
Association Studies ◽  
Genome Wide Association ◽  
Phenotypic Traits ◽  
Pathway Enrichment Analysis ◽  
Dry Matter Accumulation ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Maize Varieties

Dry matter accumulation and partitioning during the early phases of development could significantly affect crop growth and productivity. In this study, the aboveground dry matter (DM), the DM of different organs, and partition coefficients of a maize association mapping panel of 412 inbred lines were evaluated at the third and sixth leaf stages (V3 and V6). Further, the properties of these phenotypic traits were analyzed. Genome-wide association studies (GWAS) were conducted on the total aboveground biomass and the DM of different organs. Analysis of GWAS results identified a total of 1,103 unique candidate genes annotated by 678 significant SNPs (P value &lt; 1.28e–6). A total of 224 genes annotated by SNPs at the top five of each GWAS method and detected by multiple GWAS methods were regarded as having high reliability. Pathway enrichment analysis was also performed to explore the biological significance and functions of these candidate genes. Several biological pathways related to the regulation of seed growth, gibberellin-mediated signaling pathway, and long-day photoperiodism were enriched. The results of our study could provide new perspectives on breeding high-yielding maize varieties.

scholarly journals A Genome-Wide Association Study of Novel Genetic Variants Associated With Anthropometric Traits in Koreans

2021 ◽  
Vol 12 ◽  
Author(s):  
Hye-Won Cho ◽  
Hyun-Seok Jin ◽  
Yong-Bin Eom
Keyword(s):  
Genetic Variants ◽  
Genetic Factors ◽  
Genome Wide Association Study ◽  
Association Studies ◽  
Fat Distribution ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
A Genome

Most previous genome-wide association studies (GWAS) have identified genetic variants associated with anthropometric traits. However, most of the evidence were reported in European populations. Anthropometric traits such as height and body fat distribution are significantly affected by gender and genetic factors. Here we performed GWAS involving 64,193 Koreans to identify the genetic factors associated with anthropometric phenotypes including height, weight, body mass index, waist circumference, hip circumference, and waist-to-hip ratio. We found nine novel single-nucleotide polymorphisms (SNPs) and 59 independent genetic signals in genomic regions that were reported previously. Of the 19 SNPs reported previously, eight genetic variants at RP11-513I15.6 and one genetic variant at the RP11-977G19.10 region and six Asian-specific genetic variants were newly found. We compared our findings with those of previous studies in other populations. Five overlapping genetic regions (PAN2, ANKRD52, RNF41, HGMA1, and C6orf106) had been reported previously but none of the SNPs were independently identified in the current study. Seven of the nine newly found novel loci associated with height in women revealed a statistically significant skeletal expression of quantitative trait loci. Our study provides additional insight into the genetic effects of anthropometric phenotypes in East Asians.

scholarly journals Genome-Wide Association Studies of Somatic Cell Count in the Assaf Breed

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1531
Author(s):  
Yasemin Öner ◽  
Malena Serrano ◽  
Pilar Sarto ◽  
Laura Pilar Iguácel ◽  
María Piquer-Sabanza ◽  
...  
Keyword(s):  
Somatic Cell ◽  
Genome Wide Association Study ◽  
Association Studies ◽  
Significant Snps ◽  
Genome Wide Association ◽  
System Response ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
A Genome

A genome-wide association study (GWAS) was performed to identify new single nucleotide polymorphisms (SNPs) and genes associated with mastitis resistance in Assaf sheep by using the Illumina Ovine Infinium® HD SNP BeadChip (680K). In total, 6173 records from 1894 multiparous Assaf ewes with at least three test day records and aged between 2 and 7 years old were used to estimate a corrected phenotype for somatic cell score (SCS). Then, 192 ewes were selected from the top (n = 96) and bottom (n = 96) tails of the corrected SCS phenotype distribution to be used in a GWAS. Although no significant SNPs were found at the genome level, four SNPs (rs419096188, rs415580501, rs410336647, and rs424642424) were significant at the chromosome level (FDR 10%) in two different regions of OAR19. The SNP rs419096188 was located in intron 1 of the NUP210 and close to the HDAC11 genes (61 kb apart), while the other three SNPs were totally linked and located 171 kb apart from the ARPP21 gene. These three genes were related to the immune system response. These results were validated in two SNPs (rs419096188 and rs424642424) in the total population (n = 1894) by Kompetitive Allele-Specific PCR (KASP) genotyping. Furthermore, rs419096188 was also associated with lactose content.

Sign in / Sign up

Export Citation Format

Share Document