scholarly journals Genome-wide association studies uncover candidate genes for Zinc, Iron, and Selenium concentration in barley grains

2021 ◽  
Author(s):  
Samar G. Thabet ◽  
Dalia Z. Alomari ◽  
Ahmad M. Alqudah
Keyword(s):  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Association Studies ◽  
Spring Barley ◽  
Genome Wide Association ◽  
Human Consumption ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
A Genome ◽  
Barley Grains

Abstract Background Barley (Hordeum vulgare L.) is one of the most important staple food crops worldwide. Mineral concentrations in cereals are important for human health; hence improving Zn, Fe and Se accumulation in grains is an imperative need. This study was designed to understand the genetic architecture of Zn, Fe and Se grain concentrations in barley grains. Results We performed a genome-wide association study (GWAS) for grain Zn, Fe and Se concentrations in 216 spring barley accessions, using field data from 2 years. All the accessions were genotyped with a high-density 9K SNPs array from IlluminaTM. The mean values of estimated BLUEs for Zn, Fe and Se were 38.37, 35.56 and 39.45 µg g− 1 dry weight, respectively. High heritability was equaled 75.65% for Fe across the two environments, while moderate heritability values were detected for Zn and Se. Notably, wide genetic variation was found among genotypes for Zn, Fe and Se concentrations. A total of 222 SNPs associated with Zn, Fe and Se were detected on all chromosomes, where the highest significant associations is linked to Fe accumulation. Three genomic regions include newly identified putative candidate genes, which are related to Zn uptake and transport or represent Homeobox leucine zipper protein. Additionally, several significant associations were physically located inside or near genes which are potentially involved in Zn and Fe homoeostasis of which two candidate genes at 5H (502,454,312–502,455,148 bp) and 7H (205,216,091–205,221,133 bp) were found to be involved in Basic helix loop helix (BHLH) family transcription factor and Squamosa promoter binding-like protein, respectively. Conclusions These findings provide new insights into the genetic basis of Zn, Fe and Se concentration in barley grains that in turn may help plant breeders to select high Zn, Fe and Se-containing genotypes to improve human consumption and grain quality.

scholarly journals Genome-wide association studies reveal candidate genes associated to bacteraemia caused by ST93-IV CA-MRSA

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Stanley Pang ◽  
Denise A Daley ◽  
Shafi Sahibzada ◽  
Shakeel Mowlaboccus ◽  
Marc Stegger ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Virulence Genes ◽  
Genome Wide Association Study ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genetic Traits ◽  
Genome Wide ◽  
A Genome ◽  
Northern Regions

Abstract Background The global emergence of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has seen the dominance of specific clones in different regions around the world with the PVL-positive ST93-IV as the predominant CA-MRSA clone in Australia. In this study we applied a genome-wide association study (GWAS) approach on a collection of Australian ST93-IV MRSA genomes to screen for genetic traits that might have assisted the ongoing transmission of ST93-IV in Australia. We also compared the genomes of ST93-IV bacteraemia and non-bacteraemia isolates to search for potential virulence genes associated with bacteraemia. Results Based on single nucleotide polymorphism phylogenetics we revealed two distinct ST93-IV clades circulating concurrently in Australia. One of the clades contained isolates primarily isolated in the northern regions of Australia whilst isolates in the second clade were distributed across the country. Analyses of the ST93-IV genome plasticity over a 15-year period (2002–2017) revealed an observed gain in accessory genes amongst the clone’s population. GWAS analysis on the bacteraemia isolates identified two gene candidates that have previously been associated to this kind of infection. Conclusions Although this hypothesis was not tested here, it is possible that the emergence of a ST93-IV clade containing additional virulence genes might be related to the high prevalence of ST93-IV infections amongst the indigenous population living in the northern regions of Australia. More importantly, our data also demonstrated that GWAS can reveal candidate genes for further investigations on the pathogenesis and evolution of MRSA strains within a same lineage.

scholarly journals Genome-wide association study reveals candidate genes for flowering time in cowpea (Vigna unguiculata [L.] Walp)

2021 ◽  
Author(s):  
Dev Paudel ◽  
Rocheteau Dareus ◽  
Julia Rosenwald ◽  
Maria Munoz-Amatriain ◽  
Esteban Rios
Keyword(s):  
Flowering Time ◽  
Candidate Genes ◽  
Vigna Unguiculata ◽  
Association Studies ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Human Consumption ◽  
Phenotypic Variance ◽  
Genome Wide Association Studies ◽  
Genome Wide

Cowpea (Vigna unguiculata [L.] Walp., diploid, 2n = 22) is a major crop used as a protein source for human consumption as well as a quality feed for livestock. It is drought and heat tolerant and has been bred to develop varieties that are resilient to changing climates. Plant adaptation to new climates and their yield are strongly affected by flowering time. Therefore, understanding the genetic basis of flowering time is critical to advance cowpea breeding. The aim of this study was to perform genome-wide association studies (GWAS) to identify marker trait associations for flowering time in cowpea using single nucleotide polymorphism (SNP) markers. A total of 367 accessions from a cowpea mini-core collection were evaluated in Ft. Collins, CO in 2019 and 2020, and 292 accessions were evaluated in Citra, FL in 2018. These accessions were genotyped using the Cowpea iSelect Consortium Array that contained 51,128 SNPs. GWAS revealed seven reliable SNPs for flowering time that explained 8-12% of the phenotypic variance. Candidate genes including FT, GI, CRY2, LSH3, UGT87A2, LIF2, and HTA9 that are associated with flowering time were identified for the significant SNP markers. Further efforts to validate these loci will help to understand their role in flowering time in cowpea, and it could facilitate the transfer of some of this knowledge to other closely related legume species.

scholarly journals Prioritization of genes associated with the pathogenesis of leukosis in cattle

2019 ◽  
Vol 22 (8) ◽  
pp. 1063-1069 ◽  
Author(s):  
N. S. Yudin ◽  
N. L. Podkolodnyy ◽  
T. A. Agarkova ◽  
E. V. Ignatieva
Keyword(s):  
Protein Interactions ◽  
Genome Wide Association Study ◽  
Association Studies ◽  
Mammalian Species ◽  
Genome Wide Association ◽  
Farm Animals ◽  
Genome Wide Association Studies ◽  
Protein Protein Interactions ◽  
Genome Wide ◽  
A Genome

Selection by means of genetic markers is a promising approach to the eradication of infectious diseases in farm animals, especially in the absence of effective methods of treatment and prevention. Bovine leukemia virus (BLV) is spread throughout the world and represents one of the biggest problems for the livestock production and food security in Russia. However, recent genome-wide association studies have shown that sensitivity/resistance to BLV is polygenic. The aim of this study was to create a catalog of cattle genes and genes of other mammalian species involved in the pathogenesis of BLV-induced infection and to perform gene prioritization using bioinformatics methods. Based on manually collected information from a range of open sources, a total of 446 genes were included in the catalog of cattle genes and genes of other mammals involved in the pathogenesis of BLV-induced infection. The following criteria were used to prioritize 446 genes from the catalog: (1) the gene is associated with leukemia according to a genome-wide association study; (2) the gene is associated with leukemia according to a case-control study; (3) the role of the gene in leukemia development has been studied using knockout mice; (4) protein-protein interactions exist between the gene-encoded protein and either viral particles or individual viral proteins; (5) the gene is annotated with Gene Ontology terms that are overrepresented for a given list of genes; (6) the gene participates in biological pathways from the KEGG or REACTOME databases, which are over-represented for a given list of genes; (7) the protein encoded by the gene has a high number of protein-protein interactions with proteins encoded by other genes from the catalog. Based on each criterion, a rank was assigned to each gene. Then the ranks were summarized and an overall rank was determined. Prioritization of 446 candidate genes allowed us to identify 5 genes of interest (TNF,LTB,BOLA-DQA1,BOLA-DRB3,ATF2), which can affect the sensitivity/resistance of cattle to leukemia.

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.

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 Fine Mapping of Intracranial Aneurysm Susceptibility Based on a Genome-wide Association Study

2021 ◽  
Author(s):  
Eun Pyo Hong ◽  
Dong Hyuk Youn ◽  
Bong Jun Kim ◽  
Jun Hyong Ahn ◽  
Jeong Jin Park ◽  
...  
Keyword(s):  
Intracranial Aneurysm ◽  
Fine Mapping ◽  
Bayes Factor ◽  
Genome Wide Association Study ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Network Analyses ◽  
Genome Wide ◽  
A Genome

Abstract In addition to conventional genome-wide association studies (GWAS), a fine-mapping is increasingly used to identify the genetic function of variants associated with disease susceptibilities. Here, we used a fine-mapping approach to evaluate the casual variants based on a previous GWAS involving patients with intracranial aneurysm (IA). Fine-mapping analysis was conducted based on the chromosomal data provided by GWAS consisting 250 patients diagnosed with IA and 296 controls using posterior inclusion probability (PIP) and log10 transformed Bayes factor (log10BF). The narrow sense of heritability (h2) explained by each casual variant was estimated. Subsequent gene expression and functional network analyses were used to calculate the transcripts per million (TPM) values. Twenty causal candidate single nucleotide polymorphisms (SNPs) surpassed a genome-wide significance threshold for creditable evidence (log10BF > 6.1). Four SNPs including rs75822236 (R535H, GBA; log10BF = 15.06), rs112859779 (G141S, TCF24; log10BF = 12.12), rs79134766 (A208T, OLFML2A; log10BF = 14.92), and rs371331393 (Q1932X, ARHGAP32; log10BF = 20.88) showed a completed PIP value in each chromosomal region, suggesting a high probability of variant causality associated with IA. Expression in GBA was highly enriched in the whole blood (TPM = 33.13), while TCF24 were rarely expressed in all tissues and cells. No direct interaction was observed between the four casual genes; however, PSAP appeared to be particularly important via indirect correlation between other genes. Our results suggested that four mutations of GBA, TCF24, OLFML2A, and ARHGAP32 were linked to IA susceptibility and pathogenesis. Our approach may promise more informative mutations in the following GWAS.

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 Bacterial Genome wide association studies (bGWAS) and transcriptomics identifies cryptic antimicrobial resistance mechanisms in Acinetobacter baumannii

2019 ◽  
Author(s):  
Chandler Roe ◽  
Charles H.D. Williamson ◽  
Adam J. Vazquez ◽  
Kristen Kyger ◽  
Michael Valentine ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Acinetobacter Baumannii ◽  
Genome Wide Association Study ◽  
Association Studies ◽  
Bacterial Genome ◽  
Genome Wide Association ◽  
Multiple Drug ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
A Genome

AbstractAntimicrobial resistance (AMR) in the nosocomial pathogen, Acinetobacter baumannii, is becoming a serious public health threat. While some mechanisms of AMR have been reported, understanding novel mechanisms of resistance is critical for identifying emerging resistance. One of the first steps in identifying novel AMR mechanisms is performing genotype/phenotype association studies. However, performing genotype/phenotype association studies is complicated by the plastic nature of the A. baumannii pan-genome. In this study, we compared the antibiograms of 12 antimicrobials associated with multiple drug families for 84 A. baumannii isolates, many isolated in Arizona, USA. in silico screening of these genomes for known AMR mechanisms failed to identify clear correlations for most drugs. We then performed a genome wide association study (GWAS) looking for associations between all possible 21-mers; this approach generally failed to identify mechanisms that explained the resistance phenotype. In order to decrease the genomic noise associated with population stratification, we compared four phylogenetically-related pairs of isolates with differing susceptibility profiles. RNA-Sequencing (RNA-Seq) was performed on paired isolates and differentially expressed genes were identified. In these isolate pairs, we identified four different potential mechanisms, highlighting the difficulty of broad AMR surveillance in this species. To verify and validate differential expression, amplicon sequencing was performed. These results suggest that a diagnostic platform based on gene expression rather than genomics alone may be beneficial in certain surveillance efforts. The implementation of such advanced diagnostics coupled with increased AMR surveillance will potentially improve A. baumannii infection treatment and patient outcomes.

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.

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