Genome-Wide Association for Itraconazole Sensitivity in Non-Resistant Clinical Isolates of Aspergillus fumigatus

AbstractAspergillus fumigatus is a potentially lethal opportunistic pathogen that infects over ∼200,000 people and causes ∼100,000 deaths per year globally. Treating A. fumigatus infections is particularly challenging because of the recent emergence of azole-resistance. The majority of studies focusing on the molecular mechanisms underlying azole resistance have examined azole-resistant isolates. However, isolates that are susceptible to azoles also display variation in their sensitivity, presenting a unique opportunity to identify genes contributing to azole sensitivity. Here, we used genome-wide association (GWA) analysis to identify loci involved in azole sensitivity by analyzing the association between 68,853 SNPs and itraconazole (ITCZ) minimum inhibitory concentration (MIC) in 76 clinical isolates of A. fumigatus from Japan. Population structure analysis suggests the presence of four distinct populations, with ITCZ MICs distributed relatively evenly across populations. We independently conducted GWA when treating ITCZ MIC as a quantitative trait and a binary trait and identified two SNPs with strong associations that were identified in both analyses. These SNPs fell within the coding regions of Afu2g02220 and Afu2g02140. We functionally validated Afu2g02220 by knocking it out using a CRISPR/Cas-9 approach, because orthologs of this gene are involved in sterol modification and ITCZ targets the ergosterol pathway. Knockout strains displayed no difference in growth compared to the parent strain in minimal media, yet a minor but consistent inhibition of growth in the presence of 0.15 ug/ml ITCZ. Our results suggest that GWA paired with efficient gene deletion is a powerful and unbiased strategy for identifying the genetic basis of complex traits in A. fumigatus.ImportanceAspergillus fumigatus is a pathogenic mold that can infect and kill individuals with compromised immune systems. The azole class of drugs provide antifungal activity against A. fumigatus infections and have become an essential treatment strategy. Unfortunately, A. fumigatus azole resistance has recently emerged and rapidly risen in frequency making treatment more challenging. Our understanding of the molecular basis of azole sensitivity has been shaped mainly through candidate gene studies. Unbiased approaches are necessary to understand the full repertoire of genes and genetic variants underlying azole resistance and sensitivity. Here, we provide the first application of genome-wide association analysis in A. fumigatus in the identification of a gene (Afu2g02220) that contributes to itraconazole susceptibility. Our approach, which combines association mapping and CRISPR/Cas-9 for functional validation of candidate genes, has broad application for investigating the genetic basis of complex traits in fungal systems.

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Genome-Wide Association for Itraconazole Sensitivity in Non-resistant Clinical Isolates of Aspergillus fumigatus

Frontiers in Fungal Biology ◽

10.3389/ffunb.2020.617338 ◽

2021 ◽

Vol 1 ◽

Author(s):

Shu Zhao ◽

Wenbo Ge ◽

Akira Watanabe ◽

Jarrod R. Fortwendel ◽

John G. Gibbons

Keyword(s):

Aspergillus Fumigatus ◽

Complex Traits ◽

Molecular Mechanisms ◽

Clinical Isolates ◽

Genome Wide Association ◽

Ergosterol Biosynthesis ◽

Azole Resistance ◽

Genome Wide ◽

Population Structure Analysis ◽

Recent Emergence

Aspergillus fumigatus is a potentially lethal opportunistic pathogen that infects over ~200,000 people and causes ~100,000 deaths per year globally. Treating A. fumigatus infections is particularly challenging because of the recent emergence of azole-resistance. The majority of studies focusing on the molecular mechanisms underlying azole resistance have examined azole-resistant isolates. However, isolates that are susceptible to azoles also display variation in their sensitivity, presenting a unique opportunity to identify genes contributing to azole sensitivity. Here, we used genome-wide association (GWA) analysis to identify loci involved in azole sensitivity by analyzing the association between 68,853 SNPs and itraconazole (ITCZ) minimum inhibitory concentration (MIC) in 76 clinical isolates of A. fumigatus from Japan. Population structure analysis suggests the presence of four distinct populations, with ITCZ MICs distributed relatively evenly across populations. We independently conducted GWA when treating ITCZ MIC as a quantitative trait and a binary trait, and identified two SNPs with strong associations in both analyses. These SNPs fell within the coding regions of Afu2g02220 and Afu2g02140. We functionally validated Afu2g02220 by knocking it out using a CRISPR/Cas9 approach, because orthologs of this gene are involved in sterol modification and ITCZ targets the ergosterol biosynthesis pathway. Knockout strains displayed no difference in growth compared to the parent strain in minimal media, yet a minor but consistent inhibition of growth in the presence of 0.15 μg/ml ITCZ. Our results suggest that GWA paired with efficient gene deletion is a powerful and unbiased strategy for identifying the genetic basis of complex traits in A. fumigatus.

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GWAS of three molecular traits highlights core genes and pathways alongside a highly polygenic background

10.1101/2020.04.20.051631 ◽

2020 ◽

Cited By ~ 6

Author(s):

Nasa Sinnott-Armstrong ◽

Sahin Naqvi ◽

Manuel Rivas ◽

Jonathan K Pritchard

Keyword(s):

Complex Traits ◽

Genetic Basis ◽

Association Studies ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Biological Processes ◽

Uk Biobank ◽

The Core ◽

Genome Wide ◽

Core Genes

SummaryGenome-wide association studies (GWAS) have been used to study the genetic basis of a wide variety of complex diseases and other traits. However, for most traits it remains difficult to interpret what genes and biological processes are impacted by the top hits. Here, as a contrast, we describe UK Biobank GWAS results for three molecular traits—urate, IGF-1, and testosterone—that are biologically simpler than most diseases, and for which we know a great deal in advance about the core genes and pathways. Unlike most GWAS of complex traits, for all three traits we find that most top hits are readily interpretable. We observe huge enrichment of significant signals near genes involved in the relevant biosynthesis, transport, or signaling pathways. We show how GWAS data illuminate the biology of variation in each trait, including insights into differences in testosterone regulation between females and males. Meanwhile, in other respects the results are reminiscent of GWAS for more-complex traits. In particular, even these molecular traits are highly polygenic, with most of the variance coming not from core genes, but from thousands to tens of thousands of variants spread across most of the genome. Given that diseases are often impacted by many distinct biological processes, including these three, our results help to illustrate why so many variants can affect risk for any given disease.

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Genome-wide association study of biologically informed periodontal complex traits offers novel insights into the genetic basis of periodontal disease

Human Molecular Genetics ◽

10.1093/hmg/ddw069 ◽

2016 ◽

Vol 25 (10) ◽

pp. 2113-2129 ◽

Cited By ~ 63

Author(s):

Steven Offenbacher ◽

Kimon Divaris ◽

Silvana P. Barros ◽

Kevin L. Moss ◽

Julie T. Marchesan ◽

...

Keyword(s):

Periodontal Disease ◽

Association Study ◽

Complex Traits ◽

Genetic Basis ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Genome Wide

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Genome-Wide Association Studies of Leaf Angle in Maize

10.21203/rs.3.rs-329481/v1 ◽

2021 ◽

Author(s):

Bo Peng ◽

Xiaolei Zhao ◽

Yi Wang ◽

Chunhui Li ◽

Yongxiang Li ◽

...

Keyword(s):

Candidate Genes ◽

Phenotypic Variation ◽

Genetic Basis ◽

Genome Wide Association ◽

Leaf Angle ◽

Genome Wide Association Studies ◽

Major Qtls ◽

Genome Wide ◽

Population Structure Analysis ◽

A Genome

Abstract Compact plant-type with small leaf angle has increased canopy light interception, which is conducive to the photosynthesis of the population and higher population yield at high density planting in maize. In this study, a panel of 285 diverse maize inbred lines genotyped with 56,000 SNPs was used to investigate the genetic basis of leaf angle across three consecutive years using a genome-wide association study (GWAS). The leaf angle showed broad phenotypic variation and high heritability across different years. Population structure analysis subdivided the panel into four subgroups that correspond to the four major empirical germplasm origins in China, i.e., Tangsipingtou, Reid, Lancaster and P. When tested with the optimal GWAS model, we found that the Q+K model was the best in reducing false positive. In total, 96 SNPs accounting for 5.54%-10.44% of phenotypic variation were significantly (P<0.0001) associated with leaf angle across three years. According to the linkage disequilibrium decay distance, 96 SNPs were binned in 43 QTLs for leaf angle. Seven major QTLs with R2>8% stably detected in at least two years and BLUP values were clustered in four genomic regions (bins 2.01, 2.07, 5.06, and 10.04). Seven important candidate genes, Zm00001d001961, Zm00001d006348, Zm00001d006463, Zm00001d017618, Zm00001d024919, Zm00001d025018, and Zm00001d025033 were predicted for the seven stable major QTLs, respectively. The markers identified in this study can be used for molecular breeding for leaf angle, and the candidate genes would contribute to further understanding of the genetic basis of leaf angle.

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Genome-wide association study of rice rooting ability at the seedling stage

10.21203/rs.3.rs-33742/v2 ◽

2020 ◽

Author(s):

Xin Xu ◽

Junhua Ye ◽

Yingying Yang ◽

Mengchen Zhang ◽

Qun Xu ◽

...

Keyword(s):

Association Study ◽

Root Length ◽

Genetic Basis ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Root Number ◽

Expression Levels ◽

Rooting Ability ◽

Genome Wide ◽

Population Structure Analysis

Abstract BackgroundRice rooting ability is a complex agronomical trait that displays heterosis and plays an important role in rice growth and production. Only a few quantitative trait loci (QTLs) have been identified by bi-parental population. More genes or QTLs are required to dissect the genetic architecture of rice rooting ability.ResultsTo characterize the genetic basis for rice rooting ability, we used a natural rice population, genotyped by a 90K single nucleotide polymorphism (SNP) array, to identify the loci associated with rooting-related traits through the genome-wide association study (GWAS). Population structure analysis divided the natural population into two subgroups: indica and japonica. We measured four traits for evaluating rice rooting ability, namely root growth ability (RGA), maximum root length (MRL), root length (RL), and root number (RN). Using the association study in three panels consisting of one for the full population, one for indica, and one for japonica, 24 SNPs associated with rooting ability-related traits were identified. Through comparison of the relative expression levels and DNA sequences between germplasm with extreme phenotypes, results showed that LOC_Os05g11810 had non-synonymous variations at the coding region, which may cause differences in root number, and that the expression levels of LOC_Os04g09900 and LOC_Os04g10060 are closely associated with root length variation.ConclusionsThrough evaluation of the rice rooting ability-related traits and the association mapping, we provided useful information for understanding the genetic basis of rice rooting ability and also identified some candidate genes and molecular markers for rice root breeding.

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Genome-Wide Association Study of H/L Traits in Chicken

Animals ◽

10.3390/ani9050260 ◽

2019 ◽

Vol 9 (5) ◽

pp. 260 ◽

Cited By ~ 1

Author(s):

Bo Zhu ◽

Qinghe Li ◽

Ranran Liu ◽

Maiqing Zheng ◽

Jie Wen ◽

...

Keyword(s):

Disease Resistance ◽

Association Study ◽

Genetic Basis ◽

Molecular Mechanisms ◽

Genome Wide Association Study ◽

Gene Annotation ◽

Immune Defense ◽

Genome Wide Association ◽

Genome Wide ◽

A Genome

Presently, the heterophil-to-lymphocyte (H/L) ratio is being studied extensively as a disease resistance trait. Through intricate mechanisms to identify and destroy pathogenic microorganisms, heterophils play a pivotal role in the immune defense systems of avian species. To reveal the genetic basis and molecular mechanisms affecting the H/L ratio, phenotypic and H/L data from 1650 white feather chicken broilers were used in performing a genome-wide association study. A self-developed, chicken-specific 55K chip was used for heterophils, lymphocytes, and H/L classification, according to individual genomic DNA profiles. We identified five significant single nucleotide polymorphisms (SNPs) when the genome-wide significance threshold was set to 5% (p < 2.42 × 10−6). A total of 15 SNPs obtained seemingly significant levels (p < 4.84 × 10−5). Gene annotation indicated that CARD11 (Caspase recruitment domain family member 11), BRIX1 (Biogenesis of ribosomes BRX1), and BANP (BTG3 associated nuclear protein) play a role in H/L-associated cell regulation and potentially constitute candidate gene regions for cellular functions dependent on H/L ratios. These results lay the foundation for revealing the genetic basis of disease resistance and future marker-assisted selection for disease resistance.

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Genome-Wide Association Analysis for Triazole Resistance in Aspergillus fumigatus

Pathogens ◽

10.3390/pathogens10060701 ◽

2021 ◽

Vol 10 (6) ◽

pp. 701

Author(s):

Yuying Fan ◽

Yue Wang ◽

Gregory A. Korfanty ◽

Meagan Archer ◽

Jianping Xu

Keyword(s):

Aspergillus Fumigatus ◽

Target Gene ◽

Molecular Mechanisms ◽

Genome Wide Association Study ◽

Clinical Importance ◽

Genome Wide Association ◽

Missense Mutations ◽

Genome Wide ◽

Resistant Strains ◽

The Common

Aspergillus fumigatus is a ubiquitous fungus and the main agent of aspergillosis, a common fungal infection in the immunocompromised population. Triazoles such as itraconazole and voriconazole are the common first-line drugs for treating aspergillosis. However, triazole resistance in A. fumigatus has been reported in an increasing number of countries. While most studies of triazole resistance have focused on mutations in the triazole target gene cyp51A, >70% of triazole-resistant strains in certain populations showed no mutations in cyp51A. To identify potential non-cyp51A mutations associated with triazole resistance in A. fumigatus, we analyzed the whole genome sequences and triazole susceptibilities of 195 strains from 12 countries. These strains belonged to three distinct clades. Our genome-wide association study (GWAS) identified a total of six missense mutations significantly associated with itraconazole resistance and 18 missense mutations with voriconazole resistance. In addition, to investigate itraconazole and pan-azole resistance, Fisher’s exact tests revealed 26 additional missense variants tightly linked to the top 20 SNPs obtained by GWAS, of which two were consistently associated with triazole resistance. The large number of novel mutations related to triazole resistance should help further investigations into their molecular mechanisms, their clinical importance, and the development of a comprehensive molecular diagnosis toolbox for triazole resistance in A. fumigatus.

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Evaluating the power and limitations of genome-wide association mapping in C. elegans

10.1101/2021.09.09.459688 ◽

2021 ◽

Author(s):

Samuel J. Widmayer ◽

Kathryn S. Evans ◽

Stefan Zdraljevic ◽

Erik C. Andersen

Keyword(s):

Quantitative Trait ◽

Complex Traits ◽

Genetic Basis ◽

Natural Populations ◽

Evolutionary Genetics ◽

Genome Wide Association ◽

C Elegans ◽

Quantitative Genetic ◽

Genome Wide ◽

Simulation Based

A central goal of evolutionary genetics in Caenorhabditis elegans is to understand the genetic basis of traits that contribute to adaptation and fitness. Genome-wide association (GWA) mappings scan the genome for individual genetic variants that are significantly correlated with phenotypic variation in a population, or quantitative trait loci (QTL). GWA mappings are a popular choice for quantitative genetic analyses because the QTL that are discovered segregate in natural populations. Despite numerous successful mapping experiments, the empirical performance of GWA mappings has not, to date, been formally evaluated for this species. We developed an open-source GWA mapping pipeline called NemaScan and used a simulation-based approach to provide benchmarks of mapping performance among wild C. elegans strains. Simulated trait heritability and complexity determined the spectrum of QTL detected by GWA mappings. Power to detect smaller-effect QTL increased with the number of strains sampled from the C. elegans Natural Diversity Resource (CeNDR). Population structure was a major driver of variation in GWA mapping performance, with populations shaped by recent selection exhibiting significantly lower false discovery rates than populations composed of more divergent strains. We also recapitulated previous GWA mappings of experimentally validated quantitative trait variants. Our simulation-based evaluation of GWA performance provides the community with critical context for pursuing quantitative genetic studies using CeNDR to elucidate the genetic basis of complex traits in C. elegans natural populations.

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Thinking About the Evolution of Complex Traits in the Era of Genome-Wide Association Studies

Annual Review of Genomics and Human Genetics ◽

10.1146/annurev-genom-083115-022316 ◽

2019 ◽

Vol 20 (1) ◽

pp. 461-493 ◽

Cited By ~ 32

Author(s):

Guy Sella ◽

Nicholas H. Barton

Keyword(s):

Complex Traits ◽

Genetic Basis ◽

Association Studies ◽

Practical Importance ◽

Complex Trait ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Heritable Variation ◽

Genome Wide ◽

Polygenic Adaptation

Many traits of interest are highly heritable and genetically complex, meaning that much of the variation they exhibit arises from differences at numerous loci in the genome. Complex traits and their evolution have been studied for more than a century, but only in the last decade have genome-wide association studies (GWASs) in humans begun to reveal their genetic basis. Here, we bring these threads of research together to ask how findings from GWASs can further our understanding of the processes that give rise to heritable variation in complex traits and of the genetic basis of complex trait evolution in response to changing selection pressures (i.e., of polygenic adaptation). Conversely, we ask how evolutionary thinking helps us to interpret findings from GWASs and informs related efforts of practical importance.

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Genome-Wide Association Study of Rice Rooting Ability at the Seedling Stage

10.21203/rs.3.rs-33742/v1 ◽

2020 ◽

Author(s):

Xin Xu ◽

Junhua Ye ◽

Yingying Yang ◽

Mengchen Zhang ◽

Qun Xu ◽

...

Keyword(s):

Association Study ◽

Root Length ◽

Genetic Basis ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Root Number ◽

Expression Levels ◽

Rooting Ability ◽

Genome Wide ◽

Population Structure Analysis

Abstract Background Rice rooting ability is a complex agronomical trait that displays heterosis and plays an important role in rice growth and production. Only a few quantitative trait loci (QTLs) have been identified by bi-parental population. More genes or QTLs are required to dissect the genetic architecture of rice rooting ability.Results To characterize the genetic basis for rice rooting ability, we used a natural rice population, genotyped by a 90K single nucleotide polymorphism (SNP) array, to identify the loci associated with rooting-related traits through the genome-wide association study (GWAS). Population structure analysis divided the natural population into two subgroups: indica and japonica. We measured four traits for evaluating rice rooting ability, namely root growth ability (RGA), maximum root length (MRL), root length (RL), and root number (RN). Combined with the association study in three panels consisting of one for the full population, one for indica, and one for japonica, 32 SNPs associated with rooting ability-related traits were identified. Through comparison of the relative expression levels and DNA sequences between germplasms with extreme phenotypes, results showed that LOC_Os05g11810 had non-synonymous variations at the coding region, which may cause differences in root number, and that the expression levels of LOC_Os04g09900 and LOC_Os04g10060 are closely associated with root length variation.Conclusions The goal of our research was to improve understanding of the genetic basis of rice rooting ability and provide useful molecular markers and germplasms for rice root breeding.

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