scholarly journals Association Mapping across Numerous Traits Reveals Patterns of Functional Variation in Maize

2014 ◽  
Author(s):  
Jason G Wallace ◽  
Peter Bradbury ◽  
Nengyi Zhang ◽  
Yves Gibon ◽  
Mark Stitt ◽  
...  
Keyword(s):  
Phenotypic Variation ◽  
Copy Number Variants ◽  
Natural Populations ◽  
Nucleotide Polymorphisms ◽  
Functional Variation ◽  
Single Nucleotide ◽  
Gene By Environment Interactions ◽  
Genome Wide ◽  
Intergenic Regions ◽  
Regulatory Functions

Phenotypic variation in natural populations results from a combination of genetic effects, environmental effects, and gene-by-environment interactions. Despite the vast amount of genomic data becoming available, many pressing questions remain about the nature of genetic mutations that underlie functional variation. We present the results of combining genome-wide association analysis of 41 different phenotypes in ~5,000 inbred maize lines to analyze patterns of high-resolution genetic association among of 28.9 million single-nucleotide polymorphisms (SNPs) and ~800,000 copy-number variants (CNVs). We show that genic and intergenic regions have opposite patterns of enrichment, minor allele frequencies, and effect sizes, implying tradeoffs among the probability that a given polymorphism will have an effect, the detectable size of that effect, and its frequency in the population. We also find that genes tagged by GWAS are enriched for regulatory functions and are ~50% more likely to have a paralog than expected by chance, indicating that gene regulation and neofunctionalization are strong drivers of phenotypic variation. These results will likely apply to many other organisms, especially ones with large and complex genomes like maize.

scholarly journals The influence of X chromosome variants on trait neuroticism

2018 ◽  
Author(s):  
Michelle Luciano ◽  
Gail Davies ◽  
Kim M Summers ◽  
W David Hill ◽  
Caroline Hayward ◽  
...  
Keyword(s):  
X Chromosome ◽  
Nucleotide Polymorphisms ◽  
Nucleic Acid Binding ◽  
Single Nucleotide ◽  
Association Analyses ◽  
Complex Disorders ◽  
Genome Wide ◽  
Intergenic Regions ◽  
Protein Classes ◽  
Sample Maximum

Autosomal variants have successfully been associated with trait neuroticism in genome-wide analysis of adequately-powered samples. But such studies have so far excluded the X chromosome from analysis. Here, we report genetic association analyses of X chromosome and XY pseudoautosomal single nucleotide polymorphisms (SNPs) and trait neuroticism using UK Biobank samples (N = 405,274). Significant association was found with neuroticism on the X chromosome for 204 markers found within three independent loci (a further 783 were suggestive). Most of these significant neuroticism-related X chromosome variants were located in intergenic regions (n = 713). Involvement of HS6ST2, which has been previously associated with sociability behaviour in the dog, was supported by single SNP and gene-based tests. We found that the amino acid and nucleotide sequences are highly conserved between dogs and humans. From the suggestive X chromosome variants, there were 19 nearby genes which could be linked to gene ontology information. Molecular function was primarily related to binding and catalytic activity; notable biological processes were cellular and metabolic, and nucleic acid binding and transcription factor protein classes were most commonly involved. X-variant heritability of neuroticism was estimated at 0.34% (SE = 0.07). A polygenic X-variant score created in an independent sample (maximum N ≈ 7300) did not predict significant variance in neuroticism, psychological distress, or depressive disorder. We conclude that the X chromosome harbours significant variants influencing neuroticism, and might prove important for other quantitative traits and complex disorders.

scholarly journals High-throughput sequencing reveals inbreeding depression in a natural population

2014 ◽  
Vol 111 (10) ◽  
pp. 3775-3780 ◽  
Author(s):  
Joseph I. Hoffman ◽  
Fraser Simpson ◽  
Patrice David ◽  
Jolianne M. Rijks ◽  
Thijs Kuiken ◽  
...  
Keyword(s):  
Natural Population ◽  
Inbreeding Depression ◽  
High Throughput Sequencing ◽  
Natural Populations ◽  
Harbor Seals ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Peromyscus Polionotus ◽  
Genome Wide ◽  
Underlying Mechanisms

Proxy measures of genome-wide heterozygosity based on approximately 10 microsatellites have been used to uncover heterozygosity fitness correlations (HFCs) for a wealth of important fitness traits in natural populations. However, effect sizes are typically very small and the underlying mechanisms remain contentious, as a handful of markers usually provides little power to detect inbreeding. We therefore used restriction site associated DNA (RAD) sequencing to accurately estimate genome-wide heterozygosity, an approach transferrable to any organism. As a proof of concept, we first RAD sequenced oldfield mice (Peromyscus polionotus) from a known pedigree, finding strong concordance between the inbreeding coefficient and heterozygosity measured at 13,198 single-nucleotide polymorphisms (SNPs). When applied to a natural population of harbor seals (Phoca vitulina), a weak HFC for parasite infection based on 27 microsatellites strengthened considerably with 14,585 SNPs, the deviance explained by heterozygosity increasing almost fivefold to a remarkable 49%. These findings arguably provide the strongest evidence to date of an HFC being due to inbreeding depression in a natural population lacking a pedigree. They also suggest that under some circumstances heterozygosity may explain far more variation in fitness than previously envisaged.

scholarly journals Genome wide analysis reveals single nucleotide polymorphisms associated with fatness and putative novel copy number variants in three pig breeds

BMC Genomics ◽  
2013 ◽  
Vol 14 (1) ◽  
pp. 784 ◽  
Author(s):  
Katie E Fowler ◽  
Ricardo Pong-Wong ◽  
Julien Bauer ◽  
Emily J Clemente ◽  
Christopher P Reitter ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Copy Number ◽  
Copy Number Variants ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide Analysis ◽  
Pig Breeds ◽  
Genome Wide

scholarly journals Pathway-based analysis enables deeper mining of GWAS data on H/L in chickens

2020 ◽  
Author(s):  
Jie Wang ◽  
Bo Zhu ◽  
Jie Wen ◽  
Qinghe Li ◽  
Guiping Zhao
Keyword(s):  
Immune System ◽  
Single Nucleotide Polymorphisms ◽  
Pathway Analysis ◽  
Phenotypic Variation ◽  
Chromosome 1 ◽  
Phenotypic Variance ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
A Genome

Abstract Background Heterophils are refers to white blood cells with phagocytosis and killing functions in the avian immune system, These cells identify and kill pathogenic microorganisms through precise regulatory mechanisms. As a simple index, the heterophil/lymphocyte ratio (H/L) in the blood reflects the immune system status of chickens. H/L is a complex trait affected by multiple genetic loci, but single nucleotide polymorphisms (SNPs) significantly associated with traits can usually explain only part of the phenotypic variation. Combining a genome-wide association study (GWAS) with pathway analysis can improve understanding of the biological pathways affecting traits. Our objective was to conduct a SNP- and pathway-based analysis to identify possible biological mechanisms involved in H/L traits. Methods GWAS for H/L was performed in 1,317 Cobb broilers to identify significant single nucleotide polymorphisms (SNPs) associated with H/L. Eight SNPs (P< 1/8,068) reached a significant level of association. The following results were obtained through a series of analyses, including pathway-based association analysis and analysis of the proportion of phenotypic variance explained by SNPs. Results On the basis of GWAS analysis results, one associated SNP (5% genome-wide significance (6.80E-6,0.05/8,068)) on GGA 1(chicken chromosome 1) and seven suggestively associated SNPs with a trend toward significance(1.24E-4, 1/8,068) on GGAs 1, 7, 13 and 19 were detected. The significant SNP on GGA 19 was in Complement C1q Binding Protein (C1QBP). The wild-type and mutant individuals showed significant differences in H/L at five loci (P< 0.05). According to the results of pathway-based analysis, nine associated pathways (P < 0.05) were identified, including small cell lung cancer, proteoglycans in cancer, sulfur relay system, pathways in cancer, gastric acid secretion and purine metabolism. By combining GWAS with pathway analysis, we found that all SNPs after QC explained 12.4% of the phenotypic variation in H/L and 53 SNPs associated with H/L explained as much as 9.7% of the phenotypic variation in H/L. Conclusions Our findings contribute to understanding of the genetic regulation of H/L and provide theoretical support.

scholarly journals Comprehensive Genome-Wide Association Analysis Reveals the Genetic Basis of Root System Architecture in Soybean

2020 ◽  
Vol 11 ◽  
Author(s):  
Waldiodio Seck ◽  
Davoud Torkamaneh ◽  
François Belzile
Keyword(s):  
Root System ◽  
System Architecture ◽  
Phenotypic Variation ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Primary Root ◽  
Root System Architecture ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Genome Wide

Increasing the understanding genetic basis of the variability in root system architecture (RSA) is essential to improve resource-use efficiency in agriculture systems and to develop climate-resilient crop cultivars. Roots being underground, their direct observation and detailed characterization are challenging. Here, were characterized twelve RSA-related traits in a panel of 137 early maturing soybean lines (Canadian soybean core collection) using rhizoboxes and two-dimensional imaging. Significant phenotypic variation (P &lt; 0.001) was observed among these lines for different RSA-related traits. This panel was genotyped with 2.18 million genome-wide single-nucleotide polymorphisms (SNPs) using a combination of genotyping-by-sequencing and whole-genome sequencing. A total of 10 quantitative trait locus (QTL) regions were detected for root total length and primary root diameter through a comprehensive genome-wide association study. These QTL regions explained from 15 to 25% of the phenotypic variation and contained two putative candidate genes with homology to genes previously reported to play a role in RSA in other species. These genes can serve to accelerate future efforts aimed to dissect genetic architecture of RSA and breed more resilient varieties.

EpiPen: An R Package to Investigate Two-Locus Epistatic Models

2014 ◽  
Vol 17 (4) ◽  
Author(s):  
Raymond K. Walters ◽  
Charles Laurin ◽  
Gitta H. Lubke
Keyword(s):  
Power Analysis ◽  
R Package ◽  
Simulation Studies ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Epistatic Interactions ◽  
Model Interpretation ◽  
Genome Wide ◽  
Using Data ◽  
Power Analyses

Epistasis is a growing area of research in genome-wide studies, but the differences between alternative definitions of epistasis remain a source of confusion for many researchers. One problem is that models for epistasis are presented in a number of formats, some of which have difficult-to-interpret parameters. In addition, the relation between the different models is rarely explained. Existing software for testing epistatic interactions between single-nucleotide polymorphisms (SNPs) does not provide the flexibility to compare the available model parameterizations. For that reason we have developed an R package for investigating epistatic and penetrance models, EpiPen, to aid users who wish to easily compare, interpret, and utilize models for two-locus epistatic interactions. EpiPen facilitates research on SNP-SNP interactions by allowing the R user to easily convert between common parametric forms for two-locus interactions, generate data for simulation studies, and perform power analyses for the selected model with a continuous or dichotomous phenotype. The usefulness of the package for model interpretation and power analysis is illustrated using data on rheumatoid arthritis.

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