Code for: The stability of fatty acid composition in sunflower oil is dependent on environment and affected by structural variation
Code accompanying the manuscript "The stability of fatty acid composition in sunflower oil is dependent on environment and affected by structural variation" (Ingold, Hulke et al.), submitted to Theoretical and Applied Genetics.The code implements a genome-wide association study of seed fatty acid composition and its stability in the sunflower (Helianthus annuus L.) association mapping (SAM) population of 287 varieties, grown in eight field trials across North America: Vancouver, British Columbia (2010); Moorhead, Minnesota (2015, early and late plantings 2016); Ames, Iowa (2010, 2013, 2014); and Athens, Georgia (2010). Palmitic, stearic, oleic, and linoleic acid were measured by gas chromatography.Multivariate GWAS was performed on four phenotype sets: mean fatty acid composition within each environment; the same omitting high oleic varieties; within-environment stability quantified by standard errors among replicate samples (alpha stability); and across-environment stability quantified by Eberhart and Russell's beta.Included are scripts for phenotype preparation, beta stability regression, CHELSA climate data extraction and correlation, genotype and kinship analysis (ADMIXTURE, VanRaden kinship, PCA, LD blocks), multivariate GWAS with GEMMA and univariate GWAS with vcf2gwas, post-GWAS candidate gene identification, and analysis of a chromosome 5 introgression associated with stability under hot, humid conditions.The code is archived at https://doi.org/10.5281/zenodo.22001495 and developed at https://github.com/BrianSmart/SunflowerFattyAcidStabilityGWAS. SNP genotypes are third-party and available from HelianthOME (http://www.helianthome.org/download/#genotype).
Resources
2 resources available
-
Geodata ISO 19139 metadata
XML -
https://doi.org/10.5281/zenodo.22001495
HTML
Find Related Datasets
Search by Tags
Click any tag below to search for similar datasets
Complete Metadata
| @type | dcat:Dataset |
|---|---|
| accessLevel | public |
| bureauCode |
[ "005:18", "005:20" ] |
| contactPoint |
{ "fn": "Smart, Brian, C.", "hasEmail": "mailto:brian.smart@ndsu.edu" } |
| description | <p dir="ltr">Code accompanying the manuscript "The stability of fatty acid composition in sunflower oil is dependent on environment and affected by structural variation" (Ingold, Hulke et al.), submitted to Theoretical and Applied Genetics.</p><p dir="ltr">The code implements a genome-wide association study of seed fatty acid composition and its stability in the sunflower (Helianthus annuus L.) association mapping (SAM) population of 287 varieties, grown in eight field trials across North America: Vancouver, British Columbia (2010); Moorhead, Minnesota (2015, early and late plantings 2016); Ames, Iowa (2010, 2013, 2014); and Athens, Georgia (2010). Palmitic, stearic, oleic, and linoleic acid were measured by gas chromatography.</p><p dir="ltr">Multivariate GWAS was performed on four phenotype sets: mean fatty acid composition within each environment; the same omitting high oleic varieties; within-environment stability quantified by standard errors among replicate samples (alpha stability); and across-environment stability quantified by Eberhart and Russell's beta.</p><p dir="ltr">Included are scripts for phenotype preparation, beta stability regression, CHELSA climate data extraction and correlation, genotype and kinship analysis (ADMIXTURE, VanRaden kinship, PCA, LD blocks), multivariate GWAS with GEMMA and univariate GWAS with vcf2gwas, post-GWAS candidate gene identification, and analysis of a chromosome 5 introgression associated with stability under hot, humid conditions.</p><p dir="ltr">The code is archived at https://doi.org/10.5281/zenodo.22001495 and developed at https://github.com/BrianSmart/SunflowerFattyAcidStabilityGWAS. SNP genotypes are third-party and available from HelianthOME (http://www.helianthome.org/download/#genotype).</p> |
| distribution |
[ { "@type": "dcat:Distribution", "title": "Geodata ISO 19139 metadata", "format": "xml", "accessURL": "https://geodata.nal.usda.gov/geonetwork/srv/api/records/e5eb6950-5358-45a0-b524-41b33ce2b954/formatters/xml", "mediaType": "text/xml", "conformsTo": "https://www.isotc211.org/2005/gmd" }, { "@type": "dcat:Distribution", "title": "https://doi.org/10.5281/zenodo.22001495", "mediaType": "text/html", "downloadURL": "https://doi.org/10.5281/zenodo.22001495" } ] |
| identifier | 10.5281/zenodo.22001495 |
| keyword |
[ "GWAS", "Helianthus annus L.", "association mapping", "fatty acid composition", "genotype by environment (G×E) interaction", "linoleic acid", "oleic acid", "seed oil quality", "source code", "structural variation", "sunflower", "trait stability" ] |
| license | https://creativecommons.org/publicdomain/zero/1.0/ |
| modified | 2026-08-28 |
| programCode |
[ "005:040" ] |
| publisher |
{ "name": "Agricultural Research Service", "@type": "org:Organization" } |
| spatial |
"{"type": "MultiPoint", "coordinates": [[-123.1207, 49.2827], [-96.7678, 46.8738], [-93.6199, 42.0347], [-83.3576, 33.9519]]}"
|
| temporal | 2010-01-01/2016-12-31 |
| theme |
[ "geospatial" ] |
| title | Code for: The stability of fatty acid composition in sunflower oil is dependent on environment and affected by structural variation |
