DOI: 10.5061/dryad.9cnp5hqs0
title: Dataset for genome-wide association study of maize phosphorus efficiency

description: This dataset comprises genotypic data derived from 398 genotypes of maize
 (Zea mays), categorized into 100 Dent (maize_Dent), 100 Flint
 (maize_Flint), and 198 doubled haploid Landraces (maize_LR) sourced from
 six European lines. The data is provided in Variant Call Format (vcf),
 with each population having its dedicated file, analyzed separately. The
 vcf files contain meta-information lines, a header line, and subsequent
 data lines detailing genomic positions. Meta-information is included post
 the ## string. The header encompasses eight fixed fields per record,
 tab-delimited and specifying information such as chromosome (CHROM),
 position (POS), identifier (ID), reference base(s) (REF), alternate
 base(s) (ALT), quality (QUAL), filter status (FILTER), and additional
 information (INFO). Missing values are denoted by a dot ('.').
 The data format includes a FORMAT field specifying data types and order,
 followed by individual fields for each sample. Genotypes are encoded as
 allele values separated by either '/' or '|'. This
 dataset was employed in a genome-wide association study (GWAS) utilizing a
 diversity panel to analyze Phosphorus use efficiency in these genotypes.
description: All genotypes in the study had available marker data generated
 using the MaizeSNP50 BeadChip from Illumina®. To ensure data integrity,
 quality control procedures were implemented. Markers exhibiting more than
 5% heterozygotes or 50% missing values per marker were excluded, along
 with markers having an additional 20% missing values per genotype in the
 entire dataset. Subsequently, individualized quality control was applied
 to each subpopulation. Heterozygous markers were set to NA, and a minor
 allele frequency (MAF) filter of 3% was imposed. Imputation was conducted
 separately for each subpopulation using BEAGLE 5.0. The imputed data
 underwent further filtering, with a threshold set for a MAF greater than
 5%. The physical positions of Single Nucleotide Polymorphisms (SNPs) are
 referenced to the B73 genome version 4.
description: # Genome-wide association study of maize phosphorus efficiency
 [https://doi.org/10.5061/dryad.9cnp5hqs0
 ](https://doi.org/10.5061/dryad.9cnp5hqs0) ## Description of the data and
 file structure A VCF (Variant Call Format) file is a text file storing
 genetic variation data, like SNPs or insertions/deletions. It includes
 meta-information, a header defining data fields, and data lines specifying
 genomic positions with details such as chromosome, position, alleles,
 quality, and additional information. The dataset is structured with
 individual vcf files for three distinct maize populations: **Dent
 (maize_Dent), Flint (maize_Flint), and doubled haploid Landraces
 (maize_LR)**. Each vcf file contains meta-information lines, followed by a
 header line specifying eight fixed fields per sample and subsequent data
 lines detailing genomic positions. The fixed fields include information
 such as chromosome (CHROM), position (POS), identifier (ID), the reference
 base(s) (REF), alternate base(s) (ALT), quality (QUAL), filter status
 (FILTER), and additional information (INFO). Genotypes are encoded as
 allele values separated by '/' or '|'. The
 relationships between the data files lie in their shared format and
 genomic content, with each file representing a specific maize population.
 Researchers can analyze the data collectively or focus on individual
 populations based on their research objectives. Quality control measures
 have been applied uniformly across all files, involving the removal of
 markers with more than 5% heterozygotes or 50% missing values per marker.
 An additional criterion of 20% missing values per genotype in the complete
 dataset was applied. Subpopulation-specific quality control was carried
 out, such as setting heterozygous markers to 'NA' and
 implementing a minor allele frequency (MAF) filter of 3%. Imputation,
 conducted individually for each subpopulation using BEAGLE 5.0, further
 refines the dataset, with the final imputed data filtered for a MAF
 greater than 5%. ## Code/Software These files can all be opened with
 Tassel 5 as vcf files. They can also be opened with a standard text
 editor.