2026-10-14T01:29:00Z https://api.figshare.com/v2/oai

oai:figshare.com:article/34022334 2026-09-29T09:47:41Z category_24310 item_type_3 month_year_09_2026

Genome-wide SNP genotype dataset for 249 Quality Protein Maize inbred lines used for phytic acid GWAS Sushil Kumar (25136298) Sourabh Kumar (25136305) Dinesh Kumar Saini (25114485) Rainy Rainy (25136308) Abhijit Kumar Das (25136313) Chikkappa G. Karjagi (21698265) Dharampaul Chaudhary (25136315) Shailendra Singh Gaurav (25136321) Ramesh Kumar (25136324) Genomics quality protein maize (QPM) Single nucleotide polymorphism. Genotyping genome-wide association study phytic acid <p dir="ltr">This dataset contains genome-wide single nucleotide polymorphism (SNP) genotype data for a diversity panel of 249 Quality Protein Maize (QPM) inbred lines evaluated in a genome-wide association study of kernel phytic acid content. The dataset comprises 26,074 high-quality SNP markers distributed across the 10 maize chromosomes. Genotyping was performed using a sequencing-based approach. Genomic DNA was used for library preparation with the NEBNext Ultra II DNA Library Preparation Kit for Illumina, with ApeKI as the restriction enzyme, followed by sequencing on an Illumina NovaSeq 6000 S4 platform using 2 × 151-bp paired-end reads. Sequence reads were aligned to the Zea mays B73 reference genome assembly Zm-B73-REFERENCE-NAM-5.0 using BWA-MEM, and variants were called using GATK. Variant calling initially identified 11,525,180 variants. Initial filtering using VCFtools retained 115,416 chromosomal biallelic SNPs with minor allele frequency (MAF) ≥ 0.05 and genotype calls in at least 10% of samples. Markers with >10% missing genotype data or a heterozygous-call rate >20% were subsequently removed, resulting in the final set of 26,074 high-quality SNPs. The deposited genotype matrix is provided in HapMap format. Each row represents a SNP marker and includes marker identifier, alleles, chromosome, physical position, strand, standard HapMap metadata fields, and genotype calls for the 249 QPM inbred lines. SNP positions correspond to the Zm-B73-REFERENCE-NAM-5.0 reference genome assembly. Missing genotype calls are represented by “N”, and heterozygous calls are represented using standard IUPAC nucleotide ambiguity codes. These 26,074 SNPs were used for analyses of population structure, principal component analysis, genetic relatedness, linkage disequilibrium, and genome-wide association mapping of kernel phytic acid content in the associated study.</p> 2026-09-29T09:47:41Z Dataset Dataset 10.6084/m9.figshare.34022334.v1 https://figshare.com/articles/dataset/Genome-wide_SNP_genotype_dataset_for_249_Quality_Protein_Maize_inbred_lines_used_for_phytic_acid_GWAS/34022334 CC BY 4.0