Table · dataset · 2026
Genome-wide SNP genotype dataset for 249 Quality Protein Maize inbred lines used for phytic acid GWAS
Listed in ZivaHub and HKU DataHub and figshare and Loughborough Research Repository and UP Research Data Repository — shown once because both records carry DOI 10.6084/m9.figshare.34022334.v1
<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.
Description
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.
Read the rest (3 more)
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>
Links
Where it is published
- DOI doi.org/10.6084/m9.figshare.34022334.v1 ↗
DOI / persistent id · from zivahub uct ac za
Catalogue records · 1
- OAI-PMH record api.figshare.com/v2/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=oai%3Af… ↗
metadata API · from zivahub uct ac za
Topics
- From keywords
- Astronomy & Astrophysics · Chemistry · Chemistry · Computer Science & AI · Computer Science & AI · Earth & Environmental Science · Earth & Environmental Science · Earth & Environmental Science · Earth & Environmental Science · Earth & Environmental Science · Economics & Finance · Economics & Finance · Engineering · Engineering · Engineering · Genomics · Genomics · Genomics · Genomics · Genomics · Humanities · Humanities · Humanities · Life Sciences · Life Sciences · Life Sciences · Life Sciences · Life Sciences · Materials Science · Mathematics & Statistics · Medicine & Health · Medicine & Health · Ocean & Atmospheric Science · Psychology & Behavioral Science · Social Science · Social Science · Social Science
- Inferred from text
- Sequencing 75%
Provenance · 5 source records, 43 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| ZivaHub | oai:figshare.com:article/34022334 | 12 d ago | JSON v1 |
| HKU DataHub | oai:figshare.com:article/34022334 | 12 d ago | JSON v1 |
| figshare | oai:figshare.com:article/34022334 | 11 d ago | JSON v1 |
| Loughborough Research Repository | oai:figshare.com:article/34022334 | 11 d ago | JSON v1 |
| UP Research Data Repository | oai:figshare.com:article/34022334 | 11 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · zivahub uct ac za | connector:zivahub_uct_ac_za@1.0.0 | |
| concepts[field].anzsrc:field:310509 | mapping · repository lboro ac uk | vocabulary-mapper@1.0.0 | keywords['Genomics'] |
| concepts[field].anzsrc:field:310509 | mapping · figshare com | vocabulary-mapper@1.0.0 | keywords['Genomics'] |
| concepts[field].anzsrc:field:310509 | mapping · zivahub uct ac za | vocabulary-mapper@1.0.0 | keywords['Genomics'] |
| concepts[field].anzsrc:field:310509 | mapping · researchdata up ac za | vocabulary-mapper@1.0.0 | keywords['Genomics'] |
| concepts[field].anzsrc:field:310509 | mapping · datahub hku hk | vocabulary-mapper@1.0.0 | keywords['Genomics'] |
| concepts[field].local:field:astronomy | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:chemistry | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:chemistry | mapping · repository lboro ac uk | connector:repository_lboro_ac_uk@1.0.0 | |
| concepts[field].local:field:computer-science-ai | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:computer-science-ai | mapping · repository lboro ac uk | connector:repository_lboro_ac_uk@1.0.0 | |
| concepts[field].local:field:earth-environmental | mapping · zivahub uct ac za | connector:zivahub_uct_ac_za@1.0.0 | |
| concepts[field].local:field:earth-environmental | mapping · datahub hku hk | connector:datahub_hku_hk@1.0.0 | |
| concepts[field].local:field:earth-environmental | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:earth-environmental | mapping · repository lboro ac uk | connector:repository_lboro_ac_uk@1.0.0 | |
| concepts[field].local:field:earth-environmental | mapping · researchdata up ac za | connector:researchdata_up_ac_za@1.0.0 | |
| concepts[field].local:field:economics-finance | mapping · repository lboro ac uk | connector:repository_lboro_ac_uk@1.0.0 | |
| concepts[field].local:field:economics-finance | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:engineering | mapping · researchdata up ac za | connector:researchdata_up_ac_za@1.0.0 | |
| concepts[field].local:field:engineering | mapping · repository lboro ac uk | connector:repository_lboro_ac_uk@1.0.0 | |
| concepts[field].local:field:engineering | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:humanities | mapping · researchdata up ac za | connector:researchdata_up_ac_za@1.0.0 | |
| concepts[field].local:field:humanities | mapping · repository lboro ac uk | connector:repository_lboro_ac_uk@1.0.0 | |
| concepts[field].local:field:humanities | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · datahub hku hk | connector:datahub_hku_hk@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · zivahub uct ac za | connector:zivahub_uct_ac_za@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · repository lboro ac uk | connector:repository_lboro_ac_uk@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · researchdata up ac za | connector:researchdata_up_ac_za@1.0.0 | |
| concepts[field].local:field:materials-science | mapping · repository lboro ac uk | connector:repository_lboro_ac_uk@1.0.0 | |
| concepts[field].local:field:mathematics-statistics | mapping · repository lboro ac uk | connector:repository_lboro_ac_uk@1.0.0 | |
| concepts[field].local:field:medicine-health | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:medicine-health | mapping · repository lboro ac uk | connector:repository_lboro_ac_uk@1.0.0 | |
| concepts[field].local:field:ocean-atmospheric | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:psychology-behavioral | mapping · repository lboro ac uk | connector:repository_lboro_ac_uk@1.0.0 | |
| concepts[field].local:field:social-science | mapping · researchdata up ac za | connector:researchdata_up_ac_za@1.0.0 | |
| concepts[field].local:field:social-science | mapping · repository lboro ac uk | connector:repository_lboro_ac_uk@1.0.0 | |
| concepts[field].local:field:social-science | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[modality].local:modality:sequencing | enrichment · zivahub uct ac za | keyword-concept-rules@1.0.0 | title+description (75%) |
| description | source · zivahub uct ac za | connector:zivahub_uct_ac_za@1.0.0 | /metadata/dc/description |
| license | source · zivahub uct ac za | connector:zivahub_uct_ac_za@1.0.0 | /metadata/dc/rights |
| publication_date | source · zivahub uct ac za | connector:zivahub_uct_ac_za@1.0.0 | |
| title | source · zivahub uct ac za | connector:zivahub_uct_ac_za@1.0.0 | /metadata/dc/title |