BGS Hosted Metadata
Single nucleotide polymorphism genotyping of 323 wheat accessions from Pakistan, Mexico and Australia
[This dataset is embargoed until June 1, 2027]. The dataset contains single nucleotide polymorphism (SNP) genotyping data for 323 diverse wheat accessions from Pakistan, Mexico, and Australia. DNA was extracted from 21-day-old seedlings grown in a glasshouse at Rothamsted Research, UK, and genotyped using the commercially available TaNG v1.1 Affymetrix Axiom array at the Bristol Genomics Facility, University of Bristol. The genotypic data are provided in HapMap double-bit format. This work aimed to improve nitrogen use efficiency (NUE) in wheat as part of efforts toward sustainable yield enhancement and global food security. Genetic dissection of key agronomic traits presents a viable strategy for developing high-yielding, nitrogen-efficient wheat cultivars. The data support a genome-wide association study (GWAS) that related NUE traits to potential genetic markers. The research was funded by the Natural Environment Research Council (Grant NE/S009019/1). Full details about this dataset can be found at https://doi.org/10.5285/291ca8d7-6178-4e6f-98a5-f59225d884cd
Simple
- Date (Publication)
- 2025-11-26
- Citation identifier
- https://catalogue.ceh.ac.uk/id/291ca8d7-6178-4e6f-98a5-f59225d884cd
- Citation identifier
- doi: / 10.5285/291ca8d7-6178-4e6f-98a5-f59225d884cd
- Other citation details
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Iqbal, R., Bano, Z., Kiran, A., Naeem, M.K., Khan, M.R., Wakeel, A., Sajjad, H., Aziz, T., Sutton, M., Price, A., Prins, A., Shewry, P., Alabdullah, A.K., Maqsood, M.A. (2025). Single nucleotide polymorphism genotyping of 323 wheat accessions from Pakistan, Mexico and Australia. NERC EDS Environmental Information Data Centre 10.5285/291ca8d7-6178-4e6f-98a5-f59225d884cd
- Point of contact
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Organisation name Individual name Electronic mail address Role Rothamsted Research Prins, A.
Point of contact University of Agriculture Faisalabad Iqbal, R.
Author University of Agriculture Faisalabad Bano, Z.
Author University of Agriculture Faisalabad Kiran, A.
Author National Agricultural Research Center Islamabad
Naeem, M.K.
Author National Agricultural Research Center Islamabad
Khan, M.R.
Author University of Agriculture Faisalabad Wakeel, A.
Author University of Agriculture Faisalabad Sajjad, H.
Author University of Agriculture Faisalabad Aziz, T.
Author UK Centre for Ecology & Hydrology Sutton, M.
Author University of Aberdeen Price, A.
Author Rothamsted Research Prins, A.
Author Rothamsted Research Shewry, P.
Author John Innes Centre Alabdullah, A.K.
Author National Agricultural Research Center Islamabad
Maqsood, M.A.
Author University of Agriculture Faisalabad EMAIL NOT PROVIDED
Owner NERC EDS Environmental Information Data Centre Publisher NERC EDS Environmental Information Data Centre Custodian
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GEMET - Concepts, version 4.1.3
- Keywords
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- Agriculture
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nitrogen use efficiency
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Pakistan
- Access constraints
- Other restrictions
- Other constraints
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Embargoed
- Use constraints
- Other restrictions
- Use constraints
- Other restrictions
- Other constraints
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If you reuse this data, you should cite: Iqbal, R., Bano, Z., Kiran, A., Naeem, M.K., Khan, M.R., Wakeel, A., Sajjad, H., Aziz, T., Sutton, M., Price, A., Prins, A., Shewry, P., Alabdullah, A.K., Maqsood, M.A. (2025). Single nucleotide polymorphism genotyping of 323 wheat accessions from Pakistan, Mexico and Australia. NERC EDS Environmental Information Data Centre https://doi.org/10.5285/291ca8d7-6178-4e6f-98a5-f59225d884cd
- Spatial representation type
- Text, table
- Language
- English
- Character set
- UTF8
- Topic category
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- Farming
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- Unique resource identifier
- WGS 84
- Distribution format
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Name Version Comma-separated values (CSV)
- Distributor contact
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Organisation name Individual name Electronic mail address Role NERC EDS Environmental Information Data Centre
Distributor
- Hierarchy level
- Dataset
- Other
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dataset
Conformance result
- Title
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Commission Regulation (EU) No 1089/2010 of 23 November 2010 implementing Directive 2007/2/EC of the European Parliament and of the Council as regards interoperability of spatial data sets and services
- Date (Publication)
- 2010-12-08
- Statement
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DNA was extracted from 21 day old seedlings using the Wizard Genomic DNA Purification Kit (Promega, UK). Quantity and quality was checked using an ND-1000 spectrophotometer (Thermo Fisher Scientific, USA) and a Qubit 2.0 fluorometer using a Qubit dsDNA quantification kit (Invitrogen, UK). The quality thresholds were as follows: an OD260/OD280 ratio of between 1.8 and 2.0 and a OD260/OD230 ratio greater than 1.5. High-throughput SNP genotyping of 323 genotypes was performed using the TaNG v1.1 Affymetrix Axiom genotyping array (Thermo Fisher Scientific, UK) at the University of Bristol Genomics facility, University of Bristol, UK. Genotype calling was performed using the Best Practices Workflow in the Axiom Analysis Suite (AxAS) following the default SNP quality control thresholds where DCQ (dish quality control) ≥ 0.82 and CR (call rate) cut-off ≥ 97%. Markers were then classified and filtered based on the Axiom recommended criteria. Subsequently, markers that were monomorphic, had a minor allele frequency (MAF) of <5%, a missing call rate of >20%, or a heterozygote frequency >25% were removed. After filtering, a total of 6,315 best recommended and high-quality markers were retained and were used to generate the HapMap-formatted data.
Metadata
- File identifier
- 291ca8d7-6178-4e6f-98a5-f59225d884cd XML
- Metadata language
- English
- Character set
- 8859 Part 1
- Hierarchy level
- Dataset
- Hierarchy level name
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dataset
- Date stamp
- 2025-12-08T09:40:08
- Metadata standard name
- UK GEMINI
- Metadata standard version
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2.3
- Metadata author
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Organisation name Individual name Electronic mail address Role NERC EDS Environmental Information Data Centre Point of contact
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