291ca8d7-6178-4e6f-98a5-f59225d884cd English ISO/IEC 8859-1 (also known as Latin 1) dataset dataset NERC EDS Environmental Information Data Centre Lancaster Environment Centre, Library Avenue, Bailrigg Lancaster LA1 4AP UK info@eidc.ac.uk https://eidc.ac.uk/ EIDC website The Environmental Information Data Centre (EIDC) is the UK's national data centre for terrestrial and freshwater sciences. information pointOfContact 2025-12-08T09:40:08 UK GEMINI 2.3 WGS 84 Single nucleotide polymorphism genotyping of 323 wheat accessions from Pakistan, Mexico and Australia 2025-11-26 publication https://catalogue.ceh.ac.uk/id/291ca8d7-6178-4e6f-98a5-f59225d884cd 10.5285/291ca8d7-6178-4e6f-98a5-f59225d884cd doi: 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 [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 Prins, A. Rothamsted Research anneke.prins@rothamsted.ac.uk pointOfContact Iqbal, R. University of Agriculture Faisalabad rubabiqbalphd@gmail.com author Bano, Z. University of Agriculture Faisalabad banozunaira7@gmail.com author Kiran, A. University of Agriculture Faisalabad aysha.kiran@uaf.edu.pk author Naeem, M.K. National Agricultural Research Center Islamabad kashifuaar102@hotmail.com author Khan, M.R. National Agricultural Research Center Islamabad mrkhan@parc.gov.pk author Wakeel, A. University of Agriculture Faisalabad abdulwakeel77@gmail.com author Sajjad, H. University of Agriculture Faisalabad aysha.kiran@uaf.edu.pk author Aziz, T. University of Agriculture Faisalabad draziz@uaf.edu.pk author Sutton, M. UK Centre for Ecology & Hydrology enquiries@ceh.ac.uk author Price, A. University of Aberdeen a.price@abdn.ac.uk author Prins, A. Rothamsted Research anneke.prins@rothamsted.ac.uk author Shewry, P. Rothamsted Research peter.shewry@rothamsted.ac.uk author Alabdullah, A.K. John Innes Centre Abdul-Kader.Alabdullah@jic.ac.uk author Maqsood, M.A. National Agricultural Research Center Islamabad mohamgill@uaf.edu.pk author University of Agriculture Faisalabad EMAIL NOT PROVIDED owner NERC EDS Environmental Information Data Centre info@eidc.ac.uk publisher NERC EDS Environmental Information Data Centre info@eidc.ac.uk custodian nitrogenous fertiliser GEMET - Concepts, version 4.1.3 2019-01-28 creation Agriculture nitrogen use efficiency Pakistan otherRestrictions Embargoed otherRestrictions This resource is available under the terms of the Open Government Licence otherRestrictions 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 textTable English utf8 farming -0.382 -0.359 51.804 51.815 Comma-separated values (CSV) NERC EDS Environmental Information Data Centre info@eidc.ac.uk distributor dataset dataset 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 2010-12-08 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.