ArticlePloS one2011
A large maize (Zea mays L.) SNP genotyping array: development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 338 papers, 1 of them a synthesis that pooled it.
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Who cites it
338 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis and co-expression analysis revealed stable QTL and candidate genes conferring resistances to Fusarium and Gibberella ear rots while reducing mycotoxin contamination in maize.Frontiers in plant science · 2022Pooled it
- Genetic dissection of grain yield and correlated proxy traits under suboptimal conditions.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Polymorphism can extensively reshape the genome-wide crossover landscape in Arabidopsis thaliana.Nature communications · 2026Article
- Genetic Dissection and Functional Validation ofInternational journal of molecular sciences · 2026Article
- Genetic Relatedness and Heterotic Grouping in MRIZP Elite Maize Inbred Lines Using SNP Markers from 25k SNP Array and RNA-seq Data.Current issues in molecular biology · 2026Article
- Next-Generation Genotyping: Innovations Driving Plant Genomic Improvement.Life (Basel, Switzerland) · 2026Review
- Genome-wide association study identifies key loci and candidate genes for maize grain yield-related traits.BMC plant biology · 2026Article
- Genetic Variation and Quantitative Trait Loci Analysis of the Maize Ionome in Response to Phosphorus Fertilisation.Plant, cell & environment · 2025Article
- Low-call-rate SNPs and presence-absence variation identified in the rice pan-genome can improve genomic prediction of rice gene bank accessions.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Development and validation of a high-density 'Amahysnp' genotyping array in grain amaranth (Amaranthus hypochondriacus).BMC plant biology · 2025Article
- Article
- Evolution of population structure in a commercial European hybrid dent maize breeding program and consequences on genetic diversity.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- The combination of linkage mapping, genome-wide association study, and dynamic transcriptome analysis reveals conserved candidate genes for salt tolerance in maize.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- A maize landrace introgression library reveals a negative effect of root-to-shoot ratio on water-use efficiency.The plant genome · 2025Article
- Individual plant genetics reveal the control of local adaptation in European maize landraces.BMC biology · 2025Article
- Genome-Wide Association Analysis of Sweet Pepper (Plants (Basel, Switzerland) · 2025Article
- Optimization of commercial SNP arrays and the generation of a high-efficiency GenoBaits Peanut 10K panel.Scientific reports · 2025Article
- Improvement in genomic prediction of maize with prior gene ontology information depends on traits and environmental conditions.The plant genome · 2025Article
- SeqSNP-based genic markers reveal genetic architecture and candidate genes for low nitrogen tolerance in tropical maize inbred lines.Frontiers in plant science · 2025Article
- Article
278 more citing papers are in PubMed but not listed here.
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19 authors.
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No grant is acknowledged in the PubMed record.
Abstract
SNP genotyping arrays have been useful for many applications that require a large number of molecular markers such as high-density genetic mapping, genome-wide association studies (GWAS), and genomic selection. We report the establishment of a large maize SNP array and its use for diversity analysis and high density linkage mapping. The markers, taken from more than 800,000 SNPs, were selected to be preferentially located in genes and evenly distributed across the genome. The array was tested with a set of maize germplasm including North American and European inbred lines, parent/F1 combinations, and distantly related teosinte material. A total of 49,585 markers, including 33,417 within 17,520 different genes and 16,168 outside genes, were of good quality for genotyping, with an average failure rate of 4% and rates up to 8% in specific germplasm. To demonstrate this array's use in genetic mapping and for the independent validation of the B73 sequence assembly, two intermated maize recombinant inbred line populations - IBM (B73×Mo17) and LHRF (F2×F252) - were genotyped to establish two high density linkage maps with 20,913 and 14,524 markers respectively. 172 mapped markers were absent in the current B73 assembly and their placement can be used for future improvements of the B73 reference sequence. Colinearity of the genetic and physical maps was mostly conserved with some exceptions that suggest errors in the B73 assembly. Five major regions containing non-colinearities were identified on chromosomes 2, 3, 6, 7 and 9, and are supported by both independent genetic maps. Four additional non-colinear regions were found on the LHRF map only; they may be due to a lower density of IBM markers in those regions or to true structural rearrangements between lines. Given the array's high quality, it will be a valuable resource for maize genetics and many aspects of maize breeding.
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