ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2010
Development of highly polymorphic SNP markers from the complexity reduced portion of maize [Zea mays L.] genome for use in marker-assisted breeding.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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29 citing papers in PubMed.
- Genome-wide assessment of genetic diversity and selective signatures in sunflower (Helianthus annuus L.) using a 10 K SNP array.Scientific reports · 2026Article
- Genetic diversity and population structure analysis of cotton (Gossypium hirsutum L.) genotypes using DArTseq technology.BMC genomics · 2026Article
- A comprehensive catalog of single nucleotide polymorphisms (SNPs) from the black pepper (Piper nigrum L.) genome.BMC genomics · 2025Article
- Genetic diversity and population structure analyses of tropical maize inbred lines using Single Nucleotide Polymorphism markers.PloS one · 2025Article
- Validation of sorghum quality control (QC) markers across African breeding lines.The plant genome · 2024Article
- Development of Novel Markers for Yield in Hevea brasiliensis Muell. Arg. Based on Candidate Genes from Biosynthetic Pathways Associated with Latex Production.Biochemical genetics · 2022Article
- Natural variation in genes potentially involved in plant architecture and adaptation in switchgrass (Panicum virgatum L.).BMC evolutionary biology · 2018Article
- Quantitative trait loci from identification to exploitation for crop improvement.Plant cell reports · 2017Review
- Genetic Divergence between Camellia sinensis and Its Wild Relatives Revealed via Genome-Wide SNPs from RAD Sequencing.PloS one · 2016Article
- Evaluation of random forest regression for prediction of breeding value from genomewide SNPs.Journal of genetics · 2015Article
- Sequencing consolidates molecular markers with plant breeding practice.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2015Review
- Construction of Commercial Sweet Cherry Linkage Maps and QTL Analysis for Trunk Diameter.PloS one · 2015Article
- Development of maizeSNP3072, a high-throughput compatible SNP array, for DNA fingerprinting identification of Chinese maize varieties.Molecular breeding : new strategies in plant improvement · 2015Article
- Transcriptome sequencing for high throughput SNP development and genetic mapping in Pea.BMC genomics · 2014Article
- Article
- Isolation and characterization of microsatellite markers and analysis of genetic diversity in Chinese jujube (Ziziphus jujuba Mill.).PloS one · 2014Article
- Next generation sequencing technologies for next generation plant breeding.Frontiers in plant science · 2014Article
- Unraveling the genetic architecture of subtropical maize (Zea mays L.) lines to assess their utility in breeding programs.BMC genomics · 2013Article
- Article
- Genome-wide SNP discovery in mungbean by Illumina HiSeq.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2013Article
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10 authors.
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Abstract
The duplicated and the highly repetitive nature of the maize genome has historically impeded the development of true single nucleotide polymorphism (SNP) markers in this crop. Recent advances in genome complexity reduction methods coupled with sequencing-by-synthesis technologies permit the implementation of efficient genome-wide SNP discovery in maize. In this study, we have applied Complexity Reduction of Polymorphic Sequences technology (Keygene N.V., Wageningen, The Netherlands) for the identification of informative SNPs between two genetically distinct maize inbred lines of North and South American origins. This approach resulted in the discovery of 1,123 putative SNPs representing low and single copy loci. In silico and experimental (Illumina GoldenGate (GG) assay) validation of putative SNPs resulted in mapping of 604 markers, out of which 188 SNPs represented 43 haplotype blocks distributed across all ten chromosomes. We have determined and clearly stated a specific combination of stringent criteria (>0.3 minor allele frequency, >0.8 GenTrainScore and >0.5 Chi_test100 score) necessary for the identification of highly polymorphic and genetically stable SNP markers. Due to these criteria, we identified a subset of 120 high-quality SNP markers to leverage in GG assay-based marker-assisted selection projects. A total of 32 high-quality SNPs represented 21 haplotypes out of 43 identified in this study. The information on the selection criteria of highly polymorphic SNPs in a complex genome such as maize and the public availability of these SNP assays will be of great value for the maize molecular genetics and breeding community.
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