ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2013
Genetic diversity analysis of elite European maize (Zea mays L.) inbred lines using AFLP, SSR, and SNP markers reveals ascertainment bias for a subset of SNPs.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed.
- 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
- Genetic Diversity and Construction of Salt-Tolerant Core Germplasm in Maize (Plants (Basel, Switzerland) · 2025Article
- Individual plant genetics reveal the control of local adaptation in European maize landraces.BMC biology · 2025Article
- Integrating targeted genetic markers to genotyping-by-sequencing for an ultimate genotyping tool.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Genetic Diversity within a Collection of Italian Maize Inbred Lines: A Resource for Maize Genomics and Breeding.Plants (Basel, Switzerland) · 2024Article
- Molecular markers and molecular basis of plant type related traits in maize.Frontiers in genetics · 2024Article
- Genotyping of DNA pools identifies untapped landraces and genomic regions to develop next-generation varieties.Plant biotechnology journal · 2023Article
- On the usefulness of mock genomes to define heterotic pools, testers, and hybrid predictions in orphan crops.Frontiers in plant science · 2023Article
- Predicting hybrid rice performance using AIHIB model based on artificial intelligence.Scientific reports · 2022Article
- Population-tailored mock genome enables genomic studies in species without a reference genome.Molecular genetics and genomics : MGG · 2022Article
- Transposons-Based Clonal Diversity in Trematode Involves Parts of CR1 (LINE) in Eu- and Heterochromatin.Genes · 2021Article
- Article
- How array design creates SNP ascertainment bias.PloS one · 2021Article
- Application of Genomic Big Data in Plant Breeding:Past, Present, and Future.Plants (Basel, Switzerland) · 2020Review
- Deciphering the Genetic Diversity of Landraces With High-Throughput SNP Genotyping of DNA Bulks: Methodology and Application to the Maize 50k Array.Frontiers in plant science · 2020Article
- Suitability of Single-Nucleotide Polymorphism Arrays Versus Genotyping-By-Sequencing for Genebank Genomics in Wheat.Frontiers in plant science · 2020Article
- Article
- Genotyping-by-sequencing and SNP-arrays are complementary for detecting quantitative trait loci by tagging different haplotypes in association studies.BMC plant biology · 2019Article
- Article
- Small RNA-based prediction of hybrid performance in maize.BMC genomics · 2018Article
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3 authors.
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Abstract
Recent advances in high-throughput sequencing technologies have triggered a shift toward single-nucleotide polymorphism (SNP) markers. A systematic bias can be introduced if SNPs are ascertained in a small panel of genotypes and then used for characterizing a larger population (ascertainment bias). With the objective of evaluating a potential ascertainment bias of the Illumina MaizeSNP50 array with respect to elite European maize dent and flint inbred lines, we compared the genetic diversity among these materials based on 731 amplified fragment length polymorphisms (AFLPs), 186 simple sequence repeats (SSRs), 41,434 SNPs of the MaizeSNP50 array (SNP-A), and two subsets of it, i.e., 30,068 Panzea (SNP-P) and 11,366 Syngenta markers (SNP-S). We evaluated the bias effects on major allele frequency, allele number, gene diversity, modified Roger's distance (MRD), and on molecular variance (AMOVA). We revealed ascertainment bias in SNP-A, compared to AFLPs and SSRs. It affected especially European flint lines analyzed with markers (SNP-S) specifically developed to maximize differences among North American dent germplasm. The bias affected all genetic parameters, but did not substantially alter the relative distances between inbred lines within groups. For these reasons, we conclude that the SNP markers of the MaizeSNP50 array can be employed for breeding purposes in the investigated material. However, attention should be paid in case of comparisons between genotypes belonging to different heterotic groups. In this case, it is advisable to prefer a marker subset with potentially low ascertainment bias, like in our case the SNP-P marker set.
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