ArticleBMC plant biology2019
Genotyping-by-sequencing and SNP-arrays are complementary for detecting quantitative trait loci by tagging different haplotypes in association studies.
Article in BMC plant biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers, 2 of them syntheses that pooled it.
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Who cites it
43 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- metaGE: Investigating genotype x environment interactions through GWAS meta-analysis.PLoS genetics · 2025Pooled it
- Optimizing Genomic-Enabled Prediction in Small-Scale Maize Hybrid Breeding Programs: A Roadmap Review.Frontiers in plant science · 2021Pooled it
- Article
- Development and validation of a dual-purpose 60K single nucleotide polymorphism chip for simultaneous genotyping of chicken and duck.Animal bioscience · 2026Article
- Next-Generation Genotyping: Innovations Driving Plant Genomic Improvement.Life (Basel, Switzerland) · 2026Review
- Integration and imputation of GBS-derived and DArTseq-derived SNP markers in assessing genetic diversity of bread wheat genotypes.BMC genomics · 2026Article
- Genomic prediction and genetic parameter estimation for unsaturated and saturated fatty acids in Canadian dairy cattle.Scientific reports · 2025Article
- Improvement in genomic prediction of maize with prior gene ontology information depends on traits and environmental conditions.The plant genome · 2025Article
- Genetic variability of aquaporin expression in maize: From eQTLs to a MITE insertion regulating PIP2;5 expression.Plant physiology · 2024Article
- Combining genome-wide association study and linkage mapping in the genetic dissection of amylose content in maize (Zea mays L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Bridging the gap between omics research and dental practice.BDJ open · 2024Review
- Genetic Diversity within a Collection of Italian Maize Inbred Lines: A Resource for Maize Genomics and Breeding.Plants (Basel, Switzerland) · 2024Article
- DArTseq genotyping facilitates the transfer of "exotic" chromatin from aFrontiers in plant science · 2024Article
- Combining genotyping approaches improves resolution for association mapping: a case study in tropical maize under water stress conditions.Frontiers in plant science · 2024Article
- A genomic dataset integrating genotyping-by-sequencing, SolCAP array and PCR marker data on tetraploid potato advanced breeding lines.Frontiers in plant science · 2024Article
- Comparison of ddRADseq and EUChip60K SNP genotyping systems for population genetics and genomic selection inFrontiers in genetics · 2024Article
- Plasticity QTLs specifically contribute to the genotype × water availability interaction in maize.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Robotized indoor phenotyping allows genomic prediction of adaptive traits in the field.Nature communications · 2023Article
- Identifying QTLs involved in hybrid performance and heterotic group complementarity: new GWAS models applied to factorial and admixed diallel maize hybrid panels.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Genetic diversity and selection signatures in a gene bank panel of maize inbred lines from Southeast Europe compared with two West European panels.BMC plant biology · 2023Article
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9 authors.
Funding
Abstract
backgroundSingle Nucleotide Polymorphism (SNP) array and re-sequencing technologies have different properties (e.g. calling rate, minor allele frequency profile) and drawbacks (e.g. ascertainment bias). This lead us to study their complementarity and the consequences of using them separately or combined in diversity analyses and Genome-Wide Association Studies (GWAS). We performed GWAS on three traits (grain yield, plant height and male flowering time) measured in 22 environments on a panel of 247 F1 hybrids obtained by crossing 247 diverse dent maize inbred lines with a same flint line. The 247 lines were genotyped using three genotyping technologies (Genotyping-By-Sequencing, Illumina Infinium 50 K and Affymetrix Axiom 600 K arrays).
resultsThe effects of ascertainment bias of the 50 K and 600 K arrays were negligible for deciphering global genetic trends of diversity and for estimating relatedness in this panel. We developed an original approach based on linkage disequilibrium (LD) extent in order to determine whether SNPs significantly associated with a trait and that are physically linked should be considered as a single Quantitative Trait Locus (QTL) or several independent QTLs. Using this approach, we showed that the combination of the three technologies, which have different SNP distributions and densities, allowed us to detect more QTLs (gain in power) and potentially refine the localization of the causal polymorphisms (gain in resolution).
conclusionsConceptually different technologies are complementary for detecting QTLs by tagging different haplotypes in association studies. Considering LD, marker density and the combination of different technologies (SNP-arrays and re-sequencing), the genotypic data available were most likely enough to well represent polymorphisms in the centromeric regions, whereas using more markers would be beneficial for telomeric regions.
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