ArticlePlant biotechnology journal2018
Finding invisible quantitative trait loci with missing data.
Article in Plant biotechnology journal, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
25 citing papers in PubMed, 49 citations in OpenAlex.
- From research to application: evaluation of literature-based and newly identified GWAS and GP-derived loci for anthracnose resistance in white lupin, across validation panels and environments.Molecular breeding : new strategies in plant improvement · 2026Article
- Global species delimitation of smooth-shelled blue mussels in the Mytilus edulis complex.Scientific reports · 2025Article
- Harnessing genomic prediction in Brassica napus through a nested association mapping population.The plant genome · 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
- Impact of Alien Chromosome Introgression fromPlants (Basel, Switzerland) · 2025Article
- Homoeologous non-reciprocal translocation explains a major QTL for seed lignin content in oilseed rape (Brassica napus L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Accurate prediction of quantitative traits with failed SNP calls in canola and maize.Frontiers in plant science · 2023Article
- A catalogue of resistance gene homologs and a chromosome-scale reference sequence support resistance gene mapping in winter wheat.Plant biotechnology journal · 2022Article
- Homoeologous chromosome exchange explains the creation of a QTL affecting soil-borne pathogen resistance in tobacco.Plant biotechnology journal · 2022Article
- Frequent spontaneous structural rearrangements promote rapid genome diversification in aFrontiers in plant science · 2022Article
- The application of pangenomics and machine learning in genomic selection in plants.The plant genome · 2021Article
- Homoeologous recombination is recurrent in the nascent synthetic allotetraploid Arachis ipaënsis × Arachis correntina4x and its derivatives.G3 (Bethesda, Md.) · 2021Article
- A novel deletion in FLOWERING LOCUS T modulates flowering time in winter oilseed rape.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
- Long-read sequencing reveals widespread intragenic structural variants in a recent allopolyploid crop plant.Plant biotechnology journal · 2021Article
- Dissection of Quantitative Blackleg Resistance Reveals Novel Variants of Resistance GeneFrontiers in plant science · 2021Article
- Applications of Multi-Omics Technologies for Crop Improvement.Frontiers in plant science · 2021Review
- Local Duplication of TIR-NBS-LRR Gene Marks Clubroot Resistance inFrontiers in plant science · 2021Article
- A 598-bp InDel Variation in the Promoter Region ofFrontiers in plant science · 2021Article
- Overcoming polyploidy pitfalls: a user guide for effective SNP conversion into KASP markers in wheat.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Article
- Gene presence-absence variation associates with quantitative Verticillium longisporum disease resistance in Brassica napus.Scientific reports · 2020Article
Corrections and comments
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Authors and funding
13 authors at 7 institutions in 3 countries.
Funding
Abstract
Evolutionary processes during plant polyploidization and speciation have led to extensive presence-absence variation (PAV) in crop genomes, and there is increasing evidence that PAV associates with important traits. Today, high-resolution genetic analysis in major crops frequently implements simple, cost-effective, high-throughput genotyping from single nucleotide polymorphism (SNP) hybridization arrays; however, these are normally not designed to distinguish PAV from failed SNP calls caused by hybridization artefacts. Here, we describe a strategy to recover valuable information from single nucleotide absence polymorphisms (SNaPs) by population-based quality filtering of SNP hybridization data to distinguish patterns associated with genuine deletions from those caused by technical failures. We reveal that including SNaPs in genetic analyses elucidate segregation of small to large-scale structural variants in nested association mapping populations of oilseed rape (Brassica napus), a recent polyploid crop with widespread structural variation. Including SNaP markers in genomewide association studies identified numerous quantitative trait loci, invisible using SNP markers alone, for resistance to two major fungal diseases of oilseed rape, Sclerotinia stem rot and blackleg disease. Our results indicate that PAV has a strong influence on quantitative disease resistance in B. napus and that SNaP analysis using cost-effective SNP array data can provide extensive added value from 'missing data'. This strategy might also be applicable for improving the precision of genetic mapping in many important crop species.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.