ArticleThe plant genome2019
Multiple Maize Reference Genomes Impact the Identification of Variants by Genome-Wide Association Study in a Diverse Inbred Panel.
Article in The plant genome, 2019. 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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Who cites it
29 citing papers in PubMed.
- In Situ GWAS in Two Range-Edge Populations of European Beech (Fagus sylvatica L.) Identify Genetic Factors of Adaptation to Climate Change.Molecular ecology · 2026Article
- New biologically relevant resistance to bacterial wilt in heat-stressed tomato revealed by two-reference Genome Wide Association.PLoS genetics · 2026Article
- Pangenome-guided sequence assembly via binary optimization.Briefings in bioinformatics · 2026Article
- Genome-Wide, High-Density Genotyping Approaches for Plant Germplasm Characterisation (Methods and Applications).International journal of molecular sciences · 2025Review
- Structural Variants Contribute to Phenotypic Variation in Maize.Molecular ecology · 2025Article
- Pangenomes as a framework for adaptive radiation, speciation, and adaptation.American journal of botany · 2025Article
- K-mer-based Approaches to Bridging Pangenomics and Population Genetics.Molecular biology and evolution · 2025Review
- Novel breeding resources for the underutilised legume, lablab, based on a pangenome approach.Breeding science · 2025Article
- Structural variants contribute to phenotypic variation in maize.bioRxiv : the preprint server for biology · 2024Article
- k-mer genome-wide association study for anthracnose and BCMV resistance in a Phaseolus vulgaris Andean Diversity Panel.The plant genome · 2024Article
- Combined Genome-Wide Association Study and Linkage Analysis for Mining Candidate Genes for the Kernel Row Number in Maize (Plants (Basel, Switzerland) · 2024Article
- Genetic remodeling of soil diazotrophs enables partial replacement of synthetic nitrogen fertilizer with biological nitrogen fixation in maize.Scientific reports · 2024Article
- Biparental graph strategy to represent and analyze hybrid plant genomes.Plant physiology · 2024Article
- A gentle introduction to pangenomics.Briefings in bioinformatics · 2024Review
- Combined reference-free and multi-reference based GWAS uncover cryptic variation underlying rapid adaptation in a fungal plant pathogen.PLoS pathogens · 2023Article
- Genome-wide association mapping in a sweet cherry germplasm collection (Horticulture research · 2023Article
- The genomics of linkage drag in inbred lines of sunflower.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Genome-wide association study of quality traits and starch pasting properties of maize kernels.BMC genomics · 2023Article
- A pangenome analysis pipeline provides insights into functional gene identification in rice.Genome biology · 2023Article
- Editorial: Functional Genomics in Plant Breeding 2.0.International journal of molecular sciences · 2022Article
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12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Use of a single reference genome for genome-wide association studies (GWAS) limits the gene space represented to that of a single accession. This limitation can complicate identification and characterization of genes located within presence-absence variations (PAVs). In this study, we present the draft de novo genome assembly of 'PHJ89', an 'Oh43'-type inbred line of maize ( L.). From three separate reference genome assemblies ('B73', 'PH207', and PHJ89) that represent the predominant germplasm groups of maize, we generated three separate whole-seedling gene expression profiles and single nucleotide polymorphism (SNP) matrices from a panel of 942 diverse inbred lines. We identified 34,447 (B73), 39,672 (PH207), and 37,436 (PHJ89) transcripts that are not present in the respective reference genome assemblies. Genome-wide association studies were conducted in the 942 inbred panel with both the SNP and expression data values to map (SCMV) resistance. Highlighting the impact of alternative reference genomes in gene discovery, the GWAS results for SCMV resistance with expression values as a surrogate measure of PAV resulted in robust detection of the physical location of a known resistance gene when the B73 reference that contains the gene was used, but not the PH207 reference. This study provides the valuable resource of the Oh43-type PHJ89 genome assembly as well as SNP and expression data for 942 individuals generated from three different reference genomes.
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