ArticleBMC genomics2018
Sequence analysis of European maize inbred line F2 provides new insights into molecular and chromosomal characteristics of presence/absence variants.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers, 1 of them a synthesis that pooled it.
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Who cites it
18 citing papers in PubMed, 1 synthesis or guideline pooled it, 33 citations in OpenAlex.
- Multi-omics revolution to promote plant breeding efficiency.Frontiers in plant science · 2022Pooled it
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- Structural Variants Contribute to Phenotypic Variation in Maize.Molecular ecology · 2025Article
- Structural variants contribute to phenotypic variation in maize.bioRxiv : the preprint server for biology · 2024Article
- Diverse mycorrhizal maize inbred lines differentially modulate mycelial traits and the expression of plant and fungal phosphate transporters.Scientific reports · 2022Article
- Functional Study of Lipoxygenase-Mediated Resistance againstInternational journal of molecular sciences · 2022Article
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- Stability of DNA methylation and chromatin accessibility in structurally diverse maize genomes.G3 (Bethesda, Md.) · 2021Article
- Next-Generation Breeding Strategies for Climate-Ready Crops.Frontiers in plant science · 2021Review
- A systems genetics approach reveals environment-dependent associations between SNPs, protein coexpression, and drought-related traits in maize.Genome research · 2020Article
- European maize genomes highlight intraspecies variation in repeat and gene content.Nature genetics · 2020Article
- Gene presence-absence variation associates with quantitative Verticillium longisporum disease resistance in Brassica napus.Scientific reports · 2020Article
- Mapping Regulatory Determinants in Plants.Frontiers in genetics · 2020Review
- High throughput genotyping of structural variations in a complex plant genome using an original Affymetrix® axiom® array.BMC genomics · 2019Article
- Connecting genome structural variation with complex traits in crop plants.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2019Review
- A systems biology approach uncovers a gene co-expression network associated with cell wall degradability in maize.PloS one · 2019Article
- Article
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Authors and funding
12 authors at 5 institutions in 1 country.
Funding
Abstract
backgroundMaize is well known for its exceptional structural diversity, including copy number variants (CNVs) and presence/absence variants (PAVs), and there is growing evidence for the role of structural variation in maize adaptation. While PAVs have been described in this important crop species, they have been only scarcely characterized at the sequence level and the extent of presence/absence variation and relative chromosomal landscape of inbred-specific regions remain to be elucidated.
resultsDe novo genome sequencing of the French F2 maize inbred line revealed 10,044 novel genomic regions larger than 1 kb, making up 88 Mb of DNA, that are present in F2 but not in B73 (PAV). This set of maize PAV sequences allowed us to annotate PAV content and to analyze sequence breakpoints. Using PAV genotyping on a collection of 25 temperate lines, we also analyzed Linkage Disequilibrium in PAVs and flanking regions, and PAV frequencies within maize genetic groups.
conclusionsWe highlight the possible role of MMEJ-type double strand break repair in maize PAV formation and discover 395 new genes with transcriptional support. Pattern of linkage disequilibrium within PAVs strikingly differs from this of flanking regions and is in accordance with the intuition that PAVs may recombine less than other genomic regions. We show that most PAVs are ancient, while some are found only in European Flint material, thus pinpointing structural features that may be at the origin of adaptive traits involved in the success of this material. Characterization of such PAVs will provide useful material for further association genetic studies in European and temperate maize.
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