ArticleGenome biology2021
Megabase-scale presence-absence variation with Tripsacum origin was under selection during maize domestication and adaptation.
Article in Genome biology, 2021. 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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18 citing papers in PubMed, 1 synthesis or guideline pooled it.
- metaGE: Investigating genotype x environment interactions through GWAS meta-analysis.PLoS genetics · 2025Pooled it
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- How Structural Variations Influence Crop Improvement.International journal of molecular sciences · 2025Review
- The role of mobile DNA elements in the dynamics of plant genome plasticity.Journal of experimental botany · 2025Review
- Lost in translation: What we have learned from attributes that do not translate from Arabidopsis to other plants.The Plant cell · 2025Review
- Comprehensive evaluation and guidance of structural variation detection tools in chicken whole genome sequence data.BMC genomics · 2024Article
- Evolutionary patterns of DNA base composition at polymorphic sites highlight the role of the environment in shaping barley and rice genomes.The plant genome · 2024Article
- A complete telomere-to-telomere assembly of the maize genome.Nature genetics · 2023Article
- Large haplotypes highlight a complex age structure within the maize pan-genome.Genome research · 2023Article
- De novo genome assembly and analyses of 12 founder inbred lines provide insights into maize heterosis.Nature genetics · 2023Article
- QTL Mapping and a Transcriptome Integrative Analysis Uncover the Candidate Genes That Control the Cold Tolerance of Maize Introgression Lines at the Seedling Stage.International journal of molecular sciences · 2023Article
- Genetic analysis and QTL mapping of domestication-related traits in chili pepper (Frontiers in genetics · 2023Article
- Fine mapping of a stripe rust resistance gene YrZM175 in bread wheat.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
- Phylogenomic analyses highlight innovation and introgression in the continental radiations of Fagaceae across the Northern Hemisphere.Nature communications · 2022Article
- Fine mapping of theFrontiers in plant science · 2022Article
- Frequent spontaneous structural rearrangements promote rapid genome diversification in aFrontiers in plant science · 2022Article
- Megabase-scale presence-absence variation with Tripsacum origin was under selection during maize domestication and adaptation.Genome biology · 2021Article
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Authors and funding
11 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundStructural variants (SVs) significantly drive genome diversity and environmental adaptation for diverse species. Unlike the prevalent small SVs (< kilobase-scale) in higher eukaryotes, large-size SVs rarely exist in the genome, but they function as one of the key evolutionary forces for speciation and adaptation.
resultsIn this study, we discover and characterize several megabase-scale presence-absence variations (PAVs) in the maize genome. Surprisingly, we identify a 3.2 Mb PAV fragment that shows high integrity and is present as complete presence or absence in the natural diversity panel. This PAV is embedded within the nucleolus organizer region (NOR), where the suppressed recombination is found to maintain the PAV against the evolutionary variation. Interestingly, by analyzing the sequence of this PAV, we not only reveal the domestication trace from teosinte to modern maize, but also the footprints of its origin from Tripsacum, shedding light on a previously unknown contribution from Tripsacum to the speciation of Zea species. The functional consequence of the Tripsacum segment migration is also investigated, and environmental fitness conferred by the PAV may explain the whole segment as a selection target during maize domestication and improvement.
conclusionsThese findings provide a novel perspective that Tripsacum contributes to Zea speciation, and also instantiate a strategy for evolutionary and functional analysis of the "fossil" structure variations during genome evolution and speciation.
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