ArticleBMC biology2020
A genome-wide survey of copy number variations reveals an asymmetric evolution of duplicated genes in rice.
Article in BMC biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 17 citations in OpenAlex.
- Dissecting Agronomically favorable genotypes in temperate japonica rice via haplotype analysis of a Japan-MAGIC population.The Plant journal : for cell and molecular biology · 2026Article
- IbMYB1-4 positively regulates purple stem and influences leaf color via dosage effect of gene expression in sweetpotato (Ipomoea batatas (L.) Lam.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Development of SCAR and rapid detection of YMV resistant genotypes of blackgram through qRT-PCR based absolute quantification.Molecular biology reports · 2026Article
- A Systematic Review of the Advances and New Insights into Copy Number Variations in Plant Genomes.Plants (Basel, Switzerland) · 2025Review
- GrameneOryza: a comprehensive resource for Oryza genomes, genetic variation, and functional data.Database : the journal of biological databases and curation · 2025Article
- A comprehensive map of DNA-segment copy number variation in 491 genomes of common wheat uncovers genes associated with multiple agronomic traits.Plant communications · 2025Article
- Diversity of Gibberellin 2-oxidase genes in the barley genome offers opportunities for genetic improvement.Journal of advanced research · 2024Article
- The pan-tandem repeat map highlights multiallelic variants underlying gene expression and agronomic traits in rice.Nature communications · 2024Article
- Copy number variation of the restorer Rf4 underlies human selection of three-line hybrid rice breeding.Nature communications · 2023Article
- Article
- Identification of Genetic Loci for Sugarcane Leaf Angle at Different Developmental Stages by Genome-Wide Association Study.Frontiers in plant science · 2022Article
- In-Depth Sequence Analysis of Bread WheatInternational journal of molecular sciences · 2021Article
- Omics-Facilitated Crop Improvement for Climate Resilience and Superior Nutritive Value.Frontiers in plant science · 2021Review
Corrections and comments
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Authors and funding
23 authors at 4 institutions in 1 country.
Funding
Abstract
backgroundCopy number variations (CNVs) are an important type of structural variations in the genome that usually affect gene expression levels by gene dosage effect. Understanding CNVs as part of genome evolution may provide insights into the genetic basis of important agricultural traits and contribute to the crop breeding in the future. While available methods to detect CNVs utilizing next-generation sequencing technology have helped shed light on prevalence and effects of CNVs, the complexity of crop genomes poses a major challenge and requires development of additional tools.
resultsHere, we generated genomic and transcriptomic data of 93 rice (Oryza sativa L.) accessions and developed a comprehensive pipeline to call CNVs in this large-scale dataset. We analyzed the correlation between CNVs and gene expression levels and found that approximately 13% of the identified genes showed a significant correlation between their expression levels and copy numbers. Further analysis showed that about 36% of duplicate pairs were involved in pseudogenetic events while only 5% of them showed functional differentiation. Moreover, the offspring copy mainly contributed to the expression levels and seemed more likely to become a pseudogene, whereas the parent copy tended to maintain the function of ancestral gene.
conclusionWe provide a high-accuracy CNV dataset that will contribute to functional genomics studies and molecular breeding in rice. We also showed that gene dosage effect of CNVs in rice is not exponential or linear. Our work demonstrates that the evolution of duplicated genes is asymmetric in both expression levels and gene fates, shedding a new insight into the evolution of duplicated genes.
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