ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2017
Low-coverage resequencing detects meiotic recombination pattern and features in tomato RILs.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 21 citations in OpenAlex.
- Tomato and its relatives are breaking the genomics barriers.Journal of experimental botany · 2025Review
- Unraveling Plant Recombination Patterns: Insights From Genome k-mers.Plant direct · 2025Article
- haploMAGIC: accurate phasing and detection of recombination in multiparental populations despite genotyping errors.G3 (Bethesda, Md.) · 2024Article
- Methylomes as key features for predicting recombination in some plant species.Plant molecular biology · 2024Article
- Technology-driven approaches for meiosis research in tomato and wild relatives.Plant reproduction · 2023Article
- Article
- Domestication Shapes Recombination Patterns in Tomato.Molecular biology and evolution · 2022Article
- Heterogeneous transposable elements as silencers, enhancers and targets of meiotic recombination.Chromosoma · 2019Review
- Salt Tolerance Improvement in Rice through Efficient SNP Marker-Assisted Selection Coupled with Speed-Breeding.International journal of molecular sciences · 2019Article
- Translational genomics and multi-omics integrated approaches as a useful strategy for crop breeding.Genes & genomics · 2019Review
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Traditional plant breeding relies on meiotic recombination for mixing of parental alleles to create novel allele combinations. Detailed analysis of recombination patterns in model organisms shows that recombination is tightly regulated within the genome, but frequencies vary extensively along chromosomes. Despite being a model organism for fruit developmental studies, high-resolution recombination patterns are lacking in tomato. In this study, we developed a novel methodology to use low-coverage resequencing to identify genome-wide recombination patterns and applied this methodology on 60 tomato Recombinant Inbred Lines (RILs). Our methodology identifies polymorphic markers from the low-coverage resequencing population data and utilizes the same data to locate the recombination breakpoints in individuals by using a variable sliding window. We identified 1,445 recombination sites comprising 112 recombination prone regions enriched for AT-rich DNA motifs. Furthermore, the recombination prone regions in tomato preferably occurred in gene promoters over intergenic regions, an observation consistent with Arabidopsis thaliana, Zea mays and Mimulus guttatus. Overall, our cost effective method and findings enhance the understanding of meiotic recombination in tomato and suggest evolutionarily conserved recombination associated genomic features.
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