ArticleJournal of advanced research2022
A bulked segregant analysis tool for out-crossing species (BSATOS) and QTL-based genomics-assisted prediction of complex traits in apple.
Article in Journal of advanced research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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6 citing papers in PubMed, 13 citations in OpenAlex.
- Integrated BSA-seq and RNA-seq analyses revealFrontiers in plant science · 2026Article
- Natural variations in MdBPM2/MdRGLG3-MdNAC83 network controlling the quantitative segregation of apple fruit storability.Journal of integrative plant biology · 2026Article
- Application of Genome-Assisted Prediction (GAP) for Apple Fruit Weight.Plants (Basel, Switzerland) · 2025Article
- From data to decisions: a paradigm shift in fruit agriculture through the integration of multi-omics, modern phenotyping, and cutting-edge bioinformatic tools.Frontiers in plant science · 2025Review
- Genetic variations inMolecular breeding : new strategies in plant improvement · 2024Article
- The allotetraploid horseradish genome provides insights into subgenome diversification and formation of critical traits.Nature communications · 2023Article
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Authors and funding
11 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
introductionGenomic heterozygosity, self-incompatibility, and rich-in somatic mutations hinder the molecular breeding efficiency of outcrossing plants.
objectivesWe attempted to develop an efficient integrated strategy to identify quantitative trait loci (QTLs) and trait-associated genes, to develop gene markers, and to construct genomics-assisted prediction (GAP) modes.
methodsA novel protocol, bulked segregant analysis tool for out-crossing species (BSATOS), is presented here, which is characterized by taking full advantage of all segregation patterns (including AB × AB markers) and haplotype information. To verify the effectiveness of the protocol in dealing with the complex traits of outbreeding species, three apple cross populations with 9,654 individuals were adopted.
resultsBy using BSATOS, 90, 60, and 77 significant QTLs were identified successfully and candidate genes were predicted for apple fruit weight (FW), fruit ripening date (FRD), and fruit soluble solid content (SSC), respectively. The gene-based markers were developed and genotyped for 1,396 individuals in a training population, including 145 Malus accessions and 1,251 F1 plants of the three full-sib families. GAP models were trained using marker genotype effect estimates of the training population. The prediction accuracy was 0.7658, 0.6455, and 0.3758 for FW, FRD, and SSC, respectively.
conclusionThe BSATOS and GAP models provided a convenient and efficient methodology for candidate gene mining and molecular breeding in out-crossing plant species. The BSATOS pipeline can be freely downloaded from: https://github.com/maypoleflyn/BSATOS.
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