ArticleJournal of experimental botany2018
Exploring DNA variant segregation types in pooled genome sequencing enables effective mapping of weeping trait in Malus.
Article in Journal of experimental botany, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed, 38 citations in OpenAlex.
- Natural variations in MdBPM2/MdRGLG3-MdNAC83 network controlling the quantitative segregation of apple fruit storability.Journal of integrative plant biology · 2026Article
- Naturally impaired side-chain shortening of aromatic 3-ketoacyl-CoAs reveals the biosynthetic pathway of plant acetophenones.Nature plants · 2025Article
- Major Gene with Polygene Inheritance Analysis of Prostrate Growth Habit in Hybrids ofPlants (Basel, Switzerland) · 2025Article
- Mapping and characterization of a novel powdery mildew resistance locus (PM2) inFrontiers in plant science · 2025Article
- Natural variation in MdNAC5 contributes to fruit firmness and ripening divergence in apple.Horticulture research · 2025Article
- Quantitative Traits of Interest in Apple Breeding and Their Implications for Selection.Plants (Basel, Switzerland) · 2023Article
- The double flower variant of yellowhorn is due to a LINE1 transposon-mediated insertion.Plant physiology · 2023Article
- Gravity sensing and responses in the coordination of the shoot gravitropic setpoint angle.The New phytologist · 2022Review
- Pedigree reconstruction and genetic analysis of major ornamental characters of ornamental crabapple (Malus spp.) based on paternity analysis.Scientific reports · 2022Article
- De novo chromosome-level genome of a semi-dwarf cultivar of Prunus persica identifies the aquaporin PpTIP2 as responsible for temperature-sensitive semi-dwarf trait and PpB3-1 for flower type and size.Plant biotechnology journal · 2022Article
- Identification of the PmWEEP locus controlling weeping traits in Prunus mume through an integrated genome-wide association study and quantitative trait locus mapping.Horticulture research · 2021Article
- Comparative gene expression analysis reveals that multiple mechanisms regulate the weeping trait in Prunus mume.Scientific reports · 2021Article
- Identification and Characterization of an Early Leaf Senescence GeneFrontiers in plant science · 2021Article
- Article
- Comparative Transcriptomics and RNA-Seq-Based Bulked Segregant Analysis Reveals Genomic Basis UnderlyingFrontiers in microbiology · 2021Article
- Weeping candidate genes screened using comparative transcriptomic analysis of weeping and upright progeny in an F1 population of Prunus mume.Physiologia plantarum · 2020Article
- Genetic background mutations drive neural circuit hyperconnectivity in a fragile X syndrome model.BMC biology · 2020Article
- Identification of two QTLs associated with high fruit acidity in apple using pooled genome sequencing analysis.Horticulture research · 2020Article
- Exploring DNA Variant Segregation Types Enables Mapping Loci for Recessive Phenotypic Suppression of Columnar Growth in Apple.Frontiers in plant science · 2020Article
- Identification of Differentially Up-regulated Genes in Apple with White Rot Disease.The plant pathology journal · 2019Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To unlock the power of next generation sequencing-based bulked segregant analysis in allele discovery in out-crossing woody species, and to understand the genetic control of the weeping trait, an F1 population from the cross 'Cheal's Weeping' × 'Evereste' was used to create two genomic DNA pools 'weeping' (17 progeny) and 'standard' (16 progeny). Illumina pair-end (2 × 151 bp) sequencing of the pools to a 27.1× (weeping) and a 30.4× (standard) genome (742.3 Mb) coverage allowed detection of 84562 DNA variants specific to 'weeping', 92148 specific to 'standard', and 173169 common to both pools. A detailed analysis of the DNA variant genotypes in the pools predicted three informative segregation types of variants: <lm×mm> (type I) in weeping pool-specific variants, and <lm×ll> (type II) and <hk×hk> (type III) in variants common to both pools, where the first allele is assumed to be weeping linked and the allele shown in bold is a variant in relation to the reference genome. Conducting variant allele frequency and density-based mappings revealed four genomic regions with a significant association with weeping: a major locus, Weeping (W), on chromosome 13 and others on chromosomes 10 (W2), 16 (W3), and 5 (W4). The results from type I variants were noisier and less certain than those from type II and type III variants, demonstrating that although type I variants are often the first choice, type II and type III variants represent an important source of DNA variants that can be exploited for genetic mapping in out-crossing woody species. Confirmation of the mapping of W and W2, investigation into their genetic interactions, and identification of expressed genes in the W and W2 regions provided insight into the genetic control of weeping and its expressivity in Malus.
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