ArticlePlant communications2024
Haplotype-resolved T2T genome assemblies and pangenome graph of pear reveal diverse patterns of allele-specific expression and the genomic basis of fruit quality traits.
Article in Plant communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- The heterozygous pineapple genome demonstrates the importance of haplotype-resolved plant genomes.Horticulture research · 2026Article
- Haplotype-resolved genome assembly of a male Dioscorea alata cultivar reveals the structure and evolution of young sex chromosomes.The Plant journal : for cell and molecular biology · 2026Article
- Pan-Genome and Transcriptome-Guided Analysis Reveals Duplication-Driven Evolution and Candidate MYB-bHLH Modules Associated with Fruit Development in Pear.Plants (Basel, Switzerland) · 2026Article
- Haplotype-resolved genome of 'Pinot Noir' reveals DNA polymorphisms and allele-specific expression shaping terroir adaptation.Molecular horticulture · 2026Article
- Comparative transcriptomics among peach, almond and their interspecific F1 hybrid reveal key common and species-specific regulatory pathways involved in fruit development.BMC plant biology · 2026Article
- Kiwifruit genomics and applications: recent advances, current challenges, and future prospects.Horticulture research · 2026Article
- A new phased assembly of the Antarctic spiny plunderfish provides novel insights into the evolution of the notothenioid radiation.bioRxiv : the preprint server for biology · 2026Article
- Telomere-to-telomere genome assembly and comprehensive mutation library facilitate bitter gourd breeding and functional genomics research.Plant communications · 2026Article
- Complete telomere-to-telomere genomes of cowpea reveal insights into centromere evolution in Phaseoleae.Horticulture research · 2026Article
- Pangenome Analysis Reveals Structural Variations Associated With Citric Acid Accumulation in Prunus mume.Plant biotechnology journal · 2026Article
- Improved Visualization Method of DNA Sequences and its Application in Phylogenetic Analysis.Combinatorial chemistry & high throughput screening · 2026Article
- Graph pan-genome advances genetic discoveries and the improvement of eggplant.Horticulture research · 2026Article
- Chromosome-scale assembly of European flax (Linum usitatissimum L.) genotypes and pangenomic analysis provide genomic tools to improve breeding.BMC genomics · 2025Article
- From genome to gene expression: the genomic landscape of a hybrid species of Eucalyptus urophylla × Eucalyptus grandis and its divergence from parental species hybrid.BMC plant biology · 2025Article
- Mango pangenome reveals dramatic impacts of reference bias on population genomic analyses.Horticulture research · 2025Article
- Pangenome analysis of Liriodendron reveals presence/absence variations associated with growth traits.BMC plant biology · 2025Article
- Haplotype-based Pangenomics: A Blueprint for Climate Adaptation in Plants.Genomics, proteomics & bioinformatics · 2025Article
- The telomere-to-telomere genome of Pucai () (Horticulture research · 2025Article
- Haplotype-resolved T2T genome assembly of the pear cultivar 'Danxiahong'.Scientific data · 2025Article
- Telomere-to-telomere genome assembly reveals insights into the adaptive evolution of herbivore-defense mediated by volatile terpenoids in Oenanthe javanica.Plant biotechnology journal · 2025Article
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Authors and funding
18 authors.
Funding
Abstract
Hybrid crops often exhibit increased yield and greater resilience, yet the genomic mechanism(s) underlying hybrid vigor or heterosis remain unclear, hindering our ability to predict the expression of phenotypic traits in hybrid breeding. Here, we generated haplotype-resolved T2T genome assemblies of two pear hybrid varieties, 'Yuluxiang' (YLX) and 'Hongxiangsu' (HXS), which share the same maternal parent but differ in their paternal parents. We then used these assemblies to explore the genome-scale landscape of allele-specific expression (ASE) and create a pangenome graph for pear. ASE was observed for close to 6000 genes in both hybrid cultivars. A subset of ASE genes related to aspects of fruit quality such as sugars, organic acids, and cuticular wax were identified, suggesting their important contributions to heterosis. Specifically, Ma1, a gene regulating fruit acidity, is absent in the paternal haplotypes of HXS and YLX. A pangenome graph was built based on our assemblies and seven published pear genomes. Resequencing data for 139 cultivated pear genotypes (including 97 genotypes sequenced here) were subsequently aligned to the pangenome graph, revealing numerous structural variant hotspots and selective sweeps during pear diversification. As predicted, the Ma1 allele was found to be absent in varieties with low organic acid content, and this association was functionally validated by Ma1 overexpression in pear fruit and calli. Overall, these results reveal the contributions of ASE to fruit-quality heterosis and provide a robust pangenome reference for high-resolution allele discovery and association mapping.
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