ArticleBMC genomics2018
Chromosome level high-density integrated genetic maps improve the Pyrus bretschneideri 'DangshanSuli' v1.0 genome.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed.
- Haplotype-resolved chromosome-level genome assemblies of nineteen apple (Malus domestica Borkh.) cultivars.Scientific data · 2026Article
- Orchard and storage-dependent metabolic and transcriptional regulation of superficial scald in 'Packham's Triumph' pears.Frontiers in plant science · 2026Article
- Pear scab resistance gene Rvn1 from Ussurian pear is located in a cluster of receptor-like protein ethylene-inducing Xylanase (EIX) genes.BMC plant biology · 2025Article
- Comparative genomic analyses reveal different genetic basis of two types of fruit in Maloideae.Nature communications · 2025Article
- A Class of Allopolyploidy Showing High Duplicate Retention and Continued Homoeologous Exchanges.Genome biology and evolution · 2025Article
- Near-gapless and haplotype-resolved apple genomes provide insights into the genetic basis of rootstock-induced dwarfing.Nature genetics · 2024Article
- The pear genomics database (PGDB): a comprehensive multi-omics research platform for Pyrus spp.BMC plant biology · 2023Article
- DNA methylation signatures of duplicate gene evolution in angiosperms.Plant physiology · 2023Article
- QTL Analysis and CAPS Marker Development Linked with Russet in Pear (Plants (Basel, Switzerland) · 2022Article
- RNA-Seq Analysis Identifies Transcription Factors Involved in Anthocyanin Biosynthesis of 'Red Zaosu' Pear Peel and Functional Study ofInternational journal of molecular sciences · 2022Article
- Pear genetics: Recent advances, new prospects, and a roadmap for the future.Horticulture research · 2022Article
- Genome-wide clonal variability in European pear "Rocha" using high-throughput sequencing.Horticulture research · 2022Article
- Building a foundation for gene family analysis in Rosaceae genomes with a novel workflow: A case study inFrontiers in plant science · 2022Article
- A Novel Pear Scab (Plants (Basel, Switzerland) · 2021Article
- A consensus and saturated genetic map provides insight into genome anchoring, synteny of Solanaceae and leaf- and fruit-related QTLs in wolfberry (Lycium Linn.).BMC plant biology · 2021Article
- An Atlas of Genomic Resources for Studying Rosaceae Fruits and Ornamentals.Frontiers in plant science · 2021Review
- Homozygosity Mapping Reveals Population History and Trait Architecture in Self-Incompatible Pear (Frontiers in plant science · 2020Article
- TRANSNAP: a web database providing comprehensive information on Japanese pear transcriptome.Scientific reports · 2019Article
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11 authors.
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Abstract
backgroundChromosomal level reference genomes provide a crucial foundation for genomics research such as genome-wide association studies (GWAS) and whole genome selection. The chromosomal-level sequences of both the European (Pyrus communis) and Chinese (P. bretschneideri) pear genomes have not been published in public databases so far.
resultsTo anchor the scaffolds of P. bretschneideri 'DangshanSuli' (DS) v1.0 genome into pseudo-chromosomes, two genetic maps (MH and YM maps) were constructed using half sibling populations of Chinese pear crosses, 'Mantianhong' (MTH) × 'Hongxiangsu' (HXS) and 'Yuluxiang' (YLX) × MTH, from 345 and 162 seedlings, respectively, which were prepared for SNP discovery using genotyping-by-sequencing (GBS) technology. The MH and YM maps, each with 17 linkage groups (LGs), were constructed from 2606 and 2489 SNP markers and spanned 1847 and 1668 cM, respectively, with average marker intervals of 0.7. The two maps were further merged with a previously published genetic map (BD) based on the cross 'Bayuehong' (BYH) × 'Dangshansuli' (DS) to build a new integrated MH-YM-BD map. By using 7757 markers located on the integrated MH-YM-BD map, 898 scaffolds (400.57 Mb) of the DS v1.0 assembly were successfully anchored into 17 pseudo-chromosomes, accounting for 78.8% of the assembled genome size. About 88.31% of them (793 scaffolds) were directionally anchored with two or more markers on the pseudo-chromosomes. Furthermore, the errors in each pseudo-chromosome (especially 1, 5, 7 and 11) were manually corrected and pseudo-chromosomes 1, 5 and 7 were extended by adding 19, 12 and 14 scaffolds respectively in the newly constructed DS v1.1 genome. Synteny analyses revealed that the DS v1.1 genome had high collinearity with the apple genome, and the homologous fragments between pseudo-chromosomes were similar to those found in previous studies. Moreover, the red-skin trait of Asian pear was mapped to an identical locus as identified previously.
conclusionsThe accuracy of DS v1.1 genome was improved by using larger mapping populations and merged genetic map. With more than 400 MB anchored to 17 pseudo-chromosomes, the new DS v1.1 genome provides a critical tool that is essential for studies of pear genetics, genomics and molecular breeding.
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