ArticleBMC genomics2011
Identification of SNP and SSR markers in eggplant using RAD tag sequencing.
Article in BMC genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 93 papers.
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93 citing papers in PubMed.
- Genetic structure analysis and core germplasm construction of Robinia pseudoacacia and its closely related species based on SNP.BMC plant biology · 2025Article
- Repeatome Dynamics and Sex Chromosome Differentiation in the XY and XYInternational journal of molecular sciences · 2025Article
- A Compendium for Novel Marker-Based Breeding Strategies in Eggplant.Plants (Basel, Switzerland) · 2023Review
- Genome-Wide Association Study for Agro-Morphological Traits in Eggplant Core Collection.Plants (Basel, Switzerland) · 2022Article
- Genome-Wide Survey and Development of the First Microsatellite Markers Database (International journal of molecular sciences · 2022Article
- An Eggplant Recombinant Inbred Population Allows the Discovery of Metabolic QTLs Controlling Fruit Nutritional Quality.Frontiers in plant science · 2021Article
- Fine mapping of a major locus representing the lack of prickles in eggplant revealed the availability of a 0.5-kb insertion/deletion for marker-assisted selection.Breeding science · 2020Article
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- High-density genetic linkage map construction and cane cold hardiness QTL mapping for Vitis based on restriction site-associated DNA sequencing.BMC genomics · 2020Article
- The taxonomic significance of ddRADseq based microsatellite markers in the closely related species of Heracleum (Apiaceae).PloS one · 2020Article
- A First Insight into a Draft Genome of Silver Sillago (Animals : an open access journal from MDPI · 2019Article
- Genetic Analysis for Fruit Phenolics Content, Flesh Color, and Browning Related Traits in Eggplant (International journal of molecular sciences · 2019Article
- Whole-Genome Resequencing of Seven Eggplant (Frontiers in plant science · 2019Article
- De novo assembly of genome and development of polymorphic microsatellite loci in the blue swimming crab (Portunus pelagicus) using RAD approach.Molecular biology reports · 2018Article
- Analysis of evolution and genetic diversity of sweetpotato and its related different polyploidy wild species I. trifida using RAD-seq.BMC plant biology · 2018Article
- Mapping QTLs for water-use efficiency reveals the potential candidate genes involved in regulating the trait in apple under drought stress.BMC plant biology · 2018Article
- Genome re-sequencing, SNP analysis, and genetic mapping of the parental lines of a commercial FBreeding science · 2018Article
- A nuclear DNA barcode for eastern North American oaks and application to a study of hybridization in an Arboretum setting.Ecology and evolution · 2018Article
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- Genome-wide genetic variation and comparison of fruit-associated traits between kumquat (Citrus japonica) and Clementine mandarin (Citrus clementina).Plant molecular biology · 2018Article
33 more citing papers are in PubMed but not listed here.
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7 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundThe eggplant (Solanum melongena L.) genome is relatively unexplored, especially compared to those of the other major Solanaceae crops tomato and potato. In particular, no SNP markers are publicly available; on the other hand, over 1,000 SSR markers were developed and publicly available. We have combined the recently developed Restriction-site Associated DNA (RAD) approach with Illumina DNA sequencing for rapid and mass discovery of both SNP and SSR markers for eggplant.
resultsRAD tags were generated from the genomic DNA of a pair of eggplant mapping parents, and sequenced to produce ~17.5 Mb of sequences arrangeable into ~78,000 contigs. The resulting non-redundant genomic sequence dataset consisted of ~45,000 sequences, of which ~29% were putative coding sequences and ~70% were in common between the mapping parents. The shared sequences allowed the discovery of ~10,000 SNPs and nearly 1,000 indels, equivalent to a SNP frequency of 0.8 per Kb and an indel frequency of 0.07 per Kb. Over 2,000 of the SNPs are likely to be mappable via the Illumina GoldenGate assay. A subset of 384 SNPs was used to successfully fingerprint a panel of eggplant germplasm, producing a set of informative diversity data. The RAD sequences also included nearly 2,000 putative SSRs, and primer pairs were designed to amplify 1,155 loci.
conclusionThe high throughput sequencing of the RAD tags allowed the discovery of a large number of DNA markers, which will prove useful for extending our current knowledge of the genome organization of eggplant, for assisting in marker-aided selection and for carrying out comparative genomic analyses within the Solanaceae family.
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