ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2013
Development of InDel markers for Brassica rapa based on whole-genome re-sequencing.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
- Population-resourced species-specific InDel markers for identifying putative interspecific hybrids between Populus euphratica and Populus pruinosa.BMC genomic data · 2026Article
- Development of long InDel markers through whole genome resequencing for variety purity detection in cucumber.Scientific reports · 2026Article
- InDel Markers for Identifying Interspecific Hybrid Offspring of Apple and Pear.Plants (Basel, Switzerland) · 2025Article
- Development of Gene-Based InDel Markers on Putative Drought Stress-Responsive Genes and Genetic Diversity of Durian (Durio zibethinus).Biochemical genetics · 2024Article
- Identification of Insertion and Deletion (InDel) Markers for Chickpea (Plants (Basel, Switzerland) · 2024Article
- Genetic Diversity Analysis and Core Germplasm Construction ofPlants (Basel, Switzerland) · 2024Article
- Distinguishing fanged frogs (Limnonectes) species (Amphibia: Anura: Dicroglossidae), from Thailand using high resolution melting analysis.Scientific reports · 2023Article
- Development of SNP and InDel markers by genome resequencing and transcriptome sequencing in radish (Raphanus sativus L.).BMC genomics · 2023Article
- A Genomic Evaluation of Six Selected Inbred Lines of the Naturalized Plants of Milk Thistle (Plants (Basel, Switzerland) · 2023Article
- A target cultivar-specific identification system based on the chromatographic printed array strip method for eight prominent Japanese citrus cultivars.Breeding science · 2023Article
- Vegetable biology and breeding in the genomics era.Science China. Life sciences · 2023Review
- Review
- Development of Omni InDel and supporting database for maize.Frontiers in plant science · 2023Article
- Construction of a genetic linkage map and QTL mapping of fruit quality traits in guava (Frontiers in plant science · 2023Article
- Development and Application of InDel Markers Linked to Fruit-Shape and Peel-Colour Genes in Wax Gourd.Genes · 2022Article
- Genome-wide identification and development of InDel markers in tobacco (Physiology and molecular biology of plants : an international journal of functional plant biology · 2022Article
- Article
- Development of Genome-Wide Functional Markers Using Draft Genome Assembly of Guava (Frontiers in plant science · 2021Article
- Genome-Wide Discovery of InDel Markers in Sesame (Plants (Basel, Switzerland) · 2020Article
- Fine mapping of the major anthracnose resistance QTL AnRBMC plant biology · 2020Article
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9 authors.
Funding
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Abstract
Genome-wide detection of short insertion/deletion length polymorphisms (InDels, <5 bp) in Brassica rapa (named the A genome) was performed by comparing whole-genome re-sequencing data from two B. rapa accessions, L144 and Z16, to the reference genome sequence of Chiifu-401-42. In total, we identified 108,558 InDel polymorphisms between Chiifu-401-42 and L144, 26,795 InDels between Z16 and Chiifu-401-42, and 26,693 InDels between L144 and Z16. From these, 639 InDel polymorphisms of 3-5 bp in length between L144 and Z16 were selected for experimental validation; 491 (77%) yielded single PCR fragments and showed polymorphisms, 7 (1%) did not amplify a product, and 141 (22%) showed no polymorphism. For further validation of these intra-specific InDel polymorphisms, 503 candidates, randomly selected from the 639 InDels, were screened across seven accessions representing different B. rapa cultivar groups. Of these assayed markers, 387 (77%) were polymorphic, 111 (22%) were not polymorphic and 5 (1%) did not amplify a PCR product. Furthermore, we randomly selected 518 InDel markers to validate their polymorphism in B. napus (the AC genome) and B. juncea (the AB genome), of which more than 90% amplified a PCR product; 132 (25%) showed polymorphism between the two B. napus accessions and 41 (8%) between the two B. juncea accessions. This set of novel PCR-based InDel markers will be a valuable resource for genetic studies and breeding programs in B. rapa.
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