ArticleRice (New York, N.Y.)2015
Development of Genome-Wide Insertion and Deletion Polymorphism Markers from Next-Generation Sequencing Data in Rice.
Article in Rice (New York, N.Y.), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- The development of ideal insertion and deletion (InDel) markers and initial indel map variation in cucumber using re-sequenced data.BMC genomics · 2025Article
- Article
- A Genomic Evaluation of Six Selected Inbred Lines of the Naturalized Plants of Milk Thistle (Plants (Basel, Switzerland) · 2023Article
- Genome-wide identification and development of InDel markers in tobacco (Physiology and molecular biology of plants : an international journal of functional plant biology · 2022Article
- Development of InDel markers for Oryza sativa ssp. javanica based on whole-genome resequencing.PloS one · 2022Article
- Development of a genome-wide InDel marker set for allele discrimination between rice (Oryza sativa) and the other seven AA-genome Oryza species.Scientific reports · 2021Article
- Development and validation of genome-wide InDel markers with high levels of polymorphism in bitter gourd (Momordica charantia).BMC genomics · 2021Article
- Agarose-resolvable InDel markers based on whole genome re-sequencing in cucumber.Scientific reports · 2021Article
- Genome-Wide Introgression and Quantitative Trait Locus Mapping Reveals the Potential of Asian Cotton (Frontiers in plant science · 2021Article
- Indel marker analysis of putative stress-related genes reveals genetic diversity and differentiation of rice landraces in peninsular Thailand.Physiology and molecular biology of plants : an international journal of functional plant biology · 2020Article
- Development of Whole-Genome Agarose-Resolvable LInDel Markers in Rice.Rice (New York, N.Y.) · 2020Article
- Genetic diversity of Indo-China rice varieties using ISSR, SRAP and InDel markers.Journal of genetics · 2019Article
- Article
- Characterization and fine mapping of qkc7.03: a major locus for kernel cracking in maize.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2018Article
- Genome-Wide Analysis of Genetic Variations and the Detection of Rich Variants of NBS-LRR Encoding Genes in Common Wild Rice Lines.Plant molecular biology reporter · 2018Article
- Detection of Highly Differentiated Genomic Regions Between Lotus (Frontiers in plant science · 2018Article
- Allele-specific marker-based assessment revealed that the rice blast resistance genes Pi2 and Pi9 have not been widely deployed in Chinese indica rice cultivars.Rice (New York, N.Y.) · 2016Article
- Article
- Indel Group in Genomes (IGG) Molecular Genetic Markers.Plant physiology · 2016Article
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4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNext-generation sequencing technologies enable the re-sequencing of a large number of genomes and provide an unprecedented opportunity to discover numerous DNA polymorphisms throughout the genome of a species. As the second most abundant form of genetic variation, InDels, with characteristics of co-dominance, multiple alleles and high stability and density and that are easy to genotype, have received an increasing amount attention.
resultsIn this work, a total of 2,329,544 InDels were identified in 1767 rice genomes; these InDels were dispersed across all 12 rice chromosomes, with one InDel marker found, on average, every 160.22 bp. There were 162,380 highly polymorphic InDels with a polymorphism information content (PIC) ≥ 0.5, contributing 1.81 % to the unique primer set. Of these highly polymorphic InDels, we also selected InDels with major allele differences (the size difference between the most and second most frequent alleles) ≥ 3 bp or 8 bp for primer design, which provided a more flexible choice for researchers. Finally, we experimentally validated 100 highly polymorphic InDels for accuracy and polymorphism. The PCR results showed that the accuracy of the InDel markers was 95.70 %, while the average PIC value was 0.56, with a range of 0.19 to 0.78; the average allele number was 3.02, with a range of 2 to 5.
conclusionsOur genome-wide and easily used InDel markers with high polymorphism and density in both cultivated and wild rice will undoubtedly have practical implications in rice marker-assisted breeding and will also meet the need of fine-scale genetic mapping in map-based rice gene cloning.
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