ArticleBMC genomics2015
Development of genome-wide insertion and deletion markers for maize, based on next-generation sequencing data.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Different genomic footprint of small insertion-deletion and structural variants determines the genetic divergence of indica and japonica rice.BMC genomics · 2026Article
- Development of long InDel markers through whole genome resequencing for variety purity detection in cucumber.Scientific reports · 2026Article
- Genetic basis of pedicellate spikelet masculinization in maize revealed by an advanced maize-teosinte population.Planta · 2026Article
- TP-ARMS: A Cost-Effective PCR-Based Genotyping System for Precision Breeding of Small InDels in Crops.International journal of molecular sciences · 2026Article
- The development of ideal insertion and deletion (InDel) markers and initial indel map variation in cucumber using re-sequenced data.BMC genomics · 2025Article
- Article
- InDel Markers for Identifying Interspecific Hybrid Offspring of Apple and Pear.Plants (Basel, Switzerland) · 2025Article
- Article
- Maize-Tripsacum-Teosinte allopolyploid (MTP), a novel dwarf mutant inducer tool in maize.Plant biotechnology journal · 2025Article
- Fine mapping and candidate gene analysis of qSRC3 controlling the silk color in maize (Zea mays L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Deploying QTL-seq rapid identification and separation of the major QTLs of tassel branch number for fine-mapping in advanced maize populations.Molecular breeding : new strategies in plant improvement · 2023Article
- A Genomic Evaluation of Six Selected Inbred Lines of the Naturalized Plants of Milk Thistle (Plants (Basel, Switzerland) · 2023Article
- A large deletion conferring pale green leaves of maize.BMC plant biology · 2023Article
- Efficient marker-assisted breeding for clubroot resistance in elite Pol-CMS rapeseed varieties by updating theMolecular breeding : new strategies in plant improvement · 2022Article
- Identification of a major QTL and genome-wide epistatic interactions for single vs. paired spikelets in a maize-teosinte FMolecular breeding : new strategies in plant improvement · 2022Article
- Combining QTL-seq and linkage mapping to uncover the genetic basis of single vs. paired spikelets in the advanced populations of two-ranked maize×teosinte.BMC plant biology · 2021Article
- Development of genic KASP SNP markers from RNA-Seq data for map-based cloning and marker-assisted selection in maize.BMC plant biology · 2021Article
- Development and validation of genome-wide InDel markers with high levels of polymorphism in bitter gourd (Momordica charantia).BMC genomics · 2021Article
- Development of Whole-Genome Agarose-Resolvable LInDel Markers in Rice.Rice (New York, N.Y.) · 2020Article
- A cost-effective barcode system for maize genetic discrimination based on bi-allelic InDel markers.Plant methods · 2020Article
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7 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundInsertions and deletions (indels) are the most abundant form of structural variation in all genomes. Indels have been increasingly recognized as an important source of molecular markers due to high-density occurrence, cost-effectiveness, and ease of genotyping. Coupled with developments in bioinformatics, next-generation sequencing (NGS) platforms enable the discovery of millions of indel polymorphisms by comparing the whole genome sequences of individuals within a species.
resultsA total of 1,973,746 unique indels were identified in 345 maize genomes, with an overall density of 958.79 indels/Mbp, and an average allele number of 2.76, ranging from 2 to 107. There were 264,214 indels with polymorphism information content (PIC) values greater than or equal to 0.5, accounting for 13.39% of overall indels. Of these highly polymorphic indels, we designed primer pairs for 83,481 and 29,403 indels with major allele differences (i.e. the size difference between the most and second most frequent alleles) greater than or equal to 3 and 8 bp, respectively, based on the differing resolution capabilities of gel electrophoresis. The accuracy of our indel markers was experimentally validated, and among 100 indel markers, average accuracy was approximately 90%. In addition, we also validated the polymorphism of the indel markers. Of 100 highly polymorphic indel markers, all had polymorphisms with average PIC values of 0.54.
conclusionsThe maize genome is rich in indel polymorphisms. Intriguingly, the level of polymorphism in genic regions of the maize genome was higher than that in intergenic regions. The polymorphic indel markers developed from this study may enhance the efficiency of genetic research and marker-assisted breeding in maize.
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