ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2013
Development and characterization of simple sequence repeat markers providing genome-wide coverage and high resolution in maize.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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42 citing papers in PubMed, 98 citations in OpenAlex.
- Genome-wide discovery, characterization, and validation of novel SSR markers in clove (Syzygium aromaticum) and their application in genetic analysis.BMC plant biology · 2026Article
- QTL mapping, validation, and candidate gene predicting for maize plant architecture traits via bulked segregant analysis plus linkage analysis with F₂ population.BMC plant biology · 2026Article
- Genome-Wide Discovery of SSR Markers Based on Whole-Genome Resequencing Data ofPlants (Basel, Switzerland) · 2025Article
- Genome-Wide Microsatellite Characterization and Molecular Marker Development of Himalayan Griffon (Animals : an open access journal from MDPI · 2025Article
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- Genome-Wide Comparative Analysis of Five Amaranthaceae Species Reveals a Large Amount of Repeat Content.Plants (Basel, Switzerland) · 2024Article
- Genome Assembly and Microsatellite Marker Development Using Illumina and PacBio Sequencing in theGenes · 2023Article
- CRISPR/Cas9 Editing Sites Identification and Multi-Elements Association Analysis inInternational journal of molecular sciences · 2023Article
- A large deletion conferring pale green leaves of maize.BMC plant biology · 2023Article
- Comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus species.Scientific reports · 2023Article
- Genome-wide characterization and development of SSR markers for genetic diversity analysis in northwestern Himalayas Walnut (3 Biotech · 2023Article
- First Report on Development of Genome-Wide Microsatellite Markers for Stock (Plants (Basel, Switzerland) · 2023Article
- Article
- Validating a Major Quantitative Trait Locus and Predicting Candidate Genes Associated With Kernel Width Through QTL Mapping and RNA-Sequencing Technology Using Near-Isogenic Lines in Maize.Frontiers in plant science · 2022Article
- Two fingerprinting sets for Humulus lupulus based on KASP and microsatellite markers.PloS one · 2022Article
- Genome-wide simple sequence repeat markers in potato: abundance, distribution, composition, and polymorphism.DNA research : an international journal for rapid publication of reports on genes and genomes · 2021Article
- Genome-wide simple sequence repeats (SSR) markers discovered from whole-genome sequence comparisons of multiple spinach accessions.Scientific reports · 2021Article
- Comprehensive Characterization and Validation of Chromosome-Specific Highly Polymorphic SSR Markers From Pomegranate (Frontiers in plant science · 2021Article
- Comparative Chloroplast Genome Analyses of the Winter-Blooming Eastern Asian Endemic GenusFrontiers in genetics · 2021Article
- Comprehensive identification and characterization of simple sequence repeats based on the whole-genome sequences of 14 forest and fruit trees.Forestry research · 2021Article
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Authors and funding
12 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Simple sequence repeats (SSRs) have been widely used in maize genetics and breeding, because they are co-dominant, easy to score, and highly abundant. In this study, we used whole-genome sequences from 16 maize inbreds and 1 wild relative to determine SSR abundance and to develop a set of high-density polymorphic SSR markers. A total of 264 658 SSRs were identified across the 17 genomes, with an average of 135 693 SSRs per genome. Marker density was one SSR every of 15.48 kb. (C/G)n, (AT)n, (CAG/CTG)n, and (AAAT/ATTT)n were the most frequent motifs for mono, di-, tri-, and tetra-nucleotide SSRs, respectively. SSRs were most abundant in intergenic region and least frequent in untranslated regions, as revealed by comparing SSR distributions of three representative resequenced genomes. Comparing SSR sequences and e-polymerase chain reaction analysis among the 17 tested genomes created a new database, including 111 887 SSRs, that could be develop as polymorphic markers in silico. Among these markers, 58.00, 26.09, 7.20, 3.00, 3.93, and 1.78% of them had mono, di-, tri-, tetra-, penta-, and hexa-nucleotide motifs, respectively. Polymorphic information content for 35 573 polymorphic SSRs out of 111 887 loci varied from 0.05 to 0.83, with an average of 0.31 in the 17 tested genomes. Experimental validation of polymorphic SSR markers showed that over 70% of the primer pairs could generate the target bands with length polymorphism, and these markers would be very powerful when they are used for genetic populations derived from various types of maize germplasms that were sampled for this study.
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