ArticleBMC genomics2023
Pattern and variation in simple sequence repeat (SSR) at different genomic regions and its implications to maize evolution and breeding.
Article in BMC genomics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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29 citing papers in PubMed, 57 citations in OpenAlex.
- The Pan-Plastome of Walnuts (International journal of molecular sciences · 2026Article
- Development and Application of SSR Markers for the QTLInternational journal of molecular sciences · 2026Article
- Genomic distribution characteristics and interspecific differences of microsatellite landscapes in Felidae.BMC genomics · 2026Article
- Identification and Development of Pathogen- and Pest-Specific Defense-Resistance-Associated SSR Marker Candidates Assisted by Machine Learning and Discovery of Putative QTL Hotspots inPlants (Basel, Switzerland) · 2026Article
- Genome-wide identification and characterization of NAC transcription factor-derived microsatellites in wheat (Triticum aestivum L.).Journal of applied genetics · 2026Article
- Comprehensive analysis of chloroplast genome evolution in Poaceae: codon usage patterns, selection pressures, and phylogenomic relationships.BMC genomics · 2026Article
- Association Mapping Analysis of Morphological Characteristics in FPlants (Basel, Switzerland) · 2025Article
- Mutations of short tandem repeats explain abundant trait heritability in Arabidopsis.Genome biology · 2025Article
- Generation and characterization of novel transcriptome-derived SSR markers for genetic applications in blueberry.Scientific reports · 2025Article
- Phenotypic Traits, SSR Core Primer Screening, and Genetic Diversity Analysis ofEcology and evolution · 2025Article
- Molecular characterization of T-, C- and S- specific cytoplasmic male sterile (CMS) maize inbreds using mitochondrial SSRs for its utilization in baby corn breeding.Molecular biology reports · 2025Article
- Functional divergence of LncRNAs in wheat-fungal interactions: insights from stem rust-responsive wheat transcriptomes.Physiology and molecular biology of plants : an international journal of functional plant biology · 2025Article
- Article
- Genome-wide development of SSR molecular markers for modern sugarcane cultivars.Frontiers in plant science · 2025Article
- Article
- Development of Roselle (Plants (Basel, Switzerland) · 2024Article
- The Genomic SSR Millets Database (GSMDB): enhancing genetic resources for sustainable agriculture.Database : the journal of biological databases and curation · 2024Article
- pSATdb 2.0: a database of organellar common, polymorphic, and unique microsatellites.Functional & integrative genomics · 2024Article
- Streamlining of Simple Sequence Repeat Data Mining Methodologies and Pipelines for Crop Scanning.Plants (Basel, Switzerland) · 2024Review
- Genome-wide simple sequence repeat analysis and specific molecular marker development of rye.BMC genomics · 2024Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRepetitive DNA sequences accounts for over 80% of maize genome. Although simple sequence repeats (SSRs) account for only 0.03% of the genome, they have been widely used in maize genetic research and breeding as highly informative codominant DNA markers. The genome-wide distribution and polymorphism of SSRs are not well studied due to the lack of high-quality genome DNA sequence data.
resultsIn this study, using data from high-quality de novo-sequenced maize genomes of five representative maize inbred lines, we revealed that SSRs were more densely present in telomeric region than centromeric region, and were more abundant in genic sequences than intergenic sequences. On genic sequences, tri- and hexanucleotide motifs were more abundant in CDS sequence and some mono- and dinucleotide motifs were more abundant in UTR sequences. Median length and chromosomal density of SSRs were both narrowly range-bound, with median length of 14-18 bp and genome-wide average density of 3355.77 bp/Mbp. LTR-RTs of < 0.4 Mya had higher SSR density (4498-4992 bp/Mbp). The genome-specific and motif-specific SSR polymorphism were studied. Their potential breeding applications were discussed.
conclusionsWe found that the median length of SSR sequences of different SSR motifs was nearly constant. SSR density in genic regions was much higher than intergenic regions. In addition, SSR density at LTR-RTs of different evolutionary ages varied in a narrow range. The SSRs and their LTR-RT carriers evolved at an equal rate. All these observations indicated that SSR length and density were under control of yet unknown evolutionary forces. The chromosome region-specific and motif-specific SSR polymorphisms we observed supported the notion that SSR polymorphism was invaluable genome resource for developing highly informative genome and gene markers in maize genetic research and molecular breeding.
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