ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2021
Genome-wide simple sequence repeat markers in potato: abundance, distribution, composition, and polymorphism.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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8 citing papers in PubMed, 19 citations in OpenAlex.
- De Novo Hybrid Assembly of theInternational journal of molecular sciences · 2025Article
- Genome-Wide Microsatellites inAnimals : an open access journal from MDPI · 2024Article
- Repeat-mediated recombination results in Complex DNA structure of the mitochondrial genome of Trachelospermum jasminoides.BMC plant biology · 2024Article
- Functional and evolutionary comparative analysis of the DIR gene family in Nicotiana tabacum L. and Solanum tuberosum L.BMC genomics · 2024Article
- Genome-wide development of intra- and inter-specific transferable SSR markers and construction of a dynamic web resource for yam molecular breeding: Y2MD.The plant genome · 2024Article
- Article
- CRISPR/Cas9 Editing Sites Identification and Multi-Elements Association Analysis inInternational journal of molecular sciences · 2023Article
- Characterization of Microsatellites in theFrontiers in plant science · 2022Article
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Simple sequence repeats (SSRs) are important sources of genetic diversity and are widely used as markers in genetics and molecular breeding. In this study, we examined four potato genomes of DM1-3 516 R44 (DM) from Solanum phureja, RH89039-16 (RH) from Solanum tuberosum, M6 from Solanum chacoense and Solanum commersonii to determine SSR abundance and distribution and develop a larger list of polymorphic markers for a potentially wide range of uses for the potato community. A total of 1,734,619 SSRs were identified across the four genomes with an average of 433,655 SSRs per genome and 2.31kb per SSR. The most abundant repeat units for mono-, di-, tri-, and tetra-nucleotide SSRs were (A/T)n, (AT/AT)n, (AAT/ATT)n, and (ATAT/ATAT)n, respectively. The SSRs were most abundant (78.79%) in intergenic regions and least abundant (3.68%) in untranslated regions. On average, 168,069 SSRs with unique flanking sequences were identified in the four genomes. Further, we identified 16,245 polymorphic SSR markers among the four genomes. Experimental validation confirmed 99.69% of tested markers could generate target bands. The high-density potato SSR markers developed in this study will undoubtedly facilitate the application of SSR markers for genetic research and marker-pyramiding in potato breeding.
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