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A Review of Microsatellite Markers and Their Applications in Rice Breeding Programs to Improve Blast Disease Resistance
Open accessAbstract
Over the last few decades, the use of molecular markers has played an increasing role in rice breeding and genetics. Of the different types of molecular markers, microsatellites have been utilized most extensively, because they can be readily amplified by PCR and the large amount of allelic variation at each locus. Microsatellites are also known as simple sequence repeats (SSR), and they are typically composed of 1-6 nucleotide repeats. These markers are abundant, distributed throughout the genome and are highly polymorphic compared with other genetic markers, as well as being species-specific and co-dominant. For these reasons, they have become increasingly important genetic markers in rice breeding programs. The evolution of new biotypes of pests and diseases as well as the pressures of climate change pose serious challenges to rice breeders, who would like to increase rice production by introducing resistance to multiple biotic and abiotic stresses. Recent advances in rice genomics have now made it possible to identify and map a number of genes through linkage to existing DNA markers. Among the more noteworthy examples of genes that have been tightly linked to molecular markers in rice are those that confer resistance or tolerance to blast. Therefore, in combination with conventional breeding approaches, marker-assisted selection (MAS) can be used to monitor the presence or lack of these genes in breeding populations. For example, marker-assisted backcross breeding has been used to integrate important genes with significant biological effects into a number of commonly grown rice varieties. The use of cost-effective, finely mapped microsatellite markers and MAS strategies should provide opportunities for breeders to develop high-yield, blast resistance rice cultivars. The aim of this review is to summarize the current knowledge concerning the linkage of microsatellite markers to rice blast resistance genes, as well as to explore the use of MAS in rice breeding programs aimed at improving blast resistance in this species. We also discuss the various advantages, disadvantages and uses of microsatellite markers relative to other molecular marker types.
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![Figure 1 Development and applications of microsatellite markers at a glance [31].](/paper-figures/6c9ee19ffce94d1c9fed03f91ba9e00d/a-review-of-microsatellite-markers-and-their-applications-in-rice-breeding-figure-1.jpg)
![Figure 2 Frequencies of microsatellites in the rice sequences registered in the database [90].](/paper-figures/82772bd71de1489188ac57f0c62c0f9d/a-review-of-microsatellite-markers-and-their-applications-in-rice-breeding-figure-2.jpg)
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“Breeding sweet potato varieties with desirable traits could be facilitated and accelerated through marker-assisted selection (MAS, Schmitt et al., 2010; Miah et al., 2013).”
From Development and identification of SSR markers associated with starch properties and β-carotene content in the storage root of sweet potato (Ipomoea batatas L.) (2016) · cites this paper as Miah et al., 2013
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Cited by
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MISA-web: a web server for microsatellite prediction
Beier, S., Thiel, T., Münch, T., Scholz, U., & Mascher, M. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx198 · Cited by 2,644
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Genetic Diversity of Aromatic Rice Germplasm Revealed By SSR Markers
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Self-citationPlant Genetic Diversity Studies: Insights from DNA Marker Analyses
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Metadata
- Authors
- Miah, G., Rafii, M., Ismail, M., Puteh, A., Rahim, H., Islam, K., & Latif, M.
- Affiliations
- Universiti Putra Malaysia (MY)
- Malaysian Nuclear Agency (MY)
- Corresponding author
- Rafii, Mohd
- Venue
- International Journal of Molecular Sciences
- Publisher
- MDPI AG
- Published
- 2013-11-14
- Volume
- 14
- Issue
- 11
- Pages
- 22499-22528
- ISSN
- 1422-0067 (ISSN-L)
- PMC
- PMC3856076
- OpenAlex
- W2067247057
- Cited by
- 241
- References
- 165
- Citations by year
- 2026: 10 · 2025: 10 · 2024: 19 · 2023: 31 · 2022: 23 · 2021: 19 · 2020: 32 · 2019: 14 · 2018: 31 · 2017: 17 · 2016: 18 · 2015: 12 · 2014: 5
- FWCI
- 1.43
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- International Journal of Molecular Sciences (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Universiti Putra Malaysia Institutional Repository (Universiti Putra Malaysia) (acceptedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Disease Resistance and Genetics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Wheat and Barley Genetics and Pathology
- Keywords
- microsatellite markers, rice blast resistance, marker-assisted selection, rice breeding, blast resistance genes, marker-assisted backcross breeding, genetic linkage, molecular markers, rice
- MeSH terms
- Alleles, Breeding, Genetic Markers, Plant Diseases, Oryza, Microsatellite Repeats, Chromosomes, Plant, Disease Resistance
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