A review of microsatellite markers and their applications in rice breeding programs to improve blast disease resistance

Miah, Gous; Rafii, Mohd; Ismail, Mohd; Puteh, Adam; Rahim, Harun; Islam, Kh.; Latif, Mohammad

doi:10.3390/ijms141122499

Cited by 242Genetic Mapping and Diversity in Plants and AnimalsPlant Disease Resistance and GeneticsWheat and Barley Genetics and Pathology

A review of microsatellite markers and their applications in rice breeding programs to improve blast disease resistance

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Miah, Gous, Rafii, Mohd, Ismail, Mohd, Puteh, Adam, Rahim, Harun, Islam, Kh., Latif, Mohammad·2013·International Journal of Molecular Sciences

DOI 10.3390/ijms141122499PMC PMC3856076

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Abstract

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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Breeding sweet potato varieties with desirable traits could be facilitated and accelerated through marker-assisted selection.
“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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6 of the 165 references couldn’t be matched to a known paper.

Research works printed but not linked: 5

[12]Brondani C. Hideo P. Rangel N. Borba T.C.O. Brondani R.P.V. Transferability of micro-satellite and ISSR markers in Oryza species Hereditas 2003 138 187 192 14641482
[18]Fjellstrom R. McClung A. Shank A.R. Marchetti M.A. Bormans C. Park W.D. Progress on Development of Microsatellite Markers Associated with Rice Blast Resistance Genes Proceedings of the 29th Rice Technical Working Group Meeting Little Rock, AR, USA 24–27 February 2002 43 44
[19]Conaway C. Cartinhour S. Ayres N. McClung A.M. Lai X.H. Marchetti M.A. Park W.D. PCR Based Markers Linked to Blast Resistance Genes in Rice Proceedings of the 27th Rice Technical Working Group Meeting Reno-Sparks, NV, USA 1–4 March 1998 77
[75]McCouch S.R. Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.) DNA Res 2002 9 193 207 12597276
[77]Song Q.J. Fickus E.W. Cregan P.B. Characteristics of trinucleotide markers in wheat Theor. Appl. Genet 2002 104 286 293 12582699

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Mutagenesis and TILLING to Dissect Gene Function in Plants
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An Overview of Rice QTLs Associated with Disease Resistance to Three Major Rice Diseases: Blast, Sheath Blight, and Bacterial Panicle Blight
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Molecular Scree ning of Blast Resistance Genes in Rice Germplasms Resistant to Magnaporthe oryzae
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Fine Mapping and Whole-Genome Resequencing Identify the Seed Coat Color Gene in Brassica rapa
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Breeding for high grain Fe and Zn levels in cereals
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Introgression of heat shock protein (Hsp70 and sHsp) genes into the Malaysian elite chilli variety Kulai (Capsicum annuum L.) through the application of marker-assisted backcrossing (MAB)
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Mapping quantitative trait loci in selected breeding populations: A segregation distortion approach
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DNA-Based Tools to Certify Authenticity of Rice Varieties—An Overview
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Development and identification of SSR markers associated with starch properties and β-carotene content in the storage root of sweet potato (Ipomoea batatas L.)
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Distribution, function and evolution characterization of microsatellite in Sargassum thunbergii (Fucales, Phaeophyta) transcriptome and their application in marker development
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Development of 44 Novel Polymorphic SSR Markers for Determination of Shiitake Mushroom (Lentinula edodes) Cultivars
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Molecular Approaches for Disease Resistance in Rice
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Genetic diversity, population structure, and association mapping of biomass traits in maize with simple sequence repeat markers
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New microsatellite markers for population studies of Phytophthora cinnamomi, an important global pathogen
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Low temperature isothermal amplification of microsatellites drastically reduces stutter artifact formation and improves microsatellite instability detection in cancer
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Frontiers Approaches to the Diagnosis of Thrips (Thysanoptera): How Effective Are the Molecular and Electronic Detection Platforms?
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Intervarietal and intravarietal genetic structure in Douglas‐fir: nuclear SSR s bring novel insights into past population demographic processes, phylogeography, and intervarietal hybridization
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De Novo Assembly of Transcriptome Sequencing in Caragana korshinskii Kom. and Characterization of EST-SSR Markers
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Comparative assessment of genetic diversity in Albanian olive (Olea europaea L.) using SSRs from anonymous and transcribed genomic regions
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Marker-Assisted Pyramiding of Blast-Resistance Genes in a japonica Elite Rice Cultivar through Forward and Background Selection
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Refining a major QTL controlling spotted wilt disease resistance in cultivated peanut (Arachis hypogaea L.) and evaluating its contribution to the resistance variations in peanut germplasm
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Validation of Genome-Wide SSR Markers Developed for Genetic Diversity and Population Structure Study in Grain Amaranth (Amaranthus hypochondriacus)
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Kompetitive Allele-Specific PCR (KASP): An Efficient High-Throughput Genotyping Platform and Its Applications in Crop Variety Development
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Molecular Marker Technology for Genetic Improvement of Underutilised Crops
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Development and Evaluation of SSR Markers Based on Large Scale Full-Length Transcriptome Sequencing in Sugarcane
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Characterization of Cladosporium Species by Internal Transcribed Spacer-PCR and Microsatellites-PCR
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Genetic analyses of resistance to the peach root-knot nematode (Meloidogyne floridensis) using microsatellite markers
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Genetic diversity and phylogenetic relationship estimation of Shanxi indigenous goat breeds using microsatellite markers
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Exploring the journey of plant breeding from ancient traditional practices to modern advancements
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Exploiting DNA-based molecular tools to assess genetic diversity in pomegranate (Punica granatum L.) selections and cultivars
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Genotypic and Phenotypic Selection of Newly Improved Putra Rice and the Correlations among Quantitative Traits
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Rethinking underutilized cereal crops: pan-omics integration and green system biology
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A detailed analysis of second and third-generation sequencing approaches for accurate length determination of short tandem repeats and homopolymers
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Population genetic structure of a recent insect invasion: a gall midge, Asynapta groverae (Diptera: Cecidomyiidae) in South Korea since the first outbreak in 2008
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Genotyping-by-sequencing (GBS) reveals greater somatic mutations than simple sequence repeats (SSRs) in micropropagated cannabis plants
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Analysis of genetic diversity of Centella asiatica using SSR markers
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Substantial enhancement of high polymorphic SSR marker development using in silico method from 18 available rice blast fungus genome sequences and its application in genetic diversity assessment
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Clones or no clones: genetic structure of riparian Populus euphratica forests in Central Asia
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Genetic characterization and assessment of diversity in Pandharpuri buffalo breed of India using heterologous microsatellite markers
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Genetic diversity analysis in indigenous rice (Oryza sativa L.) germplasm for bacterial leaf blight (Xanthomonas oryzae pv. oryzae) (BB) using resistance genes-linked markers
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Evaluation of Genetic Diversity and Population Structure Analysis among Germplasm of Agaricus bisporus by SSR Markers
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Inflorescence Transcriptome Sequencing and Development of New EST-SSR Markers in Common Buckwheat (Fagopyrum esculentum)
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Self-citation

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
ORCID: Miah, Gous
Rafii, Mohd
Ismail, 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)
DOI: 10.3390/ijms141122499
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: cc-by
creativecommons.org/licenses/by/3.0/ (vor)
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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A review of microsatellite markers and their applications in rice breeding programs to improve blast disease resistance

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