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.
Highlights
Rice blast, which is caused by Pyricularia grisea (Cooke) Sacc., the anamorphous state of Magnaporthe grisea
An advanced backcross population of BC3F3 lines derived from the rice varieties Vandana and Moroberekan was analyzed for blast resistance by Wu et al [128], and they identified four microsatellite markers (RM21, RM168, RM215 and RM250) that were significantly associated with the resistance gene
Molecular mapping of rice populations is a prerequisite to identifying markers closely linked to the desirable Pi resistance gene
Summary
Rice blast, which is caused by Pyricularia grisea (Cooke) Sacc., the anamorphous state of Magnaporthe grisea The integration of genomics and molecular-based breeding strategies for developing disease resistance, with gene-based marker assisted selection (MAS) being effective, is a powerful method for efficient selection. The development of molecular methods to efficiently identify novel resistance genes has the potential to greatly improve modern cultivars, and such methods would help accelerate the application of MAS and marker-assisted backcross (MAB) breeding in rice improvement programs. Use of these markers should facilitate the development of multiline cultivars that carry one or more blast resistance genes, without the need for pathogenic inoculation or phenotyping. The main objectives of this review are the following: (i) to help increase the efficiency of MAS in breeding-program crosses, improving the chances of developing new lines for commercial release; (ii) to review the basic principles and characteristics of commonly used microsatellite markers; (iii) to outline the advantages and limitations of these markers; and (iv) to provide examples of how microsatellites have been used in molecular breeding programs for blast resistance
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