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

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.

SUBMITTER: Miah G

PROVIDER: S-EPMC3856076 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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

Miah Gous G Rafii Mohd Y MY Ismail Mohd R MR Puteh Adam B AB Rahim Harun A HA Islam Kh Nurul KhN Latif Mohammad Abdul MA

International journal of molecular sciences 20131114 11

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 geno ...[more]

PMID: 24240810

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Project description:Utilization of rice blast-resistance (R) genes is the most economical and environmentally friendly method to control blast disease. However, rice varieties with R genes influence the outcome of genetic architectures of Magnaporthe oryzae (M. oryzae), and mutations in avirulence (AVR) genes of M. oryzae may cause dysfunction of the corresponding R genes in rice varieties. Although monitoring and characterizing rice R genes and pathogen AVR genes in field populations may facilitate the implementation of effective R genes, little is known about the changes of R genes over time and their ultimate impact on pathogen AVR genes. In this study, 117 main cultivated rice varieties over the past five decades and 35 M. oryzae isolates collected from those diseased plants were analyzed by PCR using gene-specific markers of the nine R genes and six primer pairs targeting the coding sequence or promoter of AVR genes, respectively. The R genes Pigm, Pi9, Pi2, Piz-t, Pi-ta, Pik, Pi1, Pikp, and Pikm were identified in 5, 0, 1, 4, 18, 0, 2, 1, and 0 cultivars, respectively. Significantly, none of these R genes had significant changes that correlated to their application periods of time. Among the four identified AVR genes, AVR-Pik had the highest amplification frequency (97.14%) followed by AVR-Pita (51.43%) and AVR-Pi9 (48.57%); AVR-Piz-t had the lowest frequency (28.57%). All these AVR genes except AVR-Pi9 had 1-2 variants. Inoculation mono-genic lines contained functional genes of Pi2/9 and Pik loci with 14 representative isolates from those 35 ones revealed that the presence of certain AVR-Piz-t, AVR-Pita variants, and AVR-Pik-E + AVR-Pik-D in M. oryzae populations, and these variants negated the ability of the corresponding R genes to confer resistance. Importantly, Pi2, Pi9, and Pigm conferred broad-spectrum resistance to these local isolates. These findings reveal that the complex genetic basis of M. oryzae and some effective blast R genes should be considered in future rice blast-resistance breeding programs.

Project description:Resilience is the capacity of an animal to be minimally affected by disturbances or to rapidly return to the state pertained before exposure to a disturbance. However, indicators for general resilience to environmental disturbances have not yet been defined, and perhaps therefore resilience is not yet included in breeding goals. The current developments on big data collection give opportunities to determine new resilience indicators based on longitudinal data, which can aid to incorporate resilience in animal breeding goals. The objectives of this paper were: (1) to define resilience indicator traits based on big data, (2) to define economic values for resilience, and (3) to show the potential to improve resilience of livestock through inclusion of resilience in breeding goals. Resilience might be measured based on deviations from expected production levels over a period of time. Suitable resilience indicators could be the variance of deviations, the autocorrelation of deviations, the skewness of deviations, and the slope of a reaction norm. These (new) resilience indicators provide opportunity to include resilience in breeding programs. Economic values of resilience indicators in the selection index can be calculated based on reduced costs due to labor and treatments. For example, when labor time is restricted, the economic value of resilience increases with an increasing number of animals per farm, and can become as large as the economic value of production. This shows the importance of including resilience in breeding goals. Two scenarios were described to show the additional benefit of including resilience in breeding programs. These examples showed that it is hard to improve resilience with only production traits in the selection index, but that it is possible to greatly improve resilience by including resilience indicators in the selection index. However, when health-related traits are already present in the selection index, the effect is smaller. Nevertheless, inclusion of resilience indicators in the selection index increases the response in the breeding goal and resilience, which results in less labor-demanding, and thus easier-to-manage livestock. Current developments on massive collection of data, and new phenotypes based on these data, offer exciting opportunities to breed for improved resilience of livestock.

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

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