A Review of Microsatellite Markers and Their Applications in Rice Breeding Programs to Improve Blast Disease Resistance

Miah, Gous; Rafii, Mohd Y.; Ismail, Mohd Razi; Puteh, Adam; Harun, Abdul Rahim; Islam, Kamrul; Latif, Abdul

doi:10.3390/ijms141122499

Cited by 203 publications

(124 citation statements)

References 142 publications

(148 reference statements)

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“…STRs are important causative agents of human diseases (Pearson et al 2005;Castel et al 2010) and are useful genetic markers (Wright and Bentzen 1994;Gupta and Varshney 2000;Miah et al 2013;Abdul-Muneer 2014), but their genotyping with NGS technology is a challenge. To overcome this, we developed STR-FM, a versatile STR profiling method that is applicable to a wide range of STR lengths and motifs.…”

Section: Discussionmentioning

confidence: 99%

Accurate typing of short tandem repeats from genome-wide sequencing data and its applications

et al. 2015

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Short tandem repeats (STRs) are implicated in dozens of human genetic diseases and contribute significantly to genome variation and instability. Yet profiling STRs from short-read sequencing data is challenging because of their high sequencing error rates. Here, we developed STR-FM, short tandem repeat profiling using flank-based mapping, a computational pipeline that can detect the full spectrum of STR alleles from short-read data, can adapt to emerging read-mapping algorithms, and can be applied to heterogeneous genetic samples (e.g., tumors, viruses, and genomes of organelles). We used STR-FM to study STR error rates and patterns in publicly available human and in-house generated ultradeep plasmid sequencing data sets. We discovered that STRs sequenced with a PCR-free protocol have up to ninefold fewer errors than those sequenced with a PCR-containing protocol. We constructed an error correction model for genotyping STRs that can distinguish heterozygous alleles containing STRs with consecutive repeat numbers. Applying our model and pipeline to Illumina sequencing data with 100-bp reads, we could confidently genotype several disease-related long trinucleotide STRs. Utilizing this pipeline, for the first time we determined the genome-wide STR germline mutation rate from a deeply sequenced human pedigree. Additionally, we built a tool that recommends minimal sequencing depth for accurate STR genotyping, depending on repeat length and sequencing read length. The required read depth increases with STR length and is lower for a PCRfree protocol. This suite of tools addresses the pressing challenges surrounding STR genotyping, and thus is of wide interest to researchers investigating disease-related STRs and STR evolution.

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Section: Discussionmentioning

confidence: 99%

Accurate typing of short tandem repeats from genome-wide sequencing data and its applications

et al. 2015

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“…Usually, DNA markers are used for tracking blast resistance genes in genetically diversified rice materials. Among the various class of DNA markers, SSRs (also called microsatellite) markers are highly polymorphic, widespread in the genome and with high allelic diversity (Miah et al 2013). SSR markers have been widely applied to analyze the genetic diversity (Cho et al 2000), to locate genes and quantitative trait loci (QTLs) on rice chromosomes (Zou et al 2000;Bres-Patry et al 2001;Moncada et al 2001).…”

Section: Introductionmentioning

confidence: 99%

Identification of suitable segregating SSR markers for blast resistance in rice using inheritance and disease reaction analysis in backcross families

Tanweer

Rafii

Sijam

et al. 2015

Australasian Plant Pathol.

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The study was conducted to identify the suitable SSR markers in relation to blast disease of rice. Backcross breeding was applied and BC 2 F 1 generation was produced using rice variety Pongsu Seribu 2 as blast resistant parent and MR219 as susceptible parent. Eleven SSR markers related to blast resistance genes (Pi gene) were found highly polymorphic between the parental lines. According to single-gene model only two markers, RM208 and RM206, fitted to the expected test cross ratio (1:1) in BC 2 F 1 generation with the relation to resistant and susceptible plants. Further BC 2 F 1 population carrying 320 plants were inoculated with the highly virulent pathotype P7.2 of Magnaporthe oryze. Chi-square (χ2) test for single-gene model showed goodness of fit (p=0.45) to the expected segregation ratio (1:1) for phenotypic segregation in BC 2 F 1 population. In marker segregation analysis two markers RM208 (χ2=1.513, p=0.218) and RM206 (χ2=0.613, P=0.433) clearly produced goodness of fit to the expected test cross ratio (1:1) for the single-gene model. The present finding could help the rice breeders to monitor the blast resistance genes with appropriate and highly segregating SSR markers in rice varietal development program against blast disease.

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“…In addition, breeding programs require markers for marker-assisted selection. Cost efficiencies of markers in breeding programs have been estimated for some crops and proved to be very efficient when integrated at the right generation into the breeding program Kuchel et al, 2005;Miah et al, 2013;Morris et al, 2003;Slater et al, 2013). Progeny 12 (13.386 T x 26.1074 D) was used in this first assessment of SSR markers for marker-assisted selection in the NIFOR breeding program.…”

Section: Ssr Analyses In Progeny 12 (Nifor)mentioning

confidence: 99%

Assessment of an oil palm population from Nigerian Institute for Oil Palm Research (NIFOR) for simple sequence repeat (SSR) marker application

Ihase¹,

Horn²,

Anoliefo³

et al. 2014

Afr. J. Biotechnol.

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Oil palm (Elaeis guineensis Jacq.), a monocotyledonous plant belonging to the Arecaceae family, is one of the most important oil crops in the world. In Nigeria, oil palm has benefited immensely from conventional breeding efforts resulting in high yields that have been achieved with this breeding material. However, oil palm breeding is slow and time-consuming due to a breeding cycle of about 10 years. In addition, the process of outcrossing leads to high variation in yield components and vegetative traits. Although DNA marker technologies offer great possibilities for plant breeding through markerassisted selection, there are so far no reports of its application to oil palm breeding in Nigeria. In this study, 32 SSR markers were used for the assessment of marker application in an oil palm breeding population coming from the extensive breeding program at the Nigerian Institute for Oil Palm Research (NIFOR). Seven SSR markers out of the 32 tested (22%) segregated in the progeny 12 (tenera x Deli dura). SSR markers mEgCIR0059, mEgCIR1917, mEgCIR3260, mEgCIR3275, mEgCIR3533 and mEgCIR3557 proved to be fully informative markers following a segregation ratio of 1:1:1:1, while marker mEgCIR0074 segregated in a 1:1 ratio.

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A Review of Microsatellite Markers and Their Applications in Rice Breeding Programs to Improve Blast Disease Resistance

Cited by 203 publications

References 142 publications

Accurate typing of short tandem repeats from genome-wide sequencing data and its applications

Accurate typing of short tandem repeats from genome-wide sequencing data and its applications

Identification of suitable segregating SSR markers for blast resistance in rice using inheritance and disease reaction analysis in backcross families

Assessment of an oil palm population from Nigerian Institute for Oil Palm Research (NIFOR) for simple sequence repeat (SSR) marker application

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