Multiplex SSR-PCR approaches for semi-automated genotyping and characterization of loci linked to blast disease resistance genes in rice

Sadegh Ashkani; Mohd Yusop Rafii; Mahmoodreza Shabanimofrad; Majid Foroughi; Parisa Azizia; Mohd Sayeed Akhtar; Mahbod Sahebi; Abd Rahim Harun; Abbas Nasehi

doi:10.1016/j.crvi.2015.07.007

Multiplex SSR-PCR approaches for semi-automated genotyping and characterization of loci linked to blast disease resistance genes in rice

C R Biol. 2015 Nov;338(11):709-22. doi: 10.1016/j.crvi.2015.07.007. Epub 2015 Aug 28.

Authors

Sadegh Ashkani¹, Mohd Yusop Rafii², Mahmoodreza Shabanimofrad³, Majid Foroughi³, Parisa Azizia⁴, Mohd Sayeed Akhtar⁵, Mahbod Sahebi⁵, Abd Rahim Harun⁶, Abbas Nasehi⁷

Affiliations

¹ Laboratory of Food Crops, Institute of Tropical Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Department of Agronomy and Plant Breeding, Yadegar-e-Imam Khomeini RAH Shahre-Rey Branch, Islamic Azad University, Tehran, Iran. Electronic address: ashkani.sadegh@upm.edu.my.
² Laboratory of Food Crops, Institute of Tropical Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia. Electronic address: mrafii@upm.edu.my.
³ Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.
⁴ Laboratory of Food Crops, Institute of Tropical Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
⁵ Laboratory of Plantation Crops, Institute of Tropical Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
⁶ Agrotechnology and Bioscience Division, Malaysian Nuclear Agency, Bangi, Kajang, Selangor, Malaysia.
⁷ Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.

PMID: 26318048
DOI: 10.1016/j.crvi.2015.07.007

Abstract

In the present study, 63 polymorphic microsatellite markers related to rice blast resistance genes were fluorescently labelled at the 5'-end with either 6-FAM or HEX using the G5 dye set and incorporated into a multiplex SSR-PCR for the detection of fragments using an automated system. For rice F3 families obtained from crosses between Pongsu Seribu 2 (Malaysian blast resistant cultivar) and Mahsuri (a susceptible rice cultivar), the genotypes for 13 designated multiplex SSR panels were determined. The genotyping assays were performed using a capillary-based ABIPRISM 3100 genetic analyser. The sizes of the SSRs alleles observed in the range from 79 to 324 bp. The observed marker segregation data were analysed using the Chi(2) test. A genetic linkage map covering ten chromosomes and comprising 63 polymorphic SSR markers was constructed, and the distorted loci were localised to linkage groups. The results indicated that distorted loci are presented on eight chromosomes.

Keywords: Capillary electrophoresis; Fluorescent-labelled; Linkage map construction; Multiplex PCR; Rice (Oryza sativa L.); Rice blast (Magnaporthe oryzae); SSR genotyping; Segregation distortion analysis.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Disease Resistance / genetics*
Genes, Plant / genetics
Genetic Linkage
Genotype
Malaysia
Microsatellite Repeats
Oryza / genetics*
Plant Diseases / genetics*
Polymerase Chain Reaction / methods*
Polymorphism, Genetic