Low-cost high-resolution genotyping assay for detecting multiple biotic stress resistance genes in rice (Oryza sativa)

Document Type

Article

Publication Date

1-1-2021

Abstract

Improving rice, a major crop that feeds more than half of the world's population, has become increasingly important in enhancing food security in a rapidly changing climate. Global warming is known to exacerbate the negative effects of biotic stresses in rice, notably bacterial leaf blight (BLB), sheath blight (SB), and blast caused by the pathogens Xanthomonas oryzae, Rhizoctonia solani, and Magnoporthe oryzae, respectively. Over the last few decades, gel and capillary-based electrophoresis have been among the most commonly used techniques for screening rice genotypes for biotic stresses. However, contradictory findings from past studies have resulted in an inconclusive comparison of these techniques, including their cost and effectiveness in genotyping rice diseases in the developing world. The present study sought to identify the suitable allele-specific markers for multiplex genotyping of gene variants associated with BLB, SB, and blast, and to compare the cost and feasibility between gel and capillary electrophoresis-based genotyping methods. Using NCBI databases, 32 allele-specific markers were identified and used to screen 14 selected rice genotypes with varying levels of BLB, SB, and blast resistance. Both gel and capillary electrophoresis were used to analyse the amplification products, and the results were validated through sequencing. While capillary electrophoresis provided greater discriminatory power, we found that high-resolution gel agarose electrophoresis was less expensive and more practical for simultaneous screening of BLB, SB, and blast resistance gene variants in rice varieties. The low-cost yet high-resolution genotyping assay developed in this study is particularly useful for large-scale genotyping in laboratories with limited resources.

Publication Source (Journal or Book title)

Plant OMICS

First Page

57

Last Page

63

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