Research Article

Assessment of genetic diversity of rice based on SNP markers for selection of parents for sheath rot (Sarocladium oryzae) resistance breeding

Published in: South African Journal of Plant and Soil
Volume 35, issue 1, 2018 , pages: 51–59
DOI: 10.1080/02571862.2017.1333636
Author(s): Simon M MvuyekureAfrican Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, South Africa, Julia SibiyaAfrican Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, South Africa, John DereraAfrican Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, South Africa, John NzungizeRwanda Agriculture Board, Rwanda, Germain NkimaRwanda Agriculture Board, Rwanda

Abstract

Sheath rot of rice, caused by Sarocladium oryzae, is an important emerging rice disease not only in Rwanda, but also in other rice-growing countries. Given that cultivar resistance is a sustainable management strategy for small-scale farmers, the aim of this study was to identify genetically distant parental materials for sheath rot resistance breeding. Ten resistant and fifteen susceptible accessions were analysed using 94 single nucleotide polymorphism (SNP) markers. The number of alleles amplified per locus ranged from 1 to 4 with a mean of 2.01 and a total of 189 alleles detected from the 25 genotypes. The number of observations per marker locus ranged from 11 to 25 with an average of 23. The mean major allele frequency was 76.2%, whereas the mean polymorphic information content was 0.263, and gene diversity was estimated at 0.325. Consequently, the markers were highly informative and revealed good estimates of genetic diversity among the studied accessions. Genetic distances ranged from 0 to 0.63 and a UPGMA dendrogram distinguished resistant and susceptible genotypes. This study revealed the possibility of improving resistance to sheath rot with minimum risk of genetic depression or reduced variability among progenies through hybridisation of locally adapted germplasm.

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