Identification of microsatellite markers linked to grain discoloration disease in rice genotypes

Rice grain discoloration disease is emerging as a major threat in improved and late ripening varieties in the north of Iran that deteriorates grain quality and physical properties. Breeding for disease resistance is the preferred strategy to manage grain discoloration. An important application of molecular markers in plant systems involves improvement in the efficiency of conventional plant breeding by carrying out indirect selection through molecular markers linked to the traits of interest. In this context, association analysis was used to identify molecular markers associated with grain discoloration resistance in rice genotypes in this study. 

In this study, resistance of 94 rice genotypes (Iranian landrace and improved varieties and exotic genotypes) to grain discoloration disease was evaluated during 2017 and 2018.Genotyping was done using 128 pairs of polymorphic microsatellite markers on 94 genotypes of rice. Then association analysis was conducted through general linear model (GLM) and mixed linear model (MLM) by using TASSEL software.

Phenotypic analysis showed that there is high diversity in the studied genotypes for resistance to grain discoloration disease. The model-based structure analysis classified rice genotypes into two sub-populations. In association analysis based on GLM and MLM models, 12 and 3 QTLs showed significant relations after considering Bonferroni correction with grain discoloration in two years, respectively.

Both GLM and MLM detected 3 markers (RM242, RM5709 and RM5955) associated with grain discoloration resistance in both 2017 and 2018, suggesting that these markers can be used in rice breeding programs like marker-assisted selection (MAS).