Molecular identification of blast resistance genes in rice genotypes using gene-specific markers

Molecular identification of major blast resistance (R) genes in rice was performed in a group of 10 rice (Oryza sativa) genotypes from Egypt and Saudi Arabia using six DNA markers (T8042, NSB, YL153/YL154, RM3843, RM3330, and z4794) belonging to three classes: single-nucleotide polymorphisms (SNPs), simple sequence repeats (SSRs), and insertion-deletions (InDels). The markers were chosen based on their linkage to six major R genes (Pit, Pib, Pi39 (t), Pi40 (t), Piz/Piz-t, and Pita /Pita2 ). The studied markers showed low allelic diversity, with the number of alleles identified in a single genotype ranging between two and nine alleles. The Egyptian genotype Eg-N-7 had two alleles of the Pi40 (t) gene, while the Saudi Arabian genotype Al-Ahsa1 had nine alleles that belonged to the seven R genes. The studied genotypes were also assessed for 19 agro-morphological traits. Analysis of variance of the studied traits showed significant differences among the genotypes. The putative associations between molecular markers and the agro-morphological traits were examined using associationmapping approach by employing the unified mixed model. Eight significant marker–trait associations were detected for eight agro-morphological traits (plant height, panicle length, sterility percentage, grain width, grain shape, elongation percentage, gelatinization temperature, and days to maturity). The phenotypic variance shown by each marker ranged between 43% and 65%. The findings of the current study will assist in identifying possible blast resistance genotypes for future rice breeding programs. Additionally, the results highlight the possible dual usage of specific markers in genotypic screening as well as in determining marker–trait associations.