MOLECULAR CHARACTERIZATION AND VALIDATION OF SSR MARKERSASSOCIATED WITH SHEATH BLIGHT TOLERANCE IN MAGIC INDICA POPULATIONOF RICE (ORYZA SATIVA L.)

Abstract

Sheath blight, caused by Rhizoctonia solani Kühn, is one of the major constraints to rice production, and its quantitative
inheritance limits the effectiveness of conventional breeding. The present study aimed to validate reported simple sequence repeat
(SSR) markers associated with sheath blight resistance and assess the genetic diversity and marker–trait associations among
selected MAGIC indica rice lines. Twenty relatively tolerant and 20 susceptible lines from Among 365 MAGIC indica lines
phenotypically screened under field conditions, together with four check varieties, were selected for molecular characterization. A
total of 136 SSR markers, including 55 sheath blight QTL linked and 81 genome wide markers, were screened, of which 9 SSR
markers (6.62%) (RM336, RM224, RM209, RM216, RM205, RM202, RM12398, RM10255 and RM11229) were polymorphic.
These markers detected 26 alleles with an average of 2.89 alleles per locus. The average major allele frequency, gene diversity,
observed heterozygosity, and polymorphic information content (PIC) were 0.665, 0.457, 0.071, and 0.390, respectively. Marker
RM336 was the most informative, exhibiting the highest gene diversity (0.63) and PIC (0.59). Allelic profiling using the resistant
checks Tetep and Wazuhophek identified several MAGIC lines carrying multiple favorable alleles associated with sheath blight
resistance, with genotypes 271, 291, 66, 313, 189, and 326 showing the highest recovery of resistant alleles. Single marker
analysis revealed significant (P < 0.01) associations between all nine polymorphic markers and sheath blight related traits. RM205
showed the strongest association, explaining up to 71.2% of the phenotypic variation for relative lesion height and 63.4% for
disease score. Neighbor joining cluster analysis grouped the 46 genotypes into three major clusters with six subclusters, indicating
moderate genetic diversity and weak population structure. Tolerant and susceptible genotypes were distributed across the same
clusters, reflecting the complex quantitative inheritance of sheath blight resistance.The validated SSR markers, particularly RM205,
RM336, RM202, RM209, and RM224, together with the identified MAGIC lines carrying favorable alleles, represent valuable
genetic resources for marker assisted breeding to develop sheath blight resistant rice cultivars.