| Summary: | Drought, with its complex genetic nature possesses great challenge for resource deficient agriculture of this century. Even the climate change with its unpredictable weather pattern causes peak water scarcity. With these current challenges, genotypes with better root plasticity prove an effective way for sustainability in agriculture. Root, the ‘hidden half’ has high complexity for screening but serves as critical role for water and nutrient acquisition. Root phenomics was assessed by screening the RILs developed from Norungan and IR64 in modified transparent soil filled root box. RILs exhibiting extreme root phenome were screened under natural moisture stress condition in the field. Several candidate genes governing root development have been identified in rice. The genomic location of six candidate genes involved in root development pathway was obtained from OrygeneDB and specific microsatellites falling within and flanking these candidate genes were acquired from Gramene. Out of twenty-two microsatellites recovered and used for parental polymorphism survey, 3 microsatellites in the 3 candidate gene loci viz., OsMADS61, OsMADS23 and OsMADS27 exhibited polymorphism between IR 64 and Norungan. Association analysis of phenotypic and genotypic data indicated that all the three polymorphic markers significantly influenced the trait, maximum root length. The gene specific marker RM3558 (OsMADS61), and RM23170 (OsMADS23) also controlled the trait root volume, while the microsatellite marker, RM5789 linked to OsMADS27 had its influence on root: shoot ratio. This study identified significant candidate gene-linked microsatellites for utilization in drought tolerance breeding through marker assisted selection approach.
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