SSR marker based molecular diversity among advanced breeding lines of Katarni rice (Oryza sativa. L.) and validation of phenotypic selection through functional markers

Abstract Like Basmati, Katarni is a traditional aromatic rice cultivar grown primarily in its geographical indicated areas i.e. Bhagalpur, Banka and Munger districts of Bihar, India. However, known for exquisite grain quality characteristics, it suffers from lodging problem, and is very late maturing leading tolow productivity, constant decrease in acreage and farmer preference. Introgression of the semi-dwarfing gene ( sd1 ) in Katarni was performed through marker assisted backcross breeding and advanced to obtain the homogeneous population. The derived lines were analyzed for the presence of genes for semi-dwarfism ( sd1 ), aroma ( badh2 ), flowering date ( Hd3a ) and kernel length ( GS3 ) using functional markers. Improved lines of Katarni rice were found positive for sd1 gene in PCR and most of the entries simultaneously contained genes for short grain type, thus implicating the applicability of these markers in marker-assisted backcross breeding. Twenty three advanced breeding lines of Katarni were phenotypically evaluated for target traits viz ., plant height, days to 50% flowering, grain length, grain width and leaf aroma through sensory test alongwith their parental checks. Molecular profiling of the entries was carried out to develop DNA fingerprint using 81 SSR markers which were found to be highly informative and capable of distinguishing between genotypes. The PIC value was highest for marker RM15189 and RM182. The genetic distance detected through UPGMA clustering indicated five distinct groups, and maximum degree of similarity was observed between lines namely, ASGL11 and ASGL12 followed by ASGL9 and ASGL11. Except Hd3A , the molecular profiling through functional markers were also in congruity with the morphological data.