Assessment of genetic diversity in F2 rice seed population of a cross between Tulaipanji and Ranjit using morphological, physicochemical and SSR markers

Tulaipanji rice (Oryza sativa L.) variety is a region specific traditional cultivar of North Dinajpur district (West Bengal). It is low yielding (1.8th) cultivar due to their poor harvest index and other genetic factors such as tendency to lodging and susceptibility to foliar diseases such as blast and bacterial blight, tungro virus etc. Tulaipanji Basmati aromatic and people prefer it due to its soft fluffy grain quality with mild fragrance and easy to digest. Hence it has high demand in the market and costs Rs. 80/kg. Demand gap can be fulfilled by developing a new improved variety of Tulipanji combining its grain quality attributes with high yield potential genes/QTLs and resistance to diseases. Hybridization was made (during kharif season 2011) between Tulaipanji and Ranjit (HYV) for the introgression of short stature, high yielding responsible genes/QTLs from Ranjit to Tulaipanji for its improvement. F2 seeds population were collected and analysed based on morphological and physicochemical parameters for their genetic variability and screening. Genetic diversity among the Fl plants and parental lines were analysed using microsatellite based SSR primer in PCR amplification. SSR markers in relation to disease resistance gene/QTL such as Xa21, Pita440 and Pib sub 3-5 were used to screen the breeding lines. Xa21specific amplified band was observed in cultivar Ranjit (HYV) which was located on chromosome 6 (resistance gene/QTL for bacterial blight) and accordingly introgressed into one of the line of F1 plants (Tulaipanji x Ranjit). There was no gene/QTL specific band was amplified for SSR marker of Pi440 and Pib sub 3-5 in the parental or Fl lines for blast resistance. Grain quality QTL specific markers such as Waxy, Sbe 2 and RM225 were employed to screen the F1 and parental lines for apparent amylose content (ACC). Apparent amylose content (ACC) was 22% in Tulaipanji and 25% in Ranjit and F2 seed showed in between 22 and 25% amylose. Breeding lines showing desired traits in relation to disease resistance and quality traits can be used for the development of improved Tulaipanji rice of North Dinajpur through marker assisted selection (MAS) using SSR markers