Unveiling genetic diversity, fingerprinting, phenotypic and molecular characterization of rice (Oryza sativa L.) germplasm from Northeast India using SRAP and TRAP markers

Northeast India, a part of the Indo-Burma biodiversity hotspot, harbours the richest genetic diversity reservoir for agricultural crops. The region is not only a centre of origin of rice but also a critical area where conservation of genetic diversity in crops is required. The analysis of 197 landraces/germplasm using phenotypic, genotypic and combined genotypic/phenotypic distances revealed ample genetic variation in the collections. Multivariate analysis for phenotypic variability indicated that 11 out of 13 phenotypic traits assessed were useful in discriminating the genotypes. Cluster analysis based on phenotypic data distinguished three clusters, while a corresponding analysis with SRAP and TRAP markers indicated four groups. Also, the combined analysis for the phenotypic and genotypic data provided four distinct clusters, revealing valuable information about the diversity among economically important agronomic traits. The present study also partitions the genotypes into distinct heterotic groups, thereby making it possible for parental selection and hybridization to maximize genetic diversity in the rice breeding program. Moreover, two combinations of SRAP and SRAP5 (ME01 and EM10) and SRAP6 (ME01 and EM07) with four TRAP combinations, TRAP1 (Auxr1 and FT14), TRAP2 (Auxr1 and T03), TRAP3 (Auxr1 and FT14) and TRAP5 (Auxr1 and T13) with high informative PIC score, greater than 0.70 effectively discriminated the current collections/genotypes for a robust fingerprint system.