Morpho-molecular and nutritional profiling for yield improvement and value addition of indigenous aromatic Joha rice of Assam

Short-grain aromatic Joha rice of Assam is a unique class of specialty rice having tremendous potential in domestic and international markets. The poor yielding ability of Assam's Joha rice demands its systematic characterization for an effective breeding program. This study investigates the morphological, molecular and biochemical profiles of twenty popular Joha (aromatic) rice cultivars indigenous to Assam. Distinctiveness, Uniformity and Stability (DUS) characterization of the cultivars revealed polymorphism in thirty-seven traits, establishing distinctiveness for their utilization in breeding programs. Unweighted Neighbor Joining (UNJ) clustering based on usual Euclidean distances for the polymorphic morphological markers grouped the cultivars into three clusters with eight, eleven, and one genotypes. The Joha rice cultivars showed significant differences for all the quantitative traits except for panicle length. The genotypic and phenotypic coefficients of variability (GCV & PCV) were high for grain yield ha −1 (24.62 & 24.85%) and filled grains panicle −1 (23.69 & 25.02%). Mahalanobis D 2 analysis revealed three multi-genotypic and four mono-genotypic clusters of the cultivars. The first five principal components explain 85.87% of the variation among the cultivars for the traits under study; filled grain panicle −1 (0.91) and stem thickness (0.55) positively contributed to the first PC. The cultivars' average polyunsaturated fatty acids were 37.9% oleic acid, 39.22% linoleic acid, and 0.5% linolenic acid. Kon Joha 4 and Ronga Joha contained the highest iron (82.88 mg kg −1 ) and zinc (47.39 mg kg −1 ), respectively. Kalijeera , Kunkuni Joha , Kon Joha-5 , Manimuni Joha and Kon Joha-2 accorded a strong aroma. PCR amplified 174 alleles with a mean value 2.64 across the 66 polymorphic SSR markers. PIC values ranged from 0.091 to 0.698, with an average of 0.326. The highly informative (PIC > 0.50) markers were RM316, RM283, RM585, RM1388, RM3562, RM171, R1M30, RM118, RM11and RM29 for identification of the twenty aromatic rice cultivars. PCR amplification of 27 SSR markers identified 28 unique alleles (97–362 bp) in 13 Joha rice cultivars, which can help their identification/DNA fingerprinting. The UNJ clustering based on Jaccard's coefficients classified the cultivars into three distinct clusters with eight, ten, and two genotypes. Our study revealed the nutritional richness of these specialty Joha rice cultivars and sufficient scope for yield enhancement through their interbreeding to keep quality intact.