9. Genetic relationship among aromatic short grain and Basmati rice based on ISSR and SSR markers

Directorate of Rice Research, Hyderabad 500 030

Almost every state of indica has its own set of non-basmati aromatic rice that perform well in native areas. These short and medium-grained varieties have outstanding quality traits like aroma, kernel elongation on cooking, fluffiness, and taste. Study of genetic diversity of these rices will help in as identifying distinct varieties and selection of suitable parents for breeding for quality rice. The objective of this study was to determine the genetic relationship among a set of 30 aromatic rices (22 short grain, 8 basmati) and one non- aromatic control Jaya. DNA was extracted from seedlings by miniprep method. Standard ISSR - PCR, SSR-PCR, agarose gel electrophoresis and ethidium bromide staining procedures were followed. Seven informative ISSR primers (UBC- 810, 811, 824, 834, 840, 841, 842) amplified 55 bands and six SSR primers (RM 42, 44,155, 156, 223, 586) amplified 17 alleles. A similarity matrix based on 465 pair wise comparisons of pooled data was made using NTSYS pc. The dendrogram showed

2 major clusters - a large one consisting of 20 short grain aromatic rices and a small one consisting of 8 basmati rices and Jaya (Fig. 1). Dubraj from Madhya Pradesh and Tarunbhog grouped together distinct from all other accessions at 70% similarity. The short grain aromatic varieties were reported to cluster separately from the long grained aromatic varieties with high similarity (Ray Choudhary et al. 2001). Two unique ISSR bands amplified in Tarunbhog and Amritbhog. The locus RM 42 was monomorphic. At RM 223, 3 alleles were observed. One was present in 24 accessions, one only in Tarunbhog, Amritbhog, Tilakchandan and Kalajira and one was unique to Ganjeikali. These two loci are in the chromosome 8 region linked to aroma (Ahn et al. 1992) and show polymorphism between Basmati and non-Basmati genotypes (Jain et al. 2002). RM 155 an EST based SSR primer amplified a unique allele in Nagri. RM 586 close to the waxy locus amplified a maximum of 5 alleles one unique to Jaya. The two varieties RAU 3048 and RAU 3043 could not be distinguished. Tilakchandan and Kesar were the closest. Jaya and Kasturi grouped in one cluster as also reported earlier (Nagaraju et al. 2002). Molecular markers provide a more accurate estimation of genetic diversity as compared to morphological data. Informative markers used in this study are cost effective and would be useful in fingerprinting and diversity analysis for germplasm management and rice breeding.


Ahn, S.N., C.N. Bollich and S.D. Tanksley, 1992. RFLP tagging of a gene for aroma in rice. Theor. Appl. Genet. 84: 825-828.

Jain, N., N. Saini, P. Rana, S. Jain and R.K. Jain, 2002. Microsatellite diversity for chromosome number 8 in Basmati rice. RGN 19: 103-105.

Nagaraju, J., M. Kathirvel, R. Ramesh Kumar, E.A. Siddiq and S.E. Hasnain, 2002. Genetic analysis of traditional and evolved Basmati and non-Basmati rice varieties by using fluorescence based ISSR-PCR and SSR markers. Proc. Natl. Acad. Sci. USA 99a: 5836-5841.

Ray Choudhury, P., S. Kohli, K. Srinivasan, T. Mohapatra and R.P. Sharma, 2001. Identification and classification of aromatic rices based on DNA fingerprinting. Euphytica 118: 243-251.