Genetic diversity analysis of indigenous rice varieties in Kerala using molecular markers

Abstract

The present study entitled “Genetic diversity analysis of indigenous rice varieties in Kerala using molecular markers “was carried out in the Department of Plant Breeding and Genetics, College of Agriculture, Vellayani, Thiruvananthapuram during 2017-2018. The study was conducted with the objective to analyze the genetic diversity of traditional rice varieties in four agro climatic zones of Kerala using RAPD and SSR markers. Five varieties were collected from the each agro climatic zones viz., hill areas of Wayanad, rice growing tract of Palakkad, saline soils of Pokkali and Kuttanad soils. The DNA was isolated and RAPD analysis with 10 Operon primers and SSR analysis was done with ten RM primers. In the RAPD analysis the ten operon primers produced 88 amplicons with an average polymorphism 82%. Resolving power OPC-07 (15.4) had the highest value but its Polymorphism Information Content and Effective Multiplication Ratio (EMR) were considerably low. Considering all the three parameters together primer OPF-06 is found to be the best RAPD primer with considerably high polymorphism information content, resolving power and effective multiplication ratio. The dendrogram constructed based on the RAPD scoring showed that varieties Pokkali and VTL-2 had maximum similarity. These two were from Pokkali rice tract. PTB 12 from Pattambi was found to be unique and it clustered with others only at 30% similarity.The clustering of the genotypes did not show any correlation with the geographic origin. ABL 12 and VTL- 2 showed 70 % similarity but those two were from Wayanad Hills and Pokkali tract respectively. Vellakuttadan from Moncombu clustered with PTB 2 from pattambi at 72% a similarity. Kochuvith and Vellakuttadan from Moncombu clustered at 67 %. All the SSR markers produced two alleles except RM 210 and RM 204 which produced four alleles and one allele respectively. All the alleles of all the markers were polymorphic except that of primer RM204. The polymorphism information content of the SSR primers used in the study ranged from 0 to 0.88. In this study the highest PIC value of 0.88 was reported by RM 210 followed by RM 567 (0.85). The resolving power and EMR was also highest for RM 210. The dendrogram constructed based on the SSR markers could give a clustering of genotypes more correlated with the geographic origin. Genotypes Kochuvithu and

Vellakuttadan showed 100 % similarity both where from Kuttanad. But Karavalakochuvith, T.virippu, and PTB 2 also showed 100% similarity but these three were from Moncompu, Pokkali and Palakkad respectively. At around 90 % similarity AMB 14, AMB 22 from Wayanad, Pokkali andVTL-2 from Pokkali, PTB 13 and PTB 8 from Palakkad clustered showing more correlation to the Geographic origin. SSR markers being sequence specific and flanking the repeat sequence which has more role in evolution, are more reliable in predicting the Genetic diversity based on origin. Since both of them could not give a clear-cut clustering based on geographic origin an analysis using both the markers together was done. This gave a better picture of the clustering as it involved more number of variables. But here also the varieties from Wayanad A1 to A5 were scattered in different clusters. Only A 14 and A15 (AMB 14 and AMB 5) clustered at 60 percentage similarity. The accessions from moncompu (A6-A10) clustered at around 50 % similarity. In the accession from Pokkali tract (A11-A15) only T.virippu to VTL-2 clustered at 78 % similarity. Accession from central zone Pattambi (A16-A20) was scattered into different clusters. PTB 12 was unique from other accessions. This molecular diversity analysis of the traditional rice genotypes from four different agro climatic zones could find that the maximum similarity was 78% and that too only between two accessions. The diversity among the genotypes was 64% as all the genotypes clustered at 36% similarity. The clustering of the genotypes did not show any correlation with the geographic origin. Exchange of varieties between the farmers and some amount of natural crossing would have led to the mixture of populations of rice genotypes in different agro climatic zones.