Identification of Variety Diagnostic Molecular Mar

Authors: S S Kshirsagar Kailash Chandra Samal Mihir Rabha Debendra Nath Bastia Gyana Ranjan Rout

Publish Date: 2013/08/11

Volume: 84, Issue: 2, Pages: 389-396

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Abstract

Twenty eight inter simple sequence repeat ISSR markers were used to determine the genotypic identification and phylogenetic relationship within 48 varieties of Indica rice including four aromatic rice grown in eastern part of India Out of 44 upland and low land varieties 39 varieties released by the Orissa University of Agriculture and Technology Orissa and five released by the other National Institutes of India A total of 28 ISSR primers were screened representing di and tri nucleotide repeats out of which 12 ISSR markers were selected for varietal analysis as diagnostic markers The number of bands per locus ranged from 4 to 8 with an average of 6 The results revealed that all the primers showed distinct polymorphism among the varieties indicating the robust nature of ISSR markers Most of the primers showed highest polymorphic information content and resolving power The cluster analysis indicates that all the rice genotypes are grouped into two classes in which aromatic rice varieties clustered separately from upland and lowland varieties Principal component analysis showed the distinct differences among themselves Based on this study the larger range of similarity values using ISSR markers provides greater confidence for the assessment of genetic relationships among the varieties The information obtained from the DNA profile helps to identify the variety diagnostic markers in 48 rice genotypes This outcome of the investigation can be used in background selections during backcross breeding programsRice Oryza sativa 2n = 24 belonging to the family Poaceae and subfamily Oryzoidea is the staple food for onethird of the world’s population and occupies almost onefifth of the total land area covered under cereals It is grown under diverse conditions and over wide geographical range Most of the world’s rice is cultivated and consumed in Asia which constitutes more than half of the global population Approximately 11  of the world’s arable land is planted annually to rice and it ranks next to wheat The world’s rice production has doubled during last 25 years largely due to the use of improved technology such as high yielding varieties and better crop management practices 1 Further scope of crop improvement depends on the availability genetic diversity and variability and use of new biotechnological tools There exists a rich diversity in rice Except for a few earlier studies on classification of germplasm using isozymes there have been a few studies to assess the diversity of Indian rice varieties including landraces at the molecular level Presently some of the varieties have gone threatened Hence their conservation and characterization is of utmost important Some of the traditional varieties are not sufficiently represented to study the genetic diversity A number of molecular markers have been used for diversity study in rice 2 3 4 Inter simple sequence repeat ISSR is a microsatellitebased multi locus marker technique which is simple and useful for estimating genetic diversity in several crop plants The technique has the advantages of random amplified polymorphic DNA RAPD and in addition shows higher level of polymorphism reproducibility and costeffectiveness per polymorphism ISSR–PCR has been used in genetic diversity studies in several crop plants In rice ISSR–PCR has been used for the analysis of micro satellite motif frequency and fingerprinting of varieties determining phylogenetic relationships among Oryza species 5 6 7 8 9 The usefulness of multi locus ISSR–PCR markers in determining diversity within improved varieties landraces of rice of Orissa has not been previously investigated The objectives of this study are i to assess the extent of genetic diversity in Indian landraces of rice as compared to improved cultivars and other accessions using ISSR primers ii to compare the level of polymorphism revealed by each primer and between landraces and varieties iii to develop a rational basis for the choice of informative primers using polymorphic information content resolving power and mean genetic similarity and iv to identify the variety diagnostic ISSR markers for rice improvement program

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