Molecular Diversity Analysis for Zinc Deficiency Tolerance under Aerobic Rice (Oryza sativa L.) Ecosystem

Rice (Oryza sativa L.) is the “Global Grain” because of its use as prime staple food in about 100 countries of the world. Aerobic rice provides for effective use of water as the concept of flooding paddy fields is abandoned in this ecosystem. But due to the transition from flooding of paddy fields to aerobic system of rice cultivation many factors that determine nutrient (Zn) bioavailability changes in addition to water deficit. Achieving higher yields under aerobic conditions requires new varieties of “aerobic rice” combining both the water stress tolerance and nutrient (especially Zn) deficiency tolerance traits. Molecular marker technologies are the effective tools and they are used for the assessment of genetic variability because they are not influenced by the environment. Among the molecular markers, Simple Sequence Repeat (SSR) has proved to be the most powerful tool for variety identification in rice and has much potential in genetic and breeding studies. Among the 16 SSR markers specific to zinc deficiency tolerance used for assessing the genetic diversity, 13 primer pairs (81.25%) were polymorphic. The number of alleles per microsatellite locus ranged from 2 to 5, averaging 2.53 alleles per locus. Polymorphism information content (PIC) values ranged from 0.43 (RM242) to 0.69 (RM1089 and RM3331), with an average of 0.58. The Unweighted Pair Group Method with Arithmetic Mean (UPGMA) dendrogram revealed two major groups with three clusters and the wide range of dissimilarity values (0.68–1.00) which showed a high degree of diversity among the germplasm lines. The results of the genetic diversity will be useful for the selection of the parents for developing zinc deficiency tolerant rice variety under aerobic condition through molecular breeding programme.