121 POJ 6(2):121-127 (2013) ISSN:1836-3644 Wild rices of Eastern Indo-Gangetic plains of India constitute two sub-populations harbouring rich genetic diversity Aparajita Singh 1 , Balwant Singh 2 , Kabita Panda 2 , Ved Prakash Rai 1 , Anil Kumar Singh 1 , Sheo Pratap Singh 1 , Sandeep Kumar Chouhan 1 , Vandna Rai 2 , Pawan Kumar Singh 1* , Nagendra K. Singh 2 1 Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi221005, India 2 National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi 110 012, India *Corresponding author: pksbhu@gmail.com Abstract Analysis of variability and genetic structure of wild rice populations is important for the management and conservation of the valuable genetic resources. To better understand the relationships among wild rice accessions, we analyzed a subset of germplasm collected from the eastern Indo-Gangetic plains of Uttar Pradesh and Bihar. Thirty-five wild rice accessions were characterized for fourteen morphological traits and genotyped using 25 genome wide SSR markers. The accessions showed significant phenotypic variation for all the traits analyzed. Analysis of SSR markers revealed average 2.4 alleles per locus with PIC values ranging from 0.51 to 0.90 with an average of 0.79. Cluster analysis and principal component analysis clearly demarcated the wild rice accessions into two main groups representing Oryza rufipogon and Oryza nivara. The high level of genetic diversity found in wild rices of this region suggests that it is a valuable resource that should be conserved for utilization in rice breeding programs. Keywords: Wild rice, Genetic diversity, SSR markers, Morphological traits, Eastern Indo-Gangetic plains. Abbreviations: IGP_Indo-Gangetic plains, PCA_Principal component analysis, PIC_Polymorphism information content. Introduction The genus Oryza consists of twenty two wild and two cultivated species (O. sativa and O. glaberrima). Asian cultivated rice O. sativa (2n = 24) is the world’s most important food crop and is primary food source for more than one third of the world’s population. Rice accounts for 35 to 60% of the calories consumed by 3 billion Asians (Khush, 2005). To meet the future demands of food for ever increasing population, there is an urgent need to enhance the productivity of this crop that seems to have reached a plateau (Khush , 2003) due to a narrow genetic base of the modern rice cultivars. It is essential to search for the new traits and genes in the wild rice germplasm and landraces of rice to combat this problem. Although there are many sources of natural variation, wild relatives of cultivated crop species are increasingly recognized as a valuable repository of useful allelic variation for crop improvement. Wild species of rice are reservoir of many useful genes but a vast majority of these genes remain untapped because it is often difficult to identify and transfer these genes into cultivated indica rice. Historically, wild rice species have provided many valuable traits such as disease and pest resistance and cytoplasmic male sterility (Brar and Khush, 1997). O. rufipogon Griff. and O. nivara Sharma et Shastry are the most closely related species to Asian cultivated rice (O. sativa) and are considered its progenitors (Oka, 1988; Khush, 1997). The geographic range of O. sativa and O. rufipogon overlap throughout Asia. O. rufipogon further evolved and formed a complex which includes O. nivara and O. rufipogon. O. rufipogon is perennial, photoperiod sensitive, largely cross-fertilized, and widely distributed in South and Southeast Asia, Southern China, Papua New Guinea and Northern Australia. It grows in areas with year round water, such as swamps and lakes. In contrast, O. nivara is an annual, photoperiod insensitive and predominantly self-fertilized species which is believed to have evolved from O. rufipogon because of habitat shift. This species is restricted to South and mainland Southeast Asia and adapted to seasonally dry habitat (Vaughan and Morishima, 2003; Sang and Ge, 2007). Because of their important role in providing beneficial genes for rice breeding O. rufipogon and O. nivara have long been the subject of extensive taxonomic, phylogenetic and population studies using a variety of approaches (Khush, 1997; Vaughan et al., 2003). The two species are cross compatible and exhibit narrow genetic differentiation (Oka, 1988; Lu et al., 2002; Zhu et al., 2007). Consequently, O. rufipogon and O. nivara have sometimes been treated as two different ecotypes of the same species (Oka, 1988; Cheng et al., 2003;Vaughan and Morishima, 2003). Indian subcontinent can be divided broadly into three main geographical regions: the Himalayas in the far north, the Indo–Gangetic Plain in the north-central area and the southern Peninsula. The Indo-Gangetic plain (IGP) is one of the most intensively farmed zones of the world and is crucial for the food security (Thakur and Pandey, 2009). The eastern IGP is endowed with a great diversity of wild rice growing in its natural habitats. In recent years, a considerable amount of information about the genetic structure within and among natural populations of O. rufipogon and O. nivara has been obtained (Kuroda et al., 2007; Zhou et al., 2008), but O. rufipogon and O. nivara germplasm present in eastern IGP is not well characterized. Recently, a large number of wild rice germplasm were collected from the major rice growing areas of eastern IGP of