Population Genetics of Traditionally Cultivated Rice Varieties in the Eastern Himalayan Region of Northeast India

The Eastern Himalayan region of northeast(NE) India covers a geographical area of over 255,000 sq. km. and consists of Arunachal Pradesh, Assam, Manipur, Meghalaya, Mizoram, Nagaland and Tripura states (Figure 1.1). This region encompasses wide range of eco-geographical conditions, ranging from lowland flood plains of Brhamaputra and Barak Riverto mountains as high as 4000 m above sea level in the West Kameng and Tawang region of Arunachal Pradesh. Rice (Oryza sativa) is the staple food of the local inhabitants in NE India. Traditional farmers of the region cultivate a large number of indigenous rice varieties under diverse topographic and agroclimatic conditions and different growing seasons. However, rice genetic resources in NE India are being rapidly lost due to changes in the land use and agricultural practices that favor agronomically improved varieties. A detailed understanding of the genetic structure and diversity of rice varieties in NE India is crucial for developing conservation and management strategies of rice genetic resources and use of the rice gene pool in the region for breeding and genetic improvement programs. In this study, genetic structure and diversity of rice varieties representing several ecotypes collected from various regions of NE India were investigated using molecular tools. Chapter 1 covers a study focused on the genetic structure and diversity of 24 indigenous varieties representing Sali (12), Jum (4), Boro(3), and glutinous (5) types and five agronomically improved varieties. The results revealed that the genetic diversity among indigenous rice varieties was higher than that of the agronomically improved varieties. The Sali and Jum types showed significantly higher levels of genetic diversity as compared to agronomically improved types. Two major genetically distinct clusters were detected in this study, which corresponded to two subspecies of O. sativa, namely indica and japonica. In Chapter 2, the results of a study on characterization of rice ecotypes into japonica or indica subspecies using insertion-deletion (indel) markers are presented. The indel markers were designed based on the genome-wide DNA polymorphism database of typical indica cv 93-11 and japonica cv Nipponbare. The result showed that the traditional method of indica and japonica rice classification based on cultivation type, morphological traits, physiological and biochemical characteristics is incongruent with the indel marker based classification. Majority of the upland (Jum) and glutinous seeded varieties, which were traditionally classified as japonica clustered with indica types. Similarly, a few lowland varieties, which were traditionally classified as indica clustered with japonica types. Chapter 3 covers the nucleotide polymorphism and patterns of nucleotide diversity at two trait specific genes, Wx and OsC1. The Wx gene is associated with amylose content, which determines the glutinous nature of rice grains while theOsC1 gene is associated with the apiculus coloration. The polymorphism in the Wx gene among glutinous and non glutinous grain types, and the nucleotide diversity inthe OsC1 gene among colored and colorless apiculus rice varieties were investigated. The results revealed that trait specific nucleotide polymorphisms that were identified in previous studies did not necessarily correspond to the specific phenotypes in the indigenous rice varieties of NE India. The glutinous type varieties showed higher levels of nucleotide diversity as compared to the nonglutinous types at the Wx locus. The neutrality analysis did not reveal signature of selection among the glutinous and nonglutinous rice phenotypes at the Wx gene. On the other hand, the OsC1 gene revealed low level of selection among the colorless apiculus varieties as evident by lower nucleotide diversity in colorless types as compared to the colored apiculus varieties.