SNP Marker Based Genetic Diversity and Population Structure Study of Rice Germplasm of Arunachal Pradesh

Rice genetic resource is the primary source for rice breeding. It also makes a concrete contribution to global wealth creation and food security. India is one of the centers of origin for rice and the nutritional security of the North-Eastern (NE) states of India predominantly depends on rice. The NE region especially Arunachal Pradesh is considered to be one of the hot pockets of rice genetic resources in the world and also has diverse rice growing conditions as compared to other parts of the country. Genetic diversity of 662 rice accessions originating from the state of Arunachal Pradesh was assessed using 36 single nucleotide polymorphism (SNP) markers distributed across all 12 chromosome of rice genome. These SNP markers generated a total of 36 allelic combinations. Polymorphic Information content (PIC) ranged from 0.006 to 0.375 and major allele frequency ranged from 0.51 to 0.99. Similarly, heterozygosity and gene diversity ranged from 0.003 to 0.162 and 0.006 to 0.49, respectively. A picture of genetic relatedness was inferred using Neighbor joining tree, which grouped all the genotypes in to three major clusters. AMOVA analysis showed that, among population 31% whereas, among individual 51% diversity. Population structure from K=1 to K=20 were tested and Δk was found maximum at three population (K=3). Principal Coordinate Analysis (PCoA) showed that rice germplasm were intermixed as per Neighbour joining tree but showed three major groups based three population structure information. Hence, PCoA supports the population obtained from the model based approach. This study shows that large diversity exists in the rice germplasm of Arunachal Pradesh and can be utilized for trait-specific breeding.