Abstract
The studies on genetic variation, diversity and population structure of rice germplasm of North East India could be an important step for improvements of abiotic and biotic stress tolerance in rice. Genetic diversity and genetic relatedness among 114 rice genotypes of North East India were assessed using genotypic data of 65 SSR markers and phenotypic data. The phenotypic diversity analysis showed the considerable variation across genotypes for root, shoot and drought tolerance traits. The principal component analysis (PCA) revealed the fresh shoot weight, root volume, dry shoot weight, fresh root weight and drought score as a major contributor to diversity. Genotyping of 114 rice genotypes using 65 SSR markers detected 147 alleles with the average polymorphic information content (PIC) value of 0.51. Population structure analysis using the Bayesian clustering model approach, distance-based neighbor-joining cluster and principal coordinate analysis using genotypic data grouped the accession into three sub-populations. Population structure analysis revealed that rice accession was moderately structured based on FST value estimates. Analysis of molecular variance (AMOVA) and pairwise FST values showed significant differentiation among all the pairs of sub-population ranging from 0.152 to 0.222 suggesting that all the three subpopulations were significantly different from each other. AMOVA revealed that most of the variation in rice accession mainly occurred among individuals. The present study suggests that diverse germplasm of NE India could be used for the improvement of root and drought tolerance in rice breeding programmes.
Highlights
Rice (Oryza sativa L.) is a primary staple food crop for more than 3.5 billion population of the world and cultivated across at least 114 countries[1]
The determination of F statistic (FST) using structure analysis for the subpopulation of the present study was 0.407 which indicated high differentiation between subpopulation because genotypes were collected from a wide range of ecology and topography
SSR based diversity analysis confirmed the existence of genetic diversity in a population of 114 rice genotypes
Summary
Rice (Oryza sativa L.) is a primary staple food crop for more than 3.5 billion population of the world and cultivated across at least 114 countries[1]. Among the various groups of rice cultivated in Assam, upland rice cultivar of North East India which is directly sown in fields during March-April and harvested in July-August is known agronomically as “aus/ahu” rice[6] These are photoperiod insensitive landraces maintained by farmers endowed with tremendous genetic variability and valuable genes for various abiotic stress tolerances as they are not subjected to selective breeding over a long period. An attempt was made to study genetic diversity in a few rice genotypes of North East India, the majority of which were agronomically identified as aus/ahu cultivars along with few indica rice. No attempt has been made to study the genetic architecture of the root traits in relation to drought tolerance using rice from North East India which necessitates the study of the diversity for such traits for supplement rice improvement works. DNA based markers such as RAPD (Random Amplified Polymorphic DNA), SSR (Simple Sequence repeat), AFLP (Amplified Fragment Length Polymorphism) and SNP (Single Nucleotide Polymorphism) have been routinely used to assess the genetic divergence among the genotypes as they are not influenced by environmental factors
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