Nuclear and Chloroplast DNA Variation Provides Insights into Population Structure and Multiple Origin of Native Aromatic Rices of Odisha, India.

Pritesh Sundar Roy,Sudipta Jena,Nitiprasad Namdeorao Jambhulkar,Srigopal Sharma,Sasank Sekhar Chyau Patnaik,Trilochan Mohapatra,Rashmita Samal,Gundimeda Jwala Narasimha Rao,Ashok Patnaik,Manoj Prasad

doi:10.1371/journal.pone.0162268

Abstract

A large number of short grain aromatic rice suited to the agro-climatic conditions and local preferences are grown in niche areas of different parts of India and their diversity is evolved over centuries as a result of selection by traditional farmers. Systematic characterization of these specialty rices has not been attempted. An effort was made to characterize 126 aromatic short grain rice landraces, collected from 19 different districts in the State of Odisha, from eastern India. High level of variation for grain quality and agronomic traits among these aromatic rices was observed and genotypes having desirable phenotypic traits like erect flag leaf, thick culm, compact and dense panicles, short plant stature, early duration, superior yield and grain quality traits were identified. A total of 24 SSR markers corresponding to the hyper variable regions of rice chromosomes were used to understand the genetic diversity and to establish the genetic relationship among the aromatic short grain rice landraces at nuclear genome level. SSR analysis of 126 genotypes from Odisha and 10 genotypes from other states revealed 110 alleles with an average of 4.583 and the Nei’s genetic diversity value (He) was in the range of 0.034–0.880 revealing two sub-populations SP 1 (membership percentage-27.1%) and SP 2 (72.9%). At the organelle genomic level for the C/A repeats in PS1D sequence of chloroplasts, eight different plastid sub types and 33 haplotypes were detected. The japonica (Nipponbare) subtype (6C7A) was detected in 100 genotypes followed by O. rufipogon (KF428978) subtype (6C6A) in 13 genotypes while indica (93–11) sub type (8C8A) was seen in 14 genotypes. The tree constructed based on haplotypes suggests that short grain aromatic landraces might have independent origin of these plastid subtypes. Notably a wide range of diversity was observed among these landraces cultivated in different parts confined to the State of Odisha.

Highlights

Rice (Oryza sativa L.), the staple food crop of world, is the primary source of living for Asians
Correlation analysis between grain quality and agronomic traits of the short grain aromatic rice landraces showed that grain yield was significantly (r = 0.269ÃÃ) correlated to ear
The aromatic short grain rices characterized in the present study showed a high range of variability for various agronomic and quality traits, like plant height, duration, yield, kernel length and breadth, water uptake, alkali spreading value and amylose content

Summary

Introduction

Rice (Oryza sativa L.), the staple food crop of world, is the primary source of living for Asians. Long grain Basmatis are highly popular at global level. Apart from these, many indigenous short grain landraces with wide diversity accumulated over thousands of years of natural and artificial selection [3,4] are of preference in their niche areas for speciality preparations. Aromatic short grain rice varieties have been cultivated throughout India with most of them on a small scale in their niche areas, for religious purposes, festivals, entertaining guests and daily use and many of the states have their own distinct set of short grain aromatic rices. The erosion of these valuable resources post-green revolution is of concern from the point of germplasm asset

Methods

Results

Discussion

Conclusion