Genetic diversity and population structure of Arabidopsis thaliana along an altitudinal gradient

Antariksh Tyagi; Shivani Singh; Parneeta Mishra; Akanksha Singh; Abhinandan Mani Tripathi; Satya Narayan Jena; Sribash Roy

doi:10.1093/aobpla/plv145

Genetic diversity and population structure of Arabidopsis thaliana along an altitudinal gradient

AoB Plants. 2015 Dec 15:8:plv145. doi: 10.1093/aobpla/plv145.

Authors

Antariksh Tyagi¹, Shivani Singh², Parneeta Mishra², Akanksha Singh², Abhinandan Mani Tripathi², Satya Narayan Jena¹, Sribash Roy³

Affiliations

¹ Genetics and Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow 226001, Uttar Pradesh, India.
² Genetics and Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow 226001, Uttar Pradesh, India Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110 001, India.
³ Genetics and Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow 226001, Uttar Pradesh, India Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110 001, India Present address: CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India sribashroy@nbri.res.in.

Abstract

The natural genetic variation within a plant species is primarily a consequence of its phylogeography and evolutionary history. This variation largely determines its present-day population structure. Arabidopsis thaliana, as a model plant, has been studied in great detail including its probable origin, local as well as global genetic diversity pattern, population structure, adaptation, etc. However, no such studies have so far been reported from the Indian Himalayan region. Here, we describe a comprehensive study on the genetic diversity and population structure of A. thaliana from an altitudinal range of 700-3400 m above mean sea level the highest altitudinal range reported so far. We also compare these populations with previously reported worldwide populations. A total of 48 accessions representing six populations were analysed using 19 microsatellites and 11 chloroplast markers. Genetic diversity analysis indicated populations to be highly diverse and comparable with worldwide populations. STRUCTURE, principal coordinate and isolation by distance (IBD) analyses showed that genetic variation in different populations is structured at geographical and altitudinal level. Further analyses indicate that these populations are genetically distinct from the rest of the world populations. Different parameters of the demographic expansion model support a rapid expansion. Based on mismatch distribution, the initial time of expansion of west Himalayan populations was found to be about 130 000 years. Bayesian analysis of divergence time indicated that these populations have a long evolutionary history in this region. Based on the results of genetic diversity parameters, demographic expansion and divergence time estimation, it appears that west Himalayan populations may be the source of the west-east expansion model.

Keywords: Chloroplast loci; Indian Arabidopsis; evolution; genetic diversity; microsatellite markers; phylogeography; population structure.

Published by Oxford University Press on behalf of the Annals of Botany Company.