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Background  Population differentiation and their adaptation to a particular environment depend on their ability to respond to a new environment. This, in turn is governed to an extent, by the degree of phenotypic plasticity exhibited by the populations. The populations of same species inhabiting different climatic conditions may differ in their phenotypic plasticity. Himalayan populations of  Arabidopsis thaliana  originating from a steep altitude are exposed to different climatic conditions ranging from sub-tropical to temperate. Thus they might have experienced different selection pressures during evolution and may respond differently under common environmental condition.    Results  Phenotypic plasticity and differentiation of natural populations of  A. thaliana  grown under common garden and controlled conditions were determined. A total of seventeen morphological traits, their plasticity, association between traits and environment were performed using 45 accessions from three populations. Plants from different altitudes differed in phenotypes, their selection and fitness under two conditions. Under both the conditions lower altitude population was characterized by higher leaf count and larger silique than higher and middle altitude population. Flowering time of high altitude population increased while that of low and medium altitude decreased under controlled condition compared to open field. An increase in seed weight and germination was observed for all the population under open field than controlled. Rosette area was under divergent selection in both the condition. The heritability of lower altitude population was the highest under both the conditions, where as it was the least for higher altitude population further indicating that the high altitude populations are more responsive towards phenotypic changes under new environmental conditions. Ninety-nine percent of variability in traits and their plasticity co-varied with the altitude of their origin. The population of high altitude was more plastic and differentiated as compared to the lower altitude one.    Conclusions    Arabidopsis thaliana  population native to different altitudes of the west Himalaya responds differently when grown under common environments. The success of high altitude population is more in common garden than the controlled conditions. The significant variability in phenotype and its association with altitude of origin predicts for non-random genetic differentiation among the populations.    Electronic supplementary material  The online version of this article (10.1186/s12898-017-0149-5) contains supplementary material, which is available to authorized users.

High altitude population of Arabidopsis thaliana is more plastic and adaptive under common garden than controlled condition