Abstract
Environmental conditions play an important role in the emergence of genetic variations in natural populations. We identified genome-wide patterns of nucleotide variations in the coding regions of natural Arabidopsis thaliana populations. These populations originated from 700 m to 3400 m a.m.s.l. in the Western Himalaya. Using a pooled RNA-Seq approach, we identified the local and global level population-specific SNPs. The biological functions of the SNP-containing genes were primarily related to the high light intensity prevalent at high-altitude regions. The novel SNPs identified in these genes might have arisen de novo in these populations. In another approach, the FSTs of SNP-containing genes were correlated with the corresponding climatic factors. ‘Radiation in the growing season’ was the only environmental factor found to be strongly correlated with the gene-level FSTs. In both the approaches, the high light intensity was identified as the primary abiotic stress associated with the variations in these populations. The differential gene expression analysis between field and controlled condition grown plants also showed high light intensity as the primary abiotic stress, particularly for the high altitude populations. Our results provide a genome-wide perspective of nucleotide variations in populations along altitudinal gradient and their putative role in emergence of these variations.
Highlights
Environmental conditions play an important role in the emergence of genetic variations in natural populations
We report genome-wide polymorphisms in the coding region of West Himalayan Arabidopsis thaliana populations and their associations with the climatic variables of their natural habitat
Westram et al.[10] showed that pooled RNA-Seq is reliable for variant allele frequency estimation, given a large number of individuals are included in the pool
Summary
Environmental conditions play an important role in the emergence of genetic variations in natural populations. We identified genome-wide patterns of nucleotide variations in the coding regions of natural Arabidopsis thaliana populations. ‘Radiation in the growing season’ was the only environmental factor found to be strongly correlated with the gene-level FSTs In both the approaches, the high light intensity was identified as the primary abiotic stress associated with the variations in these populations. It aims at integrating the genomic changes with the environmental conditions to which an organism is exposed[1] This environment-driven selection is one of the most important factors behind population differentiation which functions by imposing variable selection pressure among the populations of climatically different regions. The correlations between FSTs and environmental variables is recently being applied to identify signatures of natural selection[3,4] The advantage of this approach is that it leads to a more straightforward evidence of selection in response to the local climate. Selection may act on SNPs in non-coding regions such as promoters, enhancers or small RNAs where they affect gene expression
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