Geospatial Paradigm of Nucleotide Substitution within the Gene Family Encoding Plasma Membrane H+-ATPase Pumps in Arabidopsis thaliana

Abstract

The PM H+-ATPase gene family consists of 12 members in Arabidopsis thaliana denoted to Auto-inhibited H+-ATPase 1-12 (AHA1-AHA12). This gene family performs crucial roles in many aspects of plant growth and development such as ion and metabolite transportation, pollen development, stomatal opening, signalling process, and adaptation to abiotic stresses especially thermal changes. The H+-ATPase action dynamically fluctuates during thermal changes in order to enhance adaptation strategies in plants. Based on the fact that surface temperature on average is typically warmer in lower latitudes and cooler in higher latitudes, the association of PM H+-ATPase genetic variants (SNPs) with latitude intervals was studied using chi-square testing of 1001 Genomes project data. The results indicated a significant association between nucleotide substitution and latitude interval, and therefore a geospatial paradigm of PM H+-ATPase nucleotide substitution was established. A>T and T>A substitutions showed a close positive association with higher latitudes (cold climate) and negative association with lower latitudes (warm climate), and vice versa for A>G. Most of the nucleotide substitutions were associated with extreme cold and warm climates while cold climate had more impact. The most significant signal of PM H+-ATPase genes strategy for adaptation to cold climate was A>T nucleotide substitution. Also, the results showed that the most high-impact SNPs were identified in coding regions and related to premature stop codons.