Elemental profiling and genome-wide association mapping reveal genomic variants modulating ionomic composition in Populus trichocarpa leaves

The ionome represents elemental composition in plant tissues and can be an indicator of nutrient status as well as overall plant performance. Thus, identifying genetic determinants governing elemental uptake and storage is an important goal in plant breeding and engineering. In this study, we coupled high-throughput ionome characterization with high-resolution genome-wide association studies (GWAS) to uncover genetic loci that modulate ionomic composition in leaves of 584 black cottonwood poplar (Populus trichocarpa) genotypes. Congruence of alternate ionomic profiling platforms, i.e., inductively coupled plasma-mass spectrometry (ICP-MS), neutron activation analysis (NAA) and laser-induced breakdown spectroscopy (LIBS), was performed on leaf samples from a subset of the population. Significant agreement was observed across the three platforms with some notable exceptions for individual elements. Subsequently, we used the ICP-MS platform to profile the 584 genotypes focusing on 20 elements. GWAS performed using a set of high-density (>8.2 million) single nucleotide polymorphisms (SNP), identified multiple loci significantly associated with variations in these mineral elements. The potential causal genes for variations in the ionome were significantly enriched in genes whose homologs were previously associated to ion homeostasis in other species. Notably, a polymorphic copy of the high-affinity molybdenum transporter MOT1 was found directly associated to molybdenum content in leaf tissues. The results of the GWAS also provided evidence of physiological and genetic interactions between mineral elements in poplar. The new candidate genes predicted to play a key role in cross-homeostasis of multiple elements are new targets for engineering a variety of traits of interest in tree species.