Genome-wide association studies reveal genetic basis of ionomic variation in cassava

Elemental profiling and genome-wide association studies 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 for breeding and engineering biomass feedstocks with improved performance. In this study, we coupled high-throughput ionome characterization of leaf tissues with high-resolution genome-wide association studies (GWAS) to uncover genetic loci that modulate ionomic composition in leaves of poplar (Populus trichocarpa). Significant agreement was observed across the three ionomic profiling platforms tested: inductively coupled plasma-mass spectrometry (ICP-MS), neutron activation analysis (NAA) and laser-induced breakdown spectroscopy (LIBS). Relative quantification of 20 elements using ICP-MS across a population of 584 genotypes, revealed larger variation in micro-nutrients and trace elements content than for macro-nutrients across genotypes. The GWAS performed using a set of high-density (>8.2 million) single nucleotide polymorphisms, identified over 600 loci significantly associated with variations in these mineral elements, pointing to numerous uncharacterized candidate genes. A significant enrichment for genes related to ion homeostasis and transport was observed, including several members of the cation-proton antiporters (CPA) family and MATE efflux transporters, previously reported to be critical for plant growth and fitness in other species. Our results also included a polymorphic copy of the high-affinity molybdenum transporter MOT1 found directly associated to molybdenum content. For the first time in a perennial plant, our results provide evidence of genetic control of mineral content in a model tree species.

Ionome of Lithuanian Populations of Purple Loosestrife (Lythrum salicaria) and Its Relation to Genetic Diversity and Environmental Variables

Fifteen riparian populations of Lithuanian Lythrum salicaria were assessed for leaf macronutrient, micronutrient and non-essential element concentrations and compared to the former obtained molecular data at amplified fragment length polymorphism (PLP.AFLP) loci. Inductively coupled plasma mass spectrometry was used to profile the contents of 12 elements in the leaves. The leaf nutrient concentrations were within normal ranges for growth and development and heavy metal concentrations did not reach toxic levels. The concentrations of macroelements such as nitrogen, potassium, calcium and magnesium were in the range of 23,790–38,183; 7327–11,732; 7018–12,306; and 1377–3183 µg/g dry mass (d. m.), respectively; the concentrations of micronutrients such as sodium, iron, zinc and copper varied in the ranges of 536–6328; 24.7–167.1; 10.88–26.24; and 3.72–5.30 µg/g d. m., respectively, and the concentrations of non-essential elements such as lead, nickel, chromium, and cadmium were in the intervals of 0.136–0.940; 0.353–0.783; 0.207–0.467; and 0.012–0.028 µg/g d. m., respectively. When comparing the maximum and minimum values for site elements of L. salicaria, the concentration of N varied by 1.6, K—1.6, Ca—1.8, Mg—2.3, Na—6.1, Fe—6.8, Zn—2.4, Cu—1.5, Pb—6.9, Ni—2.2, Cr—2.2, and Cd—2.3 times. The coefficient of variation (CV) of element concentrations in sites was moderate to large: N—15.4%, K—14.3%, Ca—18.6%, Mg—24.8%, Na—50.7%, Fe—47.0%, Zn—24.9%, Cu—14.5%, Pb—57.1%, Ni—30.11%, Cr—26.0%, and Cd—38.6%. Lythrum salicaria populations growing near regulated riverbeds were characterized by significantly (p < 0.05) lower concentrations of Ca and Mg, and significantly (p < 0.05) higher concentrations of N, K, Fe, Na, Ni, Cr and Cd. The PLP.AFLP was negatively correlated with concentrations of N, Na, Fe, Ni, Cr, and Cd. The L. salicaria population with the lowest leaf N and Na concentration showed the highest genetic polymorphism (PLP.AFLP = 65.4%), while the least polymorphic population (PLP.AFLP = 35.0%) did not show extreme concentrations of either element. In conclusion, our elemental analysis of L. salicaria populations showed that ionomic parameters are related to genomic parameters, and some habitat differences are reflected in the ionomes of the populations.