Leveraging GWAS data to identify metabolic pathways and networks involved in maize lipid biosynthesis

Maize (Zea mays mays) oil is a rich source of polyunsaturated fatty acids (FAs) and energy, making it a valuable resource for human food, animal feed, and bio‐energy. Although this trait has been studied via conventional genome‐wide association study (GWAS), the single nucleotide polymorphism (SNP)‐trait associations generated by GWAS may miss the underlying associations when traits are based on many genes, each with small effects that can be overshadowed by genetic background and environmental variation. Detecting these SNPs statistically is also limited by the levels set for false discovery rate. A complementary pathways analysis that emphasizes the cumulative aspects of SNP‐trait associations, rather than just the significance of single SNPs, was performed to understand the balance of lipid metabolism, conversion, and catabolism in this study. This pathway analysis indicated that acyl‐lipid pathways, including biosynthesis of wax esters, sphingolipids, phospholipids and flavonoids, along with FA and triacylglycerol (TAG) biosynthesis, were important for increasing oil and FA content. The allelic variation found among the genes involved in many degradation pathways, and many biosynthesis pathways leading from FAs and carbon partitioning pathways, was critical for determining final FA content, changing FA ratios and, ultimately, to final oil content. The pathways and pathway networks identified in this study, and especially the acyl‐lipid associated pathways identified beyond what had been found with GWAS alone, provide a real opportunity to precisely and efficiently manipulate high‐oil maize genetic improvement.     

Chloride as a macronutrient increases water‐use efficiency by anatomically driven reduced stomatal conductance and increased mesophyll diffusion to CO2

Chloride (Cl^?) has been recently described as a beneficial macronutrient, playing specific roles in promoting plant growth and water‐use efficiency (WUE). However, it is still unclear how Cl^? could be beneficial, especially in comparison with nitrate (NO₃^?), an essential source of nitrogen that shares with Cl^? similar physical and osmotic properties, as well as common transport mechanisms. In tobacco plants, macronutrient levels of Cl^? specifically reduce stomatal conductance (g_s) without a concomitant reduction in the net photosynthesis rate (A_N). As stomata‐mediated water loss through transpiration is inherent in the need of C₃ plants to capture CO₂, simultaneous increase in photosynthesis and WUE is of great relevance to achieve a sustainable increase in C₃ crop productivity. Our results showed that Cl^?‐mediated stimulation of larger leaf cells leads to a reduction in stomatal density, which in turn reduces g_s and water consumption. Conversely, Cl^? improves mesophyll diffusion conductance to CO₂ (g_m) and photosynthetic performance due to a higher surface area of chloroplasts exposed to the intercellular airspace of mesophyll cells, possibly as a consequence of the stimulation of chloroplast biogenesis. A key finding of this study is the simultaneous improvement of A_N and WUE due to macronutrient Cl^? nutrition. This work identifies relevant and specific functions in which Cl^? participates as a beneficial macronutrient for higher plants, uncovering a sustainable approach to improve crop yield.