The Sorghum Lipid Database (SoLD): population-scale lipidomics linking environmental and genetic variation in the Sorghum Association Panel

Abstract

Sorghum (Sorghum bicolor) is a climate-resilient crop whose acclimation to nutrient limitation and low temperature likely involves extensive lipidome reconfiguration. Lipids are key membrane components, carbon and energy stores, and mediators of stress signaling, yet population-scale lipidomics data for sorghum are limited. We present the Sorghum Lipid Database (SoLD), a curated lipidomics resource from the Sorghum Association Panel grown under two field regimes: (i) a nutrient-sufficient with usual planting date environment (control) and (ii) a low-input treatment with reduced nitrogen and phosphorus, earlier planting, and no application of insecticides, herbicides, or pesticides (low-input). Using high-resolution LC-MS, we quantified 244 lipid species and detected broad, largely conserved compositional shifts across field trials. However, there were four major low-input-associated lipid signatures relative to control: (i) depletion of sulfoquinovosyldiacylglycerol, (ii) triacylglycerol enrichment, (iii) phospholipid redistribution centered on phosphatidylserine, and (iv) coordinated lysophospholipid remodeling, reflected in altered lysophosphatidylcholine-to-lysophosphatidylethanolamine ratios. Analyses of lipid chemical space and lipid ontology enrichment supported these compositional changes. GWAS of lipid species, class sums, and class ratios revealed recurrent, environment-specific loci. Control-associated loci were enriched for genes involved in lipid and isoprenoid metabolism, developmental regulation, and cell-wall biosynthesis and modification. Low-input-associated loci were enriched for genes involved in nutrient-stress signaling, cell-wall remodeling, defense, developmental control, and cold-related barrier formation and proteostasis. Thus, SoLD provides a framework connecting sorghum lipid diversity with environmental and genetic variation. All information regarding the database and the experiment is freely accessible through a Shiny application: https://nirwan.shinyapps.io/SAP-Lipidomics-Database/. The database enables users to move from lipid-class to individual molecular species and associated candidate loci, for hypothesis generation, comparative analyses, and prioritization of targets for functional validation.