Genomics of Root System Architecture Adaptation in Sorghum under Nitrogen and Phosphorus Deficiency

Abstract Plant root systems play a crucial role in water and nutrient uptake so understanding the genetic mechanisms underlying root architecture adaptation to the environment is key, particularly in non-model crops. Here, we investigate the diversity of root system architecture (RSA) in Sorghum bicolor under nitrogen (N) and phosphorus (P) deficiency. We used a globally diverse sorghum panel to identify single nucleotide polymorphisms (SNPs) associated RSA responses under N and P deficiency through a genome-wide association study (GWAS). RSA adaptation under P deficiency involved development of fine exploratory roots marked by increased total root length and fine root classes (root length diameter ranges 1 and2), coupled with reduced radial expansion. Under N deficiency, adaptation also involved suppression of root radial growth but without elongation. In both cases, reduced radial growth was marked by reduced surface area and volume, more dramatically for P than N deficiency. GWAS identified SNPs associated with these RSA adaptations, some of which were in regions encoding genes such as: ILR3-like, bHLH, and a LEUNIG homolog all with known roles in root growth regulation. These findings provide novel genetic insights into sorghum root adaptation to nutrient limitations and offer potential targets for breeding resource-efficient crop varieties. Summary Plants absorb water and nutrients from the soil through their roots, yet for most crops, little is known about how root shape and structure adapt to stressful conditions such as poor soil fertility. In this study, we used a globally diverse collection of sorghum genotypes to investigate how sorghum roots respond to nitrogen and phosphorus deficiency. Specific genotypes showed strong root adaptations under these conditions, leading us to identify genetic factors significantly associated with these responses. Our findings improve our understanding of root adaptation to nutrient stress and highlight promising genetic targets for breeding more nutrient-efficient crops. Competing Interest Statement The authors have declared no competing interest. Footnotes This version of the manuscript has been revised to address comments from reviewers, including clarifications in the Methods, revisions to Figures 1, 4, and 6, and updates to the supplementary data.