Deep and shallow root ideotypes confer differential adaptation to single and combined nitrogen and phosphorus deficiency in eggplant MAGIC lines

Abstract

Increasing crop yields has traditionally relied on over-fertilization, mainly with nitrogen (N) and phosphorus (P). To move towards sustainability, breeding for optimized root system architecture (RSA) is crucial for adaptation to low inputs. Leveraging genomic information from a 325-line eggplant multiparent advanced generation intercross (MAGIC) population and root phenotyping data from a previously characterized subset of 212 lines under standard conditions, we applied genomic prediction models to identify genotypes with contrasting deep and shallow root ideotypes. Integration of 293,783 high-quality SNPs with the phenotypic training set enabled the selection of 12 promising lines. These lines were assessed at seedling stage for both above- and below-ground performance under single and combined N and P deprivation (–N, –P, and –NP) to understand root strategies for resilience. General trends showed that –N was associated with chlorosis and deeper root systems (increasing by 92.3% compared to the control), while –P exhibited the most detrimental effect on overall plant performance (aerial biomass average reduction of 78.3% relative to the control). Strikingly, a combined –NP deficiency appeared to induce a more stable physiological state, with overall performance comparable to –N alone. The analysis of the top-performing lines revealed unique strategies mainly driven by lateral root density and root depth plasticity or stability to mitigate negative impacts on aerial growth performance. Importantly, these results demonstrate that genomic prediction can effectively identify root ideotypes with functional relevance. The selected lines represent valuable genetic resources for breeding and hold potential as rootstocks, capable of thriving in nutrient-deficient environments.