Resequencing and phenotyping of the first highly inbred eggplant multiparent population reveal SmLBD13 as a key gene associated with root morphology

Abstract

The MEGGIC (Magic EGGplant InCanum) population here presented is the first highly inbred eggplant (Solanum melongena) multiparent advanced generation intercross (MAGIC) population developed so far, derived from seven cultivated accessions and one wild S. incanum from arid regions. The final 325 S5 lines were high-throughput genotyped using low-coverage whole-genome sequencing (lcWGS) at 3X, yielding 293,783 high-quality SNPs after stringent filtering. Principal component analysis (PCA) and neighbour-joining clustering revealed extensive genetic diversity, lack of genetic structure, and the distinct genetic profile of the wild founder. The eight founders and a core subset of 212 lines were phenotyped for above- and below-ground traits, revealing wide phenotypic diversity. Root morphology traits displayed moderate heritability values, and strong correlation were found between root and aerial traits, suggesting that a well-developed root system supports greater above-ground growth. Genome-wide association studies (GWAS) identified a genomic region on chromosome 6 associated with root biomass (RB), total root length (RL), and root surface area (SA). Within this region, SmLBD13, a LOB-domain protein involved in lateral root development, was identified as a candidate gene. The S. incanum haplotype in this region was linked to reduced lateral root branching density, a trait that may enhance deeper soil exploration and resource uptake. These findings provide key insights into root genetics in eggplant, demonstrating MEGGIC potential for high-resolution trait mapping. Furthermore, they highlight the role of exotic wild germplasm in breeding more resilient cultivars and rootstocks with improved root architecture and enhanced nutrient uptake efficiency.