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 Solanum 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 neighbor-joining clustering revealed extensive genetic diversity driven by the unique genetic profile of the wild founder, and lack of genetic structure, suggesting a well-mixed population with a high degree of recombination. The eight founders and a core subset of 212 lines were phenotyped for above-and belowground 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 aboveground 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, an 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.

Acknowledgements

This work has been funded by grants PID2021-128148OB-I00 funded by MICIU/AEI/10.13039/501100011033/ and by ERDF/EU, PDC2022-133513-I00 funded by MICIU/AEI/10.13039/501100011033/ and European Union Next Generation EU/PRTR, CIPROM/2021/020 from Conselleria d’Educació, Cultura, Universitats i Ocupació (Generalitat Valenciana), and by the Horizon Europe programme, project number 101094738 (Promoting a Plant Genetic Resource Community for Europe; PRO-GRACE). V.B.-F. is grateful to Conselleria d’Educació, Cultura, Universitats i Ocupació (Generalitat Valenciana), for a predoctoral contract (CIACIF/2023/238). A.S. is grateful to MICIU/AEI/10.13039/501100011033/ and FSE+ for a predoctoral grant (PRE2022-102368). P.G. is grateful for the postdoctoral grant RYC2021-031999-I funded by MICIU/AEI/10.13039/501100011033 and the European Union through NextGenerationEU/PRTR.

Author contributions

M.P., S.S., J.P., S.V., and P.G. conceived the idea and supervised the manuscript. A.A. and A.S. performed the root phenotyping trials. A.A., V.B.-F., P.G., and S.V. performed the bioinformatic analysis and analyzed the data. A.A. prepared a first draft of the manuscript. All other authors reviewed and edited the manuscript.

Data availability statement

The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ncbi.nlm.nih.gov/,PRJNA392603 and PRJNA1174391.

Conflict of interests

The authors declare no conflicts of interest.

Supplementary data

Supplementary data is available at Horticulture Research online.

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