# The worldwide population structure of over 3,400 eggplant accessions identified by SPET genotyping

Lorenzo Barchi, Ezio Portis, Sergio Lanteri, David Alonso, Maria Josè Díez, Jaime Prohens, Véronique Lefebvre, Jeremy Salinier, Hatice Filiz Boyaci, Laura Toppino, et al.

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Lorenzo Barchi, Ezio Portis, Sergio Lanteri, David Alonso, Maria Josè Díez, et al.. The world-wide population structure of over 3,400 eggplant accessions identified by SPET genotyping. XVII SOLANACEAE2022 International Conference on the Plant Family of Solanaceae, Nov 2022, THES-SALONIKI, Greece. hal-04133464

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Submitted on 19 Jun 2023

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ORAL PRESENTATIONS

The worldwide population structure of over 3,400 eggplant accessions identified by SPET genotyping.

Lorenzo Barchi1, Ezio Portis1, Sergio Lanteri1, David Alonso2, Maria Josè Díez2, Jaime Prohens2, Veronique Lefebvre3, Jeremy Salinier3, Hatice Filiz Boyaci4, Laura Toppino5, Giuseppe Leonardo Rotino6, M. Timothy Rabanus-Wallace6, Andreas Boerner6, Nils Stein6,7, Richard Finkers8, Matthijs Brouwer9, Arnaud G. Bovy9, Roland Schafleitner10, Giuseppe Aprea11 and Giovanni Giuliano11

1 DISAFA, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy

2 Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana COMAVUPV,
València, Spain

3 INRAE, GAFL, Montfavet, France

4 Bati Akdeniz Agricultural Research Institute (BATEM), Antalya, Türkiye

5 CREA-GB, Montanaso Lombardo, Italy

6 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany,

7 Center for Integrated Breeding Research, Georg-August-University Göttingen, Göttingen, Germany

8 Gennovation B.V., Wageningen, Netherlands

9 Wageningen University & Research, Plant Breeding, Wageningen, The Netherlands

10 World Vegetable Center, Tainan, Taiwan

11 ENEA, Rome, Italy

G2P-SOL (http://www.g2p-sol.eu) is an EU-funded project, bringing together the main European and international genebanks hosting germplasm of the four major Solanaceous crops: potato, tomato, pepper and eggplant. Within the project, about 5,900 eggplant accessions, including wild relatives of the crop, were inventoried. To provide genomic information on around 3,500 representative accessions, a custom set of 5K SPET probes (single primer enrichment technology, TECAN) was designed targeting SNPs evenly distributed all over the genome but mainly in gene-rich regions. After library preparation, Illumina sequencing and quality filtering, reads were aligned to the eggplant reference genome (version 4.1) using BWA-MEM and SNP calling was performed using GATK4.1.9. By removing accessions with low coverage sequencing data, 3,412 were retained and 120K polymorphic sites identified by applying stringent filtering criteria. Among them, 4,306 were SNPs targeted by the 5K probe set, while the remaining were accessory off-target SNPs. The identified SNPs provided information for identifying putative mislabeled accessions (i.e., wrong species assignment), and duplicates within and between genebanks. Moreover, they are exploitable for setting up screening protocols to avoid the acquisition of duplications by ex-situ maintainers. 34 The population structure and genetic relationships of the eggplant accessions were investigated to build up a core collection for GWAS. Furthermore, based on historical phenotypic data available in genebanks, loci associated with key agronomic traits were identified. Our results demonstrate that SPET technology represents a valid alternative to random complexity reduction methods and arrays, proving a suitable tool for the high-throughput genotyping, management, and enhancement of genebank collections.
Key words: Solanum melongena, diversity, SPET

Acknowledgment: This work was supported by the European Commission, Horizon 2020 G2P-SOL project (grant agreement no. 677379). G2P-SOL project.