Eggplant (Solanum melongena L.) stands as the second highest berry-producing solanaceous crop after tomato. Under the EU G2P-SOL project (http://www.g2p-sol.eu), seven major Genebanks made available 3,412 eggplant accessions as well as cultivated and wild relatives. The accessions were genotyped using the Single Primer Enrichment Technology (SPET) and a core collection of 450 accessions was identified, then reduced to 321 S. melongena accessions, characterized by less than 5% heterozygosity and missing data, and which captures the genetic diversity of the species. The core collection was phenotyped for 46 agronomic traits across three different locations: Montanaso Lombardo (Italy), Valencia (Spain), and Antalya (Türkiye). Additionally, in Italy and Spain, 162 semi-polar metabolites present in peel and flesh of commercially ripe fruit were measured and analysed using LC-PDA-HRMS (Q-ExactiveTM). Thanks to the availability of the eggplant genome sequence we published in 2021 (https://doi.org/10.1111/tpj.15313), the core collection was resequenced at 20X, resulting in more than 51M SNPs, over 1.9M structural variations (SVs), and upwards of 14M k-mers. After filtering for quality, a genome-wide association (GWA) study was performed on 309 eggplant accessions. Quantitative trait loci (QTLs) were identified from the markers significantly associated with the traits according to the linkage disequilibrium (LD) decay of each eggplant chromosome (LD decay was 0.2-0.3Mb). Hundreds of QTLs for both agronomic and metabolic traits were identified. As an example, for fruit size and shape traits, most of the associated regions were located on chromosome 2,3,10 and 12 A synteny analysis was also carried out among tomato, eggplant and pepper, and synteny maps were generated using GENESPACE (v0.9.3). Acknowledgments: Research supported by the H2020 G2P-SOL project (no. 677379) and PRO-GRACE project (no. 101094738).
Resequencing and phenotyping of an eggplant core collection capturing its worldwide genetic variation for GWA studies
Gaccione L.;Barchi L.;Martina M.;Portis E.;Lanteri S.
2024-01-01
Abstract
Eggplant (Solanum melongena L.) stands as the second highest berry-producing solanaceous crop after tomato. Under the EU G2P-SOL project (http://www.g2p-sol.eu), seven major Genebanks made available 3,412 eggplant accessions as well as cultivated and wild relatives. The accessions were genotyped using the Single Primer Enrichment Technology (SPET) and a core collection of 450 accessions was identified, then reduced to 321 S. melongena accessions, characterized by less than 5% heterozygosity and missing data, and which captures the genetic diversity of the species. The core collection was phenotyped for 46 agronomic traits across three different locations: Montanaso Lombardo (Italy), Valencia (Spain), and Antalya (Türkiye). Additionally, in Italy and Spain, 162 semi-polar metabolites present in peel and flesh of commercially ripe fruit were measured and analysed using LC-PDA-HRMS (Q-ExactiveTM). Thanks to the availability of the eggplant genome sequence we published in 2021 (https://doi.org/10.1111/tpj.15313), the core collection was resequenced at 20X, resulting in more than 51M SNPs, over 1.9M structural variations (SVs), and upwards of 14M k-mers. After filtering for quality, a genome-wide association (GWA) study was performed on 309 eggplant accessions. Quantitative trait loci (QTLs) were identified from the markers significantly associated with the traits according to the linkage disequilibrium (LD) decay of each eggplant chromosome (LD decay was 0.2-0.3Mb). Hundreds of QTLs for both agronomic and metabolic traits were identified. As an example, for fruit size and shape traits, most of the associated regions were located on chromosome 2,3,10 and 12 A synteny analysis was also carried out among tomato, eggplant and pepper, and synteny maps were generated using GENESPACE (v0.9.3). Acknowledgments: Research supported by the H2020 G2P-SOL project (no. 677379) and PRO-GRACE project (no. 101094738).
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