Genetic dissection of a Solanum elaeagnifolium tertiary genepool introgression associated with 4-O-caffeoylquinic acid accumulation in eggplant

Caffeoylquinic acids (CQAs) are the major phenolic compounds in eggplant (Solanum melongena) fruit, with 5-O-caffeoylquinic acid (5-CQA; chlorogenic acid) as the predominant isomer, while crop wild relatives may offer novel variation for diversifying these profiles. Previous work detected a distinct phenolic acid profile in S. elaeagnifolium, a tertiary genepool wild relative of eggplant, and in advanced backcross materials carrying introgressions from this species. This profile was characterized by a secondary chromatographic peak eluting after 5-CQA, but the identity of this compound and the associated chromosome 1 region remained unresolved. Here, we combined HPLC-MS-based metabolite identification, fine mapping, and comparative microsynteny analysis to characterize this phenotype. The secondary peak was identified as 4-O-caffeoylquinic acid (4-CQA). Fine mapping across three consecutive selfing generations, involving 612 screened individuals and 21 informative recombinants, reduced the associated interval from 2.753 Mb to 0.211 Mb, delimiting a region containing 30 annotated genes. The 4-CQA peak was detected in both homozygous and heterozygous introgression-derived materials, consistent with dominant control of the trait. Structural comparison of the fine-mapped interval revealed broad conservation between S. melongena and S. elaeagnifolium, but also identified a localized structurally divergent block potentially underlying the secondary 4-CQA peak. Within this block, the S. elaeagnifolium interval harbors acetylajmalan esterase-like/GDSL-type genes and a transcript-supported putative novel donor-specific gene. Overall, this study highlights S. elaeagnifolium introgressions as a promising source of phenolic diversification and providing markers to facilitate the development of eggplant lines with a more diverse CQA profile and potentially enhanced functional quality.