| Summary: | Abstract One hypothesis for the origin of endemic species of tomato on the Galápagos islands postulates a hybridization of Solanum pimpinellifolium and Solanum habrochaites. Solanum galapagense accession LA1141 has purple fruit pigmentation, previously described in green‐fruited wild tomatoes such as S. habrochaites or Solanum chilense. Characterization of LA1141 derived purple pigmentation provides a test of the hybridization hypothesis. Purple pigmentation was recovered in progenies derived from LA1141, and the anthocyanins malvidin 3(coumaroyl)rutinoside‐5‐glucoside, petunidin 3‐(coumaroyl) rutinoside‐5‐glucoside, and petunidin 3‐(caffeoyl)rutinoside‐5‐glucoside were abundant. Fruit color was evaluated in an introgression population, and three quantitative trait loci (QTLs) were mapped and validated in subsequent populations. The loci atroviolacium on chromosome 7, Anthocyanin fruit on chromosome 10, and uniform ripening also on chromosome 10 underly these QTLs. Sequence analysis suggested that the LA1141 alleles of Aft and atv are unique relative to those previously described from S. chilense accession LA0458 and Solanum cheesmaniae accession LA0434, respectively. Phylogenetic analysis of the LA1141 Aft genomic sequence did not support a green‐fruited origin, and the locus clustered with members of the red‐fruited tomato clade. The LA1141 allele of Aft is not the result of an ancient introgression from the green‐fruited clade and underlies a gain of anthocyanin pigmentation in the red‐fruited clade.
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