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Epistatic QTL for yield heterosis in tomato

Cite this dataset

Zamir, Dani; Torgeman, Shai (2022). Epistatic QTL for yield heterosis in tomato [Dataset]. Dryad.


Controlled population development and genome-wide association studies have proven powerful in uncovering genes and alleles underlying complex traits. An underexplored dimension of such studies is the phenotypic contribution of non-additive interactions between quantitative trait loci (QTL). Capturing such epistasis in a genome-wide manner requires very large populations to represent replicated combinations of loci whose interactions determine phenotypic outcomes. Here, we dissect epistasis using a densely genotyped population of 1400 backcross-inbred lines (BILs) between a modern processing tomato inbred (Solanum lycopersicum) and the Lost Accession of a distant, green-fruited, drought-tolerant wild species, Solanum pennellii. The homozygous BILs, each representing an average of 11 introgressions, and their hybrids with the recurrent parents were phenotyped for tomato yield components. Population-wide mean yield of the BILs was less than 50% of that of their hybrids (BILH), and correspondingly, homozygous introgressions across the genome reduced yield relative to recurrent parent while several QTL of the BILHs independently improved productivity. Analysis of two QTL scans showed 32 cases of less than additive and 48 cases of more than additive interactions. Strikingly, one epistatic interaction involving S. pennellii QTL on chromosomes 1 and 7, which independently did not affect yield, increased fruit yield by 20-50% in the double introgression hybrid grown in irrigated and dry fields over a period of three years and varied genetic backgrounds. Our work demonstrates the power of large, interspecific controlled population development to uncover hidden QTL phenotypes, and how rare epistatic interactions can improve crop productivity via heterosis.


Fruits of all the genotypes were harvested when 95-100% of the tomatoes were red (105-115 days after transplanting). The following measurements were taken for each of the plants: Plant weight (PW kg) of the vegetative part, average fruit weight (FW g) calculated from a random sample of 10 red fruits per plants, total soluble solids concentration (Brix) of the fruit (Bx%) assayed on the same 10 red fruits, and total fresh yield per plant (TY) (including both red and green fruits if there were any).

Usage notes

R software


Israel Science Foundation, Award: 2365/20

European Commission, Award: 677379

European Commission, Award: 727929

European Commission, Award: 101000716