Lara Pereira, Lei Zhang, Manoj Sapkota, Alexis Ramos, Hamid Razifard, Ana L. Caicedo & Esther van der Knaap

Theoretical and Applied Genetics October 2021; vol. 134: 3363–3378

Key Message

Six novel fruit weight QTLs were identified in tomato using multiple bi-parental populations developed from ancestral accessions. Beneficial alleles at these loci arose in semi-domesticated subpopulations and were likely left behind. This study paves the way to introgress these alleles into breeding programs.

Abstract

The size and weight of edible organs have been strongly selected during crop domestication. Concurrently, human have also focused on nutritional and cultural characteristics of fruits and vegetables, at times countering selective pressures on beneficial size and weight alleles. Therefore, it is likely that novel improvement alleles for organ weight still segregate in ancestral germplasm. To date, five domestication and diversification genes affecting tomato fruit weight have been identified, yet the genetic basis for increases in weight has not been fully accounted for. We found that fruit weight increased gradually during domestication and diversification, and semi-domesticated subpopulations featured high phenotypic and nucleotide diversity. Columella and septum fruit tissues were proportionally increased, suggesting targeted selection. We developed twenty-one F₂ populations with parents fixed for the known fruit weight genes, corresponding to putative key transitions from wild to fully domesticated tomatoes. These parents also showed differences in fruit weight attributes as well as the developmental timing of size increase. A subset of populations was targeted for QTL-seq, leading to the identification of six uncloned fruit weight QTLs. Three QTLs, located on chromosomes 1, 2 and 3, were subsequently validated by progeny testing. By exploring the segregation of the known fruit weight genes and the identified QTLs, we estimated that most beneficial alleles in the newly identified loci arose in semi-domesticated subpopulations from South America and were not likely transmitted to fully domesticated landraces. Therefore, these alleles could be incorporated into breeding programs using the germplasm and genetic resources identified in this study.

See: https://link.springer.com/article/10.1007/s00122-021-03902-2

Figure 1: A. Phylogenetic tree using genome-wide fourfold-degenerate SNPs after quality filtering. Population group is represented by color and indicated at each accession. Population delimitation of three accessions (*) was manually corrected according to their physical traits and previous phylogenetic study (Razifard et al, 2020). Accessions representing diversity of SP and SLC populations (red dot at tree tip) were selected for in-depth fruit phenotyping. B. Nucleotide diversity in each population, estimated based on π and Watterson's θ in 100-kb genomic windows.