An integrated genomic and biochemical approach to investigate the potentiality of heirloom tomatoes: Breeding resources for food quality and sustainable agriculture

Abstract

A revival of interest in traditional varieties reflects the change in consumer preferences and the greater awareness of the quality of locally grown products. As ancient cultivars, heirlooms have been selected for decades in specific habitats and represent nowadays potential germplasm sources to consider for breeding high-quality products and cultivation in sustainable agriculture. In this study, 60 heirloom tomato (Solanum lycopersicum L.) accessions, including diverse varietal types (beefsteak, globe, oxheart, plum, and cherry), were profiled over two seasons for the main chemical and biochemical fruit traits. A medium-high level of heritability was found for all traits ranging from 0.52 for soluble solids to 0.99 for fruit weight. The average content of ascorbic acid was ~31 mg 100 g^-1 of fw in both seasons, while the greatest variability was found for carotenoids with peaks of 245.65 μg g^-1 of fw for total lycopene and 32.29 μg g^-1 of fw for β-carotene. Dissection of genotypic (G) and seasonal (Y) factors highlighted genotype as the main source of variation for all traits. No significant effect of Y and G × Y was found for ascorbic acid and fruit weight, respectively, whereas a high influence of Y was found on the variation of lycopene. Molecular fingerprinting was performed using the 10K SolCAP array, yielding a total of 7,591 SNPs. Population structure, phylogenetic relationships, and principal components analysis highlighted a differentiation of plum and cherry genotypes with respect to the beefsteak and globe types. These results were confirmed by multivariate analysis of phenotypic traits, shedding light on how breeding and selection focused on fruit characteristics have influenced the genetic and phenotypic makeup of heirlooms. Marker-trait association showed 11 significantly associated loci for β-carotene and fruit weight. For β-carotene, a single variant on chromosome 8 was found at 12 kb to CCD8, a cleavage dioxygenase playing a key role in the biosynthesis of apocarotenoids. For fruit weight, a single association was located at less than 3 Mbp from SLSUN31 and fw11.3, two candidates involved in the increasing of fruit mass. These results highlight the potentiality of heirlooms for genetic improvement and candidate gene identification.

Keywords: SNP array; breeding; carotenoids; genotype × year interaction; population structure; quality; tomato heirlooms; vitamin C.

Figure 1

Variation for fruit weight and chemical traits in the five heirloom groups across two seasons. Boxplots showing the average value and quartiles (first and third) for traits scored in the first (above) and the second (below) seasons, respectively. The measurement scale for each trait is reported on the Y-axis. Means with different letters are significantly different (P = 0.05) according to Tukey’s.

Figure 2

Variation for ascorbic acid and β-carotene in 60 heirloom genotypes in the two years of evaluation. Vertical bars show the average values for each accession. For each trait, data of the first and the second seasons are on the left and the right, respectively. Genotypes are ordered based on cultivar group. Acronyms are listed in Supplementary Table 1.

Figure 3

Variation for trans- and cis-lycopene in 60 heirloom genotypes in the 2 years of evaluation. Vertical bars show the average values for each accession. For each trait, data of the first and the second seasons are on the left and the right, respectively. 9-Cis, 13-cis, and 15-cis lycopene are indicated in blue, orange, and gray colors, respectively. Genotypes are ordered based on cultivar group. Acronyms are listed in Supplementary Table 1.

Figure 4

Principal component analysis. Loading plot of the first (PC₁) and second (PC₂) principal components showing the variation for 10 traits scored across two seasons. Accessions of different cultivar groups are represented by different colored symbols. Examples of the morphological characteristics of the fruits for the studied accessions are included in the figure. Color and symbols are listed in the graph’s legend. The first and second component centroids for each cultivar group are indicated by filled yellow symbols with shape and edge color according to cultivar groups (see legend). The direction and distance from the center of the biplot indicate how each trait scored contributes to the first two components. Trait acronyms are listed in Table 1.

Figure 5

Pearson’s rank correlation coefficients between pairs of phenotypes. Correlation coefficients are indicated in each cell. Colored correlations are those with a P-value<0.05. Color intensity is directly proportional to the coefficients. On the right side of the correlogram, the legend color shows the correlation coefficients and the corresponding colors. The correlogram for traits scored during Y1 is placed below the diagonal, and the correlogram for traits scored during Y2 is placed above the diagonal. Trait acronyms are listed in Table 1.

Figure 6

Phylogenetic analysis and population structure of 60 tomato accessions based on 7,591 SNPs. On the left, the neighbor-joining phylogenetic tree was computed using the maximum composite likelihood method. Numbers at the nodes are bootstrap values for 1,000 replicates. Accessions of different cultivar groups are represented by different colored symbols as listed in the legend. On the right, STRUCTURE analysis considering the most likely number of subpopulations K = 2 based on Evanno’s test. Clustering at K = 4 and K = 6 is shown. Horizontal solid bars for each genotype represent the allele frequency (indicated with numbers) for each K.

Figure 7

Loading plots in the first four components, showing the genomic diversity of 60 studied tomato accessions. (A) PC₁ vs. PC₂; (B) PC₁ vs. PC₃; (C) PC₁ vs. PC₄; (D) PC₂ vs. PC₃; (E) PC₃ vs. PC₄. The percentage of variation explained is shown in the grey plot. The orange line (above) indicates the cumulative variation of the components from 1 to 10; the blue line (below) indicates the variation explained by each component.

Figure 8

Marker–trait association analysis. Manhattan plots showing SNP associations for β-carotene (above) and fruit weight (below). Analysis has been performed considering 7,591 SNPs on 60 accessions evaluated across 2 years. The black horizontal line indicates a significant threshold (−log₁₀ P-value) according to Bonferroni. The X-axis indicates the chromosome position and SNP density in 1 MB window following the legend on the right of each graph. For the associated traits, the QQ plot is reported on the left.