A clarified position for Solanum lycopersicum var. cerasiforme in the evolutionary history of tomatoes (solanaceae)

Abstract

Background: The natural phenotypic variability present in the germplasm of cultivated plants can be linked to molecular polymorphisms using association genetics. However it is necessary to consider the genetic structure of the germplasm used to avoid false association. The knowledge of genetic structure of plant populations can help in inferring plant evolutionary history. In this context, we genotyped 360 wild, feral and cultivated accessions with 20 simple sequence repeat markers and investigated the extent and structure of the genetic variation. The study focused on the red fruited tomato clade involved in the domestication of tomato and confirmed the admixture status of cherry tomatoes (Solanum lycopersicum var. cerasiforme). We used a nested sample strategy to set-up core collection maximizing the genetic diversity with a minimum of individuals.

Results: Molecular diversity was considerably lower in S. lycopersicum i.e. the domesticated form. Model-based analysis showed that the 144 S. lycopersicum var. cerasiforme accessions were structured into two groups: one close to the domesticated group and one resulting from the admixture of the S. lycopersicum and S. pimpinellifolium genomes. SSR genotyping also indicates that domesticated and wild tomatoes have evolved as a species complex with intensive level of hybridization. We compiled genotypic and phenotypic data to identify sub-samples of 8, 24, 32 and 64 cherry tomato accessions that captured most of the genetic and morphological diversity present in the entire S. lycopersicum var. cerasiforme collection.

Conclusion: The extent and structure of allelic variation is discussed in relation to historical events like domestication and modern selection. The potential use of the admixed group of S. lycopersicum var. cerasiforme for association genetics studies is also discussed. Nested core collections sampled to represent tomato diversity will be useful in diversity studies. Molecular and phenotypic variability of these core collections is defined. These collections are available for the scientific community and can be used as standardized panels for coordinating efforts on identifying novel interesting genes and on examining the domestication process in more detail.

Figure 1

Determination of Kopt following the method of Evanno et al. (2005). The rate of change of the posterior probability of the data given the number of clusters is plotted against K, the number of clusters. ΔK was calculated as |L"(K)|/s[Pr(x|k)] (see Materials and Methods). The first peak (K = 2) corresponds to the optimum number of clusters. The secondary peak (K = 4) indicates a sublevel clustering.

Figure 2

Classification of individuals using Structure2.0 according to the previous classification into species. The distribution of the individuals to different clusters by the model-based method is indicated by the color code in the legend box.

Figure 3

Principal Coordinate Analysis of the Eulycopersicon sample with Structure2.0 clustering information. The 'red-fruited' sample did not contain S. cheesmaniae accessions. The subdivision of the collection assuming Kopt = 2 separates group 1 (triangle) and group 2, (square) accessions. When assuming Kopt = 4, large fruited accessions: subgroup D (black square) and small-size fruit accessions: subgroup C (white square) are divided. For wild accessions, subgroup A (white triangle) and subgroup D (black triangle) were divided. 'Wild'/'domesticated' admixed accessions are represented by grey diamonds. Intra-specific admixed accessions are not identified. Inertia values are 22.09% and 4.84% for factorial coordinates axes 1 and 2, respectively.

Figure 4

Comparison of efficiency of random and maximization (M) sampling strategy in S. l. cerasiforme sample (n = 143 accessions). Score, which represents allelic richness, is plotted against size of core collection. The efficiency of the M strategy is represented by a straight line and the random strategy is represented by a dashed line. A. Core collections were sampled with alleles from 20 SSR loci and were cross validated by the same alleles. B. Core collections were sampled with alleles from 20 SSR loci and were cross validated by alleles from twelve phenotypic data split in 5 classes. C. Core collections were sampled with alleles from 20 SSR markers and twelve phenotypic data and were cross validated by the same alleles.

Figure 5

Core collection representativeness for fruit weight, Soluble Solid Content and Titratable Acidity. Classes are those used for core collections (cc) design.