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. 2015 Apr 1;16(1):257.
doi: 10.1186/s12864-015-1444-1.

Genomic variation in tomato, from wild ancestors to contemporary breeding accessions

José Blanca  1 , Javier Montero-Pau  2 , Christopher Sauvage  3 , Guillaume Bauchet  4   5 , Eudald Illa  6 , María José Díez  7 , David Francis  8 , Mathilde Causse  9 , Esther van der Knaap  10 , Joaquín Cañizares  11
Affiliations

Genomic variation in tomato, from wild ancestors to contemporary breeding accessions

José Blanca et al. BMC Genomics. .

Abstract

Background: Domestication modifies the genomic variation of species. Quantifying this variation provides insights into the domestication process, facilitates the management of resources used by breeders and germplasm centers, and enables the design of experiments to associate traits with genes. We described and analyzed the genetic diversity of 1,008 tomato accessions including Solanum lycopersicum var. lycopersicum (SLL), S. lycopersicum var. cerasiforme (SLC), and S. pimpinellifolium (SP) that were genotyped using 7,720 SNPs. Additionally, we explored the allelic frequency of six loci affecting fruit weight and shape to infer patterns of selection.

Results: Our results revealed a pattern of variation that strongly supported a two-step domestication process, occasional hybridization in the wild, and differentiation through human selection. These interpretations were consistent with the observed allele frequencies for the six loci affecting fruit weight and shape. Fruit weight was strongly selected in SLC in the Andean region of Ecuador and Northern Peru prior to the domestication of tomato in Mesoamerica. Alleles affecting fruit shape were differentially selected among SLL genetic subgroups. Our results also clarified the biological status of SLC. True SLC was phylogenetically positioned between SP and SLL and its fruit morphology was diverse. SLC and "cherry tomato" are not synonymous terms. The morphologically-based term "cherry tomato" included some SLC, contemporary varieties, as well as many admixtures between SP and SLL. Contemporary SLL showed a moderate increase in nucleotide diversity, when compared with vintage groups.

Conclusions: This study presents a broad and detailed representation of the genomic variation in tomato. Tomato domestication seems to have followed a two step-process; a first domestication in South America and a second step in Mesoamerica. The distribution of fruit weight and shape alleles supports that domestication of SLC occurred in the Andean region. Our results also clarify the biological status of SLC as true phylogenetic group within tomato. We detect Ecuadorian and Peruvian accessions that may represent a pool of unexplored variation that could be of interest for crop improvement.

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Figures

Figure 1
Figure 1
Principal component analysis using all 952 uniquely named accessions and based on 2,313 markers.
Figure 2
Figure 2
Principal Component Analysis for SP, SLC, SLL and SLL Mesoamerica and genetically close SLC subgroups. (A) SP, (B) SLC, (C) SLL and (D) SLL Mesoamerica and genetically close SLC subgroups. Solid lines encircle the main genetic groups and different colors and markers represent genetic subgroups.
Figure 3
Figure 3
Tomatoes from SLC vintage subgroup (source http://www.ars.usda.gov ).
Figure 4
Figure 4
Comparison between the passport-based classification (columns) and genetic-based classification (rows). The genetic classifications correspond to the clusters shown in Additional file 1: Table S1 and, passport classification is based on information provided (see Material and Methods for further details). Size of the squares is proportional to the number of samples corresponding to each genetic and passport group and, background colors highlight different species and botanical varieties.
Figure 5
Figure 5
Neighbor network for the genetic subgroups; Neighbor network based on genetic distances (D est ) for the genetic subgroups. (A) Complete network and (B) close up of the region squared in panel A. Only subgroups with more than 5 individuals are represented. Different colors represent genetic groups.
Figure 6
Figure 6
Phylogenetic tree based on SNP data. Phylogenetic tree based on SNP data computed with Bayesian based SNAPP algorithm. Posterior support of nodes is shown.
Figure 7
Figure 7
Rarefaction analysis of the number of alleles per locus and frequency of private alleles. Rarefaction analysis of the number of alleles per locus (A, B) and frequency of private alleles (C, D) for SP, SLC Andean (Ecuadorian and Northern Peruvian SLC), SLC non-Andean, SLL vintage, SLL fresh and SLL processing for two sets of markers. A and C show the results for a set of 2,312 markers spread at least 0.1 cM and B and D for 6343 SNPs (see text for details). Include which genetic subgroups are included in each category.
Figure 8
Figure 8
Fruit weight and shape gene frequencies across genetic groups. Ancestral allele in blue, derived allele in red. Black lines show binomial confidence intervals at 95%.Indicate which genetic subgroups are pooled in each category.
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