Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole‐genome sequencing

Abstract

SUMMARYWe explored genetic variation by sequencing a selection of 84 tomato accessions and related wild species representative of the Lycopersicon, Arcanum, Eriopersicon and Neolycopersicon groups, which has yielded a huge amount of precious data on sequence diversity in the tomato clade. Three new reference genomes were reconstructed to support our comparative genome analyses. Comparative sequence alignment revealed group-, species-and accession-specific polymorphisms, explaining characteristic fruit traits and growth habits in the various cultivars. Using gene models from the annotated Heinz 1706 reference genome, we observed differences in the ratio between non-synonymous and synonymous SNPs (dN/dS) in fruit diversification and plant growth genes compared to a random set of genes, indicating positive selection and differences in selection pressure between crop accessions and wild species. In wild species, the number of single-nucleotide polymorphisms (SNPs) exceeds 10 million, i.e. 20-fold higher than found in most of the crop accessions, indicating dramatic genetic erosion of crop and heirloom tomatoes. In addition, the highest levels of heterozygosity were found for allogamous self-incompatible wild species, while facultative and autogamous self-compatible species display a lower heterozygosity level. Using whole-genome SNP information for maximum-likelihood analysis, we achieved complete tree resolution, whereas maximum-likelihood trees based on SNPs from ten fruit and growth genes show incomplete resolution for the crop accessions, partly due to the effect of heterozygous SNPs. Finally, results suggest that phylogenetic relationships are correlated with habitat, indicating the occurrence of geographical races within these groups, which is of practical importance for Solanum genome evolution studies.

De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing

“…In addition, the metabolite content of LYC1722 differed from that of LA716 (Supplemental Figure 2). Taken together, these characteristics highlight the high level of diversity within S. pennellii (Rick and Tanksley, 1981) and show that LA716 and LYC1722 are relatively diverged accessions, which as such might provide different beneficial traits or alleles (Aflitos et al, 2014).…”

“…Using the shortread sequencing data to identify variants such as single nucleotide polymorphisms (SNPs) and small insertions and deletions (InDels) versus the S. pennellii LA716 reference revealed 6.2 million predicted variants where the highest variant rate was found on chromosomes 1 and 4 ( Figure 1A; Supplemental Table 1). For comparison, in a large panel of cultivated tomatoes (S. lycopersicum) there were only a few cases where more than 2 million variants were found (Aflitos et al, 2014). In addition, the metabolite content of LYC1722 differed from that of LA716 (Supplemental Figure 2).…”

Phylogenomics of 42 tomato chloroplasts using assembly and alignment-free method

“…(iv) Neolycopersicon group containing only Solanum penellii, which was considered to be sister to the rest of the section based on its lack of the sterile anther that occurs as a morphological synapomorphy in S. habrochaites and the rest of the core tomatoes 8 . More recent studies using conserved orthologous sequence markers (COSII) 11 , genome-wide single nucleotide polymorphisms (SNPs) 7,12 and genomic repeat elements 13 have largely supported previous hypotheses with respect to major clades within the tomatoes, although individual species relationships are less clear cut for some taxa. Thus, given the general acceptance of this informal classification, in the present study we will often use it as reference in order to better clarify the results here presented.…”

NGS-Based Genotyping, High-Throughput Phenotyping and Genome-Wide Association Studies Laid the Foundations for Next-Generation Breeding in Horticultural Crops

“…NGS, coupled with the availability of high-quality reference genomes of horticultural crops, have expedited the re-sequencing of many individuals to identify a large number of SNPs and investigate within-and between-species sequence variation [5,[55][56][57][58]. Although the above cited re-sequencing projects were fruitful from a scientific standpoint, the re-sequencing was characterized by low depth of coverage for several individuals.…”