The genome of the stress-tolerant wild tomato species Solanum pennellii

Abstract

Solanum pennellii is a wild tomato species endemic to Andean regions in South America, where it has evolved to thrive in arid habitats. Because of its extreme stress tolerance and unusual morphology, it is an important donor of germplasm for the cultivated tomato Solanum lycopersicum. Introgression lines (ILs) in which large genomic regions of S. lycopersicum are replaced with the corresponding segments from S. pennellii can show remarkably superior agronomic performance. Here we describe a high-quality genome assembly of the parents of the IL population. By anchoring the S. pennellii genome to the genetic map, we define candidate genes for stress tolerance and provide evidence that transposable elements had a role in the evolution of these traits. Our work paves a path toward further tomato improvement and for deciphering the mechanisms underlying the myriad other agronomic traits that can be improved with S. pennellii germplasm.

Figure 1. Genomic landscape of S. pennellii chromosome 1.

(a–d) Densities of genes (a), retrotransposons (b), DNA transposons (c) and simple repeats (d) are shown for a 500-kb window. (e) Average RNA sequencing coverage in a 500-kb window. (f–h) Percentages of variants relative to S. pimpinellifolium (f), S. lycopersicum (g) and S. tuberosum (h).

Figure 2. Expression of cuticle biosynthesis–related genes.

(a–d) The expression of genes related to cutin biosynthesis (a) and wax biosynthesis (b) and of genes putatively (c) or known to be (d) associated with the formation of cuticular aromatic components was analyzed using quantitative PCR to validate data from RNA sequencing experiments and biochemical analysis. Statistical analysis was performed using a two-tailed t test. *P < 0.05, **P < 0.01, ***P < 0.001. Gene expression shown is relative to that for actin (Solyc05g054480). Error bars, s.e.m.; four biological replicates, each with three technical replicates.

Figure 3. Chromosome mapping of stress-related candidate genes.

Candidate genes related to salt stress and drought are visualized on their respective IL QTLs for selected ILs 2-5, 7-4-1, 8-3 and 9-1. Colored squares next to each gene represent the magnitude of differential expression (log₂) across a range of different tissues and conditions. Red indicates higher expression in S. pennellii, and blue indicates higher expression in S. lycopersicum. Underlined genes are those characterized by large differences in expression between S. lycopersicum cv. M82 and S. pennellii at the promoter and/or coding sequence level. Large differences are characterized as large (>30-bp) indels in the promoter region and/or at least one significant amino acid change in the coding sequence as determined by the P value predicted by SIFT Blink. Brix × yield, total agronomic yield.