Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding

Abstract

Solanum pimpinellifolium (SP) is the wild progenitor of cultivated tomato. Because of its remarkable stress tolerance and intense flavor, SP has been used as an important germplasm donor in modern tomato breeding. Here, we present a high-quality chromosome-scale genome sequence of SP LA2093. Genome comparison identifies more than 92,000 structural variants (SVs) between LA2093 and the modern cultivar, Heinz 1706. Genotyping these SVs in ~600 representative tomato accessions identifies alleles under selection during tomato domestication, improvement and modern breeding, and discovers numerous SVs overlapping genes known to regulate important breeding traits such as fruit weight and lycopene content. Expression quantitative trait locus (eQTL) analysis detects hotspots harboring master regulators controlling important fruit quality traits, including cuticular wax accumulation and flavonoid biosynthesis, and SVs contributing to these complex regulatory networks. The LA2093 genome sequence and the identified SVs provide rich resources for future research and biodiversity-based breeding.

A Genetic Map and Linkage Panel for the Large-fruited Fresh-market Tomato

“…As a resource to the scientific community, we have provided the full allelic information of 58 core lines in the UFTLP 1.0, and information about allelic agreement between the UFTLP and SolCAP array SNP sites (Supplemental Table S1). Recently, several draft tomato sequence assemblies from long-read data were released (Alonge et al, 2020;Mazo-Molina et al, 2019;Schmidt et al, 2017;Wang et al, 2020). High-density linkage analysis, together with long sequence reads data and DNA insert libraries, were used to order and orient draft sequence assemblies into pseudo-molecule chromosomes (Ghurye and Pop, 2019;Rice and Green, 2019).…”

De novo genome assembly of two tomato ancestors, Solanum pimpinellifolium and Solanum lycopersicum var. cerasiforme, by long-read sequencing

“…Wild tomato species most likely have a higher number of identifiable intact LTRs and/or longer internal regions than cultivated species, as the LAI score of other SP (LA2079; LAI = 13.14) and S. pennellii (LAI = 14.8) is higher than that of SLL. 16 , 18 According to these quality assessment results, the SP and SLC genomes were classified to be of reference quality based on the assembly of repetitive and intergenic sequence spaces (draft quality, LAI < 10; reference quality, 10 < LAI < 20; and gold quality LAI > 20). 19 …”

“… 15 Recently, chromosome-scale genome sequence of ‘LA2093’ was determined using a long-read PacBio sequencer and was annotated to contain 35,761 protein-coding genes, of which 35,535 were validated by the published transcriptome data and/or homologs in the NCBI non-redundant protein database. 16 Furthermore, draft genome sequences of several SP and SLC accessions have been determined using a long-read Nanopore sequencer, and several structural variant hotspots have been identified. 14 However, chromosome-level genome assemblies, particularly those generated using long-read sequencers, are still limited and should be further improved.…”

A High-continuity and Annotated Tomato Reference Genome

“…Human domestication and improvement have increased the size of modern tomato fruits about 100 times relative to their ancestors [30]. At the same time, the avor and resistance of tomatoes have been greatly reduced [35]. Comparative genomic analysis of the SLT1.0 and S. pimpinellifolium LA2093 genomes identi ed structural variations in some important genes that affect tomato fruit weight, such as SlT11G021690 (oxidoreductase activity).…”