Resequencing at ≥40-Fold Depth of the Parental Genomes of a Solanum lycopersicum × S. pimpinellifolium Recombinant Inbred Line Population and Characterization of Frame-Shift InDels That Are Highly Likely to Perturb Protein Function

Abstract

A recombinant in-bred line population derived from a cross between Solanum lycopersicum var. cerasiforme (E9) and S. pimpinellifolium (L5) has been used extensively to discover quantitative trait loci (QTL), including those that act via rootstock genotype, however, high-resolution single-nucleotide polymorphism genotyping data for this population are not yet publically available. Next-generation resequencing of parental lines allows the vast majority of polymorphisms to be characterized and used to progress from QTL to causative gene. We sequenced E9 and L5 genomes to 40- and 44-fold depth, respectively, and reads were mapped to the reference Heinz 1706 genome. In L5 there were three clear regions on chromosome 1, chromosome 4, and chromosome 8 with increased rates of polymorphism. Two other regions were highly polymorphic when we compared Heinz 1706 with both E9 and L5 on chromosome 1 and chromosome 10, suggesting that the reference sequence contains a divergent introgression in these locations. We also identified a region on chromosome 4 consistent with an introgression from S. pimpinellifolium into Heinz 1706. A large dataset of polymorphisms for the use in fine-mapping QTL in a specific tomato recombinant in-bred line population was created, including a high density of InDels validated as simple size-based polymerase chain reaction markers. By careful filtering and interpreting the SnpEff prediction tool, we have created a list of genes that are predicted to have highly perturbed protein functions in the E9 and L5 parental lines.

The Genome Sequence of the Wild Tomato Solanum pimpinellifolium Provides Insights Into Salinity Tolerance

“…The availability of the cultivated tomato genome has led to several important advances, such as the identification of candidate genes (CG) related to fruit development ( Zhong et al, 2013 ; Liu et al, 2016 ), the development of single nucleotide polymorphism (SNP) genotyping arrays ( Sim et al, 2012a , b ; Víquez-Zamora et al, 2014 ), the design of the CRISPR-cas9 gene-editing system ( Brooks et al, 2014 ), and the identification of loci contributing to improved tomato flavor quality ( Tieman et al, 2017 ). While the draft genome sequence of S. pimpinellifolium ‘LA1589’ has been used in several previous studies (e.g., Kevei et al, 2015 ), the fragmented nature of the assembly (309,180 contigs), the low sequencing coverage of the genome and the limitations of the available genome annotation constrain the usefulness of this assembly. Additionally, a further three accessions of S. pimpinellifolium (LYC2798, LA1584 and LA1578) were sequenced by the 100 Tomato Genome Project ( The 100 Tomato Genome Sequencing Consortium et al, 2014 ), but genome assemblies and annotations for these accessions have not been performed.…”

BIFURCATE FLOWER TRUSS: a novel locus controlling inflorescence branching in tomato contains a defective MAP kinase gene

“…This pipeline produced variant call format (VCF) files which were annotated by SnpEff (version 4.0) using ITAG2.40, associated with genome reference version SL2.50) ( http://solgenomics.net/ , last accessed 12 March, 2018; Fernandez-Pozo et al , 2015 ). Finally, the variants were filtered using GATK’s variant filtration tool (Quality Depth <2, Fisher Strand >60, Mapping Quality <40, Haplotype Score >13, and Mapping Quality RankSum <12.5) ( Kevei et al , 2015 ). Unique variants were filtered using a custom BASH script which excluded polymorphisms shared between the data sets, similar to the mechanism of bedtools ( Quinlan and Hall, 2010 ).…”

De novogenome assembly and transcriptome analysis for the drought and salt resistantSolanum sitiens

“…Extensive resequencing data mapped against cultivated tomato is available from over 500 accessions, including all wild species [18] [19] [20], and a pan-genome has been created for tomato using 725 accessions [21], but this included limited numbers of wild species and only within the Solanum sect. Lycopersicon.…”