Mapping in the era of sequencing: high density genotyping and its application for mapping TYLCV resistance in Solanum pimpinellifolium

Abstract

BackgroundA RIL population between Solanum lycopersicum cv. Moneymaker and S. pimpinellifolium G1.1554 was genotyped with a custom made SNP array. Additionally, a subset of the lines was genotyped by sequencing (GBS).ResultsA total of 1974 polymorphic SNPs were selected to develop a linkage map of 715 unique genetic loci. We generated plots for visualizing the recombination patterns of the population relating physical and genetic positions along the genome.This linkage map was used to identify two QTLs for TYLCV resistance which contained favourable alleles derived from S. pimpinellifolium. Further GBS was used to saturate regions of interest, and the mapping resolution of the two QTLs was improved. The analysis showed highest significance on Chromosome 11 close to the region of 51.3 Mb (qTy-p11) and another on Chromosome 3 near 46.5 Mb (qTy-p3). Furthermore, we explored the population using untargeted metabolic profiling, and the most significant differences between susceptible and resistant plants were mainly associated with sucrose and flavonoid glycosides.ConclusionsThe SNP information obtained from an array allowed a first QTL screening of our RIL population. With additional SNP data of a RILs subset, obtained through GBS, we were able to perform an in silico mapping improvement to further confirm regions associated with our trait of interest. With the combination of different ~ omics platforms we provide valuable insight into the genetics of S. pimpinellifolium-derived TYLCV resistance.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1152) contains supplementary material, which is available to authorized users.

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

“…Furthermore, horticultural traits of commercial tomato, such as fruit size, have been influenced by the introduction of S. pimpinellifolium alleles (as reviewed by Tanksley, 2004 ; Azzi et al, 2015 ), some of which were identified by the molecular mapping of backcross populations developed from S. pimpinellifolium ( Tanksley et al, 1996 ). Additionally, numerous quantitative trait loci (QTLs) have been identified using S. pimpinellifolium , such as those for biotic stress ( Salinas et al, 2013 ; Chen et al, 2014 ; Víquez-Zamora et al, 2014 ; Ni et al, 2017 ), abiotic stress ( Villalta et al, 2008 ; Lin et al, 2010 ), fruit quality traits ( Tanksley et al, 1996 ; Chen et al, 1999 ; Xiao et al, 2008 ; Capel et al, 2016 ), and other agronomic traits ( Doganlar et al, 2002 ; Cagas et al, 2008 ; Nakano et al, 2016 ). Numerous S. pimpinellifolium accessions have been previously characterized as having a high salinity tolerance (ST) and are promising sources of genes and alleles for improvement of ST in cultivated tomato ( Bolarin et al, 1991 ; Cuartero et al, 1992 ; Foolad and Lin, 1997 ; Foolad et al, 1998 ; Cuartero and Fernandez-Munoz, 1999 ; Foolad, 1999 ; Foolad and Chen, 1999 ; Bolarin et al, 2001 ; Foolad et al, 2001 ; Zhang et al, 2003 ; Villalta et al, 2008 ; Estan et al, 2009 ; Rao et al, 2013 , 2015 ).…”

“…‘Heinz 1706,’ as well as a draft sequence of S. pimpinellifolium accession ‘LA1589’ ( The Tomato Genome Consortium, 2012 ). 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.…”

The genome sequence of the wild tomato Solanum pimpinellifolium provides insights into salinity tolerance

“…Furthermore, horticultural traits of commercial tomato, such as fruit size, have been influenced by the introduction of S. pimpinellifolium alleles (as reviewed by Tanksley, 2004;Azzi et al, 2015), some of which were identified by the molecular mapping of backcross populations developed from S. pimpinellifolium (Tanksley et al, 1996). Additionally, numerous quantitative trait loci (QTLs) have been identified using S. pimpinellifolium, such as those for biotic stress (Salinas et al, 2013;Chen et al, 2014;Víquez-Zamora et al, 2014;Ni et al, 2017), abiotic stress (Villalta et al, 2008;Lin et al, 2010), fruit quality traits (Tanksley et al, 1996;Chen et al, 1999;Xiao et al, 2008;Capel et al, 2016), and other agronomic traits (Doganlar et al, 2002;Cagas et al, 2008;Nakano et al, 2016). In fact, S. pimpinellifolium is known to have high salinity tolerance and is a promising source for improvement of salinity tolerance in cultivated tomato (Bolarín et al, 1991;Villalta et al, 2008;Estan et al, 2009;Rao et al, 2013;Rao et al, 2015).…”

“…'Heinz 1706', as well as a draft sequence of S. pimpinellifolium accession 'LA1589' (The Tomato Genome Consortium, 2012). The availability of the cultivated tomato genome has greatly contributed to several fields of research, such as the identification of candidate genes related to fruit development (Zhong et al, 2013;Liu et al, 2016), the development of SNP genotyping arrays (Sim et al, 2012a;Sim et al, 2012b;Víquez-Zamora et al, 2014), the design of the CRISPR-cas9 gene-editing system (Brooks et al, 2014), and the identification of loci associated with traits contributing to improved tomato flavor quality (Tieman et al, 2017). Despite the availability of the draft genome sequence of S. pimpinellifolium 'LA1589', limited advances in the genetic studies of this species have been described so far (e.g.…”

Identification of metabolites involved in heat stress response in different tomato genotypes

“…A proportion of these metabolites are specific to a certain tissue, a species, or a condition and this expands the use of metabolomics analyses as a deep chemical phenotyping tool (Fritsche-Neto et al 2015). For instance, associations between genotype and metabolic phenotype have been studied to identify related markers to for instance fruit and vegetable quality, and biotic and abiotic stress resistance (Tikunov et al 2005, Riedelsheimer et al 2012, Wahyuni et al 2013, Viquez-Zamora et al 2014and Xu et al 2013. Metabolomics analyses generally include the following five major steps: (i) sample preparation, (ii) sample analysis, preferably using different analytical platforms, such as Gas Chromatography and Liquid Chromatography coupled to Mass Spectrometry (GC-MS and LC-MS, respectively), (iii) data processing, including peak picking, peak alignment and compound annotation, as far as is possible, (iv) statistical analysis and (v) data interpretation (Fiehn 2002).…”