A Solanum neorickii introgression population providing a powerful complement to the extensively characterized Solanum pennellii population

Abstract

We present a complementary resource for trait fine-mapping in tomato to those based on the intra-specific cross between cultivated tomato and the wild tomato species Solanum pennellii, which have been extensively used for quantitative genetics in tomato over the last 20 years. The current population of backcross inbred lines (BILs) is composed of 107 lines derived after three backcrosses of progeny of the wild species Solanum neorickii (LA2133) and cultivated tomato (cultivar TA209) and is freely available to the scientific community. These S. neorickii BILs were genotyped using the 10K SolCAP single nucleotide polymorphism chip, and 3111 polymorphic markers were used to map recombination break points relative to the physical map of Solanum lycopersicum. The BILs harbor on average 4.3 introgressions per line, with a mean introgression length of 34.7 Mbp, allowing partitioning of the genome into 340 bins and thereby facilitating rapid trait mapping. We demonstrate the power of using this resource in comparison with archival data from the S. pennellii resources by carrying out metabolic quantitative trait locus analysis following gas chromatography-mass spectrometry on fruits harvested from the S. neorickii BILs. The metabolic candidate genes phenylalanine ammonia-lyase and cystathionine gamma-lyase were then tested and validated in F populations and via agroinfiltration-based overexpression in order to exemplify the fidelity of this method in identifying the genes that drive tomato metabolic phenotypes.

A Solanum lycopersicoides reference genome facilitates insights into tomato specialized metabolism and immunity

“…Another mQTL on chromosome 10 resulted in up to five‐fold elevation of total phenylpropanoids (Figure 5, Table S11, and Figure S11). PAL5 resides at this locus as it does for a Solanum neorickii phenylalanine mQTL (Brog et al., 2019). In contrast to cultivated tomato, wild tomato species accumulate significant phenolics in fruit pericarp (Willits et al., 2005) as do lines with the S. lycopersicoides allele of this mQTL locus (Figure S12).…”

Genome-wide association studies of seed metabolites identify loci controlling specialized metabolites in Arabidopsis thaliana

“…This results in greater phenotypic variance compared to the NIL population between Col-0 and C24 as exemplified by differences in flavonoid levels. However, the overlap suggests, as previously stated (Brog et al, 2019), that genome-wide association and QTL mapping are complementary techniques to study seed specialized metabolism.…”

Genome-wide association studies: assessing trait characteristics in model and crop plants

“…Rather than employing the cross-validation approach which can prove incredibly time and labor intensive several other more direct approaches have been taken. For example, the confirmation of many metabolic QTL has been provided by the reduction of the expression of candidate genes via virus-induced gene silencing [93,95,116] or alternatively via their transient or inducible expression [20]. Given that the repertoire of species amenable to both methods are currently being considerably expanded.…”