Development of a PCR-based, genetic marker resource for the tomato-like nightshade relative, Solanum lycopersicoides using whole genome sequence analysis

Abstract

Solanum lycopersicoidesis a wild nightshade relative of tomato with known resistance to a wide range of pests and pathogens, as well as tolerance to cold, drought and salt stress. To effectively utilizeS.lycopersicoidesas a genetic resource in breeding for tomato improvement, the underlying basis of observable traits in the species needs to be understood. Molecular markers are important tools that can unlock the genetic underpinnings of phenotypic variation in wild crop relatives. Unfortunately, DNA markers that are specific toS.lycopersicoidesare limited in number, distribution and polymorphism rate. In this study, we developed a suite ofS.lycopersicoides-specific SSR and indel markers by sequencing, building and analyzing a draft assembly of the wild nightshade genome. Mapping of a total of 1.45 Gb ofS.lycopersicoidescontigs against the tomato reference genome assembled a moderate number of contiguous reads into longer scaffolds. Interrogation of the obtained draft yielded SSR information for more than 55,000 loci inS.lycopersicoidesfor which more than 35,000 primers pairs were designed. Additionally, indel markers were developed based on sequence alignments betweenS.lycopersicoidesand tomato. Synthesis and experimental validation of 345 primer sets resulted in the amplification of single and multilocus targets inS.lycopersicoidesand polymorphic loci betweenS.lycopersicoidesand tomato. Cross-species amplification of the 345 markers in tomato, eggplant, silverleaf nightshade and pepper resulted in varying degrees of transferability that ranged from 55 to 83%. The markers reported in this study significantly expands the genetic marker resource forS.lycopersicoides, as well as for relatedSolanum spp. for applications in genetics and breeding studies.