title: Mapping in the era of sequencing: high density genotyping and its application for mapping TYLCV resistance in Solanum pimpinellifolium.
abstract: BACKGROUND
  A 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).
  
  
  RESULTS
  A 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.
  
  
  CONCLUSIONS
  The 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.
authors.forename: Marcela
authors.initials: M
authors.lastname: Víquez-Zamora
authors.forename: Myluska
authors.initials: M
authors.lastname: Caro
authors.forename: Richard
authors.initials: R
authors.lastname: Finkers
authors.forename: Yury
authors.initials: Y
authors.lastname: Tikunov
authors.forename: Arnaud
authors.initials: A
authors.lastname: Bovy
authors.forename: Richard G F
authors.initials: RG
authors.lastname: Visser
authors.forename: Yuling
authors.initials: Y
authors.lastname: Bai
authors.affiliation: Wageningen UR Plant Breeding, Wageningen University & Research Centre, P,O, Box 386, Wageningen, AJ 6700, the Netherlands. sjaak.vanheusden@wur.nl.
authors.forename: Sjaak
authors.initials: S
authors.lastname: van Heusden
mesh_terms: D000483:Alleles; D002874:Chromosome Mapping; D003198:Computer Simulation; D060467:Disease Resistance / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics; D060005:Genotyping Techniques; D007178:Inbreeding; D055442:Metabolome; D010935:Plant Diseases / Q000276:immunology / Q000821:virology*; D010942:Plant Viruses / Q000502:physiology*; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci / Q000235:genetics; D017421:Sequence Analysis; D032322:Solanum / Q000235:genetics* / Q000276:immunology / Q000378:metabolism / Q000821:virology*