title: Association analysis for disease resistance to Fusarium oxysporum in cape gooseberry (Physalis peruviana L).
abstract: BACKGROUND
  Vascular wilt caused by Fusarium oxysporum is the most important disease in cape gooseberry (Physalis peruviana L.) in Colombia. The development of resistant cultivars is considered one of the most cost-effective means to reduce the impact of this disease. In order to do so, it is necessary to provide breeders with molecular markers and promising germplasm for introgression of different resistance loci as part of breeding schemes. Here we described an association mapping study in cape gooseberry with the goal to: (i) select promising materials for use in plant breeding and (ii) identify SNPs associated with the cape gooseberry resistance response to the F. oxysporum pathogen under greenhouse conditions, as potential markers for cape gooseberry breeding.
  
  
  RESULTS
  We found a total of 21 accessions with different resistance responses within a diversity panel of 100 cape gooseberry accessions. A total of 60,663 SNPs were also identified within the same panel by means of GBS (Genotyping By Sequencing). Model-based population structure and neighbor-joining analyses showed three populations comprising the cape gooseberry panel. After correction for population structure and kinship, we identified SNPs markers associated with the resistance response against F. oxysporum. The identification of markers was based on common tags using the reference genomes of tomato and potato as well as the root/stem transcriptome of cape gooseberry. By comparing their location with the tomato genome, 16 SNPs were found in genes involved in defense/resistance response to pathogens, likewise when compared with the genome of potato, 12 markers were related.
  
  
  CONCLUSIONS
  The work presented herein provides the first association mapping study in cape gooseberry showing both the identification of promising accessions with resistance response phenotypes and the identification of a set of SNP markers mapped to defense/resistance response genes of reference genomes. Thus, the work also provides new knowledge on candidate genes involved in the P. peruviana - F. oxysporum pathosystem as a foundation for further validation in marker-assisted selection. The results have important implications for conservation and breeding strategies in cape gooseberry.
authors.affiliation: Tibaitatá Research Center, Colombian Corporation for Agricultural Research, Corpoica, Km 14 vía Mosquera, Bogotá, Colombia.
authors.forename: Jaime A
authors.initials: JA
authors.lastname: Osorio-Guarín
authors.affiliation: Tibaitatá Research Center, Colombian Corporation for Agricultural Research, Corpoica, Km 14 vía Mosquera, Bogotá, Colombia.
authors.forename: Felix E
authors.initials: FE
authors.lastname: Enciso-Rodríguez
authors.affiliation: Tibaitatá Research Center, Colombian Corporation for Agricultural Research, Corpoica, Km 14 vía Mosquera, Bogotá, Colombia.
authors.forename: Carolina
authors.initials: C
authors.lastname: González
authors.affiliation: Boyce Thompson Institute for Plant Research, Ithaca, NY, USA.
authors.forename: Noé
authors.initials: N
authors.lastname: Fernández-Pozo
authors.affiliation: Boyce Thompson Institute for Plant Research, Ithaca, NY, USA.
authors.forename: Lukas A
authors.initials: LA
authors.lastname: Mueller
authors.affiliation: Agrobiodiversity Department, National Direction of Research and Development, Corpoica, Km 14 vía Mosquera, Bogotá, Colombia. lbarrero@corpoica.org.co.
authors.forename: Luz Stella
authors.initials: LS
authors.lastname: Barrero
mesh_terms: D002874:Chromosome Mapping; D060467:Disease Resistance / Q000235:genetics*; D005670:Fusarium; D005819:Genetic Markers; D005838:Genotype; D010641:Phenotype; D032321:Physalis / Q000235:genetics* / Q000382:microbiology; D010935:Plant Diseases / Q000235:genetics* / Q000382:microbiology; D020641:Polymorphism, Single Nucleotide; D059467:Transcriptome
chemical_list: D005819:Genetic Markers
keywords: Association mapping; Cape gooseberry; Fusarium oxysporum; Genotyping by sequencing