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Background  Downy mildew, the most devastating disease of spinach ( Spinacia oleracea  L.), is caused by the oomycete  Peronospora effusa  [= P. farinosa  f. sp.  spinaciae ]. The  P. effusa  shows race specificities to the resistant host and comprises 19 reported races and many novel isolates. Sixteen new  P. effusa  races were identified during the past three decades, and the new pathogen races are continually overcoming the genetic resistances used in commercial cultivars. A spinach breeding population derived from the cross between cultivars Whale and Lazio was inoculated with  P. effusa  race 16 in an environment-controlled facility; disease response was recorded and genotyped using genotyping by sequencing (GBS). The main objective of this study was to identify resistance-associated single nucleotide polymorphism (SNP) markers from the cultivar Whale against the  P. effusa  race 16.    Results  Association analysis conducted using GBS markers identified six significant SNPs (S3_658,306, S3_692697, S3_1050601, S3_1227787, S3_1227802, S3_1231197). The downy mildew resistance locus from cultivar Whale was mapped to a 0.57 Mb region on chromosome 3, including four disease resistance candidate genes (Spo12736, Spo12784, Spo12908, and Spo12821) within 2.69–11.28 Kb of the peak SNP.    Conclusions  Genomewide association analysis approach was used to map the  P. effusa  race 16 resistance loci and identify associated SNP markers and the candidate genes. The results from this study could be valuable in understanding the genetic basis of downy mildew resistance, and the SNP marker will be useful in spinach breeding to select resistant lines.

High resolution mapping and candidate gene identification of downy mildew race 16 resistance in spinach