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

Gehendra Bhattarai,James C Correll,Chunda Feng,Ainong Shi,Braham Dhillon,Wei Yang,Beiquan Mou

doi:10.1186/s12864-021-07788-8

Abstract

BackgroundDowny 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.ResultsAssociation 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.ConclusionsGenomewide 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.

Highlights

Downy mildew, the most devastating disease of spinach (Spinacia oleracea L.), is caused by the oomycete Peronospora effusa [=P. farinosa f. sp. spinaciae]
Downy mildew response Spinach cultivar Whale is resistant to P. effusa race 16, while Lazio is susceptible [5, 6]
Qualitative disease incidence data scored for each line were used as phenotype data, and association analysis was conducted using the binary disease scores of 172 spinach lines (123 resistant and 49 susceptible) that remained after filtering for the individual lines with high missing single nucleotide polymorphism (SNP) calls and parental lines

Summary

Introduction

The most devastating disease of spinach (Spinacia oleracea L.), is caused by the oomycete Peronospora effusa [=P. farinosa f. sp. spinaciae]. The most devastating disease of spinach (Spinacia oleracea L.), is caused by the oomycete Peronospora effusa [=P. farinosa f. 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. Significant increase in the production area in last two decades, planting in a higher density, year-round production, and planting of resistant cultivars with narrow genetic background increases selection pressure, continuous increase in organic production area provides a niche for P. effusa growth and multiplication, and these phenomena in combination are conducive for the emergence of a new race. New races are likely a result of asexual variation [13] and sexual recombination [13, 14] within the pathogen populations

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