Haplotype-resolved powdery mildew resistance loci reveal the impact of heterozygous structural variation on NLR genes inMuscadinia rotundifolia

Abstract

Muscadinia rotundifolia cv. Trayshed is a valuable source of resistance to grape powdery mildew (PM). It carries two PM resistance (R) loci, Run1.2 on chromosome 12 and Run2.2 on chromosome 18. This study identified the nucleotide-binding leucine-rich repeat (NLR) genes composing each R locus and their associated defense mechanisms. Evaluation of PM disease development showed that introgression of both loci confers resistance to PM in a V. vinifera background, but with varying speed and intensity of the response. To better understand the effect of NLR composition on PM resistance, both haplotypes of each R locus were reconstructed and the gene models within each haplotype were manually refined. We found that the number and classes of NLR genes differed between Run1.2 and Run2.2 loci and between the haplotypes of each R locus. In addition, NLR genes composing Run1.2b or Run2.2 loci exhibited different levels of gene expression, pointing to candidate NLR genes responsible for PM resistance in Trayshed. Finally, a transcriptomic analysis that included six additional R loci showed differences in the defense mechanisms associated with Run1.2b and Run2.2 in response to PM and at constitutive level. Altogether, our results reveal that Trayshed’s R loci are composed of distinct NLRs that trigger different plant defense mechanisms in response to PM and at constitutive level, which would explain the variation of pathogen restriction between the two loci.

Genome of the North American wild apple speciesMalus angustifolia

“…Additionally, 1,977,328 small InDels were identified between the haplotypes -roughly the same amount as in M. fusca. Notably, in plants with high heterozygosity, the source of genetic diversity extends beyond single nucleotide polymorphisms, and it has been shown that large structural variations (SVs) play a significant role in haplotypic diversity (Guan et al, 2021;Mansfeld et al, 2021;Yuan et al, 2021;Massonnet et al, 2022). Using our approach, we identified SVs of different types ranging in size from 50 bp -50 Kb.…”

The grape powdery mildew resistance lociRen2, Ren3, Ren4D, Ren4U, Run1, Run1.2b, Run2.1, andRun2.2activate different transcriptional responses toErysiphe necator

“…Because PCD occurs in epidermal cells post-penetration of E. necator, the recognition of E. necator's effectors by intracellular nucleotide-binding leucine-rich repeat (NLR) proteins is likely the trigger of PCD (Qiu et al, 2015;Dry et al, 2019). Only one NLR gene associated with PM resistance, MrRUN1, has been characterized in M. rotundifolia G52 (Feechan et al, 2013) and candidate NLR genes associated with Run1.2b and Run2.2 have been proposed for M. rotundifolia Trayshed (Massonnet et al, 2022).…”

“…So far, thirteen PM resistance (R) loci have been genetically mapped (Dry et al, 2019;Karn et al, 2021) and named Resistance to Uncinula necator (Run) or Resistance to Erysiphe necator (Ren). Different allelic forms have been found for some of Run and Ren loci (Dry et al, 2019;Massonnet et al, 2022).…”