Gene duplication and transposition of mobile elements drive evolution of the Rpv3 resistance locus in grapevine

Abstract

Summary A wild grape haplotype (Rpv3‐1) confers resistance to Plasmopara viticola. We mapped the causal factor for resistance to an interval containing a TIR‐NB‐LRR (TNL) gene pair that originated 1.6–2.6 million years ago by a tandem segmental duplication. Transient coexpression of the TNL pair in Vitis vinifera leaves activated pathogen‐induced necrosis and reduced sporulation compared with control leaves. Even though transcripts of the TNL pair from the wild haplotype appear to be partially subject to nonsense‐mediated mRNA decay, mature mRNA levels in a homozygous resistant genotype were individually higher than the mRNA trace levels observed for the orthologous single‐copy TNL in sensitive genotypes. Allelic expression imbalance in a resistant heterozygote confirmed that cis‐acting regulatory variation promotes expression in the wild haplotype. The movement of transposable elements had a major impact on the generation of haplotype diversity, altering the DNA context around similar TNL coding sequences and the GC‐content in their proximal 5′‐intergenic regions. The wild and domesticated haplotypes also diverged in conserved single‐copy intergenic DNA, but the highest divergence was observed in intraspecific and not in interspecific comparisons. In this case, introgression breeding did not transgress the genetic boundaries of the domesticated species, because haplotypes present in modern varieties sometimes predate speciation events between wild and cultivated species.

Two-omics data revealed commonalities and differences between Rpv12- and Rpv3-mediated resistance in grapevine

“…Despite the inherent limitations of this kind of comparative experiments, we observed that changes leading to a common metabolic reprogramming necessary for triggering and operating cell death at the infection sites and for SA-dependent synthesis of PR-proteins have occurred in Rpv12-mediated resistance with similar timing and in the same direction as observed for Rpv3mediated resistance. While the causal factor that triggers Rpv3-mediated HR has been identified in the gene products of two nearby TIR-NB-LRRs 58 , the causal gene that would explain the observed Mendelian inheritance of Rpv12-mediated resistance has not been isolated yet 21 . The sequence of the reference grapevine genome that has been assembled from a DM sensitive genotype predicts the presence of allelic forms of CC-NB-LRR genes in the Rpv12 locus 21,59 .…”

“…Reads were aligned to the grapevine PN40024 reference transcriptome 59,78 Use of RnA-Seq data for the description of the genetic makeup of the genotype under-study. We also used RNA-Seq reads from all samples and stages to perform allele-specific read alignment against a modified version of the grapevine genome reference that included the reference Rpv3-PN40024 haplotype and the alternative resistance Rpv3-1 haplotype and called variant sites using the procedure described in 58 . RNA reads revealed a substantial number of homozygous sites in transcribed genes of the Rpv3-1 sequence, which allowed us to exclude that the genotype analysed in this study had inherited from its parent 'Bianca' the resistance haplotype at the Rpv3 locus.…”

“…S7), approximately 2 Mb downstream of the reported location of the Rpv12 locus 21 . A closer inspection into the introgression around the Rpv12 locus was conducted using available DNA sequencing reads of 'Merlot Khorus' , a variety known to carry the Rpv12 resistance haplotype, which derived from the backcross to vinifera of a full-sibling of the genotype under study (uncle-nephew relationship), and UD-21076 58 , which derived from the selfing of 'Bianca' , the second parent of the genotype under study ( Supplementary Fig. S8).…”

Plasmopara viticola infection affects mineral elements allocation and distribution in Vitis vinifera leaves

“…Several Quantitative Trait Loci (QTLs), named Resistance to P. viticola ( Rpv ) genes, have been identified in different grapevine species and they have been associated with major phenotypic traits of resistance to downy mildew disease. In particular, Rpv1 and Rpv2 were found to be responsible for the resistance in Muscadinia rotundifolia 29 , Rpv3 was associated with the resistance in ‘Villard blanc’ 30 , whilst the resistance traits in V. amurensis was ascribed to Rpv8 , Rpv10 and Rpv12 31 – 33 . Since the discovery of the resistance traits to P. viticola , breeding programs have been undertaken in order to introduce the features related to downy mildew resistance in susceptible species 34 – 38 .…”

Rpv29, Rpv30 and Rpv31: Three Novel Genomic Loci Associated With Resistance to Plasmopara viticola in Vitis vinifera

“…), exhibit varying levels of resistance, ranging from moderate to high, due to co-evolution with the pathogen ( Jürges et al, 2009 ). Several QTL (Quantitative Trait Loci), conferring downy mildew resistance, at different levels ranging from weak to total, were discovered in Vitis species background: Rpv1 and Rpv2 in Muscadinia rotundifolia Michaux ( Merdinoglu et al, 2003 ; Wiedemann-Merdinoglu et al, 2006 ); Rpv3 and Rpv19 in Vitis rupestris Scheele ( Welter et al, 2007 ; Bellin et al, 2009 ; Divilov et al, 2018 ; Vezzulli et al, 2019 ; Foria et al, 2020 ); Rpv4 , Rpv7 , Rpv11 , Rpv17 , Rpv18 , Rpv20 , and Rpv21 , in unspecified American species ( Fischer et al, 2004 ; Welter et al, 2007 ; Bellin et al, 2009 ; Divilov et al, 2018 ); Rpv5 , Rpv6 , Rpv9 , and Rpv13 in V. riparia ( Marguerit et al, 2009 ; Moreira et al, 2011 ); Rpv8 , Rpv10 , Rpv12 , Rpv22 , Rpv23 , Rpv24 , Rpv25 , and Rpv26 in V . amurensis ( Blasi et al, 2011 ; Schwander et al, 2012 ; Venuti et al, 2013 ; Song et al, 2018 ; Lin et al, 2019 ); Rpv14 in V. cinerea ( Ochssner et al, 2016 ); Rpv15 and Rpv16 in Vitis piasezkii Maxim.…”