The Amur grape (Vitis amurensis Rupr.) thrives naturally in cool climates of Northeast Asia. Resistance against the introduced pathogen Plasmopara viticola is common among wild ecotypes that were propagated from Manchuria into Chinese vineyards or collected by Soviet botanists in Siberia, and used for the introgression of resistance into wine grapes (Vitis vinifera L.). A QTL analysis revealed a dominant gene Rpv12 that explained 79% of the phenotypic variance for downy mildew resistance and was inherited independently of other resistance genes. A Mendelian component of resistance–a hypersensitive response in leaves challenged with P. viticola–was mapped in an interval of 0.2 cM containing an array of coiled-coil NB-LRR genes on chromosome 14. We sequenced 10-kb genic regions in the Rpv12+ haplotype and identified polymorphisms in 12 varieties of V. vinifera using next-generation sequencing. The combination of two SNPs in single-copy genes flanking the NB-LRR cluster distinguished the resistant haplotype from all others found in 200 accessions of V. vinifera, V. amurensis, and V. amurensis x V. vinifera crosses. The Rpv12+ haplotype is shared by 15 varieties, the most ancestral of which are the century-old ‘Zarja severa’ and ‘Michurinets’. Before this knowledge, the chromosome segment around Rpv12+ became introgressed, shortened, and pyramided with another downy mildew resistance gene from North American grapevines (Rpv3) only by phenotypic selection. Rpv12+ has an additive effect with Rpv3+ to protect vines against natural infections, and confers foliar resistance to strains that are virulent on Rpv3+ plants.

BackgroundThe increasing temperature associated with climate change impacts grapevine phenology and development with critical effects on grape yield and composition. Plant breeding has the potential to deliver new cultivars with stable yield and quality under warmer climate conditions, but this requires the identification of stable genetic determinants. This study tested the potentialities of the microvine to boost genetics in grapevine. A mapping population of 129 microvines derived from Picovine x Ugni Blanc flb, was genotyped with the Illumina® 18 K SNP (Single Nucleotide Polymorphism) chip. Forty-three vegetative and reproductive traits were phenotyped outdoors over four cropping cycles, and a subset of 22 traits over two cropping cycles in growth rooms with two contrasted temperatures, in order to map stable QTLs (Quantitative Trait Loci).ResultsTen stable QTLs for berry development and quality or leaf area were identified on the parental maps. A new major QTL explaining up to 44 % of total variance of berry weight was identified on chromosome 7 in Ugni Blanc flb, and co-localized with QTLs for seed number (up to 76 % total variance), major berry acids at green lag phase (up to 35 %), and other yield components (up to 25 %). In addition, a minor QTL for leaf area was found on chromosome 4 of the same parent. In contrast, only minor QTLs for berry acidity and leaf area could be found as moderately stable in Picovine. None of the transporters recently identified as mutated in low acidity apples or Cucurbits were included in the several hundreds of candidate genes underlying the above berry QTLs, which could be reduced to a few dozen candidate genes when a priori pertinent biological functions and organ specific expression were considered.ConclusionsThis study combining the use of microvine and a high throughput genotyping technology was innovative for grapevine genetics. It allowed the identification of 10 stable QTLs, including the first berry acidity QTLs reported so far in a Vitis vinifera intra-specific cross. Robustness of a set of QTLs was assessed with respect to temperature variation.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0588-0) contains supplementary material, which is available to authorized users.

Grape varieties with resistance to downy mildew (DM) carry alien chromosome segments in Vitis vinifera backgrounds. We previously showed that the largest descent group shares a non‐vinifera haplotype at the locus Rpv3. Here, we performed a common garden experiment with 76 varieties to evaluate the level of field resistance across four years. All varieties exhibited effector‐triggered immunity (ETI)‐associated necrosis. On a scale of 1–9, the median OIV452 value for foliar resistance was 7.1 in the resistant lineage vs. 3.2 in vinifera controls. Genotype, year and their interaction significantly affected the level of resistance. Some resistant genotypes showed high mean values of OIV452 and low variance among years. Other resistant genotypes showed lower mean OIV452 and higher variance. They were capable of activating ETI, but the intensity was inadequate to restrict pathogen growth under highly conducive conditions. Rpv3‐dependent responses were stronger in highly native genetic backgrounds and tended to attenuate in late backcross generations. Genetic backgrounds donated by European winegrapes of the convarietas occidentalis provided on average higher levels of Rpv3 resistance than backgrounds of orientalis table grapes.

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.

Over the past two centuries, introgression through repeated backcrossing has introduced disease resistance from wild grape species into the domesticated lineage Vitis vinifera subsp. sativa. Introgression lines are being cultivated over increasing vineyard surface areas, as their wines now rival in quality those obtained from preexisting varieties. There is, however, a lot of debate about whether and how wine laws defining commercial product categories, which are based on the classification of V. vinifera and interspecific hybrid grapes, should be revised to accommodate novel varieties that do not fit either category. Here, we developed a method of multilocus genotype analysis using short–read resequencing to identify haplotypic blocks of wild ancestry in introgression lines and quantify the physical length of chromosome segments free–of–introgression or with monoallelic and biallelic introgression. We used this genomic data to characterize species, hybrids and introgression lines and show that newly released resistant varieties contain 76.5–94.8% of V. vinifera DNA. We found that varietal wine ratings are not always commensurate with the percentage of V. vinifera ancestry and linkage drag of wild alleles around known resistance genes persists over at least 7.1–11.5 Mb, slowing down the recovery of the recurrent parental genome. This method also allowed us to identify the donor species of known resistance haplotypes, define the ancestry of wild genetic background in introgression lines with complex pedigrees, validate the ancestry of the historic varieties Concord and Norton, and unravel sample curation errors in public databases.

Plasmopara viticola is the causal agent of grapevine downy mildew (DM). DM resistant varieties deploy effector-triggered immunity (ETI) to inhibit pathogen growth, which is activated by major resistance loci, the most common of which are Rpv3 and Rpv12. We previously showed that a quick metabolome response lies behind the eti conferred by Rpv3 tiR-nB-LRR genes. Here we used a grape variety operating Rpv12-mediated eti, which is conferred by an independent locus containing cc-nB-LRR genes, to investigate the defence response using Gc/MS, UpLc, UHpLc and RnA-Seq analyses. Eighty-eight metabolites showed significantly different concentration and 432 genes showed differential expression between inoculated resistant leaves and controls. Most metabolite changes in sugars, fatty acids and phenols were similar in timing and direction to those observed in Rpv3-mediated eti but some of them were stronger or more persistent. Activators, elicitors and signal transducers for the formation of reactive oxygen species were early observed in samples undergoing Rpv12-mediated eti and were paralleled and followed by the upregulation of genes belonging to ontology categories associated with salicylic acid signalling, signal transduction, WRKY transcription factors and synthesis of PR-1, PR-2, PR-5 pathogenesis-related proteins. Downy mildew is one of the most destructive diseases of the grapevine, causing significant limitations on grape production in the absence of chemical protection of vineyards. Downy mildew is caused by the biotrophic oomycete Plasmopara viticola (Berk. And Curt) Berl. and Toni, which is native to North America and was introduced into Europe at the end of the nineteenth century. The European bunch grape (Vitis vinifera L.) does not normally activate the immune system in response to P. viticola with a few exceptions 1,2. The introgression of resistant genes from other grape species (i.e. V. rupestris, V. amurensis, V. cinerea, V. riparia and Muscadinia rotundifolia) into the crop germplasm can alleviate the dependence of viticulture on the use of fungicides 3. The pathogen can cause serious damage to any green organ of the grapevine. P. viticola deploys a specialized structure called haustorium to establish a close interaction with grapevines and to leak nutrients from viable host cells 4,5. P. viticola can feed on both susceptible and resistant grapevines and complete its life cycle on both hosts. Resistant grapevines are, however, able to detect the invading pathogen and operate defence responses. The initial phases of the infection are similar on both hosts, but mycelial growth is restricted in resistant hosts and sporangia are released at lower rates than in susceptible hosts. The similarity during early phases of infection suggests the presence of post-infection mechanisms of resistance, including callose deposition, cell wall-associated

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