Grapevine powdery mildew resistance and susceptibility loci identified on a high-resolution SNP map

Abstract

Improved efficacy and durability of powdery mildew resistance can be enhanced via knowledge of the genetics of resistance and susceptibility coupled with the development of high-resolution maps to facilitate the stacking of multiple resistance genes and other desirable traits. We studied the inheritance of powdery mildew (Erysiphe necator) resistance and susceptibility of wild Vitis rupestris B38 and cultivated V. vinifera ‘Chardonnay’, finding evidence for quantitative variation. Molecular markers were identified using genotyping-by-sequencing, resulting in 16,833 single nucleotide polymorphisms (SNPs) based on alignment to the V. vinifera ‘PN40024’ reference genome sequence. With an average density of 36 SNPs/Mbp and uniform coverage of the genome, this 17K set was used to identify 11 SNPs on chromosome 7 associated with a resistance locus from V. rupestris B38 and ten SNPs on chromosome 9 associated with a locus for susceptibility from ‘Chardonnay’ using single marker association and linkage disequilibrium analysis. Linkage maps for V. rupestris B38 (1,146 SNPs) and ‘Chardonnay’ (1,215 SNPs) were constructed and used to corroborate the ‘Chardonnay’ locus named Sen1 (Susceptibility to Erysiphe necator 1), providing the first insight into the genetics of susceptibility to powdery mildew from V. vinifera. The identification of markers associated with a susceptibility locus in a V. vinifera background can be used for negative selection among breeding progenies. This work improves our understanding of the nature of powdery mildew resistance in V. rupestris B38 and ‘Chardonnay’, while applying next-generation sequencing tools to advance grapevine genomics and breeding.

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Acknowledgments

We thank Edward Buckler and Qi Sun for support with GBS procedures and genetic analysis; Alex Lipka for statistical advice; and Laura Shannon for her help in R/QTL use and linkage map construction. This research was supported by BecasChile, the USDA Viticulture Consortium—East, the New York Wine & Grape Foundation, and the Lake Erie Regional Grape Processors Fund. Partial funding was also provided by a USDA-National Institute of Food and Agriculture—Specialty Crop Research Initiative Competitive Grant, Award No. 2011-51181-30635.

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Correspondence to Bruce Reisch.

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Communicated by R. Töpfer.

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Suppl. S1 Number of crossovers per individual as a function of percentage of missing data. Individuals 2, 36, 45, 50, 55, 62, 66, 70, 74 and 76 showing an increased proportion of crossing over were discarded from the linkage analysis (TIFF 81 kb)

Suppl. S2 The allelic state of each significant SNP in each of the parents and progeny. For each progeny, ‘Chardonnay’ (Ch) and Vitis rupestris B38 (R), each of these biallelic SNPs is coded as dark red or light red, with a blank for missing data. Marker name corresponds with chromosome location in the PN40024 reference genome. S20 markers have not been assigned to a chromosome, and S27 corresponds to unassembled portions of chromosome 7. Locus LD reports the reference chromosome to which the marker was in linkage disequilibrium. S10_16893872 was not in LD with any PN40024 reference chromosome (PDF 36 kb)

Suppl. S3 Linkage disequilibrium of single SNPs with whole genome SNPs from the corresponding parent, measured as D′. X axis indicates SNP position based on alignment to the physical map (PN40024). Additional information for each of these significant SNPs is provided in Table 2 (PDF 1072 kb)

Suppl. S4 Linkage disequilibrium (LD) analysis based on D′ calculations for a full matrix of selected chromosomes of V. rupestris B38 (A) and ‘Chardonnay’ (B). Chromosomes 7 and 9 contain SNPs associated with powdery mildew resistance and chromosomes 6 and 16 are representative of the pattern observed among the remaining chromosomes. X- and Y-axes indicate SNP positions based on alignment to the physical map (PN40024). Markers with high D′ values are in LD (red to purple) as commonly seen by the within chromosome comparisons. Panel (C) represents an enlargement of the comparison between chromosomes 9 and 16 of ‘Chardonnay’. The arrow shows the position of significant marker S16_11260816. Alignment to the physical map placed this marker in chromosome 16, but LD analysis and the linkage map placed it on chromosome 9. (TIFF 586 kb)

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Barba, P., Cadle-Davidson, L., Harriman, J. et al. Grapevine powdery mildew resistance and susceptibility loci identified on a high-resolution SNP map. Theor Appl Genet 127, 73–84 (2014). https://doi.org/10.1007/s00122-013-2202-x

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Keywords

  • Quantitative Trait Locus
  • Single Nucleotide Polymorphism
  • Powdery Mildew
  • Reference Genome
  • Interval Mapping