Abstract
Key messageRapid characterization of novel NB-LRR-associated resistance to Phomopsis cane spot on grapevine using high-throughput sampling and low-coverage sequencing for genotyping, locus mapping and transcriptome analysis provides insights into genetic resistance to a hemibiotrophic fungus.Phomopsis cane and leaf spot, caused by the hemibiotrophic fungus Diaporthe ampelina (syn = Phomopsis viticola), reduces the productivity in grapevines. Host resistance was studied on three F1 families derived from crosses involving resistant genotypes ‘Horizon’, Illinois 547-1, Vitis cinerea B9 and V. vinifera ‘Chardonnay’. All families had progeny with extremely susceptible phenotypes, developing lesions on both dormant canes and maturing fruit clusters. Segregation of symptoms was observed under natural levels of inoculum in the field, while phenotypes on green shoots were confirmed under controlled inoculations in greenhouse. High-density genetic maps were used to localize novel qualitative resistance loci named Rda1 and Rda2 from V. cinerea B9 and ‘Horizon’, respectively. Co-linearity between reference genetic and physical maps allowed localization of Rda2 locus between 1.5 and 2.4 Mbp on chromosome 7, and Rda1 locus between 19.3 and 19.6 Mbp of chromosome 15, which spans a cluster of five NB-LRR genes. Further dissection of this locus was obtained by QTL mapping of gene expression values 14 h after inoculation across a subset of the ‘Chardonnay’ × V. cinerea B9 progeny. This provided evidence for the association between transcript levels of two of these NB-LRR genes with Rda1, with increased NB-LRR expression among susceptible progeny. In resistant parent V. cinerea B9, inoculation with D. ampelina was characterized by up-regulation of SA-associated genes and down-regulation of ethylene pathways, suggesting an R-gene-mediated response. With dominant effects associated with disease-free berries and minimal symptoms on canes, Rda1 and Rda2 are promising loci for grapevine genetic improvement.
Highlights
Agricultural producers are facing increasing pressure to reduce the use of fungicides, for which deployment of cultivars with disease resistance is one viable solution.1 3 Vol.:(0123456789)Theoretical and Applied Genetics (2018) 131:1173–1189several sources of resistance to major crop diseases have been identified and introgressed
All parental genotypes showed few to no symptoms, having either a score of 0, or a score of 1
Cluster symptoms were absent from female parents and were not possible to observe with the dioecious male parents V. cinerea B9 and Illinois 547-1
Summary
Agricultural producers are facing increasing pressure to reduce the use of fungicides, for which deployment of cultivars with disease resistance is one viable solution.1 3 Vol.:(0123456789)Theoretical and Applied Genetics (2018) 131:1173–1189several sources of resistance to major crop diseases have been identified and introgressed. Once genetic control of major diseases and the subsequent reduction in fungicide applications is achieved, other problems may emerge, namely pathogens that were secondary targets of routine fungicide applications. This phenomenon has been observed in powdery and downy mildewresistant vineyards, where the incidence of grapevine black rot increased (Molitor and Beyer 2014; Rex et al 2014). Phomopsis cane and leaf spot of grapevine (“Phomopsis”) is caused by Diaporthe ampelina Host cells become necrotic and shoot lesions and leaf spots usually appear 3–4 weeks after infection (Wilcox et al 2015). Phomopsis can cause lesions on the rachis, resulting in loss of up to 30% of yields (Anco et al 2012)
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