Two dominant loci determine resistance to Phomopsis cane lesions in F1 families of hybrid grapevines

• Published in: Theoretical and applied genetics Vol. 131; no. 5; pp. 1173 - 1189
• Main Authors: Barba, Paola, Lillis, Jacquelyn, Luce, R. Stephen, Travadon, Renaud, Osier, Michael, Baumgartner, Kendra, Wilcox, Wayne F., Reisch, Bruce I., Cadle-Davidson, Lance
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01.05.2018; Springer Nature B.V
• Subjects: Agriculture; Biochemistry; Biomedical and Life Sciences; Biotechnology; Chromosome 15; Chromosome 7; Fruits; Fungi; Gene expression; Gene mapping; Gene regulation; Genetic analysis; Genetic crosses; Genotypes; Genotyping; Inoculation; Inoculum; Leafspot; Life Sciences; Localization; Original; Original Article; Phomopsis viticola; Plant Biochemistry; Plant Breeding/Biotechnology; Plant Genetics and Genomics; Quantitative trait loci; Transcription; Vitis cinerea; Vitis vinifera
• ISSN: 0040-5752; 1432-2242
• DOI: 10.1007/s00122-018-3070-1

Key message Rapid 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 F 1 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 Rda 1 and Rda 2 from V. cinerea B9 and ‘Horizon’, respectively. Co-linearity between reference genetic and physical maps allowed localization of Rda 2 locus between 1.5 and 2.4 Mbp on chromosome 7, and Rda 1 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 Rda 1, 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, Rda 1 and Rda 2 are promising loci for grapevine genetic improvement.