International collaboration advances research into grape disease resistance
By Janet van Zoeren
Food security and sustainability are a focus of research and innovation around the world. This global challenge provides the opportunity for discoveries to take place through collaboration across institutions and between countries. Unfortunately, these partnerships can be hard to organize, and indeed multiple research groups often address the same questions with limited communication. But an international collaborative effort between the VitisGen2 project and a German research institution has shown that such collaborations can be possible and productive.
Since joining the VitisGen2 team, I have been impressed with how the project facilitates scientists coming together across the country to map the grape genome and to use this information to breed disease-resistant varieties, promoting more sustainably-produced fruit. This past summer, the VitisGen2 team took this a step further with a collaboration involving German scientist Daniel Zendler, a leading expert on the Ren3 gene for powdery mildew resistance. Dr. Zendler, of the Julius-Kühn Institute for Grapevine Breeding Geilweilerhof (JKI), spent three months working with Lance Cadle-Davidson and David Gadoury in Geneva, NY at Cornell AgriTech’s campus.
Start of a collaboration
Zendler and Cadle-Davidson met at the International Conference on Grapevine Breeding and Genetics in France in 2018. Cadle-Davidson had heard of Zendler after reading his recent publication on Ren3 and Ren9 genes, which both influence grapevine resistance to powdery mildew (PM), the most economically important grape disease worldwide. Zendler knew about Cadle-Davidson and the VitisGen2 project from Cadle-Davidson’s presentation earlier that day and his extensive publications on grapevine powdery mildew resistance.
While talking, they discussed their similar research goals, which they are tackling from different angles and with different equipment. To bring together their knowledge and perspectives, they decided that Zendler would spend the summer working at the Cornell AgriTech campus. Luckily, the German Research Foundation (DFG) also values the importance of “initiating international collaborations” and funded a grant to provide Zendler’s travel and project expenses. During the visit, Zendler, Gadoury and Cadle-Davidson followed up on and brought together their previous research experiences to achieve concrete advances in the understanding of grapevine powdery mildew resistance.
For his PhD project, Zendler was studying the specific region of the genome where Ren3 is located. However, he found that the region associated with this resistance shifted during the season. Because of this observation, Zendler and his colleagues discovered — entirely by accident — that the previously published Ren3 region (what geneticists call a Quantitative Trait Locus or QTL) is comprised of two independent resistances, both on chromosome 15, now named Ren3 and Ren9. This is important because it means that these two different resistance loci can be combined (“pyramided”) to provide more long-lasting resistance to PM.
To develop such fine-grain information about these genetic regions, Zendler and his colleagues used a ‘mapping population’, meaning they compared several hundred progeny of two crosses (“Regent” x “Lemberger” and “Regent” x “Cabernet Sauvignon”) to locate new DNA markers associated with the observed resistance. These genetically distinct progeny each carried different combinations of genes from the Regent parent (with Ren3 PM resistance) and the Lemberger or Cabernet Sauvignon parents (having no PM resistance genes).
The observation of new genetic markers with known linkage to PM resistance allowed a very detailed mapping of the Ren3 QTL. In Germany, Zendler and his colleagues observed and recorded PM susceptibility and resistance scores on these genetic lines in the field at the beginning and at the end of an infection period. Combining these data with genetic marker information, they found that the QTL region, which had previously been described as associated with Ren3 (Welter et. al, 2004), shifted during the growing season. At different times of the year the major QTL was either associated with the previously described region of Ren3, or with a genetic region elsewhere on chromosome 15.
Targeted inoculation experiments of selected individuals from the mapping population revealed that those with “Regent” associated alleles in the previously described Ren3 region exhibited a necrosis at the penetration sites of the PM pathogen. The same reaction was observed for the second, newly found QTL, confirming a second resistance-associated region, which is now named Ren9. These artificial inoculation experiments also helped to clarify the location of Ren3 to a very precise region on chromosome 15.
Goals of collaboration
Following completion of his PhD research, as part of a post-doctoral position, Zendler arrived in Geneva in June 2019 to begin work on the next steps toward a more in-depth understanding of the Ren9 PM resistance gene. Over the summer, Cadle-Davidson, Gadoury and Zendler worked together to narrow down the DNA sequence region of the newly-discovered Ren9 locus. The automated phenotyping equipment in Cadle-Davidson’s and Gadoury’s labs (see Martinson and Cadle-Davidson 2018) greatly accelerated the process of screening different lines for PM resistance and mapping the Ren9 locus. In addition, Zendler was able to use this phenotyping equipment to test two other of his research goals: determining whether the resistance conferred by Ren9 is effective against the many strains of PM that are maintained at Cornell AgriTech, and seeing if there is an additive effect to having both Ren3 and Ren9 resistances.
To achieve these goals, Zendler brought leaves from 103 different grape genotypes from Germany. These genotypes were carefully selected according to their specific genetic variability within the Ren9 and Ren3 regions. They were inoculated in the lab at Cornell AgriTech, and the Blackbird phenotyping platform, being developed by VitisGen2, was used to assess the PM hyphal growth on leaves from grape carrying the Ren9 and Ren3 genes. In addition, Zendler’s knowledge of the locus enabled re-analysis of 2000 VitisGen2 breeding lines from Anne Fennell, Bruce Reisch, and Matthew Clark, to rapidly discover 61 vines with useful variation in their genetic makeup at the Ren3 and Ren9 associated regions on chromosome 15. Leaves from these 61 vines were screened using three different powdery mildew strains collected in North America, which will provide important information for U.S. grape breeders.
For Zendler, the research done at Cornell AgriTech provided access to leaves of grape breeding lines, PM isolates, and the phenotyping platform developed by the VitisGen2 project. Zendler mentioned that he had already been able to get some results after working on this project here for less than a month – he suspects it would have been a much slower process working with a microscope at his lab in Germany. After returning to Germany, he’ll do some staining and microscopic follow up studies, providing valuable results for both North American and European grape breeders and growers.
This collaboration provided the VitisGen2 project with access to Zendler’s detailed knowledge of these two widely used resistance genes, and analysis of the German breeding lines relative to U.S. breeding lines, accelerating progress for both countries. The connections established through this visit will foster continued collaboration to move forward on the global quest for more sustainably-produced grapes.
Martinson, T. & L. Cadle-Davidson. 2018. The Phenotyping Bottleneck: How grape breeders link desired traits to DNA markers. Wines and Vines.