Haplotype diversity and marker development at grapevine (Vitis) disease resistance loci

Abstract

Studying disease resistance loci in grapevines (Vitis) is a complex process because resistance QTL often coincide with highly-repetitive NLR gene clusters that are difficult to analysis bioinformatically, requiring extra time and attention to fully characterize. With the ever-increasing use of next generation sequencing, long-read genome assemblies, and efforts like the USDA-funded VitisGen3 grape breeding and genetics project, these regions have become more accessible to researchers and breeders alike. Ahallmark endeavor of VitisGen3 has been to identify and characterize resistance loci, test candidate gene function, develop markers for marker-assisted selection, and create bioinformatic pipelines to expedite selection on these loci for breeding programs world-wide. This effort wouldn’t be possible without the creation of the Vitis colinear core genome rhAmpSeq panel. Available as a service to anyone in the world, the panel has been used to genotype more than 80,000 grapevines since its publication in 2019, including the accessions from the USDAgermplasm repository. To date, rhAmpSeq alleles have been utilized for the prediction of more than 30 resistance loci and other traits of interest for marker-assisted selection. With rhAmpSeq discovery and screening of resistance QTL now routine, VitisGen3 has expanded into QTL fine mapping, KASP marker development, chromosome painting, and studies on haplotype diversity. In this talk, I aim to highlight the strategies used by VitisGen3 for characterizing the haplotypes at resistance loci such as Rpv3, among others, and the development of low-cost KASP markers.

Acknowledgements

We would like to thank the entire VitisGen3 team but especially the project director, Matthew Clark, and project manager, Kate Fessler. VitisGen3 is funded by a Specialty Crop Research Initiative Competitive Grant, Award No. 2022-51181-38240, from the USDANational Institute of Food and Agriculture.