Documenting and mining disease resistance alleles in the USDA Vitis repositories

Abstract

The USDAAgricultural Research Service maintains Vitis germplasm repositories in Geneva, NY and Davis, CAcollectively preserving approximately 5,000 unique accessions representing 30 Vitis species. Over the past two decades, biparental mapping families derived from selected accessions have been evaluated for resistance to powdery mildew and downy mildew, resulting in the discovery of numerous quantitative trait loci (QTL) and resistance alleles that are now actively used in breeding programs. Over this time, genotyping and phenotyping technologies have evolved to enable higher throughput approaches to allele mining, driven by innovations in the VitisGen projects. Given the allelic diversity at resistance loci, QTL mapping remains the most reliable approach for discovering novel resistance alleles. Currently, the primary bottleneck is generating sufficient seedling populations to support accelerated allele mining pipelines. Open data initiatives like the VIVC database (https://www.vivc.de/) and the Grapevine QTL Browser (https://grapedia.org/qtl-browser/) are leading the way to making genetic discoveries accessible to breeding programs. In USDA, we plan to use the GRIN database (https://www.ars-grin.gov/) to document known resistance alleles and chromosome painting of species representation for each accession. The next challenges are to rapidly introgress multiple novel resistance alleles into high quality genetic backgrounds for grape breeding and cultivar release.