Deciphering resistance to Tomato brown rugose fruit virus (ToBRFV) using Genome-Wide Association Studies

Tomato Brown Rugose Fruit Virus (ToBRFV) is an emerging, highly virulent virus that seriously threatens global production of tomatoes and peppers. Following its initial discovery in Israel and subsequent isolation in Jordan, the virus has spread to more than 50 countries in Asia, Africa, Europe, and America. During the last few years, the virus has become a significant concern due to its ability to spread through various ways, including infected seeds, mechanical contact, pollinators like bumble bees (Bombus terrestris) and pests such as invasive tomato leafminer (Tuta absoluta). Furthermore, the lack of commercially resistant varieties and the hurdle of disinfecting contaminated areas underscore the critical importance of addressing the threat posed by ToBRFV. Therefore, the main objective of this study was to explore genomic regions related to ToBRFV resistance and to identify accessions that could serve as a source of resistance. To achieve this, we evaluated 161 tomato accessions from Varitome collection and conducted Genome-Wide Association Studies (GWAS) utilizing 8,265,571 SNPs, 2,735,297 INDELs, and 27,477 SVs. GWAS led to identification of six INDELs and eight SNPs associated with ToBRFV Disease Severity Index, and we identified 14 QTLs using FarmCPU, GLM, and BLINK models. Furthermore, we identified five tomato accessions that exhibit high resistance to ToBRFV, namely BGV006370, BGV007366, BGV012615 from Varitome collection, along with LA0716 and LA1777. The identified ToBRFV resistant accessions and genomic loci will aid in further finemapping QTLs controlling ToBRFV tolerance, which could be utilized to develop commercial cultivars with desired phenotypic performance.