Screening resistant germplasms and quantitative trait locus mapping of resistance to Tomato chlorosis virus

Tomato chlorosis virus (ToCV) is an emerging plant virus, posing a substantial threat to the cultivation of economically vital vegetable crops, particularly tomato ( Solanum lycopersicum ). Despite its substantial impact on crop yield, resistant or tolerant tomato germplasms have not been well-documented, and the genetic basis of resistance to ToCV remains poorly understood. In this study, two wild accessions that were immune to ToCV and five accessions that were highly resistant to ToCV were identified from 58 tomato accessions. Additionally, a novel method was developed for evaluating resistance to ToCV in tomatoes and observed that tomatoes exhibited typical pathological features on day 15 and day 30 after ToCV inoculation, referred to as Stage 1 and Stage 2, respectively. Using quantitative trait locus (QTL) sequencing in conjunction with classical QTL approaches, ToCV resistance loci were identified in two F2 populations derived from the crosses between SG11 (susceptible) and LA1028(resistant) and between SP15 (susceptible) and LA0444(resistant). Genetic analysis indicated that resistance to ToCV in the wild-type ToCV-resistant tomato accessions LA1028 and LA0444 was quantitative and mainly governed by four loci ( Qtc1.1 and Qtc11.1 from LA1028 and Qtc7.1 and Qtc9.1 from LA0444). Subsequently, transcriptome analysis of three resistant accessions (LA2157, LA0444, and LA1028) and two susceptible accessions (SG11 and SP15) revealed unique differentially expressed genes and specific biological processes at the two stages of ToCV infection. This study provides new resistant germplasms and potential genetic resources for ToCV resistance, which can be valuable in tomato molecular breeding programs to obtain resistant varieties.