Diagnosis and characterization of plant viruses in Mexico using HTS: an approach to guide virus management and marker-assisted selection

High-throughput sequencing (HTS) has revolutionized plant virus detection through viral genome reconstruction and comprehensive identification of known and novel viruses. Where available, marker-assisted breeding programs have successfully deployed molecular markers for developing virus-resistant cultivars. However, the systematic integration of these complementary approaches remains limited in practical breeding applications. This review compares rRNA-depleted RNA and siRNA-based approaches for plant virus detection. Evidence supports that siRNA-based methods have superior reliability across diverse viral genome types. Here, we document the implementation of HTS siRNA at our lab over 10 years in common bean, with recent diagnostic applications in chickpeas and tomatoes, enabling precise identification and genome characterization of viral species, variants, and strains in specific geographical areas. This characterization allows for appropriate management strategies, including vector control, sanitary practices, and resistance breeding based on virus-specific transmission biology. Our approach integrates composite sampling strategies, systematic confirmation workflows using PCR, RT-PCR, or RCA, and marker-assisted selection. Its implementation confirmed BCMV, BCMNV, and BGYMV as predominant threats to common bean production, guiding the development of a multiplex RT-PCR diagnostic tool and marker-assisted breeding strategies. This resulted in nine common bean cultivars resistant to viruses prevalent in different regions. Additionally, we discovered new viral species: Phaseolus vulgaris severe mosaic virus, bean latent virus, chickpea leaf roll virus, the putative novel species Phaseolus rotundatus endornavirus, and a novel tomato mosaic virus variant. This integrated approach addresses practical challenges in implementing HTS for breeding applications, including cost management and technical expertise requirements to select appropriate control methods and guide marker-assisted breeding efforts toward developing virus-resistant cultivars.