Genome-wide approaches for the identification of markers and genes associated with sugarcane yellow leaf virus resistance

Abstract The breeding of sugarcane, a leading sugar and energy crop, is particularly hampered by the extremely complex sugarcane genome. One of the main diseases that affect this crop is sugarcane yellow leaf (SCYL), caused by the sugarcane yellow leaf virus (SCYLV). Regardless of the manifestation of SCYL symptoms, infection by SCYLV can lead to substantial yield losses, making resistance to this virus highly relevant to sugarcane breeding. However, the genetic basis of this trait has not been unraveled or widely explored. In this context, several methodologies have arisen as promising tools for the identification of molecular markers associated with SCYLV resistance, which are crucial for marker-assisted selection and can contribute to the understanding of the mechanisms involved in the response to this virus. Here, we investigated the genetic basis of SCYLV resistance in sugarcane using dominant and codominant markers and genotypes of interest for breeding. A sugarcane panel inoculated with SCYLV was analyzed for SCYL symptom severity, and viral titer was estimated by reverse transcription quantitative PCR. This panel was genotyped with 662 dominant markers, as well as by genotyping-by-sequencing, which enabled the identification of 70,888 SNPs and indels with information on allele proportion and position on the Saccharum spontaneum genome. We then performed polyploid-adapted genome-wide association analyses and used machine-learning algorithms coupled with feature selection methods to establish marker-trait associations. While each approach identified a unique set of markers associated with the phenotypes, we also observed convergences between them, demonstrating their complementarity. Finally, by aligning the sequences neighboring these markers to the genomic coding sequences of closely related plant species, we annotated genes harboring 176 of these markers. With this procedure, we identified genes encoding emblematic participants in virus resistance mechanisms, as well as other candidates whose involvement in the responses to viruses has not been reported before. Our approach has the potential to accelerate sugarcane breeding targeting SCYLV resistance and is a powerful tool for studies on the biological processes leading to this trait.