Effect of Sugarcane Cultivars Infected with Sugarcane Yellow Leaf Virus (ScYLV) on Feeding Behavior and Biological Performance of Melanaphis sacchari (Hemiptera: Aphididae)

Sugarcane yellow leaf virus (ScYLV), Polerovirus, Luteoviridae, is one of the main viruses that infect sugarcane worldwide. The virus is transmitted by the aphid Melanaphis sacchari in a persistent, circulative manner. To better understand the interactions between ScYLV, sugarcane genotypes and M. sacchari, we explored the effect of sugarcane cultivars on the feeding behavior and biological performance of the vector. The number of nymphs, adults, winged, total number of aphids and dead aphids was assayed, and an electrical penetration graph (EPG) was used to monitor the stylet activities. Multivariate analysis showed changes in the vector’s behavior and biology on cultivars, identifying specific groups of resistance. In the cultivar 7569, only 5.5% of the insects were able to stay longer on sustained phloem ingestion, while in the other seven cultivars these values varied from 20% to 60%. M. sacchari showed low phloem activities in cultivars 7569 and Bio266. Overall, cultivar 7569 showed the worst biological performance of aphids, with the insects presenting mechanical difficulties for feeding and a shorter duration of the phloem period, and thus being considered the most resistant. We conclude that ScYLV virus infection in different sugarcane cultivars induced specific changes in the host plant, modifying the behavior of its main vector, which may favor or impair virus transmission.

Survey of Sugarcane Yellow Leaf Virus in the Canal Point Breeding and Cultivar Development Program

Sugarcane yellow leaf virus (SCYLV), a Polerovirus in the family Luteoviridea, causes yellow leaf disease (YLD). Yield losses from YLD have been reported from several countries in both symptomatic and asymptomatic sugarcane cultivars. The breeding nursery at Canal Point (CP) in 2016 and primary and secondary seed increases in the CP cultivar development program at grower’s farm from 2015 to 2019 were surveyed for SCYLV infection by the tissue-blot immunoassay using polyclonal antibodies raised against SCYLV. More than 32% of varieties in the CP breeding nursery were infected with SCYLV in 2016. The SCYLV data of primary and secondary seedcane increases from 2015 to 2019 showed that out of 54 varieties screened at different locations, 12 had no SCYLV-positive plants, 24 had less than 5%, 5 had 6% to 12%, and 13 had 20% to 75% of the plants infected with SCYLV. The SCYLV screenings in varieties in the primary and secondary seed increase plantings provide growers an opportunity to acquire virus-free clean seedcane by apical meristem propagation to minimize the spread of the SCYLV and avoid yield losses.

Potential Targets for Evaluation of Sugarcane Yellow Leaf Virus Resistance in Sugarcane Cultivars: In silico Sugarcane miRNA and Target Network Prediction

The Sugarcane yellow leaf virus (SCYLV) is associated with sugarcane yellow leaf disease (SCYLD) and is considered to be the most economically deleterious emerging pathogen that represents a potential threat and danger to sugarcane cultivation in China. Over the last two decades, high genetic diversity in the SCYLV genotypes was observed worldwide, with a greater chance of YLD incidence for sugarcane injury. SCYLV infection has significantly damaged its economic traits and is responsible for substantial losses in biomass production in sugarcane cultivars. This study aims to identify and comprehensively analyze sugarcane microRNAs (miRNAs) as therapeutic targets against SCYLV using plant miRNA prediction tools. Mature sugarcane miRNAs are retrieved and are used for hybridization of the SCYLV. A total of seven common sugarcane miRNAs were selected based on consensus genomic positions. The biologically significant, top ranked ssp-miR528 was consensually predicted to have a potentially unique hybridization site at nucleotide position 4162 for targeting the ORF5 of the SCYLV genome; this was predicted by all the algorithms used in this study. Then, the miRNA–mRNA regulatory network was generated using the Circos algorithm, which was used to predict novel targets. There are no acceptable commercial SCYLV-resistant sugarcane varieties available at present. Therefore, the predicted biological data offer valuable evidence for the generation of SCYLV-resistant sugarcane plants.

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

Sugarcane yellow leaf (SCYL), caused by the sugarcane yellow leaf virus (SCYLV) is a major disease affecting sugarcane, a leading sugar and energy crop. Despite damages caused by SCYLV, the genetic base of resistance to this virus remains largely unknown. Several methodologies have arisen to identify molecular markers associated with SCYLV resistance, which are crucial for marker-assisted selection and understanding response mechanisms to this virus. We investigated the genetic base of SCYLV resistance using dominant and codominant markers and genotypes of interest for sugarcane breeding. A sugarcane panel inoculated with SCYLV was analyzed for SCYL symptoms, and viral titer was estimated by RT-qPCR. This panel was genotyped with 662 dominant markers and 70,888 SNPs and indels with allele proportion information. We used polyploid-adapted genome-wide association analyses and machine-learning algorithms coupled with feature selection methods to establish marker-trait associations. While each approach identified unique marker sets associated with phenotypes, convergences were observed between them and demonstrated their complementarity. Lastly, we annotated these markers, identifying genes encoding emblematic participants in virus resistance mechanisms and previously unreported candidates involved in viral responses. Our approach could accelerate sugarcane breeding targeting SCYLV resistance and facilitate studies on biological processes leading to this trait.

Comparative genomics reveals insights into genetic variability and molecular evolution among sugarcane yellow leaf virus populations

Yellow leaf disease caused by sugarcane yellow leaf virus (SCYLV) is one of the most prevalent diseases worldwide. In this study, six near-complete genome sequences of SCYLV were determined to be 5775–5881 bp in length. Phylogenetic analysis revealed that the two SCYLV isolates from Réunion Island, France, and four from China were clustered into REU and CUB genotypes, respectively, based on 50 genomic sequences (this study = 6, GenBank = 44). Meanwhile, all 50 isolates were clustered into three phylogroups (G1–G3). Twelve significant recombinant events occurred in intra- and inter-phylogroups between geographical origins and host crops. Most recombinant hotspots were distributed in coat protein read-through protein (RTD), followed by ORF0 (P0) and ORF1 (P1). High genetic divergences of 12.4% for genomic sequences and 6.0–24.9% for individual genes were determined at nucleotide levels. The highest nucleotide diversity (π) was found in P0, followed by P1 and RdRP. In addition, purifying selection was a main factor restricting variability in SCYLV populations. Infrequent gene flow between Africa and the two subpopulations (Asia and America) were found, whereas frequent gene flow between Asia and America subpopulations was observed. Taken together, our findings facilitate understanding of genetic diversity and evolutionary dynamics of SCYLV.

Genome-Wide Association Mapping of Sugarcane Yellow Leaf Virus Resistance

The breeding of sugarcane, a leading sugar and energy crop, is complicated by the extremely complex sugarcane genome, which burdens research in the area and delays the development of new cultivars. One of the main viral diseases that affect this crop is sugarcane yellow leaf (SCYL), which is caused by the sugarcane yellow leaf virus (SCYLV). The most common symptom of SCYL is the yellowing of leaf midribs and blades, but asymptomatic cases are frequent. Regardless of the manifestation of SCYL, 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 widely explored or explained. In this context, genome-wide association studies (GWASs) have arisen as promising tools for the identification of molecular markers associated with SCYLV resistance that can be employed in marker-assisted selection. In the present work, we performed a GWAS on sugarcane using codominant markers and genotypes of interest for breeding. A panel of 97 sugarcane genotypes inoculated with SCYLV was analyzed for SCYL symptom severity, and viral titer was estimated by reverse transcription quantitative PCR (RT-qPCR). A genotyping-by-sequencing (GBS) library was constructed for 94 individuals of this population, enabling the identification of 38,710 SNPs and 32,178 indels with information on allele proportion (AP) and position on the Saccharum spontaneum genome. For association analyses, several combinations of population structure and kinship were tested to reduce model inflation, and diverse marker-trait association mixed models were employed. We identified 35 markers significantly associated with SCYL symptom severity and 22 markers strongly associated with SCYLV titer that can be applied in breeding programs upon validation. By aligning the sequences flanking these markers with their coding sequences in several plant species, we annotated the functions of 7 genes. The possible involvement of these candidates in the response to SCYLV infection is discussed.