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The sugarcane leaf diseases such as mosaic and streak mosaic are difficult to differentiate using Image processing techniques because both diseases show similar visual attributes such as pattern and color. To identify the type of diseases, we need to perform Polymerase Chain Reaction (PCR) testing which is used for the classification of diseases in laboratories. The accuracy of the PCR test depends on reaction mix preparation, reaction time, and DNA/RNA extraction. The major problem influencing the PCR test accuracy is the Annealing temperature of the primers and needs a standardized set of samples. In addition, it is a time-consuming process. In this paper, we proposed a Diversified Deep Learning Architecture (DDLA) which is developed with the input images after various pre-processing steps such as denoising using Discrete Wavelet Transform (DWT) and enhancing using histogram equalization in HSI color space to improve the similar pattern disease prediction accuracy. The performance of the proposed model is analyzed for a set of diseased leaves and the results are compared with the output of the popular pertained models such asVGG16, InceptionV3, ResNET50, Inception ResNET, and DenseNET201 with and without pre-processing. The training accuracy of the proposed model is 97% and the testing accuracy is 87%. The DDLA model produces ground truth test results with an accuracy of 88.7% for mosaic and 85.7% for streak mosaic with a less computational time of 152sec compared to the lab test duration of 6 hrs. The performance of the model is also measured in terms of Precision, F1 Score, Specificity, and Sensitivity. The Proposed DDLA model’s F1 score is higher than the pre-trained models with a minimum test loss of 1.167. Moreover, the DDLA structure occupies less memory space when compared to the pertained models.

Mosaic is one of the most important sugarcane diseases, caused by single or compound infection of Sugarcane mosaic virus (SCMV), Sorghum mosaic virus (SrMV), and/or Sugarcane streak mosaic virus (SCSMV). The compound infection of mosaic has become increasingly serious in the last few years. The disease directly affects the photosynthesis and growth of sugarcane, leading to a significant decrease in cane yield and sucrose content, and thus serious economic losses. This review covers four aspects of sugarcane mosaic disease management: first, the current situation of sugarcane mosaic disease and its epidemic characteristics; second, the pathogenicity and genetic diversity of the three viruses; third, the identification methods of mosaic and its pathogen species; and fourth, the prevention and control measures for sugarcane mosaic disease and potential future research focus. The review is expected to provide scientific literature and guidance for the effective prevention and control of mosaic through resistance breeding in sugarcane.

Mosaic viral diseases affect sugarcane productivity worldwide. Mining disease resistance-associated molecular markers or genes is a key component of disease resistance breeding programs. In the present study, 285 F 1 progeny were produced from a cross between Yuetang 93-159, a moderately resistant variety, and ROC22, a highly susceptible variety. The mosaic disease symptoms of these progenies, with ROC22 as the control, were surveyed by natural infection under 11 different environmental conditions in the field and by artificial infections with a mixed sugarcane mosaic virus (SCMV) and sorghum mosaic virus (SrMV) inoculum. Analysis of consolidated survey data enabled the identification of 29 immune, 55 highly resistant, 70 moderately resistant, 62 susceptible, and 40 highly susceptible progenies. The disease response data and a high-quality SNP genetic map were used in quantitative trait locus (QTL) mapping. The results showed that the correlation coefficients (0.26~0.91) between mosaic disease resistance and test environments were significant ( p < 0.001), and that mosaic disease resistance was a highly heritable quantitative trait ( H 2 = 0.85). Seven mosaic resistance QTLs were located to the SNP genetic map, each QTL accounted for 3.57% ~ 17.10% of the phenotypic variation explained (PVE). Furthermore, 110 pathogen response genes and 69 transcription factors were identified in the QTLs interval. The expression levels of nine genes ( Soffic.07G0015370-1P , Soffic.09G0015410-2T , Soffic.09G0016460-1T , Soffic.09G0016460-1P , Soffic.09G0017080-3C , Soffic.09G0018730-3P , Soffic.09G0018730-3C , Soffic.09G0019920-3C and Soffic.03G0019710-2C ) were significantly different between resistant and susceptible progenies, indicating their key roles in sugarcane resistance to SCMV and SrMV infection. The seven QTLs and nine genes can provide a certain scientific reference to help sugarcane breeders develop varieties resistant to mosaic diseases.

Sorghum mosaic virus (SrMV) causes sugarcane mosaic disease and has significant adverse economic impacts on the cultivation of sugarcane. This study aimed to develop a rapid isotherm nucleic acid amplification method for detecting SrMV. Specific primers were designed to target the conserved region of the P3 gene of SrMV. The reverse transcription recombinase-aided amplification (RT-RAA) method was developed by screening primers and optimizing reaction conditions. Comparative analyses with RT-PCR demonstrated that the RT-RAA method exhibited superior specificity, sensitivity, and reliability for SrMV detection. Notably, using a standard plasmid diluted 10-fold continuously as a template, the sensitivity of RT-RAA was 100-fold higher than that of RT-PCR. Moreover, the RT-RAA reaction displayed flexibility in a temperature range of 24–49 °C, eliminating the need for expensive and complex temperature control equipment. Thus, this method could be utilized at ambient or even human body temperature. Within a short duration of 10 min at 39 °C, the target sequence of SrMV could be effectively amplified. Specificity analysis revealed no cross-reactivity between SrMV and other common sugarcane viruses detected via the RT-RAA. With its high sensitivity, rapid reaction time, and minimal equipment requirements, this method presents a promising diagnostic tool for the reliable and expedited detection of SrMV. Furthermore, it indicates broad applicability for successfully detecting other sugarcane viruses.

In this study, we investigated 78 sugarcane samples with severe mosaic symptoms collected from four provinces of southern China: Guangxi, Yunnan, Hainan, and Guangdong, which cover nearly 85 % of commercial sugarcane planting zones in China. Using RT-PCR, sequencing and phylogenetic analysis, we identified 72 hybrid sugarcane samples containing causal agents of sugarcane mosaic disease. Among these, 66 virus isolates were identified as Sorghum mosaic virus (SrMV) (84.6 %), four were identified as Sugarcane streak mosaic virus (SCSMV) (5.1 %), and two were identified as Sugarcane mosaic virus (SCMV) (2.6 %). The isolates of SrMV were classified into three subgroups: I, II, and III with a 95 % similarity level. The two largest subgroups, SrMV I containing 36 sugarcane mosaic diseases isolates (46.2 %), and SrMV III containing 20 isolates (25.6 %), were prevalent in Guangdong and Guangxi provinces; however, SrMV II containing five isolates (6.4 %) did not exhibit any close association with geographical distribution. The popular sugarcane cultivar, ROC22, was found to be infected with all the three subgroup types of SrMV. According to our knowledge, this is the first reported detection of the co-infection of SrMV and SCSMV in Saccharum hybrid (YN-bs-9). Recombination analysis indicated recombination between different isolates mostly occurring in Yunnan and Guangxi provinces among the SrMV I group. This study provides insight into the species diversity and geographical distribution of causal agents of sugarcane mosaic disease, and provides the basis for its identification, prevention, and future control efforts.

Objective The selection of reference genes in sugarcane under Sugarcane mosaic virus (SCMV) infection has not been reported and is indispensable to get reliable reverse transcription quantitative PCR (RT-qPCR) results for validation of transcriptome analysis. In this regard, seven potential reference genes were tested by RT-qPCR and ranked according to their stability using BestKeeper, NormFinder and GeNorm algorithms, and RefFinder WEB-based software in an experiment performed with samples from two sugarcane cultivars contrasting for SCMV resistance, when mechanically inoculated with a severe SCMV strain and using mock inoculated plant controls. Results The genes Uridylate kinase (UK) and Ubiquitin-conjugating enzyme 18 (UBC18) were the most stable according to GeNorm algorithm and the Pearson correlation coefficients with the BestKeeper index. On the other hand, ribosomal protein L35-4 (RPL1), Actin (ACT) and Ubiquitin1 (UBQ1) were the least stable genes for all algorithms tested.

Five sugarcane leaf samples exhibiting mosaic symptoms and collected in 1999-2003 in Bangladesh, India, Sri Lanka, Thailand, and Vietnam tested negative in serological assays (ELISA and TBIA) using antiserum to sugarcane mosaic virus (SCMV) and a potyvirus specific monoclonal antibody. In addition, these samples reacted negative in RT-PCR assays with SCMV, sorghum mosaic virus (SrMV), and potyvirus specific primers. Mosaic symptoms were reproduced after mechanical inoculation of sugarcane, maize, and sorghum plants with diseased leaf extracts, but symptoms were less severe than those of SCMV and SrMV. Electron microscopy of partially purified virions from inoculated plants showed flexuous filaments characteristic of the Potyviridae family. The five sugarcane leaf samples tested positive in RT-PCR assays with two primer pairs designed to detect sugarcane streak mosaic virus (SCSMV), and in immunological assays with SCSMV antisera. SCSMV was detected by ELISA with three different antisera and by RT-PCR in 34 leaf samples from 30 cultivars exhibiting mosaic symptoms and originating from six Asian countries (the five mentioned above and Pakistan). The sequences of the RT-PCR amplicons (376 nucleotides) showed 98.5-100% identity with SCSMV isolates from GenBank. The immunological, molecular, and pathogenic characteristics of SCSMV were different from those of SCMV and SrMV. Our results suggested that SCSMV was already widespread in Asia more than two decades ago. Furthermore, immunological variation occurs among SCSMV isolates, which needs to be considered for serological diagnosis of the virus. RT-PCR primers developed in this study proved to be very efficient for detection of SCSMV from different countries.

The viral genome-linked protein, VPg, of potyviruses is involved in viral genome replication and translation. To determine host proteins that interact with Sugarcane mosaic virus (SCMV) VPg, a yeast two-hybrid screen was used and a maize (Zea mays) Elongin C (ZmElc) protein was identified. ZmELC transcript was observed in all maize organs, but most highly in leaves and pistil extracts, and ZmElc was present in the cytoplasm and nucleus of maize cells in the presence or absence of SCMV. ZmELC expression was increased in maize tissue at 4 and 6 d post SCMV inoculation. When ZmELC was transiently overexpressed in maize protoplasts the accumulation of SCMV RNA was approximately doubled compared with the amount of virus in control protoplasts. Silencing ZmELC expression using a Brome mosaic virus-based gene silencing vector (virus-induced gene silencing) did not influence maize plant growth and development, but did decrease RNA accumulation of two isolates of SCMV and host transcript encoding ZmeIF4E during SCMV infection. Interestingly, Maize chlorotic mottle virus, from outside the Potyviridae, was increased in accumulation after silencing ZmELC expression. Our results describe both the location of ZmElc expression in maize and a new activity associated with an Elc: support of potyvirus accumulation.

KEY MESSAGE : Genome-wide association analysis in tropical and subtropical maize germplasm revealed that MLND resistance is influenced by multiple genomic regions with small to medium effects. The maize lethal necrosis disease (MLND) caused by synergistic interaction of Maize chlorotic mottle virus and Sugarcane mosaic virus, and has emerged as a serious threat to maize production in eastern Africa since 2011. Our objective was to gain insights into the genetic architecture underlying the resistance to MLND by genome-wide association study (GWAS) and genomic selection. We used two association mapping (AM) panels comprising a total of 615 diverse tropical/subtropical maize inbred lines. All the lines were evaluated against MLND under artificial inoculation. Both the panels were genotyped using genotyping-by-sequencing. Phenotypic variation for MLND resistance was significant and heritability was moderately high in both the panels. Few promising lines with high resistance to MLND were identified to be used as potential donors. GWAS revealed 24 SNPs that were significantly associated (P < 3 × 10⁻⁵) with MLND resistance. These SNPs are located within or adjacent to 20 putative candidate genes that are associated with plant disease resistance. Ridge regression best linear unbiased prediction with five-fold cross-validation revealed higher prediction accuracy for IMAS-AM panel (0.56) over DTMA-AM (0.36) panel. The prediction accuracy for both within and across panels is promising; inclusion of MLND resistance associated SNPs into the prediction model further improved the accuracy. Overall, the study revealed that resistance to MLND is controlled by multiple loci with small to medium effects and the SNPs identified by GWAS can be used as potential candidates in MLND resistance breeding program.

Seventy-seven mosaic leaf samples from new sugarcane varieties from national regional trials in Kaiyuan, Mile and Yuanjiang, Yunnan Province, China, were collected in 2015 and analyzed using reverse-transcription polymerase chain reaction (RT-PCR) to determine the pathogen causing mosaic symptoms in sugarcane. Three viruses, Sugarcane streak mosaic virus (SCSMV), Sorghum mosaic virus (SrMV) and Sugarcane mosaic virus (SCMV), were detected in 100, 27.3 and 1.3% of the samples respectively. Co-infection with SCSMV, SrMV and SCMV was also found for the first time in the new variety Qiantang 5. Nucleotide sequences of the coat protein (CP) gene of 48 SCSMV and 17 SrMV isolates were subsequently sequenced and analyzed with the CP gene sequences of SCSMV and SrMV reported in GenBank to perform phylogenetic analyses. Geographic differences were observed in the phylogenetic tree of SCSMV and all SCSMV isolates from China clustered into a single China group. Moreover, SCSMV isolates from different new varieties were distributed across all subgroups or clustered into an independent branch in the China group. SrMV isolates obtained in this study and those published in GenBank clustered into two groups and were distributed into different subgroups within these groups. Furthermore, the distribution of SrMV isolates from different new varieties overlapped in these different groups and subgroups, with no obvious geographic differences. These results provide a scientific basis for sugarcane mosaic or streak mosaic disease resistance breeding and effective control of this disease.