Research on Variation of Sugarcane Red Rot (Colletotrichum falcatum Went) and Sugarcane Disease Resi

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  Abstract Sugarcane red rot caused by Colletotrichum falcatum Went is one of the important fungal diseases causing significant losses to sugarcane production, commonly known as "cancer" of sugarcane. It has risen from a minor disease to a major disease, resulting in the death of sugarcane in Lincang, Menglian and Shiping sugarcane areas in Yunnan Province. Due to the frequent variation of this pathogen, it is difficult to control, the pesticide control effect is not ideal at present, and there is still no effective and radical cure measures. The research on the variation of C. falcatum and sugarcane disease resistance is the only way to achieve the sustainable control of sugarcane disease. This paper mainly reviewed the genetic variation on the morphological, pathogenic and molecular variation of C. falcatum, and rapid molecular detection methods, and sugarcane disease resistance research in combination with the latest research at home and abroad. An outlook for further research on sugarcane red rot in the future was also given, to provide a theoretical basis for the research and control of sugarcane red rot in China.
  Key words Sugarcane; Colletotrichum falcatum Went; Variation; Molecular identification; Disease resistance
  Sugarcane (Saccharum officinarum L.) is one of the important sugar crops, and sugarcane red rot (Colletotrichum falcatum Went) is one of the most serious fungal diseases on sugarcane, mainly affecting sugarcane stems (i.e., sugarcane stem red rot) and leaf midrib (i.e., midrib red rot). In severe cases, sugarcane red rot can cause a yield reduction of sugarcane by 29.1% and a sucrose loss by more than 30.8%[1], thereby seriously affecting sugarcane yield and quality. Sugarcane red rot has occurred in various sugarcane areas in China. In recent years, due to continuous cropping of sugarcane, climate change, high humidity and rain and the mixing of various pests and diseases, favorable conditions have been provided for the occurrence of sugarcane red rot. Some sugarcane areas seriously suffer from sugarcane red rot, which has become a major disease from a minor disease. At present, there are no high-resistance varieties in production. Plus not ideal prevention and control effect of pharmaceuticals, frequent variation of sugarcane red rot pathogens and long-term cultivation of single susceptible varieties, disease-resistant varieties are often obliged to lose resistance and become susceptible varieties.
  The asexual stage of sugarcane red rot pathogens is C. falcatum[2], and the lethal temperature of the conidia is 60 ℃ for 10 min[3], so warm water treatment of seedlings is not effective in killing red rot pathogens carried in sugarcane varieties. However, it has been proved in practice that the use of suitable agents to disinfect the stems before sugarcane planting is one of the effective ways to reduce the incidence of the disease[4]. Pathogenic strain variation research and variety disease resistance research is the only way for disease prevention and control. Therefore, This paper mainly reviewed the genetic variation on the morphological, pathogenic and molecular variation of C. falcatum, and rapid molecular detection methods, and sugarcane disease resistance research in combination with the latest research at home and abroad, aiming at providing an important theoretical basis for the research and prevention of sugarcane red rot in China.   Sugarcane Red Rot Varation
  Sugarcane red rot fungus is highly prone to variation, and there have been a lot of researches on morphological variation, pathogenic variation and molecular variation. It has been concluded that the morphological classification of most strains is positively correlated with pathogenicity variation, but molecular diversity shows no such correlation[5].
  Morphological variation
  There are morphological variations in sugarcane red rot. Early researchers divided ret rot pathogens into light-colored races and dark races (light type and dark type) according to the culture colony color, hyphal morphology and sporulation[5-7]. The light-colored races produce abundant conidia and are more toxic than darker races[6]. Malathi et al.[8]conducted a study on the pathogenicity of parental varieties and found that although each strain can infect all the tested varieties, the tropical pathogenic type was more virulence. It was also concluded that acervulus initiation and sporulation were related to pathogenic  virulence.
  Pathogenicity variation
  Although the strains showed variations in culture traits and morphological characteristics, it is not reliable to use these traits to carry out variation classification. Therefore, pathogenicity assays based on different hosts are used for variation studies. The differences in pathogenicity of sugarcane red rot pathogens are mainly caused by the different pathogenicity of the same strain to different hosts or the different pathogenicity of different strains to the same host.
  At the beginning of the last century, the United States first reported the athogenicity variation of sugarcane red rot pathogens[9], and many researchers at broad have done a lot of research on the pathogenicity of the disease pathogens, especially in India. Sangdit et al.[10]classified the Thai sugarcane red rot pathogens into two races (pathogenic and non-pathogenic) according to pathogenicity. However, there are 11 pathogenic types (CF01-CF11) of Indian sugarcane red rot pathogens, including 7 species in subtropical regions and 4 species in tropical regions[11-12]. In the early days, Beniwal et al.[13]identified three pathogenic types from the subtropical local varieties Co 1148, Co 7717 and CoJ 64, which were CF01, CF02 and CF03. Subsequently, Padmanaban  et al.[14]isolated three pathogenic types from the varieties Co 419, Co 997 and CoC 671, which were Cf 419, Cf 997 and Cf 671, and were named CF04, CF05, CF06 later, respectively. In the 1980s, pathogenic strains isolated from the tropical varieties Co 419, Co 658, Co 997 and Co 6304 were used for the screening of sugarcane varieties against red rot[15]. However, Viswanathan et al.[16]showed that strains isolated from the varieties CoC 671, CoC 85061, CoC 86062 and CoC 92061 showed stronger pathogenicity than the previously used pathogenic types, and pathogenic Cf 671 and Cf 92061 had strong infectivity and have caused huge losses to sugarcane in many parts of Tamil Nadu and Andhra Pradesh and some parts of Gujarat and Karnataka[17]. Although new pathogenic types such as Cf 92061, Cf 90063 and Cf 767 are more toxic than Cf 671[18], they do not maintain their virulence for a long time and are less virulent after a few years[12], while the new pathogenic Cf 671 can maintain its virulence for many years, and has been used for screening of resistance to red rot for more than 20 years in India[15]. However, in 2004, Viswanathan[15]isolated the new pathogenic Cf 94012 from the variety Co 94012, and used 32 sugarcane varieties for pathogenicity test on pathogenic Cf 671 and new pathogenic Cf 94012 for seven consecutive years. The results showed that the new pathogenic Cf 94012 was more virulent than the pathogenic Cf 671. Similarly, the cf CHA strain isolated by Prittesh  et al. was more virulent and could infect seven sugarcane varieties, and the highly-resistant sugarcane variety Co 94004 was screened. A series of pathogenicity studies in foreign countries have shown that pathogenicity variation of sugarcane red rot pathogens is frequent, which often causes many resistant varieties to lose resistance and become susceptible varieties[19]. The pathogenicity of pathogens is the basis and key to the excavation and screening of disease-resistant resources. However, the pathogenicity and variation of sugarcane red rot in China are still unclear, and relevant research work is urgently needed.   Molecular variation
  With the rapid development of molecular technology, PCR molecular marker technology has been widely used in molecular variation research, providing new methods and means for genetic difference identification of plant pathogens, such as RAPD, ISSR and other techniques. Using RAPD molecular marker technique, Madan et al.[20]used six pairs of primers to study the diversity of five strains isolated from Haryana. The polymorphism was only 23%, and UPGMA cluster analysis divided all strains into two groups. Mohan et al.[21]used 61 pairs of RAPD primers to amplify red rot fungi, giving a polymorphism of 76%. Suman et al.[22]used 40 pairs of RAPD markers to amplify six standard strains, exhibiting a polymorphism of 78.6% and a genetic difference of more than 50%. And UPGMA cluster analysis divided all strains into two groups. Malathi et al.[8]used ITS to classify nine pathogenic types from tropical and subtropical regions of India into two groups. Kumar et al.[23]carried out a population genetic structure study on sugarcane red rot fungi isolated from subtropical regions of India. Using RAPD, URP and ISSR molecular markers, 25 strains were divided into six groups with a genetic similarity of 34%, indicating that these strains are genetically diverse.
  Rapid Molecular Detection Technology for Sugarcane Red Rot
  At present, a rapid molecular detection technology for sugarcane red rot has been developed. Nithya et al.[24]amplified a 560 bp fragment from the red rot fungus genome using RAPD primer OPE-01, and designed a pair of SCAR-labeled primers based on this sequence, i.e., the SCAR-F/R primers, which were highly specific to sugarcane red rot, but not specific to other colletotrichum. The primers were SCAR-F 5′-CCTACCCAACCGAGTATCG-3′ and SCAR-R 5′-GCGCAGCTTGCTCTCAAGAGC-3′, and the amplification product was 442 bp. Wu et al.[24-26]established a dual PCR detection system for sugarcane smut and red rot, including the sugarcane smut primers CLS 320F/R and the sugarcane red rot fungus primers SCAR-F/R[24-26]. Chandra  et al.[27]screened three sets of LAMP-specific primers (RRSC1, RRSC4, RRSC5) by designing two pairs of external primers and two pairs of internal primers, and established a loop-mediated isothermal amplification technique (LAMP) for the detection of sugarcane red rot fungi. The specificity and sensitivity of the LAMP reaction system were tested, and the method showed the sensitivity 5-10 times higher than that of the common PCR (SCAR-F/R primer) detection techniques, thereby realizing visualization detection of the fungi.   Research on Sugarcane Red Rot
  At present, the research on sugarcane resistance to red rot is mainly focused on disease resistance, disease resistance molecular markers and induced disease resistance of sugarcane varieties.
  Research on disease resistance in sugarcane varieties
  The host resistance and sucrose content of sugarcane varieties are correlated with the virulence of pathogens. Malathi & Viswanathan studied the relationship between red rot pathogen variation and host resistance using 12 genotypes of six sugarcane varieties. The culture study showed that virulence-related factors (growth, sporulation and conidial germination) of red rot pathogens were negatively correlated with host resistance, but positively correlated with the sucrose contents of different sugarcane varieties. The pathogenicity study showed that identifying the resistance of different host varieties by the pathogenic types of red rot pathogens should be selective, and the strains with weak virulence had especially good infection effects on sugarcane varieties with low sucrose contents. Therefore, for effective screening, the selection of genotypes of different varieties depends on pathogenic virulence, and it is necessary to choose the dominant strains that infect well[28].
  After crops suffer from pathogen infection, ultraviolet radiation, low temperature and other adverse stimuli, they will synthesize various secondary metabolites and disease-related proteins for defense. In the early days, Viswanathan et al.[29]reported that phytoalexin synthesis was more  in sugarcane varieties resistant to sugarcane red rot than in susceptible varieties. Malathi et al.[30]carried out further research to analyze the synthesis of phytoalexins after the inoculation of red rot pathogens in resistant sugarcane variety (Co 93009) and susceptible sugarcane variety (COC 671) by high performance liquid chromatography. Two phytoalexins, luteolinidin and apigeninidin, were synthesized after the inoculation with red rot, and luteolinidin was detected in both the resistant and susceptible varieties 24 h after inoculation, but after 48-72 h, it increased in the disease-resistant variety and remained unchanged in the susceptible variety. In addition, 48-72 h after the inoculation of the red rot pathogens, apigeninidin was detected only in the resistant variety, and it was very clear that the resistant variety specifically induced 3-deoxyanthocyanidins at a high level, which was also found to be rapid in the resistant variety. Viswanathan et al. showed that the disease-resistant (PR) proteins such as chitinase and thaumatin-like protein accumulated earlier in the resistant variety Co 93009 after inoculation with the red rot pathogens, while this type of induction in the susceptible variety CoC 671 was significantly delayed.   Disease resistance molecular markers
  The development of disease resistance molecular marker technology can speed up the breeding process for disease resistance. Alvi et al. used RAPD molecular technique to study the genetic differences between the genotypes of 12 red rot-resistant sugarcane varieties and five susceptible cultivars. The average genetic similarity between disease susceptible and resistant sugarcane genotypes was 74.37%, indicating that most genomes were similar, and the degree of polymorphism in sugarcane genotypes was not associated with resistance and susceptibility to red rot. Virupakshi & Naik used ISSR markers to analyze the chloroplast and mitochondrial genomes of seven resistant/moderately resistant and five susceptible sugarcane varieties. The UPGMA cluster analysis divided the sugarcane varieties into two groups: the resistant/moderately resistant group and the susceptible group. This result indicates that the marker is a new powerful tool for disease resistance identification, genetic relationship analysis and diversity evaluation. Using the resistance gene homologous sequence (RGA) strategy, Jayashree et al. designed 29 RGA primers from the conserved domains of resistance proteins, and analyzed the genetic diversity of 40 sugarcane varieties with different resistance to red rot. The genetic similarity ranged from 58.4 to 90%, and the average genetic similarity was 74.2%. The cluster analysis clearly distinguished the susceptible and resistant varieties, and identified 25 specific fragments amplified by 14 pairs of primers to be related to resistance and eight specific fragments amplified by eight pairs of primers to be related to susceptibility. These resistance gene homologous sequences, which are found to be associated with resistance and susceptibility in varieties, are a valuable marker source for screening for materials resistant to red rot in breeding. Similarly, Sharma & Tamta identified 18 fragments to be associated with resistance to red rot and seven fragments to be associated with susceptibility to red rot by the disease resistance gene homologous sequence strategy. The 18 fragments can be used as specific markers of disease resistance, and the seven fragments can be used as specific markers of disease susceptibility. Singh et al. used SSR markers to study the genetic diversity of 30 sugarcane genotypes with different resistance to red rot. The cluster analysis clearly distinguished all genotypes. Specifically, the resistant genotypes (ISH150 and SES594) were clearly into one cluster, while the remaining genotypes were divided into two distinct clusters, separating the moderately resistant and susceptible sugarcane genotypes. Singh et al. found that UGSM316850 and UGSM31660 in SSR markers were closely related to the medium-resistant varieties, while UGSM316400 was closely related to the highly-susceptible varieties.   Agricultural Biotechnology2019
  Study on induced disease resistance
  Induced disease resistance is mainly to resist infection by foreign pathogens through the stimulation of plants by foreign factors to activate and regulate the plants autoimmune response. At present, there are more systematic studies on system acquired resistance (SAR) and induced system resistance (ISR).
  Acibenzolar-S-methyl, benzo(1,2,3-thiadiazole-7-carbothioic acid-S-methyl (BTH), is a synthetic SA analog, which does not have a direct antimicrobial effect, but can induce the resistance of plants to effectively resist the infection of pathogens. Sundar et al. compared the system acquired resistance(SAR)  in varieties CoC 671 and CoC 92061 highly susceptible to red rot with 100 μg/ml acibenzolar-S-methyl, salicylic acid, isoicotinic acid and succinic acid. The results showed that all the sugarcane treated with inducers for plant disease resistance changed from highly susceptible to moderately resistant. Among the different inducers, acibenzolar-S-methyl induced higher level of tissue resistance, effectively limiting the colonization of pathogens, accompanied by a significant increase in peroxidase (POX) and polyphenol oxidase (PPO), demonstrating that the induction of oxidases is one of the mechanisms of system acquired resistance. Similarly, the results of Ashwin et al. also demonstrated that acibenzolar-S-methyl was the most effective of the several inducers for plant diseases resistance that induce resistance against sugarcane red rot.
  Early studies by Viswanathan & Samiyappan showed that Pseudomonas fluorescens can induce induced system resistance (ISR), which significantly reduces the colonization of red rot pathogens and reduces sugar loss. Subsequently, the induction of system resistance by P. fluorescens was carried out on different resistant sugarcane varieties. The results showed that the induced disease resistance of highly-susceptible varieties was more significant than that of the moderately-resistant and moderately-susceptible varieties. The results showed that for the resistance to red rot, compared with the inherent host defense mechanism of sugarcane against red rot, the induced system resistance was not significant. Furthermore, the use of P. fluorescens also reduced invertase and improved the quality of cane juice.
  Prospects
  Prevention and control of sugarcane red rot
  Sugarcane red rot can cause huge economic losses to sugarcane. The initial infection source of red rot is diseased sugarcane and the residual leaves of diseased plants in the field, which can reinfect plants with wind and rain and dew, and it is difficult to effectively control. For a long time, sugarcane red rot is a minor disease in Chinas sugarcane area, which is rarely studied. However, in recent years, sugarcane stem red rot has occurred locally, while there is a lack of accurate diagnosis and effective control technology. Plus heavy economic loss, sugarcane stem red rot has risen to the major disease of sugarcane. Sugarcane red rot fungi are prone to variation, and the emergence of new pathogenic races leads to the "loss of disease resistance" of sugarcane varieties.  Even if resistant varieties are planted, they will be susceptible due to emergence of new races with higher pathogenicity within 8-10 years. A single control method cannot effectively reduce the losses caused by sugarcane red rot. It is necessary to avoid long-term cultivation of single highly-susceptible varieties ROC 1, ROC 22, ROC 16, Taitang 89-1626, Yuetang 93-159, Yuetang 00-236[2, 45]. The disease can be controlled by the treatment of sugarcane seeds and soil with biological control agents such as Tichoderma spp., Pseudomonas spp., and Bacillus spp. Borer channels on cane stems are the main invasive channels of red rot spores[2], and the monitoring of borers should be strengthened. Frequency-vibrancy pest-killing lamps or sexual attractants are used to trap the adults, or trichogrammatid is released to prevent borers.  Meanwhile, field management should be strengthened to reduce the use of fungicides, and combined with a variety of green control methods, comprehensive green prevention and control can be applied to effectively control widespread epidemics of diseases, reduce damage losses and achieve sustainable control of sugarcane red rot.   Research on genetic structure of sugarcane red rot pathogens
  Compared with foreign countries, the research on this disease is relatively weak in China. At present, it is mainly concentrated in the indoor screening stage of fungicides and biocontrol bacteria, and there is a blank of in-depth systematic research. The genetic structure of sugarcane red rot pathogens and the resistance of  sugarcane varieties are still not clear, which hinders the use of disease-resistant varieties and the implementation of precise  prevention and control. In the future, researchers should actively carry out identification, systematic evolution and diversity research of different geographical environmental pathogens of sugarcane red rot, to master the main pathogens of sugarcane red rot in different ecological regions and study the pathogenic mechanisms of red rot pathogens and the law of disasters, which is of great significance for the development of corresponding resistance research and  utilization. The resistance to red rot pathogens should be monitored in real time, and detected using the developed simple, fast and efficient loop-mediated isothermal amplification technique (LAMP) without the need for expensive instruments and experimental conditions, which is beneficial for popularization at the grassroots level.
  Discovery of sugarcane red rot resistance genes
  Chinas National Nursery of Sugarcane Germplasm Resources contain more than 2 800 sugarcane germplasm resources from 16 varieties in 6 genera. It is a huge precious gene pool for sugarcane genetic improvement in China and the world, as well as an important source of disease resistance genes. Stable multi-resistant sugarcane variety germplasm resources are the basis and key to the breeding for the resistance to red rot. In the future research work, the molecular marker breeding technology can be used to improve the breeding efficiency. With the use of this technology, the disease resistance genes of sugarcane varieties can be fully excavated from the huge planting resource pool to screen excellent germplasm resources, and the heredity laws and resistance mechanism of sugarcane red rot disease are comprehensively analyzed, so as to discover and locate major QTLs that can be stably expressed in different environments.
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