Search

Sugarcane is the world’s most widely grown sugar crop accounts for almost 75% of world sugar production. Diseases are the major productivity constraints for sugarcane that considerably reduce yield and sugar recovery. Identification of disease resistance is an important and sustainable approach for disease management. More recently, Brazilian researchers have characterized the whole genome sequences of a commercial sugarcane cv SP80-3280 and mapped 373,869 genes or ninety nine percent of the total genome. Use of next- generation sequencing (NGS) techniques have facilitated the availability of complete genomic information of various sugarcane pathogens, have led to the understanding of organization of the disease resistance gene clusters for unraveling the genetic mechanism involved in developing new resistance strategies to manage sugarcane diseases. Genome wide association study (GWAS) reveal polymorphisms related with composite characters in the whole genome. In the omics era, whole genome sequencing of host and pathogens combined with the availability of bioinformatics tools for their analyses led to the emergence of GWAS, a potent method for identifying genomics region covering resistance loci in various plants. This review summarizes the literature generated during last the 10 years on GWAS in sugarcane related to disease resistance and along with novel single nucleotide polymorphism and quantitative trait loci’s hotspots identified for economically important diseases of sugarcane.

Sugarcane is an important sugar crop contributes more than 80% of world sugar production. Mosaic, leaf fleck, and yellow leaf (YL) are the major viral diseases affecting sugarcane, amongst YL occurrence is widely reported in all the sugarcane growing countries. It is caused by Sugarcane yellow leaf virus (SCYLV) and detailed works were done on complete genome characterization, transmission, and management. However, in countries like Egypt, South Africa, Cuba, Mauritius and Hawaii, the disease was reported to the cause of sugarcane yellow leaf phytoplasma (SCYP) and/or SCYLV as single/combined infections. Hence, we have investigated in detail to identify the exact Candidatus phytoplasma taxon associated in Indian cultivars affected with YL. The sequencing results and the restriction fragment length polymorphism pattern of the PCR products using the universal phytoplasma primers confirmed presence of sugarcane grassy shoot (SCGS) phytoplasma (16SrXI group) in the YL-affected plants. Mixed infection of SCYLV and SCGS phytoplasma was estimated as 32.8% in YL affected plants. Evolutionary genetic relationship between SCYP and SCGS phytoplasma representatively taken from different countries showed that SCYP from South Africa and Cuba were diverged from others and had a highest similarity with SCGS phytoplasma. Although we wanted to identify SCYP from YL affected Indian sugarcane cultivars, the study clearly indicated a clear absence of SCYP in YL affected plants and we found SCYLV as the primary cause for the disease.

Among 10 proteins encoded by Papaya ringspot virus (PRSV), only coat protein (CP) has been studied extensively from mainly the papaya-originated isolates i.e. PRSV-P. In this study, besides CP, the helper component proteinase (HC-pro) and nuclear inclusion protein-a (NIa-pro) coding regions from 19 PRSV-P and -W isolates originating from different geo-climatic locations and hosts were analyzed. Unlike CP, both HC-pro and NIa-pro did not reveal the variability in their length. HC-pro and NIa-pro sequences revealed less than 10% deduced amino acid (daa) diversity worldwide, the CP was found highly variable (up to 20% daa diversity). Highest variability in CP sequence was noticed among the cucurbit-originating PRSV-P Indian isolates, especially from Warm semi-arid climate, which was attributed to a large number of aa insertions/deletions. However, papaya-originating PRSV-P isolates from the Oceanic climate were less variable (up to 5% daa diversity). In NIa-pro, besides already known host/pathotype-specific switching of aa Lys/Asp27, switching of Lys27 → Arg27 and Asp27 → Glu27 was identified within P and W pathotypes. Additionally, a novel aa switching from Ser/Met134 → Thr134 between P and W pathotypes respectively was identified. The phylogeny of PRSV isolates was largely based on the geo-climatic locations and hosts. Through recombination detection analysis, three recombinant isolates were detected based on both NIa-pro and CP sequences, which possessed cucurbit-originated PRSV (either -P or -W) isolates as one of their parents (either major or minor.) Patterns of codon usage among the three protein coding sequences generated further revealed that the CP gene is under maximum selection pressure (with six sites) followed by NIa-pro gene (with one site). This investigation shows that the genetic recombination between the isolates originating from different hosts and geo-climatic locations as well as mutations are the significant mechanisms playing their role in generating diverse populations of PRSV.

Loop-mediated isothermal amplification (LAMP) is a rapid, highly specific and reliable technique, which is widely incorporated in the field for diagnosis of pathogens at their early stage of infection. In present study, RT-LAMP assay was developed successfully to detect Sugarcane yellow leaf virus (SCYLV) causing yellow leaf disease in sugarcane and compared with conventional reverse transcription-polymerase chain reaction (RT-PCR) and quantitative real-time polymerase chain reaction (qRT-PCR) to assess its sensitivity. RT-LAMP was able to detect the SCYLV up to a limit of 10 pg (picogram), while RT-PCR assays were able to detect this virus up to 100 pg only. The sensitivity of the RT-LAMP method was tenfold higher than that of conventional RT-PCR assay. This study revealed high sensitivity of RT-LAMP in detecting SCYLV in Indian sugarcane cultivars.

Sugarcane, an important field crop, is cultivated under tropical and subtropical regions around the world. Fusarium sacchari causing wilt, is a stalk disease, inflicting severe damage to the crop in India and other countries. Similarly, pokkah boeng (PB) a foliar disease caused by different species of Fusarium also infects the crop throughout the world. In India, both the diseases occur in different states in various sugarcane varieties. Although both diseases occur independently in the field, we recorded that they occur together in a plant. Hence, a detailed investigation was conducted to characterize different Fusarium isolates from wilt- and PB-affected sugarcane varieties by sequencing TEF1-α gene. Gene sequencing of 48 isolates revealed that 44 were of F. sacchari and the remaining four belonged to F. proliferatum. Of the four F. proliferatum, three were associated with PB and one with wilt. Almost all the 41 wilt-associated isolates belonged to F. sacchari. Investigation carried out to identify Fusarium isolates from the plants exhibiting both the wilt and the PB in two varieties Co 0238 and MS 901 revealed that only F. sacchari caused wilt and PB symptoms in both. Further, several varieties showed progressive disease severity through different phases of PB and that resulted in wilt development. The results clearly established for the first time that the same fungal pathogen systematically infects sugarcane plant and exhibits both the diseases.

Sugarcane is one of the important commercial cash crops grown widely for sugar production. Red rot, smut, wilt, grassy shoot and yellow leaf are the major diseases of sugarcane worldwide; however the sugarcane grassy shoot (SCGS) is considered the most destructive one due to the associated total loss of millable canes production. Although the crop is cultivated in tropical and sub-tropical regions across the globe, widespread occurrence of the disease is mostly reported only from South and South East Asian countries. The disease was first reported in India in 1949. Based on its symptomatology, it is known as grassy shoot in India, Pakistan, and white leaf in Thailand, Vietnam, Myanmar, China and known by both names in Sri Lanka. The past seven decades witnessed several research advancements in symptomatology recognition, diagnosis and management of this disease. The nested PCR based diagnostic approach initiatives taken during 1990s followed by the in silico virtual RFLP analyses development in the period of 2007–2009 revolutionized the molecular characterization of the pathogen based on the variability analyses which resulted in the description of reports of many phytoplasma strains infecting sugarcane. Several phloem sap feeding leafhoppers such as Deltocephalus vulgaris, Cofana unimaculata, Exitianus indicus and Maiestas portica in India, Matsumuratettix hiroglyphicus and Yamatotettix flavovittatus in Thailand and D. menoni in Sri Lanka were reported as insect vectors during the last ten years. The recent use of next generation sequencing technologies helped to sequence whole genome of the SCGS phytoplasma. Currently, heat therapy and pathogen elimination through meristem tissue culture based seedling production are the only available management techniques to prevent the disease spread into new areas. Despite the fast pace of research in pathogen detection and genomics, the research on disease management under field conditions still remain grey and pose challenges to sugarcane pathologists.

The family Luteoviridae comprises of three genera Luteovirus, Enamovirus and Polerovirus, of which, only two genera Luteovirus and Polerovirus are known in India. Though luteovirus and polerovirus infects many crops throughout the world, only a few have been documented in India. Luteoviruses were reported in field crops like barley (barley yellow dwarf virus) and chickpea (chickpea stunt virus), while polerovirus was recorded from potato, jute (potato leaf roll virus [PLRV]) sugarcane (sugarcane yellow leaf virus [SCYLV]) and cotton (cotton leaf roll dwarf virus) crops from India. SCYLV and PLRV are the most important poleroviruses as they are of serious constraints in all the sugarcane and potato growing states of India. SCYLV infection causes 39–43% reductions in plant growth and 30–34% loss in yield in sugarcane. The virus is mainly transmitted through infected seed canes. The secondary spread of the virus in the field is by the aphid vectors. PLRV is reported to cause 50–60% yield losses in potato crop and this virus is tuber borne and transmitted mainly by aphid vectors in a circulative non-propagative manner. The complete genome sequences SCYLV and PLRV isolates from sugarcane and potato are available from India. This book chapter deals with an uptodate information available on distribution, biological properties, identification, serological relationships, genetic diversity and transmission of the luteoviruses and poleroviruses reported on different crops from India.

In India, potyvirus infection is common in Solanaceae, Cucurbitaceae, Poaceae and Leguminosae families. Economically important crops like potato, tomato, papaya, banana, sugarcane and pepper are affected by potyviruses as one of the major production constraints. There are as many as 39 different potyviruses recorded in India of which the virus species Potato virus Y, Papaya ringspot virus, Sugarcane mosaic virus and Banana bract mosaic virus are economically more significant. An up-to-date information on the occurrence, biology, serology and molecular biology of the potyviruses that has been investigated in India is presented in this chapter.

Pathogenic Behaviour Pattern of Colletotrichum falcatum Isolates of Sugarcane in Sub-tropical India Red rot caused by Colletotrichum falcatum is the most serious disease of sugarcane affecting cane production in different states in India. Since the pathogenic variants very frequently emerge in the field we have assessed pathogenic variation in 12 C. falcatum isolates collected from subtropical India along with previously designated pathotypes on a set of 16 host differentials for the eight seasons. By and large, a variable virulence pattern in C. falcatum isolates was recorded on most of the host differentials. The results showed that the predominant sub-tropical pathotypes (CF09 and CF08) isolated from then the ruling cultivars CoS 767 and CoJ 64, respectively showed less virulence and the pathotype CF02 isolated from Co 7717 showed higher virulence over the period of time on the host differentials. The higher aggressiveness exhibited by CF02 over on the differentials such as Co1148, Co 975 and Khakai and known susceptible differentials Co 997, Co 62399, CoC 671, CoJ 64 and another variety Co 89003 clearly revealed higher virulence of CF11 pathotype. Even though the pathotype CF08 remained virulent on its host cultivar CoJ 64, it could not cause same type of virulence on the recently developed cultivars and it suggests that the pathotype no longer maintains its virulence once a popular cultivar CoJ 64 removed from the cultivation. Among the 11 new C. falcatum isolates evaluated, the isolate Cf8436 Karnal was found to be virulent and the differential CoS 8436 succumbed to this isolate only. Of the different CoJ 64 pathotypes, Cf64-I exhibited higher virulence and showed susceptible to intermediate reaction on different host differentials. This study suggests continuous evolution of red rot pathogen and its adaptation to the new host cultivars in subtropical India....