Red Rot Resistance Research Articles

Marker-assisted screening of promising forms in the strawberry breeding

The results of the use diagnostic DNA-markers in the breeding of strawberry (Fragaria × ananassa Duch.) were shown. The carriers of target alleles of red stele root rot resistance (F. virginiana Duch. ssp. platypetala, Bylinnaya, 69-29 (Feyerverk × Bylinnaya), 72-24 and 72-71 (Privlekatelnaya × Bylinnaya)), anthracnose resistance (Borovitskaya, Sudarushka, Elianny, Troubadour, 933-4 (F. virginiana Duch. ssp. platypetala × Rubinovyy kulon)), high mesifurane content in fruits (F. orientalis Los., F. moschata Duch., F. virginiana Duch. ssp platypetala, Lastochka, Torpeda, Flora, Samson, 932-29 (F. virginiana Duch. ssp. platypetala × Feyerverk), 56-5 (Gigantella × Privlekatelnaya)) and γ-decalactone content in fruits (F. orientalis Los., F. moschata Duch., F. ovalis Rydb., Bylinnaya, Kupchikha, Sonata, Vima Tarda) were identified. These genotypes are valuable initial forms for involvement in the breeding process to improve the strawberry assortment.

Молекулярно-генетический анализ отборных и элитных форм земляники по генам резистентности <i>Rpf1</i> и <i>Rca2</i>

Исследования проведены в 2019 – 2020 гг. в Тамбовской области. В качестве биологических объектов использованы перспективные отборные и элитные формы земляники садовой селекции Федерального научного центра им. И. В. Мичурина. Показаны результаты молекулярно-генетического анализа отборных и элитных форм земляники по генам устойчивости к фитофторозному увяданию Rpf1 и антракнозу Rca2. Маркер SCAR-R1A, сцепленный с геном Rpf1, выявлен у форм 62-41 (Былинная × Фейерверк), 69-29 (Фейерверк × Былинная) (предполагаемый генотип по гену устойчивости — Rpf1rpf1). Маркер STS-Rca2_240, сцепленный с геном Rca2, выявлен у отборной формы 933-4 (Fragaria virginiana Duch. ssp. platypetala × Рубиновый кулон) (предполагаемый генотип по гену устойчивости — Rca2rca2). У остальных изученных генотипов земляники маркеры SCAR-R1A и STS-Rca2_240 не выявлены (предполагаемый генотип по локусам устойчивости — rpf1rpf1rca2rca2). Для получения перспективных форм земляники садовой, совмещающих в генотипе гены устойчивости к антракнозной чёрной гнили (Rca2) и фитофторозному увяданию (Rpf1), необходимо дальнейшее проведение целенаправленной селекционной работы с привлечением в гибридизацию идентифицированных источников целевых аллелей генов резистентности.

Transcriptional reprogramming of major defense-signaling pathways during defense priming and sugarcane-Colletotrichum falcatum interaction.

Red rot caused by Colletotrichum falcatum poses a serious threat to sugarcane cultivation in many tropical and sub-tropical countries. Deciphering the molecular network of major defense-signaling pathways in sugarcane cultivars with varying red rot resistance is essential to elucidate the phenomenon of defense priming exerted by resistance inducers. Therefore, in this study, expression pattern of transcripts coding for major defense-signaling pathway regulatory genes was profiled during compatible and incompatible interactions and in response to defense priming using qRT-PCR. Candidate genes that were profiled are involved in or related to hypersensitive response and reactive oxygen species production (HR/ROS), salicylic acid (SA), and jasmonic acid/ethylene (JA/ET) pathways. For compatible and incompatible interactions, susceptible (CoC 671), field tolerant (Co 86032) and resistant (Co 93009) sugarcane cultivars were used, whereas for defense priming, benzothiadiazole (BTH) and the pathogen-associated molecular patterns (PAMPs) of C. falcatum viz., CfEPL1 (eliciting plant response-like) and CfPDIP1 (plant defense inducing protein) were used in CoC 671 cultivar. Results indicated that the master regulator of defense pathways, nonexpressor of pathogenesis-related genes 1 (NPR1) was highly upregulated in incompatible interactions (in both Co 86032 and Co 93009) than the compatible interaction along with SA pathway-associated genes. Similarly, in response to defense priming with BTH, CfEPL1 and CfPDIP1, only the SA pathway-associated genes showed considerable upregulation at 0h post inoculation (hpi) and other intermittent time points. Overall, this study showed that SA-mediated defense pathway is the most predominant pathway reprogrammed during priming with BTH, CfEPL1 and CfPDIP1 and substantiated the earlier findings that these agents indeed induce systemic resistance against red rot of sugarcane.

Sustainable Sugarcane Cultivation in India Through Threats of Red Rot by Varietal Management

Sugarcane is traditionally cultivated in India since time immemorial to extract gur and Khandsari sugar. In the country, white sugar manufacturing started ~ 300 years ago the with imported Saccharum officinarum genotypes. After 1850s, sugar industry expanded rapidly and such expansion also led to emergence of new threats in the form of red rot caused by the dreaded fungal pathogen Colletotrichum falcatum. The new threat caused production losses in the then Presidencies of Madras, Bombay and Bengal. Sugarcane Breeding Institute (SBI) was established in 1912 to breed sugarcane varieties for red rot resistance with other desirable agronomical traits. The institute achieved commercial success by releasing the first interspecific hybrid variety Co 205 during 1918 and release of many such varieties to the subtropical region revolutionized sugarcane cultivation by improved cane yield leading to attaining self-sufficiency in sugar requirement. Although the new varieties sustained the boom, red rot started attacking the elite varieties in different decades through a series of epidemics. These epidemics hindered sugarcane cultivation for a while in different states; however after each epidemic, new varieties were deployed to counter the disease onslaught and saved sugar industry from the brink. Many superior varieties with red rot resistance have benefitted the industry, but evolution of new C. falcatum pathotypes caused breakdown of resistance and made the life of many elite varieties short-lived. In the recent decades, variation in C. falcatum was characterized, designated into new pathotypes, and new pathotypes were used for red rot screening. The historical red rot epidemics in the country over the decades resembled to ‘boom and bust cycle’ reported in cereal rust diseases. Domination of single variety combined with flood during monsoon seasons/waterlogging favoured red rot epidemics. Notwithstanding red rot epidemics, red rot-resistant varieties played a vital role to manage the disease and to sustain sugarcane cultivation in India for more than 100 years.

Genetic variation in sugarcane cultivars for red rot resistance revealed by resistant gene analog polymorphism markers

Genetic diversity among 55 different sugarcane (Saccharum) cultivars varying in their response for red rot disease (Colletotrichum falcatum) was studied using Resistance Gene Analog Polymorphism (RGAP) markers. A total of 28 primers were used in the present study to screen 30 moderately resistant, five resistant, seven moderately susceptible, nine susceptible and four highly susceptible cultivars resulted in the generation of 87 distinct fragments with 91.9% polymorphism. Polymorphism Information Content (PIC) and Resolving Power (RP) were also calculated and the values were found to be 16.28 and 52.36 respectively. On analyzing the dendrogram, a clear distinctive grouping was observed between red rot resistant and red rot susceptible cultivars. This study, therefore clearly revealed that Resistant Gene Analog (RGA) markers showed greater genetic diversity and hence, constitute a rich source for analyzing the genetic diversity and phylogenetic relationships. The genotypes belonging to different clusters can be crossbreed to gain high variability of good combinations of characters.

Emergence of New Pathogenic Variants in Colletotrichum falcatum, Stalk Infecting Ascomycete in Sugarcane: Role of Host Varieties

Red rot caused by Colletotrichum falcatum is more than a century old disease in sugarcane, responsible for several epiphytotics in India. Due to breakdown of many elite hybrid varieties to the pathogen, they were removed from cultivation in different decades. Overall, red rot resistance in sugarcane varieties was found to be short lived. Since emergence of new variants is regular under our conditions a 10-year (2007–2017) detailed field study was taken up to assess behavior of 12 C. falcatum isolates including four designated pathotypes of the tropical region on 20 popular varieties varying in disease resistance under field conditions. Virulence behavior of C. falcatum isolates was grouped under virulent, moderately virulent and less virulent categories. The results revealed that the isolates always exhibited virulence on the susceptible varieties but not on the resistant and moderately susceptible varieties. The isolates originated from susceptible and moderately susceptible varieties did not show any distinction in their virulence. Virulence frequencies of the isolates on the moderately susceptible varieties ranged of 21.3–40% as compared to 62.9–97.9% on the susceptible varieties. One of the eight resistant varieties succumbed to the pathogen virulence on a few occasions which indicated that the pathogen is able to breach the barriers of resistance and caused disease on the variety. Further, the isolates of more than 20 years such as Cf419, Cf671 and Cf997 exhibited less virulence with more than 50% as compared to the nine isolates originated after 2000 except Cf95020. Overall, the present study revealed that C. falcatum isolates exhibited a year to year variation in their virulence on the host varieties, attempting to overpower host resistance, leading to emergence of new variants.

Susceptibility of sugarcane to red rot caused by two Fusarium species and its impact on stalk sugar level

Red rot of sugarcane is caused by Colletotrichum falcatum. A recent survey, however, indicates that other fungal species may be associated with red rot-infected sugarcane leaves. This study 1) investigates the cause of the red rot-like symptoms using a polyphasic approach, 2) determines the pathogenicity of the fungi in sugarcane leaves and infection potential in leaves and stalks in detached-plant assays, and 3) assesses their effect on the stalk sugar level. Based on combined morpho-cultural and molecular characterization, the associated fungi were identified as Fusarium sacchari and F. proliferatum. The two Fusarium species induced red rot in leaves and stalk, as did the C. falcatum control isolate. Stalks infected with the two Fusarium species had reduced sugar level after 14 days, compared to the healthy stalk checks. To our knowledge, this is the first record of Fusarium species associated with red rot in sugarcane. These results suggest that the causal agent of red rot in the field is likely to be considered when developing or implementing disease control measures. Further, sugarcane breeding programs for red rot resistance would be likely aimed at all known causal pathogens.

Somaclonal variations for red rot and sugarcane mosaic virus resistance and candidate genes integrity assessment in somaclones of selected sugarcane varieties (Saccharum officinarum L.)

Sugarcane is a complex allopolyploid hybrid with erratic flowering due to various geo -climatic factors hence deliberate hybridization for varietal improvement is a dilemma in most of the countries where sugarcane is cultivated. Somaclonal variations is an alternate strategy used for development of disease resistance and improvement in yield attributes, but point mutation in candidate genes is questionable. The aim of this study was to develop somaclones resistant to red rot and Sugarcane mosaic virus (SCMV) in obsolete sugarcane varieties and their genetic integrity assessment in candidate gene's exon regions. A total of 581 somaclones were developed, of which 201 survived after hardening and 121 after transplantation and screened against red rot and SCMV. Only 10% somaclones were found resistant to red rot in susceptible and moderately susceptible varieties while SCMV concentration was recorded less than negative control in somaclones. Four candidate genes namely; catalase (CAT1), sucrose phosphate synthase (SPS), gibberellin 2-xidase 4 (GA 2-oxidase 4) and tillering branched 1 (TB1) were evaluated for possible SNPs in their exon regions. Sequences of five representative somaclones were aligned with their parental clones and no possible SNP changes were observed. Somaclonal variations was a good source of genetic improvement of sugarcane for disease resistance with no SNP changes in candidate genes.

Analysis of strawberry genetic collection (Fragaria L.) for Rca2 and Rpfl genes with molecular markers

Strawberry (Fragaria x ananassa Duch.) varieties are susceptible to many fungal diseases. Identification of forms, carrying resistance genes, is an important stage in breeding programs leading to resistant varieties. The use of molecular markers allows to determine with high reliability the presence of the necessary genes in the genome and to identify promising forms. Some of the common strawberry's diseases, causing significant damage to strawberry plantations, are anthracnose (Colletotrichum acutatum Simmonds) and red stele root rot (Phytophthora fragariae var. fragariae Hickman). Dominant Rca2 gene is involved in monogenic resistance to C. acutatum pathogenicity group 2. Rpf1, Rpf2, Rpf3 genes are determined in monogenic resistance to red stele root rot. The purpose of this study was molecular genetic testing genotypes of genus Fragaria L. to identify carriers of Rca2 allele anthracnose resistance and Rpf1 allele red stele root rot resistance. The objects of study were the wild species of the genus Fragaria L. and strawberry varieties (Fragaria x ananassa Duch.) of different ecological and geographic origin. To assess allelic state Rca2 anthracnose resistance gene the dominant SCAR marker STS-Rca2_240 was used, was linked to the resistance gene Rca2 with a genetic distance of 2.8 cM. Rpf1 gene red stele root rot resistance was identified with the dominant SCAR marker R1A, was linked to the resistance gene Rpf1 with a genetic distance of 3.0 cM. The resistant allele of the marker STS-Rca2_240 was identified in the Laetitia variety (Rca2Rca2 or Rca2rca2 genotype), which allows us to recommend it as a promising source in breeding for anthracnose resistance. The other studied forms have homozygous recessive state of the marker STS-Rca2_240 (putative genotype rca2rca2). The resistant allele of the marker SCAR-R1A in the varieties and wild species of strawberry under study is absent, which presumably indicates their homozygous recessive genotype of Rpf1 gene (rpf1rpf1).

Evaluation of mid-late Sugarcane clones for yield, quality and red rot resistance in Zonal Varietal Trials

Evaluation of mid-late Sugarcane clones for yield, quality and red rot resistance in Zonal Varietal Trials

Characterization of an intergeneric hybrid of Erianthus procerus × Saccharum officinarum and its backcross progenies

Erianthus, a related genus grouped under ‘Saccharum complex’ is seriously considered as a potential genetic resource for imparting high biomass production, multi ratooning ability, resistance to major diseases and pests and tolerance to abiotic stresses to sugarcane varieties. However introgression of Erianthus had limited success in the past in view of the high genetic distance between the two genera and the consequent low compatibility of such crosses. The inherent difficulty in precisely identifying the true hybrids from the selfed progenies from such crosses also remains a difficult task. In this article we report the production of an intergeneric hybrid GU04(28) EO2 involving Erianthus and Saccharum. The hybrid was characterized using 5s rDNA markers and evaluated for agro-morphological traits. The chromosome number of the Erianthus procerus × Saccharum officinarum hybrid approximated to 2n + n transmission with elimination of few chromosomes. The hybrid showed relatively low stalk weight and thickness, but had high yield potential in view of the high stalk population. The hybrid also showed high drought tolerance and resistance to red rot disease. This hybrid was backcrossed to a commercial sugarcane variety Co 06027. Erianthus-specific 5s rDNA marker was present in five of the BC1 progenies, thus confirming their Erianthus derivation. The chromosome number of the BC1 progenies ranged from 2n = 88–94, consistent with n + n transmission. The BC1 progenies showed significant improvement in stalk weight and juice sucrose over the F1 hybrid and it may be possible to develop varieties with commercial potential with few more backcrosses. The Erianthus × Saccharum hybrid GU04(28) EO2 is thus a potential source for diversifying the genetic base of the sugarcane varieties as it combines the genomes of two distantly related genera and also in view of its yield potential, red rot resistance and drought tolerance.

Red rot resistant gene characterization using RGAP markers among sugarcane cultivars resistant and susceptible to the red rot disease.

Sugarcane is the major source of sugar in Asia and Europe, grown primarily in the tropical and sub-tropical zones of the world. The main disease responsible for its low yield is red rot. Therefore, in the present study, characterization of red rot disease was performed among 55 different sugarcane cultivars varying in red rot resistance level. 18 fragments were found to be associated with red rot resistance and were identified as resistant specific markers. The resistant specific fragments were amplified by RGA169, RGA396, RGA129, RGA231, RGA251, RGA057, RGA118, RGA152, RGA327, RGA542, RGA012, RGA173, RGA184, RGA275, RGA019, RGA267, RGA281 and RGA533. 7 fragments were found to be associated with red rot susceptibility and were considered as susceptible specific markers amplified by RGA088, RGA162, RGA396, RGA231, RGA251, RGA087 and RGA275. Sequencing of five resistant fragments, viz., RGA169, RGA231, RGA251, RGA267 and RGA533 was performed and the data thus obtained showed 80-99% similarity when compared with other resistant gene sequences previously submitted in NCBI database.

Single nucleotide polymorphism in sugar pathway and disease resistance genes in sugarcane.

Single nucleotide polymorphism in sugar pathway and disease resistance genes showing genetic association with sugar content and red rot resistance would be useful in marker-assisted genetic improvement of sugarcane. Validation and genotyping of potential sequence variants in candidate genes are necessary to understand their functional significance and trait association potential. We discovered, characterized, validated and genotyped SNPs and InDels in sugar pathway and disease resistance genes of Saccharum complex and sugarcane varieties using amplicon sequencing and CAPS assays. The SNPs were abundant in the non-coding 3'UTRs than 5'UTRs and coding sequences depicting a strong bias toward C to T transition substitutions than transversions. Sequencing of cloned amplicons validated 61.6 and 45.2% SNPs detected in silico in 21 sugar pathway and 16 disease resistance genes, respectively. Sixteen SNPs in four sugar pathway genes and 10 SNPs in nine disease resistance genes were validated through cost-effective CAPS assay. Functional and adaptive significance of SNP and protein haplotypes identified in sugar pathway and disease resistance genes was assessed by correlating their allelic variation with missense amino acid substitutions in the functional domains, alteration in protein structure models and possible modulation of catalytic enzyme activity in contrasting high and low sugar and moderately red rot resistant and highly susceptible sugarcane genotypes. A strong genetic association of five SNPs in the sugar pathway and disease resistance genes, and an InDel marker in the promoter sequence of sucrose synthase-2 gene, with sugar content and red rot resistance, was evident. The functionally relevant SNPs and InDels, detected and validated in sugar pathway and disease resistance genes, and genic CAPS markers designed, would be of immense use in marker-assisted genetic improvement of sugarcane for sugar content and disease resistance.

Pathogen Virulence in Sugarcane Red Rot Pathogen Versus Varieties in Cultivation: Classical Case of Loss in Virulence in the Pathotype CF06 (Cf671)

In India, red rot caused by Colletotrichum falcatum exhibits enormous variation in pathogenicity on sugarcane. The new cultivars released for commercial cultivation succumb to new pathotypes of the pathogen after some years in disease endemic regions. Due to the variability in C. falcatum, screening for red rot resistance in sugarcane progenies is being taken up with designated pathotype(s) separately for each agroclimatic regions in the country. The predominant C. falcatum pathotype of tropical India Cf671 (CF06) isolated from the then ruling cultivar CoC 671 is being used in tropical regions for disease screening. However, recently the pathotype has exhibited a reduced virulence on new cultivars and that has resulted in inconsistencies in disease reaction between artificial testing and field reaction under natural conditions. Hence, a detailed study was conducted during the past seven seasons on its pathogenicity on a set of 32 cultivars varying in red rot resistance in comparison with a new pathotype Cf94012 isolated from the cultivar Co 94012. The resistant cultivars such as BO 91, CoS 8436 and Co 98010 exhibited resistance reaction to both the pathotypes. However, other resistant cultivars such as Co 94008, Co 99006, Co 2001-15, Co 0238 and CoV 92102 showed a shift in their reaction to the new pathotype Cf94012 as moderately susceptible (MS) or susceptible (S) from resistant (R)/moderately resistant (MR) reactions in case of Cf671. Further, disease reaction on eight cultivars with MS behaviour and 11 susceptible cultivars clearly revealed a higher virulence of Cf94012 as compared to Cf671. Overall, the pathogenic behaviour of the two pathotypes during seven seasons revealed a higher virulence of Cf94012 as compared to Cf671 on resistant, moderately susceptible and susceptible cultivars. Although the pathotype Cf671 remained virulent on its host cultivar CoC 671, it could not exhibit such virulence on the cultivars developed in the recent years. Further, the study revealed that once a popular cultivar is removed from cultivation as in the case of CoC 671, the pathotype adapted to it no longer maintains its virulence, whereas the recently originated pathotype exhibits a higher virulence on the new cultivars of the host. This study also suggests adaptation of C. falcatum to the host cultivars.

Identification of putative candidate genes for red rot resistance in sugarcane (Saccharum species hybrid) using LD-based association mapping

Red rot is a serious disease of sugarcane caused by the fungus Colletotrichum falcatum that has a colossal damage potential. The fungus, prevalent mainly in the Indian sub-continent, keeps on producing new pathogenic strains leading to breakdown of resistance in newly released varieties and hence the deployment of linked markers for marker-assisted selection for resistance to this disease can fine tune the breeding programme. This study based on a panel of 119 sugarcane genotypes fingerprinted for 944 SSR alleles was undertaken with an aim to identify marker-trait associations (MTAs) for resistance to red rot. Mixed linear model containing population structure and kinship as co-factor detected four MTAs that were able to explain 10-16% of the trait variation, individually. Among the four MTAs, EST sequences diagnostic of three could be BLAST searched to the sorghum genome with significant sequence homology. Several genes encoding important plant defence related proteins, viz., cytochrome P450, Glycerol-3-phosphate transporter-1, MAP Kinase-4, Serine/threonine-protein kinase, Ring finger domain protein and others were localized to the vicinity of these MTAs. These positional candidate genes are worth of further investigation and possibly these could contribute directly to red rot resistance, and may find a potential application in marker-assisted sugarcane breeding.

Screening sugarcane somaclones and their parent varieties against red rot (Colletotrichum falcatum) and assessment of Variability by RAPD and SSR markers

The experiment was conducted to find out red rot disease causing pathogenic reactions of somaclones (R0) and their respective parents at BSRI farm in the cropping season 2011-2012. A total number of sugarcane genotypes 24 including 4 sugarcane varieties viz. Isd 37, Isd 38, Isd 39 and also Isd 40 were inoculated to screen red rot resistant levels (R = Resistant, MR = Moderately Resistant) to susceptible levels (S = Susceptible, MS = Moderately Susceptible, HS = Highly Susceptible) after 7 months of planting. As a result, Isd 37 variety (source/parent) and its somaclones CC–37–12 and CC–37–86 were found to be resistant while 7 somaclones showed moderately resistant reaction. Furthermore, somaclones of Isd 38 variety viz. CC–38–2 as moderately resistant, CC–38–10 as moderately susceptible and also CC–11(38)–8 as susceptible reaction were recorded while Isd 38 variety showed resistant reaction. On the other hand, Isd 39 and Isd 40 source varieties with their somaclones were found as resistant reaction against red rot pathogen. Some somaclones showed different reaction from their source varieties such as moderately resistant somaclones were obtained from resistant source variety Isd 37 while somaclones CC–38–2 as moderately resistant, CC–38–10 as moderately susceptible and somaclone CC–38–8 as susceptible were obtained from resistant source variety Isd 38 against red rot pathogens respectively. Besides, some somaclones showed similar reaction from their resistant source varieties Isd 37, Isd 39 and also Isd 40. It revealed that reaction against red rot pathogen, induced somaclones showed variation with their source varieties. Red rot resistance somaclones were isolated and assessed for the presence of variability through RAPD and SSR markers. Cluster and sub cluster formation verified the presence of variability in the red rot resistance somaclones with respect to the parent.SAARC J. Agri., 13(2): 173-182 (2015)

Differential Induction of 3-deoxyanthocyanidin Phytoalexins in Relation to Colletotrichum falcatum Resistance in Sugarcane

Sugarcane secrets a reddish pigment presumed to contain phytoalexin compounds in the stalk tissues in response to infection of Colletotrichum falcatum, causing red rot. To identify the phytoalexin compounds involved in red rot resistance, detailed HPLC analyses were conducted using the phytoalexin standards in a set of sugarcane cultivars varying in red rot resistance, after pathogen inoculation. We found nine different 3-deoxyanthocyanidin phytoalexin compounds, which are differentially induced upon C. falcatum infection in sugarcane varieties with varying degrees of disease resistance. Among the nine compounds, four compounds were identified as luteolinidin, 5-methoxy luteolinidin, apigeninidin and arabinosyl-5-O-apigeninidin. Multifold induction of luteolinidin, apigeninidin and arabinosyl-5-O-apigeninidinin were recorded in the stalk tissues in disease resistant cvs Co 93009, BO 91 and Baragua, respectively after pathogen inoculation as compared to the susceptible cv CoC 671. In addition to the known compounds one to three unknown compounds were detected in the resistant cultivars. The susceptible cultivars exhibited a placid induction of phytoalexin compounds after pathogen infections. The results very clearly demonstrated a specific induction of 3-deoxyanthocyanidins in resistant cultivars at a higher level as compared to susceptible cultivars after C. falcatum infection in sugarcane. Total extracts of the induced phytoalexins in the calorimetric assays, also revealed similar results. Probably induction of either luteolinidin or apigeninidin compounds alone or in combination at higher concentrations in the resistant cultivars may enable the effective arrest of pathogen invasion and further development inside the stalk tissues.

Differential Regulation of Defense-Related Gene Expression in Response to Red Rot Pathogen Colletotrichum falcatum Infection in Sugarcane

Red rot is a serious disease of sugarcane caused by the fungus Colletotrichum falcatum imposing a considerable economic loss annually in all sugarcane-producing countries. In this study, we analyzed the early resistance response of sugarcane to red rot fungus by comparing the differences between control and inoculated stalk tissues. Differential display reverse transcription polymerase chain reaction (DD-RT-PCR) was employed to identify altered expression of genes in disease-resistant cv Co 93009, in response to pathogen infection. DD-RT-PCR identified 300 differentially expressed transcripts of which 112 were selected for further analysis. Cloning and sequence analysis of the isolated cDNA fragments resulted in functional categorization of these clones into five categories, of which the defense/stress/signaling group was the largest, with clones homologous to genes known to be actively involved in various pathogenesis-related functions in plant species. This group showed overexpression of several transcripts related to ethylene-mediated and jasmonic acid pathway of plant defense mechanisms. Of the 112 expressed sequence tags, validation of expression was carried out for five important genes whose role in plant defense mechanisms is well established. This is the first report of Colletotrichum-mediated gene regulation in sugarcane which has provided a set of candidate genes for detailed molecular dissection of signaling and defense responses in tropical sugarcane during the onset of red rot resistance.

Expression profiling of transcription factors (TFs) in sugarcane X Colletotrichum falcatum interaction

Sugarcane is one of the most important commercial crops in India, supporting the second largest agro-based sugar industry. However for more than a century, the production is imperiled by the most devastating fungus Colletotrichum falcatum Went, which causes red rot in sugarcane. Complex polyploidy and limited understanding on the inheritance to red rot resistance makes breeding efforts more complicated in sugarcane. Transcription factors (TFs) play a key role in regulating defense response, which offers much promise for the manipulation of metabolic pathways, potential in regulating multiple signaling networks leading to plant defense against pathogens. In order to better manage red rot disease in sugarcane, we sought to screen the TFs possibly involving in pathogen defense by analyzing 5 major defense-related TF classes (WRKY, bZIP, MYB, NAC and TLP). In this study two parallel sets of experiments were carried out to compare the differential regulation of these classes of TFs upon pathogen challenge and SAR priming. Among the 41 TFs studied, differential regulation of 24 TFs upon pathogen challenge and 15 TFs upon SAR inducer priming were observed. Comparison of incompatible interaction and SAR inducer priming revealed that 8 TFs were highly induced in both the cases. Collectively, the results showed that TFs which are significantly induced early may involve actively in triggering or co-ordinating defense against pathogen invasion.

Identification of Pathogenicity Determinants in Colletotrichum falcatum Using Wild and Mutant Cultures

Colletotrichum falcatum causing red rot in sugarcane is a dynamic pathogen exhibiting enormous variation. As pathogen variability plays a crucial role in the breakdown of red rot resistance in sugarcane, investigations were made to characterize possible factors responsible for the development of newer pathotypes in the fungal pathogen. We have studied production of metabolites viz., toxin and melanin and hydrolytic enzymes in relation to disease expression with wild and temperature adapted mutants which are deficient in pathogenicity on sugarcane hosts. The nine major pathotypes used for disease screening programme were found to vary significantly in toxin production. It was found that symptom production on leaves by the pathotypes and loss of electrolytes caused by them on the host tissues increased with their virulence. The pathotypes varied in the production of pectinolytic and cellulolytic enzymes particularly exo-PG and its production corresponded with virulence. Production of melanin during host pathogen interaction was found to have a positive relation with virulence when pathogenicity assay was conducted in stalks and leaves.