Status of Late Blight Management in India Sanjeev Sharma ICAR-Central Potato Research Institute, Shimla E-mail: sanjeevsharma.cpri@gmail.com, Sanjeev.Sharma1@icar.gov.in IICCAARR----CCPPRRII Potato in Indian Agriculture  Potato contributes about 2.48% of the total agricultural output from only 1.07% of the total cropped area  In comparison, rice and wheat contributes about 14.54% from 30.29% area and 10.95% from 19.48% area, respectively  Potato contributes about 4.0 times more than both wheat and paddy from unit area to the national economy in agricultural sub-sector IICCAARR----CCPPRRII Status of Potato in India Area: 2.16 m ha Production: 53 mt Northern hills Productivity: 23t/ha Northern plains Plains 90% Plateau 4% Hills 6% Plateau region Southern hills Per cent area (million ha) under potato in different states of India Punjab 4% Others Gujarat 19% UP 4% 29% Karnataka 2% MP 5% Bihar 16% WB 21% IICCAARR----CCPPRRII Distribution of late blight Eastern Hills 19-90% NW Hills 11-90% Southern Hills 31-80% N W Plains 20-90% Eastern Plains 10-85% Plateau 50-100% Av crop loss 15% IICCAARR----CCPPRRII What has been studied? 1. The Pathogen : Variability 2. The Host : Resistance (nature and extent, genes) 3. Epidemiology : Forecasting 4. Management :  Host resistance  Chemicals  Disease forecasting  Bio-control IICCAARR----CCPPRRII Pathogen variability and its Relevance in Resistance Breeding P. infestans is highly variable:  Changes with host genotype, environment and management practices  It calls for regular monitoring of variability i.e. physiological races, mating types, mt haplotypes, RAPDs, SSRs IICCAARR----CCPPRRII Variability in Phytophthora infestans  Phenotypic Markers  Races (1958)  Mating types (1990)  Fungicide resistance (1995)  Genetic Markers  Isozymes  Ploidy  RAPDs  Mt.DNA  SSR  RFLP  AFLP IICCAARR----CCPPRRII Phenotypic Diversity: Race Spectrum  Presently P. infestans population is composed of most complex races (10-11 virulence genes) Location Race HP hills 11 UP 10-11 Karantaka 11 Uttarakhand 11 Tamil Nadu 11 West Bengal 10-11 Punjab 11 Meghalaya 11 Assam 11 Bihar 11 Rajasthan 11 IICCAARR----CCPPRRII Impact of New Virulences Break down of resistance in cv. Kufri Jyoti  KJ possesses 3, 4, 7 R-genes  Released for cultivation in 1968  Became popular in temperate Kufri Girdhari highlands in mid seventies  Matching race 3.4.7 detected in Shillong in 1974, Shimla in 1975  First late blight attack Kufri Jyoti observed in 1974-75  In 1984 - LB severity 30-40%  In 1988 - LB severity 90- 100%. IICCAARR----CCPPRRII Phenotypic Diversity: Mating Type A1 (%) A2 (%) 100 80 60 40 20 0 Location Uptill 1990 only A1 was present in India Hills – A2 dominant Plains – A1 dominant IICCAARR----CCPPRRII Frequency (%) Implications of Introduction of A2 Mating Type  A2 mating type isolates are more aggressive  Leads to development of sexual population which is  More aggressive  Composed of new virulence/polyploids/genotypes IICCAARR----CCPPRRII DDiisseeaassee sseevveerriittyy ((%%)) Impact of introduction of A2 mating type - A2 mating type more aggressive 120 A1 A2 % DI 100 80 60 40 20 0 6 June 17-18 June 28-Jun 29 June -2 6 July 22-23 July July Date of isolate collection IICCAARR----CCPPRRII MMaattiinngg ttyyppee ((%%)) Phenotypic Diversity: Metalaxyl sensitivity HP hills North eastern hills Indo-Gangetic plains Year Tolerance at ppm level (% isolates) 100 200 400 100 200 400 100 200 400 2001-02 15 0 0 10 0 0 0 0 0 2004-05 13 0 0 5 0 0 8 0 0 2006-07 100 75 11 32 0 0 58 71 38 2007-08 100 90 17 32 0 0 60 45 0 2008-09 100 86 39 100 33 0 60 54 22 2009-10 100 68 0 100 100 0 80 20 - 2010-11 100 100 0 100 100 83 100 67 0 2011-12 100 100 1 - - - 100 100 0 2012-13 100 100 0 100 100 0 100 100 0 2015-16 100 88 0 100 100 0 100 100 0 2016-17 100 90 0 - - - 100 80 0 IICCAARR----CCPPRRII Implications of Metalaxyl Resistance  MR isolates are more aggressive  reduce the efficacy of metalaxyl based formulations Failure of metalaxyl based fungicides in managing late blight in India (2006-07) Untreated Metalaxyl based fungicide control States No. of Disease severity Disease severity sprays (%) (%) Uttar Pradesh 3-4 40-95 85-100 West Bengal 3-4 40-80 80-100 Karnataka 2-3 60-90 80-100 Maharashtra 2-3 50-80 80-100 IICCAARR----CCPPRRII Frequency of Polyploids in Different Regions Polyploids (%) Region Diploid Triploid Tetraploid North -western hills 91 6 3 North-eastern hills 89 11 0 Southern hills 75 25 0 Indo-Gangetic plains 74 20 6 Plateau 100 0 0 P. infestans in India is polyploid consisting of diploids, triploids and tetraploids IICCAARR----CCPPRRII Effect of temperature on germination of sporangia of P. infestansIICCAARR----CCPPRRII Aggressiveness of polyploids of P. infestans at different temperature Temp IP (hr) LP (hr) LA (cm2) SP (x 104) (oC) Dip Tri Tet Dip Tri Tet Dip Tri Tet Dip Tri Tet 10 120 108 84 - - - 0.25 0.25 0.25 - - - 15 96 84 84 144 144 96 6.25 6.34 5.81 4.3 2.68 3.53 18 96 84 72 120 120 120 16.0 9.13 20.05 4.5 2.48 3.08 20 72 72 72 120 120 120 20.25 12.32 20.25 1.8 1.5 1.25 24 72 72 60 - - 120 7.50 7.00 14.25 - - 0.68 28 - - 72 - - - - - 0.25 - - - Mean 91.2 84 74 128 128 114 10.05 7.01 10.14 3.43 2.22 2.14 IICCAARR----CCPPRRII Genotypic Diversity: Mitochondrial haplotypes Haplotype Year Ia Ib IIa IIb 1996-2001 - + - - 2002 + + - - 2003 - + - - 2004 + + - + 2005 + - - - 2008-09 + + - - 2009-10 +(62.5%) + (37.5%) - - 2010-11 + (76%) + (24%) - - 2011-12 + (100%) - - - 2012-13 + (100%) - - - 2013-14 + (100%) - - - ~167bp Ia type Ib type 50 bp 394 bp 361 bp 209 bp IICCAARR----CCPPRRII Pathogen variability and its Relevance in Resistance Breeding P. infestans is highly variable:  Changes with host genotype, environment and management practices  It calls for regular monitoring of variability i.e. physiological races, mating types, mt haplotypes, RAPDs, SSRs IICCAARR----CCPPRRII Resistance breeding programme at CPRI Mainly based on transfer of R-genes from S. demissum background First set of LB resistant varieties released in: 1968 – Kufri Jyoti, Khasigaro (NEH), Kufri Naveen Kufri Jeevan, Kufri Muthu (Nilgri hills) 1979 - Kufri Badshah (Plains) 1985 - Kufri Swarna (Nilgiri hills) 1989 - Kufri Megha (NEH region) 1996 - Kufri Satlej Kufri Jawahar (Plains) 1998 - Kufri Anand IICCAARR----CCPPRRII What Happened to R-Genes? Hills Plains Defeated Defeated Disease severity very high Disease severity low to moderate Conclusion: R-genes are also valuable and can provide slow blighting effect in the plains where disease pressure is low IICCAARR----CCPPRRII Breeding for Field Resistance Sources exploited  Solanum wild spp. (diploid) S. verrucosum (1974) S. microdontum (1994-95) S. chacoense (1994-95) S. bulbocastanum (1996) S. phureja (1996) S. stoloniferum (1996) S. tuberosum ssp. andigena S. demissum (Since, 1980) IICCAARR----CCPPRRII Potato Varieties Carrying Field Resistance to Late Blight Hills  Kufri Giriraj (1998), Kufri Kanchan (1999), Kufri Shailja (2005), Kufri Himalini (2006), Kufri Himsona (2008), Kufri Giridhari (2008), Kufri Neelima (2010), Kufri Karan (2019) Plains  Kufri Pukhraj (1998), Kufri Anand (1998), Kufri Chipsona-1 &2 (1998) ,- 3 (2006), and -4 (2010), Kufri Arun (2005), Kufri Pushkar (2005), Kufri Sadabahar (2008), Kufri Khyati (2008), Kufri Lalit (2013), Kufri Mohan (2016), Kufri Neelkanth (2018) IICCAARR----CCPPRRII Use of RB Gene for Managing Late Blight (i) Kufri Bahar Katahdin x SP 951 (ii) Kufri Jyoti TPS Confirmation of RB gene Seedlings (F1C1) Screening of LB resistance LB Resistance identification Glass house test Limited Field testing Based on yield potential and Late blight resistance selected five promising hybrid lines RNAi transgenic for late blight Silencing of Phytophthora infestans Avr3a gene for imparting resistance in popular Indian cultivar LB SacI KpnI XbaI Hind III RB BamHI Avra3-AS Intron Avr3a-S NosT CaMV 35S NosT npt II Nos P iIR-Avr3a Map of the T-DNA region of the binary vector cassette, pBI121:iIR-Avr3a 1 2 3 4 5 6 siRNA - 2173 Non transgenic siRNA - 2086 Non transgenic siRNA - 1037 Non transgenic Results: Moderately resistant (25% infection) >>> Silencing of single effector is not sufficient for imparting late blight resistance Marker Assisted Selection Identification of resistance (LB, PVY & PCN) genes using MAS Diagnostic markers scored or validated for different traits : Late blight (R1, R2 and R3a), PVY (Rysto Ryadg,) and Potato cyst nematodes (H1, Gro1-4HC_QRL) Parents R1 R2 R3a Ryadg Rysto H1 Gro 1-4 HC- QRL identified (LB): 20 (LB): 28 (LB): 43 (PVY): 18 (PVY): 4 (PCN): 14 (PCN): 47 (PCN): 27 IICCAARR----CCPPRRII Stacking of multiple genes A: Phenotype of the clone#13 having stacked genes R1 and R3a compared with parents of the cross (CP 4045 × CP1945a) B: Clone#15 compared with parents, SM92338 & K. Girdhari. Both of these clones were scored as highly resistant; while CP 1945, CP 4045 and SM /92-338 scored MR and K. Girdhari scored resistant. 1 2 3 4 5 6 7 8 9 Graphical representation of the selected stacked clones with R1 and R3a genes IICCAARR----CCPPRRII Resistance grade scale1-9 Scale Somatic Hybridization Protoplast fusion: S. tuberosum & S. pinnatisectum and S. tuberosum & S. cardiophyllum a A B Somatic hybrids produced tubers C C D E A B C (a) Protoplast fusion between S. tuberosum and S. pinnatisectum. A E F heterokaryon (arrow) formed after electrofusion (A), and post-fusion D E F rounding up (B); leaves (C), flowers (D) and tubers (E) of dihaploid C-13 Somatic hybrids of S. pinnatisectum: field view (A, B, C), Parent S. pinnatisecturm (D), Parent C-13 (E) and somatic hybrid P-7 (F) Somatic Hybrids Developed C-13: dihaploid of Kufri Chipsona-2 E1-3: Solanum tuberosum (C-13) & S. etuberosum P-7: Solanum tuberosum (C-13) & S. pinnatisectum Crd-6: Solanum tuberosum (C-13) & S. cardiophyllum IICCAARR----CCPPRRII Late Blight Forecasting in Indian Hills Bhattacharyya et al. (1982) They compared various methods of disease prediction viz. Beaumont Rules, Cook and Hyre method and Hyre and Bonde method using 15 years weather data from Shimla, Shillong and Ooty hills CONCLUSIONS None of the method successfully predicted the disease in any of the areas IICCAARR----CCPPRRII Modifications proposed by Bhattacharyya et al. (1982) 1st Forecast If 7-day moving precipitation of at least 30 mm for Shimla, 28.9 mm for Ootacamund and 38.5 mm for Shillong hills with mean temp. of 23.9 oC or less continues for 7-consecutive days, late blight would appear within three weeks time 2nd Forecast If hourly temp. remains in between 10-20 oC associated with RH 80% or more for continuous 18 hrs for at least two consecutive days, late blight would appear within a week time IICCAARR----CCPPRRII Late Blight Forecasting for Plains Fitness of models based on temp. and RH in UP Expected data of appearance Actual date of Year Bhattacharyya et al Beaumont appearance (1982) 2nd forecast Rules 1986-87 13-17 Dec. 8-22 Dec. 15 Dec. 1987-88 -- 13-27 Dec. No LB 1988-89 10-17 Jan. 8-22 Jan. 12 Jan. 1989-90 28 Dec.-4 Jan. 28 Dec.-11Jan. 30 Dec. 1991-92 2-9 Dec. 17-31 Dec. 24 Dec. 1992-93 - - 16 Dec. 1993-94 - - 14 Jan. 1994-95 - - 15 Dec. 1996-97 - - No LB Success : 55% 55% IICCAARR----CCPPRRII Fitness of temperature and rainfall based models in Uttar Pradesh Expected data of appearance Actual date of Year Cook (1947) Hyre (1954) appearance model model 1986-87 - - 15 Dec. 1987-88 - - No LB 1988-89 7 Jan. - 12 Jan. 1989-90 31 Dec. 30 Dec.-13 Jan. 30 Dec. 1991-92 31 Dec. 7-21 Jan. 24 Dec. 1992-93 - - 16 Dec. 1993-94 - - 14 Jan. 1994-95 - 25 Jan.-9 Feb. 15 Dec. 1996-97 - - No LB Success : 44% 33% IICCAARR----CCPPRRII Late Blight Forecasting for Plains Model for Rainy Years  Measurable rains (0.1-0.5 mm) for a minimum of two consecutive days  5-day moving ≥ 85% RH period ≥ 50 hrs  5-day moving congenial temp.(7.2-26.6 oC) ≥100 hrs If above conditions prevail for 5- consecutive days, blight would appear within 7-10 days IICCAARR----CCPPRRII Model for Non-Rainy Years  7-day moving ≥ 85% RH period ≥ 50 hrs  7-day moving congenial temp (7.2- 26.6 oC) ≥ 115 hrs or more If above conditions prevail for 7-consecutive days, blight would appear within 7-10 days IICCAARR----CCPPRRII JHULSACAST – A computerized system for LB forecasting Data JHULSACAST transfer DATA ENTRY JHULSACAST LB FORECAST MENU RUN through interface Message transferred to Warning AIR & Doordarshan Late Blight may appear within 8-10 days IICCAARR----CCPPRRII JHULSACAST – A computerized system for LB forecasting for Punjab Data JHULSACAST JHULSACAST transfer DATA ENTRY MENU LB FORECAST RUN through interface  7-day moving ≥ 85% RH period ≥ 90 hrs Message  7-day moving transferred to Warning congenial temp. (7.2- AIR & Doordarshan Late Blight may 26.6oC) ≥ 115 hrs appear within 8-10 days IICCAARR----CCPPRRII JHULSACAST – A computerized system for LB forecasting for tarai region of Uttarakhand Data JHULSACAST JHULSACAST transfer DATA ENTRY MENU LB FORECAST RUN through interface  7-day moving ≥ 85% RH period ≥ 85 Message hrs transferred to Warning  7-day moving AIR & Late B congenial temp. Doordarshan light may appear within (7.2-26.6oC) ≥ 8-10 days 135 hrs IICCAARR----CCPPRRII JHULSACAST – A computerized system for LB forecasting for plains of West Bengal Data transfer JHULSACAST JHULSACAST DATA ENTRY MENU LB FORECAST RUN through interface  Rains (>2.5 mm) for a minimum of two days  5-day moving ≥ 90% RH period ≥ 65 hrs Message  5-day moving congenial transferred to temp. (7.2-26.6oC) Warning AIR & ≥105 hrs Doordarshan Late Blight may appear within  7-day moving ≥ 90% 8-10 days RH period ≥ 105 hrs  7-day moving congenial temp. (7.2-26.6oC) ≥150 hrs IICCAARR----CCPPRRII Decision Support System (DSS) for LB Management Prediction models Database for disease Disease appearance management programmes Meteorolo Decision rules for Yield loss Fungicides gical data JHULSACAST need based assessment database application of models fungicides • Hourly Relative Humidity (%) • Hourly Temperature (oC) Apply/ Not • Daily Rainfall (mm) apply fungicides IICCAARR----CCPPRRII Performance of Jhulsacast Model Year Expected date of late Actual date of late blight appearance blight appearance 1997-1998 8-18 November 9 November 1998-1999 13-23 November 24 November 1999-2000 9-18 November 14 November 2000-2001 20-29 November 28 November 2001-2002 4-14 January 6 January 2002-2003 17-26 December 18 December 2003-2004 12-21 December 12 December 2004-2005 18-27 December 22 December 2005-2006 Not predicted Did not appear 2006-2007 16-25 November 12 November 2007-2008 ------- ------- 2009-2010 1-10 January 7 January 2010-2011 19-28 December 27 December 2011-2012 25 Dec -3 Jan 27 December 2012-2013 26 Dec -5 Jan 4 January 2013-2014 30 Nov -9 Dec 9 December 2014-2015 28 Dec - 7 January 6 January IICCAARR----CCPPRRII Limitations of LB Forecasting Models  The forecasting models available are location specific e.g. Initiation of PLB when 7-day moving ≥85% RH (≥50 hours) and congenial temperature (7.2-26.6oC) periods (≥105 hours) these values vary from location to location  Thermohygrograph data is not available for most of the locations.  Meteorological conditions vary widely at different locations – and this determines the time of appearance and disease severity.  Calibration to each location is a slow process. 35 100 90 30 Jalandhar 80 25 70 60 20 50 15 40 Kalyani 10 30 20 5 10 0 0 45 46 47 48 49 50 51 52 1 2 3 4 5 6 7 8 Standard weeks Rainfall Max Temp Min Temp Max RH Min RH IICCAARR----CCPPRRII Temp (oC) and Rainfall(mm) RH(%) Objectives of the new model Model should be applicable across locations without local calibration.  It should use simple easily available meteorological data It should forecast disease appearance and also be amenable to use as decision support. IICCAARR----CCPPRRII Model Developed Using Data Location Latitude Longitude Height Jalandhar, Punjab 31.33° N 77.58° E 240 m Modipuram, Uttar 29.06° N 75.76° E 237 m Pradesh Pantnagar, Uttarakhand 29.05° N 79.51° E 244m Kalyani, West Bengal 22.98° N 88.48° E 11 m Test Locations Location Latitude Longitude Height Data used (Years) Faizabad (UP) 26.78° N 82.13° E 97 m 5 Patna (Bihar) 25.61° N 85.14° E 53 m 4 Jorhat (Assam) 26.75° N 94.22° E 116 m 5 Hassan (Karnataka) 13.00° N 76.00° E 923 m 6 Dharwad (Karnataka) 15.45° N 75.00° E 750 m 5 Shimla (HP) 31.1° N 77.12° E 2000 m 5 Shillong (Meghalaya) 25.50° N 91.88° E 1496 m 3 Ootacamund (TN) 11.40° N 76.70° E 2240 m 5 IICCAARR----CCPPRRII Attributes of receiver operating characteristic curve at different RH and P-days combinations Sl. No. RH/P days* combination Accuracy AUC** 1 475/47.5 0.2632 0.307 2 475/50 0.2632 0.307 3 475/52.5 0.5526 0.600 4 475/55 0.5263 0.678 5 475/57.5 0.4474 0.625 6 500/47.5 0.34211 0.361 7 500/50 0.3158 0.600 8 500/52.5 0.5526 0.407 9 500/55 0.5263 0.678 10 500/57.5 0.4737 0.643 11 525/47.5 0.42105 0.4143 12 525/50 0.4737 0.5143 13 525/52.5 0.7368 0.725 14 525/55 0.6517 0.7678 15 525/57.5 0.553 0.696 16 550/47.5 0.263 0.339 17 550/50 0.447 0.496 18 550/52.5 0.6579 0.7035 19 550/55 0.605 0.732 20 550/57.5 0.579 0.714 21 575/47.5 0.4453 0.593 22 575/50 0.4737 0.643 23 575/52.5 0.553 0.696 24 575/55 0.42105 0.6428 25 575/57.5 0.6579 0.607 *Cumulative RH and P-days over 7 days, ** Area under the curve IICCAARR----CCPPRRII IICCAARR----CCPPRRII Window for data entry (restricted) IICCAARR----CCPPRRII Window for getting forecast (unrestricted) IICCAARR----CCPPRRII Performance of Indo-Blightcast Model Location Prediction date of late blight Actual date of late blight appearance Shimla (HP) 25.06.2015 07.07.2015 Ludhiana (Punjab) 06.12.2015 12.12.2015 Modipuram (UP) 15.11.2015 27.11.2015 Kalyani (WB) 26.01.2016 30.01.2016 Pantnagar (Ukd) 05.12.2015 08.12.2015 Jorhat (Assam) 18.01.2016 22.01.2016 Shimla (HP) 25.06.2016 04.07.2016 Jalandhar (Punjab) Blight appearance not likely Did not appear Modipuram (UP) 10.12.2016 28.12.2016 Kalyani (WB) 13.01.2017 31.01.2017 Pantnagar (Ukd) 12.12.2016 11.12.2016 Jalpaiguri(WB) Blight appearance not likely Did not appear West Midnapur (WB) Blight appearance not likely Did not appear Bankura (WB) Blight appearance not likely Did not appear IICCAARR----CCPPRRII Performance of Indo-Blightcast Model Location Prediction date of late Actual date of late blight blight appearance Shimla (HP) 27.06.2017 29.06.2017 Jalandhar (Punjab) Blight appearance not likely Did not appear Modipuram (UP) 12.12.2017 19.12.2017 (Bijnor) Pantnagar (Ukd) 13.12.2017 29.12.2017 Kalyani (WB) 13.01.2018 Did not appear Jalpaiguri(WB) 23.12.2017 27.12.2017 West Midnapur (WB) Blight appearance not likely Did not appear Bankura (WB) Blight appearance not likely Did not appear Hooghly (WB) Blight appearance not likely Did not appear Burdwan (WB) Blight appearance not likely Did not appear Patna 26.12.2017 10.01.2018 Faizabad Blight appearance not likely Did not appear Kanpur 20.12.2017 22.12.2017 Jorhat 7.12.2017 19.12.2017 IICCAARR----CCPPRRII Issuance of Agro-advisories IICCAARR----CCPPRRII Biological approaches • Two isolates of Pseudomonas aeruginosa were promising Tuber slice on 9th days after treatment for bio-surfectant production as well as inhibition of P. infestans. Detached leaf 48 hr old culture filtrates IICCAARR----CCPPRRII Efficacy of rhamnolipid based formulation against late blight T1: Rhamnolipid (0.25%), T2: Mancozeb (0.2%), T3: Chlorothalonil (0.2%), T4: Propineb (0.2%), T5- control Control Rhamnolipid Mancozeb IICCAARR----CCPPRRII Biological approaches Screening of endophytes against Phytophthora infestans Out of 120 bacterial endophytes; 15 showed promising results against P. infestans. Control EB-14 Control EB-50 IICCAARR----CCPPRRII Development of dsRNA based fungicide against late blight In-vitro synthesized dsRNA encoding P. infestans genes (sporulation, metabolism and protein machinery genes) subjected to P.infestans pathogenicity P.infestans dsRNA Control dsRNA Development of dsRNA based fungicide against late blight Without dsRNA WitH dsRNA Bacterailly expressed P.infestans dsRNA Susceptible Reaction Resistant Reaction With dsRNA With dsRNA IPTG induced small RNA encoding P.infestans genes P.infestans small RNA Resistant Reaction Resistant Reaction Bio efficacy of nano clay dsRNA formulation against Late blight • Disease severity: 80% • 1% Disease severity: 5% • Sporulation: 3 x 103 • Sporulation: 1 x 102 Alternative to trasnngeic approach: dsRNA formulation would become eco-friendly new generation plant protection fungicides IICCAARR----CCPPRRII Thank you The Organizers for the invite---- ----- and to everyone else for listening IICCAARR----CCPPRRII