July 30th, 2016: Latest version of Mehtaensis newsletter published by DWR, Flowerdale, Shimla: Comprehensive updated information on rusts in India and South Asia

The latest version of the Mehtaensis newsletter (a 6 monthly newsletter named after Prof. K.C. Mehta) has just been published by ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Flowerdale, Shimla. Compiled and edited by Pramod Prasad, Hanif Khan, O.P. Gangwar, and S.C. Bhardwaj with technical assistance from S.B. Singh and Subodh Kumar. Mehtaensis contains a detailed summary of all the rust activities and race analysis results from India and neighbouring South Asian countries during the period Jan – July 2016. The executive summary is reproduced here:

“A new Lr gene was identified in local wheat LWH2. This gene confers resistance to all the pathotypes of Puccinia triticina (except pathotype 5R9-7) in India. Wheat rusts did not appear in epidemic form during 2015-16 in India. The sporadic occurrence of yellow rust was reported from few areas of North western plains and northern hills zones, but its further spread was halted through joint efforts of ICAR-IIWBR, SAUs, State Department of Agriculture and farmers. Black rust was restricted to Central and Peninsular India whereas brown rust was observed across all the zones but their severity and incidence was quite low. During 2015-16, 1028 samples of different rusts of wheat and barley were received/collected for pathotype analyses from Ravi and off season crops. About 580 samples of three rusts of wheat and yellow rust of barley were analyzed. Many of the yellow rust samples could not be revived. Yellow rust population was avirulent to resistance genes Yr5, Yr10, Yr11, Yr12, Yr13, Yr14, Yr15 & YrSp and black rust to Sr 26, Sr 27, Sr31, Sr32, Sr 35, Sr39, Sr 40, Sr 43, SrTt3 & SrTmp; and brown rust to Lr24, Lr25, Lr29, Lr32, Lr39, Lr42 and Lr45. The frequency of pathotype 46S119 (virulent on Yr2, Yr3, Yr4, Yr6, Yr7, Yr8, Yr9, Yr17, Yr18, Yr19, Yr21, Yr22, Yr23, Yr25, YrA) of yellow rust, 79G31 (virulent on Sr2, Sr5, Sr6, Sr7b Sr9a, Sr9b,Sr9c, Sr9d, Sr9f, Sr9g, Sr10, Sr13, Sr14, Sr15, Sr16, Sr17, Sr18, Sr19, Sr20, Sr21, Sr28, Sr29, Sr30, Sr34, Sr36, Sr38, SrMcN) of black rust and 121R60-1 (virulent on Lr1, Lr3, Lr10, Lr11, Lr12, Lr13, Lr14a, Lr14b,Lr14ab, Lr15, Lr16, Lr17a, Lr17b, Lr18, Lr20, Lr21, Lr22a, Lr22b, Lr23, Lr26,Lr27+31, Lr30, Lr33, Lr34, Lr35, Lr36, Lr37, Lr38, Lr44, Lr46, Lr48, Lr49) of brown rust was the maximum in their respective categories. Continue reading

May 30th, 2016: Race Analysis Data from 2015 Indicates a Possible Shift in Stem Rust Populations in East Africa

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Digalu crop destroyed by race TKTTF. Ethiopia 2013

Race analysis undertaken by EIAR, Ambo, GRRC, Denmark and USDA-ARS CDL on samples collected in 2015 from Ethiopia and Kenya indicates that stem rust populations in East Africa are changing. The detection of race TKTTF (“Digalu” race) in Ethiopia in 2012 and the subsequent epidemics in 2013, 2014 and 2015 (see Olivera et al 2015) appears to have profoundly influenced the stem rust populations in East Africa. For over a decade the Ug99 race group has dominated in both Ethiopia and Kenya, however the latest results indicate that this situation is now changing.

A total of 214 stem rust samples from Ethiopia in 2015 were analysed by the 3 different laboratories. The results indicated that the original Digalu race (TKTTF) dominated throughout the country, with 86% (n=185) of samples being this race. Other presumed variants of the Digalu race were also detected – TTTTF (n=9), TTTTC (n=3), TRTTF (n=3), PKPTF (n=4), PKPTC (n=2), PTTTF (n=1), PTPTF (n=1). Other races included: SJPQC (n=1), JRCSF (n=1), JRCQC (n=1). Ug99 (race TTKSK) was still present at very low frequency, only 2 samples out of 214.

In Kenya, only 17 isolates were analysed by USDA-ARS CDL however the results indicated that the Digalu group of races were also emerging. A total of 7 races were identified in Kenya. Races presumed to be variants of the Digalu race pre-dominated. The most frequent race was PTTTF (n=7), with PKPTC (n=3) and PKPTF (n=1) also detected. Interestingly, the original Digalu race (TKTTF) was not detected in the Kenya samples. Three Ug99 races were also detected in the Kenya 2015 samples: Races TTKSK (n=4), TTKTT (n=1) and TTKTT (n=1).

Feb 1st, 2016: Latest version of Mehtaensis newsletter published by Indian Inst of Wheat and Barley Research, Flowerdale, Shimla: Comprehensive updated information on rusts in India and South Asia

Prof Mehta v2 (2)The latest version of the Mehtaensis newsletter (a 6 monthly newsletter named after Prof. K.C. Mehta) has just been published by the IIWBR, Regional Station, Flowerdale, Shimla. Compiled and edited by Dr. S.C. Bhardwaj, O.P. Gangwar, Pramod Prasad and Hanif Khan with technical assistance from S.B. Singh and Subodh Kumar. Mehtaensis contains a detailed summary of all the rust activities and race analysis results from India and neighbouring South Asian countries during the period July – Dec 2015. The executive summary is reproduced here:

“During offseason 135 samples of three rusts of wheat were received from Himachal Pradesh, Punjab, Tamil Nadu and Uttarakhand. 49 samples of all three rusts of wheat were analyzed, some of which were spill over of main season. Ug99 type of virulence was not identified anywhere in India. In brown rust pathotype77-5 (121R63-1) of brown rust, 46S119 and 110S119 of yellow rust and 40A (62G29) of black rust were found most frequently among the analyzed samples. Nucleus inocula of three rusts were also supplied to 38 Scientists/Research centres to facilitate research work elsewhere in India. More than 2850 lines of wheat and barley were evaluated against the pathotypes of different rusts. The tested material included the breeding lines provided by breeders from various parts of India, exotic wheat lines from CIMMYT and ICARDA. In addition 150 lines of AVT I and II are being evaluated against different pathotypes to identify rust resistant wheat lines. For monitoring the occurrence/spread of different diseases of wheat, Wheat Disease Monitoring Nursery (WDMN) and SAARC-WDMN were planted at 50 and 28 locations, respectively. Early occurrence of yellow rust was reported from Ropar, Anandpur Sahib and Hoshiarpur district of Punjab. Three Ug99 resistant genetic stocks namely FLW31, FLW32 and FLW33 have been developed. FLW31 and FLW33 are completely resistant against black and brown rusts while FLW32 has resistance to black rust and adult plant resistance against yellow and brown rusts. Work on standardization of doubled haploid production in wheat using maize pollination induced chromosome elimination was initiated. Offseason nursery was used for selection and generation advancement of 325 wheat lines. Under frontline demonstration of wheat variety, HS542 was planted in five adopted villages (12 farmers) of Tehsil Arki (Solan district of Himachal Pradesh).”

Jan 12, 2016: Molecular diagnostics indicate presence of race TKTTF (“Digalu” race) in Kenya

Analysis of dead, single pustule stem rust pathogen samples (D-samples) using molecular diagnostic SNP assay at the USDA-ARS Cereals Disease Lab, Minnesota has detected a race TKTTF (“Digalu” race) genotype in Kenya for the first time. Five samples from 2014 and 7 samples from 2015, all collected by Ruth Wanyera and the pathology team from KALRO, Njoro, tested positive for race TKTTF genotype. These results indicated that a single genotype (clade IV-B) was present in Kenya. Clade IV-B is the predominant genotype in Ethiopia.

The D-sample results indicate that race TKTTF is distributed (probably at low frequency) throughout the major wheat growing regions of Kenya. The 2014 positive samples were collected from North Rift (n=2), Central Rift (n=1) and Mount Kenya (n=2). In 2015, positive samples were collected from South Rift (n=1), Central Rift (n=1) and Mount Kenya (n=5). Most of the TKTTF genotype positive samples were collected from the cultivar ‘Robin’ (n=9), but ‘KS Mwamba’ (n=1), ‘Kwale’ (n=1) and an unknown barley variety (n=1) also produced positive results for TKTTF genotype.

At present no race analysis studies on live samples collected in Kenya have detected the presence of race TKTTF. Testing of the SNP assay against known isolates of TKTTF and negative controls has proven 100% reliable, but until there is confirmation by race analysis the D-sample results are considered indicative.

Race TKTTF now totally dominates the stem rust pathogen population in all the wheat growing regions of neighbouring Ethiopia, so its presence in Kenya is not unexpected.

Jan 6, 2016: First reports of stripe rust appearing in India

YR_suscStripe rust was detected on 18th Dec 2015 in Anandpur Sahib and Ropar districts, Punjab and subsequently in Hoshiarpur district. The variety affected was HD-2967.  Following the first detection, the Indian Institute of Wheat and Barley Research (IIWBR) and other authorities are stepping up their efforts to curb the spread of the disease and urging farmers to be vigilant and take appropriate control measures. These first reports are slightly earlier than in previous years, but the locations are consistently the first places in India where stripe rust is detected. Several Indian media sources are reporting the first appearance of stripe rust in Punjab (see The Tribune, Business Standard, The Hindu, Times of India, The Tribune). As in previous years, Indian authorities are responding to these initial outbreaks in a rapid, effective and well organized way.

Dec 20, 2015: Five new variants of Ug99 confirmed from 2013/2014 samples in East Africa

stem rust bannerCombined results from race analysis undertaken at several different labs indicate that five new variants in the Ug99 lineage were detected from samples collected in East Africa during 2013 or 2014. Probably most significant were the two new SrTmp variants (Races TTKTK and TTKTT) previously reported (see “16 April 2015: BGRI report two new Ug99 variants with virulence to SrTmp detected in Kenya” and Patpour et al. 2015). Further analysis has revealed the presence of three additional new Ug99 lineage races. Details of these additional new races are:

These latest results bring the total of known variants within the Ug99 lineage to 13, with yet another SrTmp variant being detected in Kenya. All five of the new variants were detected in Kenya, but as previously reported race TTKTK was also detected in Uganda, Rwanda, Eritrea and Egypt in 2014. The results indicate that the Ug99 race group continues to evolve at a rapid rate.

Sep 2, 2015: Emergence and spread of virulence to SrTmp in the Ug99 race group in Africa – note published in Plant Disease

Mehran Patpour (Global Rust Reference Center in Denmark) and co-authors have just published details of the emergence and spread of virulence to SrTmp in the Ug99 race group in Africa. The note is now available as a First Look in Plant Disease  (see http://apsjournals.apsnet.org/doi/abs/10.1094/PDIS-06-15-0668-PDN). The report details the results of combined race analysis undertaken by the GRRC, Denmark and the USDA-ARS Cereals Disease Lab, Minnesota on 84 stem rust samples collected in 2014 from Kenya, Uganda, Rwanda and Egypt.

Seedling reaction of Race TTKTK on selected differentials (Photo: GRRC, Denmark)

Seedling reaction of Race TTKTK on selected differentials (Photo: GRRC, Denmark)

The presence of two new Ug99 race group variants – race TTKTK (Ug99 + virulent on SrTmp) and race TTKTT (Ug99 + virulent on SrTmp and Sr24) were confirmed in Kenya. Race TTKTK was also confirmed in Uganda, Rwanda and Egypt. Detection of these new variants in the Ug99 race group across several countries in a single year indicates the relevance of coordinated surveillance activities and also indicates potentially very rapid geographical dispersal of race TTKTK.

16 April 2015: BGRI report two new Ug99 variants with virulence to SrTmp detected in Kenya

The following is extracted from the BGRI Newsletter Special Edition, 3rd April 2015:

Kenyan Variety Robin Overcome by Two New Ug99 Variants

A popular wheat cultivar, Robin, sustained severe damage in some farmers’ fields by stem rust in the 2014 crop season in Kenya. Robin became popular because of high yield potential and resistance to previously known Ug99 races. The resistance was conferred by stem rust gene SrTmp, which was effective to the previous races of the Ug99 race group. KALRO scientists collected several samples from various field sites, including the stem rust resistance screening nurseries at Njoro, and race analyses conducted by CDL and GRRC identified two new variants in the Ug99 race group, both of which were virulent to SrTmp. One of the two new variants was also detected in the 2014 samples from neighboring countries. The detection of these new races is a result of worldwide efforts in recent years on stem rust surveillance to detect and monitor Ug99 and other significant races that pose a continuous threat to wheat production. During the past years KALRO has released several stem rust resistant wheat varieties and others are at advanced stages of testing in national variety registration trials. Varieties such as ‘Kingbird’, ‘Kenya Tai’, ‘Eagle 10’, ‘Kenya Sunbird’ and ‘Kenya Hawk 10’ continue to be resistant to the new SrTmp virulent variants.

9 April 2015: CAUTION – Increased vigilance needed in eastern Mediterranean countries following confirmation of Ug99 (race TTKSK) in Egypt

Fig 1: Modeled spore dispersal based on a source location in the central Nile Delta, Egypt for March, April, May 2014. Pink areas indicate where 95% of released spores are predicted to be deposited. Given high seasonal consistency, similar dispersal patterns would be expected to occur in March-May 2015.

Fig 1: Modeled spore dispersal based on a source location in the central Nile Delta, Egypt for March, April, May 2014. Pink areas indicate where 95% of released spores are predicted to be deposited. Given high seasonal consistency, similar dispersal patterns would be expected to occur in March-May 2015.

Following the confirmed detection of Ug99 (race TTKSK) in Egypt in 2014 (BGRI special newsletter report April 2015) increased vigilance is needed for stem rust in the eastern Mediterranean. Although no confirmed reports of race TTKSK have been obtained from Egypt in 2015, trace amounts of stem rust (race unknown) were detected in the central delta of Egypt in early March 2015. No further reports of stem rust outbreaks have been reported from Egypt in 2015. Crops in Egypt are now approaching maturity, with harvesting occurring between mid April to mid May. However, if any stem rust inoculum were to build up in Egypt then spore deposition models run jointly by the UK Met Office and Cambridge University indicate that there is a risk of onward movement of spores to the eastern Mediterranean basin. Model results show consistent seasonal deposition patterns over the last 12 years, indicating  a higher risk, relative to other areas, of spore deposition for Israel, Lebanon, Jordan, eastern Syria and southern Turkey. During the months April and May typically there is a large spatial variation of deposition patterns, with long-distance dispersal of spores that reach eastern Mediterranean countries (see Fig 1 – Data from March, April, May 2014 used as an illustrative example of typical spore dispersal patterns). The most recent spore deposition forecast maps for the period 8 – 14 April 2015, based on confirmed sites for Ug99 (race TTKSK) in Egypt in 2014 agree well with the long-term dispersal trends. Increased surveillance and monitoring is advised in Israel, Lebanon, Jordan, eastern Syria and southern Turkey. Sampling of any stem rust detected in the eastern Mediterranean and rapid race identity confirmation is recommended (either by race analysis on live samples or through the USDA CDL SNP assay for the Ug99 race group). Please contact Dave Hodson, CIMMYT (d.hodson@cgiar.org) for more details on sampling options.

20 March 2015: CAUTION – Increasing risk of stripe (yellow) rust outbreaks North Africa to South Asia

stripe rustFavourable weather conditions for stripe rust are occurring across North Africa to South Asia. Cool, wet conditions across many parts of the region are producing a conducive environment for disease outbreaks. Aggressive races with virulence to Yr27 are known to be widely distributed in several countries and susceptible Yr27 carrying cultivars are still planted on large areas. In addition, the Warrior race (virulent on: Yr1,2,3,4,-,6,7,-,9,-,-,17,-,25,-,32,Sp,Avs,Amb) has spread into the region from Europe. Many of the resistant cultivars to the Yr27 race are likely to carry some of the genes defeated by the Warrior race, particularly in winter wheat material. After first detection in 2010, the Warrior race has spread rapidly across Europe. Most previously resistant cultivars became susceptible to this new race and widespread damage resulted in major European wheat growing areas. The Warrior race was confirmed in 2013 from Morocco, and subsequently in Algeria in 2014 (GRRC, Denmark) and Turkey in 2014 (Field Crops Research Institute, Ankara and Regional Cereal Rust Research Center, Izmir, Turkey). Under current conditions, this race is likely to spread in North Africa and the Middle East. The combined presence of the Yr27 aggressive race and the Warrior race may result in susceptibility of many existing spring and winter wheat cultivars. Although not recorded at present, acquisition of virulence for Yr27 by the Warrior race is not impossible and needs to be carefully monitored.

Serious stripe rust outbreaks are now being reported from Morocco (March 2015), and outbreaks have occurred in India (Feb 2015 http://www.tribuneindia.com/news/haryana/yellow-rust-hits-wheat-over-2000-acres-in-y-nagar/47843.html). First reports of stripe rust appearance have also been reported from south-west Iran at the end of Feb 2015. Other countries e.g., Yemen currently only have low levels of disease or are currently reported to be disease free.

Given the current and forecasted favourable weather conditions for disease development and the presence of the Yr27 aggressive race and the Warrior race, extreme caution and vigilance is advised with respect to stripe rust. Early detection, sampling, reporting and timely effective control of any outbreaks on susceptible cultivars is recommended.

Reporting of new outbreaks to Borlaug Global Rust Initiative (BGRI) staff, K. Nazari (ICARDA) k.nazari@cgiar.org and D. Hodson (CIMMYT) d.hodson@cgiar.org is encouraged. Pathotype analysis of representative samples of stripe rust would provide additional information about which sources of resistances in wheat may be at particular risk. The Global Rust Reference Centre in Denmark may undertake such analysis, but only on a limited number of samples. Please contact K Nazari or D. Hodson for essential sampling and dispatching procedures.