Sridhar Bhavani. Decade of stem rust research on Ug99 Progress and Challenges. B. Girma Bekele Abeyo A. Badebo G. Woldeab. R.P. Singh J.

Transcription

1 Decade of stem rust research on Ug99 Progress and Challenges P. Njau R. Wanyera B. Girma Bekele Abeyo A. Badebo G. Woldeab Sridhar Bhavani R.P. Singh J. Huerta-Espino Gordon Cesar EIAR

2 Why Ug99 is a global threat? Highly aggressive - broad virulence spectrum Several genes rendered ineffective >80% of wheat lines world wide found Susceptible when tested in Kenya Migrated from Uganda to Kenya, Ethiopia, Yemen, Sudan and reported in Iran (2007) Early epidemics can cause >70% losses Mutations have identified two new races TTKST TTTSK and more recently TTKTT??

3 Successful Pathogen Tracking: Spread of Ug99 Race Group /9: 1 Ug99 race (TTKSK) detected in 1 country (Uganda) Ug99 is mutating and migrating 2015: 13 Ug99 races detected across 13 countries (Africa and Middle East) In 2013/14: 5 new Ug99 races detected in Kenya In 2014: 1 new variant (TTKTK Ug99 + SrTmp vir) detected in Kenya, Uganda, Rwanda, Eritrea and Egypt Ug99 races getting more virulent over time serious implications for other regions

4 New Technologies: Molecular diagnostics and population genetics Molecular diagnostics: Rapid + robust diagnostic SNP assay for wheat stem rust Ug99 race group (field collected single pustules). Stage 1: Ug99 Race Group Yes / No. Stage 2: Diagnostic for key races Population genetics: Developed two highthroughput genotyping SNP chips for studying population genetics and diagnostics of wheat stem rust 1. PgtSNP 1.5k (Illumina GoldenGate) - 50% genome coverage 2. PgtSNP 3.0k (Illumina Infinium) - 98% genome coverage + Newcomb et al Phytopatholog United States Department of Agriculture Agricultural Research Service Credit: CDL, Dr Les Szabo

5 Implementation of Strategies-KARI,EIAR KARI Njoro (14ha) Bread wheat screening-most activities EIAR Debre Zeit (12 ha) Durum and bread wheat screening 2185 MSL 980mm 200km w 1850 MSL 839mm 40km SE Wheat growing environments-good adaptation, growth and high disease pressure Pathotypes available (Ug99 lineage-ug99, Ug99+Sr24, Ug99+Sr36) Facilities supported by BGRI (DRRW) and CIMMYT Breeding - fits with shuttle breeding (2 seasons)-kenya

6 Wheat accessions phenotyped during for Ug99 resistance at Njoro (Kenya) and Debre Zeit (Ethiopia), and participating countries, in partnership with KALRO and EIAR 400,000 accessions screened 50,000 annual capacity

7 Status of resistance to Ug99 in wheat accessions phenotyped during at Njoro, Kenya

8 Rapid cycling of breeding materials through field based selection Mexico (Cd. Obregon-Toluca/El Batan)- Kenya International Shuttle Breeding A five-year recurrent breeding cycle Cd. Obregón 39 masl High yield (irrigated), Water-use efficiency, Heat tolerance, Leaf rust, stem rust (not Ug99) Njoro, Kenya 2185 masl Stem rust (Ug99 group) Yellow rust Toluca 2640 masl Yellow rust Septoria tritici Fusarium El Batán 2249 masl Leaf rust, Fusarium Tan spot Since 2008: Mexico-Kenya Shuttle breeding 2000 F3/F4 populations shuttled each year High yielding, resistant lines distributed worldwide since 2011 Njoro, Oct. 2014

9 Selection & phenotyping for Ug99 race group Segregating populations: F3 and F4 selected bulk populations received from Toluca, Mexico grown at Njoro off- season, selected and harvested (Jan-May) F4 and F5 selected bulk populations grown again at Njoro main-season, selected, harvested and sent back to Mexico (June- November) for planting at Obregon Advanced lines: > 8000 new lines in 1 st year yield trials in Obregon phenotyped simultaneously for stem rust at Njoro in the off-season. >1400 lines selected based on yield, stem rust and other agronomic traits phenotyped in the main-season at Njoro and for various traits in Mexico >1100 lines retained for 2 nd year yield trials under 6 environments at Obregon phenotyped for stem rust at Njoro during the off and main-seasons Between selected lines phenotyped at seedling stage in USDA-ARS greenhouse, Highest severity recorded during the four seasons of field evaluation, seedling CDL, St. Paul, MN. reactions and marker information (where relevant) used in assigning a reaction category for lines distributed internationally

10 Diversity: race-specific genes effective to Ug99 and other important races Genes available for immediate use: Sr22, Sr26, Sr35, Sr42/SrCad, Sr45, Sr50, SrSha7, SrNing, SrND643, SrHUW234, Sr1A1R, SrWeb/SrGabo56 Under development 10 genes on reduced alien chromosome segments: Sr32, Sr37, Sr39, Sr40, Sr43, Sr44, Sr47, Sr50, Sr51, Sr53 New genes from wild tetraploids, landraces, Ae. tauschii, T. monococcum (SrTm4, SrTm5)] New alien genes (H. villosa, Ae. sharonensis, Ae. searsii, Th. ponticum, Th. intermedium, Ae. caudata, etc.) Stacking/Pyramiding multiple race specific genes (Sr22, Sr25, Sr26) Race specific genes do not confer immunity when deployed singlyenhanced phenotypic effects of intermediate effect genes can be achieved in combination with APR genes

11 Strategies for resistance breeding Race-specific genes large to small effect Seeding and adult plant effective Diverse hypersensitive host reactions Few genes with large effect and most of them are intermediate types Challenge of Boom and Bust Cycles, epistatic effects Partial or slow rusting genes or race non specific genes Minor genes with small to intermediate effects Gene effects are additive Resistance does not involve hypersensitivity Genes confer slow disease progress through: Reduced infection frequency Lower disease severity, Increased latent period Small to large compatible pustules on stems Reduced spore production, Only a few genes characterized Seedling reactions- stem rust

12 Mapping of APR to Ug99 and other Pgt races Bi-parental recombinant inbred lines mapping populations (Bhavani et al. 2011, Njau et al. 2012) 15 RIL populations developed and phenotyped QTL analysis completed for six populations Pleiotropic effects of Lr34/Yr18, Lr46/Y29 & Lr67/Yr46 on slow rusting to stem rust established; corresponding resistance genes designated as Sr57, Sr58 and Sr55, respectively Association mapping identified various genomic regions (Yu et al. 2011) Lr34 mutant Lr34

13 Breeding options available Adult plant resistance Sr2, Sr55, Sr56, Sr57, Sr58 and other QTLs: 2BS, 5BL, etc. Sr loci: high levels of APR in CIMMYT wheat backgrounds Thatcher+Sr57 (or Sr55) also has high level of APR in the absence of Sr2: QTL on 3BS overlapping Sr12, 1AL & 2BS in Thatcher/McNeal population (Rouse et al. 2014) Other sources: semi-dwarf CIMMYT and old tall Kenyan varieties APR identified in improved wheat lines e.g. Kingbird, Kiritati, Juchi, Pavon, Parula Older Kenyan varieties Kenya swara, Kenya nyangumi, Kenya Fahari, K.kudu etc. Kingbird- continues to the best source of APR

14 Ug99 stem rust resistance in wheat entries identified for international distribution in 2015 (Based on highest disease severity recorded in four seasons of field testing at Njoro, Kenya and seedling test ) Entries Entries Resistance Category % Severity No. % Resistance Category No. % High-Adequate APR (44.8%): Race-specific (28.8%): NIR (Near-Immune resistant) Sr R (Resistant) Sr R-MR (Res.-Moderately Res.) Sr MR (Moderately resistant) Sr Sr1A.1R Adequate APR depending on location of deployment SrBau (15.9%): MR-MS (Mod. Res.-Mod. Sus.) SrHuw SrND Inadequate-Susceptible (10.5%) SrYanac MS (Moderately Susceptible) Sr? MS-S (Mod. Sus.-Susceptible) Durable APR gene Sr2 present in >80% lines Our goal is to increase the frequency of high yielding lines in NIR and R categories for deployment in East Africa S (Susceptible)

15 Capacity building 4 th stem rust training course on Standardization of stem rust note taking and evaluation of germplasm with emphasis on emerging threats of Yellow rust and Leaf rust (September 25th - October 5th, 2012) was conducted with 31 participants from 14 different countries.

16

17 Emerging challenges: Race TKTTF (Digalu race) Digalu race (race TKTTF) not in Ug99 race group; genetically unrelated. In Turkey since at least Increasingly detected across a wide geographical range. Germany and Denmark detected TKTTFlike variants in 2013 (virulence on 4 additional Sr genes: Sr33, Sr7a, SrTt-3, Sr45 (Olivera et al., 2015)) Race TKTTF was first detected in Ethiopia in August 2012 (trace). Epidemics in Ethiopia on cv Digalu 2013, 2014 and very distinct genotypes (type A and type B) (Olivera et al., 2015) New variants being detected becoming the predominant race group in East Africa (replacing Ug99)

18 Ethiopia: Digelu race (TKTTF) Success: Rapid detection and identification within season Outstanding global collaboration (see Olivera et al 2015) Germplasm screening started immediately in Ethiopia (seedling + adult plant single race nurseries) Catalyst for advanced early warning systems Would not have been possible without prior investments around Ug99

19 Rust never sleeps Dr. Norman Borlaug Thanks!!!