Australian Cereal Rust Control Program Consultative Committee March 22nd 2012 Director’s Report Professor Robert F. Park robert.park@sydney.edu.au

The Australian Cereal Rust Control Program -linking pathology, genetics & breeding for Australian graingrowers The University of Sydney: Lead organisation Research and breeding CIMMYT: Polygenic rust resistance CIMMYT CSIRO Plant Industry: Molecular genetics The University of Adelaide: Alien rust resistances ACRCP = PBI

Personnel Scientific staff: Honorary Associates: General staff: Urmil Bansal Harbans Bariana Robert Park Colin Wellings Peng Zhang Davinder Singh Haydar Karaoglu William Cuddy Honorary Associates: Bob McIntosh Ray Hare General staff: Muhammed Gill Sami Hoxa Keshab Kandel Paul Kavanagh Hanif Miah Gary Standen Beate Wildner Matthew Williams Postgraduate students: Jordan Bailey Mumta Chettri Lida Derevnina Banchgize Temesgen Leila Kamino Tolera Keno Sambasivam Kuppasamy Mandeep Randhawa Seipati Seketemi Karanjeet Sandhu Lisle Snyman Arvinder Toor 3

Personnel Scientific staff: Honorary Associates: General staff: Urmil Bansal Harbans Bariana Robert Park Colin Wellings Peng Zhang Davinder Singh Haydar Karaoglu William Cuddy Honorary Associates: Bob McIntosh Ray Hare General staff: Muhammed Gill Sami Hoxa Keshab Kandel Paul Kavanagh Hanif Miah Gary Standen Beate Wildner Matthew Williams Postgraduate students: Jordan Bailey Mumta Chettri Lida Derevnina Banchgize Temesgen Leila Kamino Tolera Keno Sambasivam Kuppasamy Mandeep Randhawa Seipati Seketemi Karanjeet Sandhu Lisle Snyman Arvinder Toor 4

Personnel Scientific staff: Honorary Associates: General staff: Urmil Bansal Harbans Bariana Robert Park Colin Wellings Peng Zhang Davinder Singh Haydar Karaoglu William Cuddy Honorary Associates: Bob McIntosh Ray Hare General staff: Muhammed Gill Sami Hoxa Keshab Kandel Paul Kavanagh Hanif Miah Gary Standen Beate Wildner Matthew Williams Postgraduate students: Jordan Bailey Mumta Chettri Lida Derevnina Banchgize Temesgen Leila Kamino Tolera Keno Sambasivam Kuppasamy Mandeep Randhawa Seipati Seketemi Karanjeet Sandhu Lisle Snyman Arvinder Toor 5

Adjunct Prof. Colin Wellings awarded the 2011 Farrer Medal 6

University Economic Model University of Sydney will move to a new funding model in 2012 All externally earned funding will be paid directly to the centre that earns it (e.g. RIBG) Centres will pay central administration for resources used 7

PBI Infrastructure – greenhouse polycarbonate 8

PBI Infrastructure – greenhouse polycarbonate 9

PBI Infrastructure – Karalee field redevelopment 10

PBI Infrastructure – Karalee field redevelopment “Cage” 2 “Cage” 1 11

PBI Infrastructure – controlled environment growth room complex 12

PBI Infrastructure – controlled environment growth room complex 13

PBI Infrastructure – controlled environment growth room complex 14

PBI Infrastructure – controlled environment growth room complex 15

PBI Infrastructure – controlled environment growth cabinets 16

PBI Infrastructure – Karalee field redevelopment “Cage 2” “Cage 1” Roadway Dam 17

PBI Infrastructure – Karalee field redevelopment “Cage 2” X “Cage 1” X Year 1 Year 2 Year3 Roadway Dam Shadehouse Tunnelhouses (horticulture) 18

PBI Infrastructure – Field sites Lansdowne 3 Year rotation, 4.5ha Horseunit 3 Year rotation, 3.6ha Breakwell 3 Year rotation, 1ha Karalee 3 Year rotation, 0.7ha J.B. Pye* 3 Year rotation, 0.8ha Sheep Unit 3 Year rotation, 1.2ha * Fungicide Block only; also have a further 7.5ha (2.5ha x 3 year rotation) available from 2013 19

PBI Infrastructure – Field sites Lansdowne 3 Year rotation, 4.5ha Horseunit 3 Year rotation, 3.6ha Breakwell 3 Year rotation, 1ha Karalee 3 Year rotation, 0.7ha J.B. Pye* 3 Year rotation, 0.8ha Sheep Unit 3 Year rotation, 1.2ha * Fungicide Block only; also have a further 7.5ha (2.5ha x 3 year rotation) available from 2013 Maximum numbers we can accommodate: 100,000 Routine tests 800 Long rows 20

Field rust inoculations in 2011 (spray only) - 20 pathotypes across 5 field sites Date Disease Field site 25 July Wheat rusts Lansdowne Sheep Unit Horse Unit 26 July Karalee 28 July 3 August 10 August 11 August 18 August 25 August JB Pye 29 August BGYR & WYR Breakwell Barley LR 31 August Oat rusts 13 September 21 September 22 September   21

Field rust pathotypes – leaf rust as @ early September Site   104-VPM 104-Lr24 76-VPM 10-1,3,9,10,12 Karalee 10% 80% Lansdowne Top 90% Bottom 20% 60% Horse Unit Bay 1 40% FFS 22

Rust testing of breeding material - field   Number of entries 2007 2008 2009 2010 2011 Wheat Routine Tests 117,745 81,383 100,339 104,816 61,338* Detailed Tests 427 252 35 568 520 F2 Long Rows 297 277 942 611 Non-wheat 10,934 11,802 12,964 11,403 9,528** 234 408 178 214 357 All 128,679 93,185 113,303 116,219 66,781 661 660 213 224 102** * Includes durum wheat ** Barley, oats, triticale 23

Rust testing of breeding material - field   Number of entries 2007 2008 2009 2010 2011 Wheat Routine Tests 117,745 81,383 100,339 104,816 61,338* Detailed Tests 427 252 35 568 520 F2 Long Rows 297 277 942 611 Non-wheat 10,934 11,802 12,964 11,403 9,528** 234 408 178 214 357 All 128,679 93,185 113,303 116,219 66,781 661 660 213 224 102** Maximum numbers we can accommodate: 100,000 Routine tests 800 Long rows * Includes durum wheat ** Barley, oats, triticale 24

Rust testing of breeding material - greenhouse G’house:   Number of tests 2007 2008 2009 2010 2011 Wheat Routine Tests 29,114 15,217 7,657 20,919 28,000* Detailed Tests 13,962 636 630 10.925 9,880 Non-wheat 10,412 11,802 12,964 11,403 19,991** 2,106 1,924 2,057 5,924 5,002 All Cereals 39,526 27,019 20,621 32,322 16,068 2,560 2,687 3,048 * Includes durum wheat ** Barley, oats, triticale 25

USyd ACRCP Outputs, 4.5 years, 01/07/2007 to 31/12/2011 - Surveys 4,206 cereal and grass rust samples processed, 4,293 pathotype IDs Identified and characterised 13 new rust pathotypes 174 differential genotypes used for race typing maintained Liquid nitrogen rust collection maintained and expanded to include new pts SSR development in rusts: 44 for P. graminis 30 for P. triticina 21 for P. hordei 26

USyd ACRCP Outputs, 4.5 years, 01/07/2007 to 31/12/2011 – Germplasm screening and enhancement Routine Field Tests on (ca.): 466,000 wheat; 5,500 barley; 27,400 oat; 12,500 triticales. Detailed Field Tests on (ca.): 1,802 wheat; 615 barley; 115 oat; 319 triticales. Routine Seedling Rust Assays ca.: 72,000 wheat; 5,500 barley; 27,400 oat; 31,500 triticale. Detailed Seedling Rust Assays on ca.: 15,000 wheat; 4,700 barley; 1,420 oat; 1,370 triticales. 2,379 F2 Long Rows (1,500 plants, space planted and harvested). Returned more than 3,800 wheat backcross derivatives to breeders. Returned some leaf rust resistant backcross material to barley breeders. 27

USyd ACRCP Outputs, 4.5 years, 01/07/2007 to 31/12/2011 – Gene discovery Identified and characterised at least 12 APR genes and 15 seedling genes: 5 resistance genes conferring APR in wheat 5 conferring seedling resistance in wheat (Sr48, Sr49, Sr57, Yr47, Lr71 catalogued) 3 conferring APR and 6 conferring seedling resistance in barley 3 conferring APR and 3 conferring seedling resistance to crown rust in oats 1 conferring seedling resistance and 1 conferring APR to stripe rust in triticale 28

USyd ACRCP Outputs, 4.5 years, 01/07/2007 to 31/12/2011 – Extension and training Wrote/ distributed/completed: 4 Annual Pathogenicity Survey reports 38 Cereal Rust Updates 68 extension articles for newspapers (incl. Ground Cover) etc 41 media releases including radio interviews. Contributed to 33 grower/ agronomist workshops/ field days Participated in 21 national/ international conferences/ meetings Published 68 peer-reviewed journal articles/ book chapters Completed 12 PhD and 3 Masters students, in rust pathology and genetics 29

The frequency of exotic incursions is increasing: Future perspectives The frequency of exotic incursions is increasing: Number of incursions 1915-1935 1936-1955 1956-1975 1976-1995 1996-2010 Year

The Triple3 (wheat, triticale, barley) - Double (oats) Rust Initiative Four projects instead of one: - surveillance genetics markers (led by CSIRO) Fee for Service Proposals include: reducing Director’s salary to zero, incrementally, over project life GRDC to fund (50%) Business Manager Fee for Service subsidy to reduce to zero (wheat by year 3, barley by year 4) full review of FFS, including costings, once Business Manager is appointed Initiatives to include: - approaching 100 years of continuous rust race analysis in Australia (2018) even greater emphasis on APR to all rust diseases in all crops accelerated characterisation & marker development in barley, oats targeted off-shore rust testing (Mexico, Kenya etc) tools for pre-breeding for barley stripe rust resistance rust pathogen genome sequencing to develop tools for rapid diagnosis new technologies for information flows 31

The Triple3 (wheat, triticale, barley) - Double (oats) Rust Initiative Four projects instead of one: - surveillance genetics markers (led by CSIRO) Fee for Service Proposals include: reducing Director’s salary to zero, incrementally, over project life GRDC to fund (50%) Business Manager Fee for Service subsidy to reduce to zero (wheat by year 3, barley by year 4) full review of FFS, including costings, once Business Manager is appointed Initiatives to include: - approaching 100 years of continuous rust race analysis in Australia (2018) even greater emphasis on APR to all rust diseases in all crops accelerated characterisation & marker development in barley, oats targeted off-shore rust testing (Mexico, Kenya etc) tools for pre-breeding for barley stripe rust resistance rust pathogen genome sequencing to develop tools for rapid diagnosis new technologies for information flows 32

The Triple3 (wheat, triticale, barley) - Double (oats) Rust Initiative Four projects instead of one: - surveillance genetics markers (led by CSIRO) Fee for Service Proposals include: reducing Director’s salary to zero, incrementally, over project life GRDC to fund (50%) Business Manager Fee for Service subsidy to reduce to zero (wheat by year 3, barley by year 4) full review of FFS, including costings, once Business Manager is appointed Initiatives to include: - approaching 100 years of continuous rust race analysis in Australia (2018) even greater emphasis on APR to all rust diseases in all crops accelerated characterisation & marker development in barley, oats targeted off-shore rust testing (Mexico, Kenya etc) tools for pre-breeding for barley stripe rust resistance rust pathogen genome sequencing to develop tools for rapid diagnosis new technologies for information flows 33

© University of Sydney

Australian Cereal Rust Control Program Consultative Committee March 22nd 2012 Pathogenicity surveys - wheat stem rust and wheat leaf rust - barley leaf rust - oat crown rust Australian Cereal Rust Control Program Professor Robert F. Park robert.park@sydney.edu.au 35

Pathogenicity surveys, rust database Database, including cereal rust collection and rust surveys, set up ca. 15 years ago In recent years, demand for rapid notification of results has increased In the past 2 years, Dr Wellings has done this manually Dr Nabil Ahmad (PBI) kindly restructured the database in FileMaker Pro, early 2011 All samples received for pathoytping are now acknowledged, and results sent as soon as they are generated, by email Moving towards integrating GPS and graphical representation of survey data on web Yields in Australian cereal crops are generally low & hence genetic resistance is the most effective and economical means of diseas control The ACRCP is a national program targeting control of cereal rust diseases by genetic resistance Why is a nationally coordinated approach needed? Rust diseases have caused significant losses to Australian cereal crops (some estimates are given)

Pathogenicity surveys, EpiCollect Will integrate EpiCollect Smartphone app. for data collection sometime in 2012: Yields in Australian cereal crops are generally low & hence genetic resistance is the most effective and economical means of diseas control The ACRCP is a national program targeting control of cereal rust diseases by genetic resistance Why is a nationally coordinated approach needed? Rust diseases have caused significant losses to Australian cereal crops (some estimates are given) http://www.epicollect.net/

Pathogenicity surveys, 2004 - 2011 -number of samples received and processed 747 samples received to date, ? from artificially inoculated material Wheat stem rust Common in commercial wheat crops in south eastern Australia Found on Yitpi volunteers in the Mallee in late February 2011 60 samples received, 4 pts identified: 34-2,12,13 (nNSW, 3 isolates) 34-2,12,13 +Sr21 (nNSW 1 isolate) 34-1,2,7 +Sr38 (45 isolates) 34-1,2,7 +Sr38 [Yalta Low] (6 isolates)   Year Pathogen 2005 2006 2007 2008 2009 2010 2011 WSR 51 125 21 18 11 60 80 WLR 122 40 13 23 19 100 90 WYR 393 167 350 830 552 650 370 BLR 27 31 65 62 123 63 BSR 10 4 5 2 OCR 46 34 24 49 17 165 83 OSR 41 42 20 94 Total 690 424 438 1,032 705 1,197 701 38

Pathogenicity surveys, 2011 – wheat stem rust 80 samples received to date most from eastern Australia, first samples from EA received in April 11 samples not yet processed; 88 IDs, 7 pts identified: Pathotype Number of isolates 34-1,2,7 +Sr38 58 34-1,2,7 +Sr38 [Yalta Low] 16 34-1,2,7 +Sr38 +51209 1 34-1,2,7 98-1,2,3,5,6,7 1 (Victoria) 343-1,2,3,5,6 9 34-2,12,13 2 TOTAL 88 39

Pathogenicity surveys, 2011 – wheat stem rust 80 samples received to date most from eastern Australia, first samples from EA received in April 11 samples not yet processed; 88 IDs, 7 pts identified: Pathotype Number of isolates 34-1,2,7 +Sr38 58 34-1,2,7 +Sr38 [Yalta Low] 16 34-1,2,7 +Sr38 +51209 1 34-1,2,7 98-1,2,3,5,6,7 1 (Victoria) 343-1,2,3,5,6 9 34-2,12,13 2 TOTAL 88 Pt. 34-1,2,3,7,8,9 detected from WA (2), Victoria (1) and Qld (3) 40

Pathogenicity surveys, 2011 – wheat leaf rust 90 samples received to date most from eastern Australia 6 not yet processed 128 IDs, 9 pts identified: Pathotype # isolates 104-1,2,3,(6),(7),11 12 104-1,2,3,(6),(7),11 [Gaza high] 4 104-1,2,3,(6),(7),11,13 8 104-1,2,3,(6),(7),11 +Lr37 37 76-3,5,7,9,10 +Lr37 1 76-3,5,7,9,10,12 +Lr37 33 76-1,3,5,7,9,10,12 +Lr37 29 76-1,3,5,9,10,12 10-1,3,7,9,10,12 3 TOTAL 128 Pt. 10-1,2,3,4 isolated from Qld 41

* * * * Pathogenicity surveys, 2011 – barley leaf rust 63 samples received to date most from eastern Australia 15 not yet processed 75 IDs, 11 pts identified: Pathotype # isolates 5453P- 11 5453P+ 32 5473P+ 4 5457P+ 7 (Qld, nNSW, SA) 5472P+ 1 5652P+ 5 5656P+ 2 (Vic, SA) 5672P+ 8 5673P+ 5673P+ +Rph13 220P+ 3 TOTAL 75 5453P- * 5453P+ +Rph19 * 5473P+ +Rph5 * 5457P+ +Rph3 * 42

Pathogenicity surveys, 2011 – oat crown rust 83 samples received to date, 61 IDs, 15 pathotypes: No. Common Region Lineage pts Qld/ nNSW sNSW/Vic/SA WA 0000 1 0000-2 P 0001 2 0001-0 “Pc61”* 0071-0   “Pc38/Pc39/Pc55/Pc71”** 7 0307-5,6,10 +Warrego * incl. pathotypes virulent on Amby, Nobby, Bettong, Barcoo ** incl. pathotypes virulent on Nugene, Warrego, Graza 68, Gwydir, Volta, Genie Now have 3 pathotypes virulent on Genie