Sustainability of Global Durum Wheat Production Karim Ammar Head, - - PowerPoint PPT Presentation

Enhancing the Sustainability of Global Durum Wheat Production

Karim Ammar Head, Durum Wheat & Triticale Breeding Global Wheat Program, CIMMYT-Mexico

 Wheat & Maize Genetic Improvement ■ Spring Wheat: Mexico, Winter Wheat: Turkey ■ Maize: Decentralized (Africa, India)

CIMMYT

Mission

 Wheat & Maize-based Systems Agronomy ■ Input-saving technologies, Conservation Agriculture, Precision Agriculture  Curator of Wheat & Maize Genetic Resources ■ > 140,000 accessions of wheat & wild relatives  Wheat & Maize-related Capacity Enhancement ■ Practical training, graduate studies, visiting scientists

CIMMYT Spring Wheat Breeding

General Scheme & Outlet = International Nurseries

Crossing Selection Evaluation of fixed lines in Mexico

Distribution of improved germplasm: International Nurseries National Programs Private Companies Research Institutions Local / Regional Selection Use in crosses Use in research Direct release

CIMMYT Spring Wheat Breeding

Global Impact … And Responsibility

> 40% area, spring types < 40% area, spring types Winter types

CIMMYT Spring Wheat Breeding

Reasons for global success: a program with “eyes” worldwide

Crossing Selection Evaluation of fixed lines in Mexico Distribution of improved germplasm through IWIN

Collection and interpretation of multi-location data IWIN

CIMMYT Spring Wheat Breeding

Reasons for global success: Wide-adaptation through “Shuttle-Breeding”

Obregon

Longitude: 109° 54´ W Latitude: 27° 21´ N Altitude: 40 masl

Winter Cycle: Obregón (28oN, 35 masl) November - May. Irrigated + simulated drought Diseases: Leaf Rust Photoperiod: Increasing Soils: +/- alkaline Summer Cycle: Toluca/El Batan (18.5oN, 2600 masl) May - October. Rainfed, High Rainfal Diseases: Yellow Rust, Septoria, Fusarium Photoperiod: Decreasing Soils: +/- acid Toluca

Longitude: 99° 33´ W Latitude: 19° 13´ N Altitude: 2640 masl

F2, F4, F6 F3, F5

CIMMYT Spring Wheat Breeding

Reasons for global success: Reliable and relevant phenotyping conditions

Obregón

1 2 3 4 5 6 7 8 9 . . . 50

Egypt

1 2 7 4 5 6 3 8 9 . . . 50

India

1 4 3 2 5 6 7 8 9 . . . 50

Pakistan

1 2 3 4 5 6 7 8 9 . . . 50

Iran

1 2 3 4 5 6 7 8 9 . . . 50

 Yield Potential: Predicts ranking of performances in other important environments worldwide

Durum Wheat Worldwide

Globally minor, locally major

7.6% % Area % Production Bread Wheat Durum Wheat 5.4%

Source: International Grains Council, 2013

Durum Wheat Worldwide

Globally minor, locally major

Bread Wheat Durum Wheat

Morocco Algeria Tunisia Lybia Syria Jordan Italy Spain Mexico 0% 20% 40% 60% 80% 100%

Durum Wheat Worldwide

Area Sown (average of last 10 years): 16.9 Million Ha.

Area Area Country x1000 ha. Country x1000 ha. Kazakhstan 2280 France 429 Canada 1970 Mexico 311 Turkey 1670 China 305 Italy 1417 Australia 258 Algeria 1264 Ethiopia 248 Morocco 982 Afghanistan 194 United States 933 Iran 175 Syria 901 Pakistan 126 India (?) 693 Iraq 107 Tunisia (?) 669 Argentina 89 Spain 635 Saudi Arabia 65 Russia 610 Egypt 46 Greece 488 Chile 13

Source: International Grains Council, 2013

Durum Wheat Worldwide

Production (average of last 10 years): 35.9 Million tons

Area Area Country x1000 tons Country x1000 tons Canada 4493 China 1245 Italy 4281 India 1060 Turkey 3030 Greece 991 Kazakhstan 2400 Australia 470 United States 2305 Afghanistan 386 France 2070 Iran 339 Algeria 2045 Pakistan 331 Syria 1962 Ethiopia 321 Mexico 1772 Egypt 280 Morocco 1452 Saudi Arabia 277 Russia 1315 Iraq 222 Spain 1287 Argentina 210 Tunisia 1259 Chile 56

Source: International Grains Council, 2013

Durum Wheat Worldwide

National Yield (average of last 10 years): 2.65 t/ha

Source: International Grains Council, 2013

Yield Yield Country Tons/ha. Country Tons/ha. Egypt 5.69 Syria 2.15 Mexico 5.67 Greece 2.03 France 4.83 Spain 2.03 Chile 4.50 Afghanistan 1.99 Saudi Arabia 4.16 Iran 1.93 China 4.10 Tunisia 1.87 Italy 3.04 Turkey 1.82 Pakistan 2.63 Australia 1.82 United States 2.47 Algeria 1.59 Argentina 2.37 India 1.55 Iraq 2.36 Morocco 1.46 Canada 2.30 Ethiopia 1.38 Russia 2.16 Kazakhstan 1.04

Durum Wheat: Sustainability of Global Production

What makes the world keep growing Durum Wheat?

Sustainability of Global Durum Wheat Production

Durum Wheat: Sustainability of Global Production

Limiting or key factors…

Sustainability of Global Durum Wheat Production Continued Progress in Yield Potential (vs. Bread Wheat) Disease Resistance Rusts & Septoria Yield Stability & Drought Tolerance Performance Stability under Heat Market Access & Industrial Quality Grain “Safeness” FHB Resistance

Durum Wheat: Sustainability of Global Production

Limiting or key factors… How they are addressed at CIMMYT

Sustainability of Global Durum Wheat Production

Primary Breeding Objectives

Continued Progress in Yield Potential (vs. Bread Wheat) Disease Resistance Rusts & Septoria Yield Stability & Drought Tolerance Performance Stability under Heat

Secondary Breeding Objective

Market Access & Industrial Quality

Primary Breeding Objective (Pasta Quality)

Grain “Safeness” FHB Resistance

Not Addressed

Durum Wheat: Sustainability of Global Production

Limiting or key factors… How they are addressed at CIMMYT

Sustainability of Global Durum Wheat Production

Primary Breeding Objectives

Continued Progress in Yield Potential (vs. Bread Wheat) Disease Resistance Rusts & Septoria Yield Stability & Drought Tolerance Performance Stability under Heat

Secondary Breeding Objective

Market Access & Industrial Quality

Primary Breeding Objective (Pasta Quality)

Grain “Safeness” FHB Resistance

Not Addressed

Durum Wheat: Progress in Yield Potential

CIMMYT

Ammar, Espinosa et al., (unpublished)

All semi-dwarf

Durum Wheat: Progress in Yield Potential

Competitiveness with bread wheat: Mexico - Nationwide

3.00 3.50 4.00 4.50 5.00 5.50 6.00 6.50 7.00 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 YIELD (tons/ha) YEAR BREAD WHEAT DURUM WHEAT Source: Official Statistics Mexico (SIAP), 2013

Durum Wheat: Progress Yield Potential + Drought Tolerance

Competitiveness with bread wheat: Internationally (Meta-study)

Source: Marti & Slafer, 2013

 Under favorable conditions: Durum Wheat has higher yield potential than Bread Wheat ■ When water is not extremely limiting ■ More nitrogen and water use efficient, ■ Mostly due to higher kernel weight ■ Faster progress through breeding  Under extremely water-limited conditions: Durum Wheat is less competitive than Bread Wheat ■ Less water and nitrogen use efficient ■ However: difference is getting rapidly smaller with time ■ Significant progress through breeding

Durum Wheat: Sustainability of Global Production

Limiting or key factors… How they are addressed at CIMMYT

Sustainability of Global Durum Wheat Production

Primary Breeding Objectives

Continued Progress in Yield Potential (vs. Bread Wheat) Disease Resistance Rusts & Septoria Yield Stability & Drought Tolerance Performance Stability under Heat

Secondary Breeding Objective

Market Access & Industrial Quality

Primary Breeding Objective (Pasta Quality)

Grain “Safeness” FHB Resistance

Not Addressed

Durum Wheat: Yield Potential + Drought Tolerance

Testing infrastructure at CIMMYT

Drip Irrigation-simulated drought, 17 ha

Durum Wheat: Yield Potential + Drought Tolerance

Challenge in combining them in a breeding program

Correlation Lines Full Drought Full Irrigation Selectable Outstanding Year Tested Irrigation Irrigation Drought (+90% check) (+100% check) 2015 1037 6.1 2.3

• 0.16

77 30 2014 831 7.9 2.1 0.01 48 18 2013 1049 7.9 2.3 0.02 60 12 2012 875 8.3 2.8 0.35 53 10 2010 560 7.9 2.8 0.12 40 2 2009 813 6.3 3.0 0.39 73 24 2008 672 7.6 3.4 0.59 38 6 Yield Average % lines in both conditions

 Genes favorable to Yield Potential are generally/mostly different from those favorable to Drought Tolerance  New lines evaluated for first time under both favorable & water-limited conditions

Durum Wheat: Yield Potential + Drought Tolerance

Challenge in combining them in a breeding program

Grain Yield in % JUPARE y = -0.0352x + 81.765 R2 = 0.0002 r = 0.04

20 40 60 80 100 120 140 70 80 90 100 110 120

FULL IRRIGATION GRAVITY DROUGHT DRIP

 Combining genes favorable to Yield Potential and Drought Tolerance in a single genotype

High YP & Water Efficient

Durum Wheat: Yield Potential + Drought Tolerance

Testing protocol for combining them in CIMMYT breeding program

 Preliminary YT (PYT): FULL Irrigation + Drought ■ 4,500-5,000 F6 lines ■ Non-replicated, augmented design with repeated checks  Advanced YT-A (AYT-A): FULL Irrigation + Drought ■ 900-1,200 lines ■ 2 reps (FI), 3 reps (DR) in 8x8 lattice designs  Advanced YT-B (AYT-B): FULL Irrigation + Drought ■ 300-500 lines ■ 2 reps (FI), 3 reps (DR) in 8x8 lattice designs

Selection of candidates for International Nurseries

 Informal indication of success: New germplasm competitive with bread wheat in some drought prone environments (Mexico, Spain, Tunisia, Italy…)

Durum Wheat: Sustainability of Global Production

Yield Potential and Drought Tolerance – Any help from genomics or markers?

 QTLs for Yield or Yield Components ■ Many published, several interesting ■ More sophisticated marker technologies enhances capacity to identify interesting genomic regions ■ NOT used in breeding due to lack of proof of significant/substantial effect in relevant backgrounds  Mutagenesis, TILLING, ... In relation to Yield or Yield Components ■ Some promising events, more to be identified ■ Still under study and need to be evaluated considering wheat plant’s tendency to compensate between yield components  Still in research and/or validation phases!  Genomic Selection ■ ??? No Comments yet! ■ CIMMYT: Proof of concept in bread wheat

Durum Wheat: Sustainability of Global Production

Limiting or key factors… How they are addressed at CIMMYT

Sustainability of Global Durum Wheat Production

Primary Breeding Objectives

Continued Progress in Yield Potential (vs. Bread Wheat) Disease Resistance Rusts & Septoria Yield Stability & Drought Tolerance Performance Stability under Heat

Secondary Breeding Objective

Market Access & Industrial Quality

Primary Breeding Objective (Pasta Quality)

Grain “Safeness” FHB Resistance

Not Addressed

 Relevance of CIMMYT Germplasm challenged by: ■ Leaf Rust, in the Mediterranean and Latin America ■ Stem Rust, in Ethiopia (more than Ug99!) ■ Septoria Tritici, in North Africa (Tunisia) & the Mediterranean Basin

Durum Wheat: Sustainability of Global Production

Main abiotic threats to sustainability… all requiring durum-specific research

Threat of Leaf Rust

Addressed primarily from Mexico… Since 2001

 No LR virulence on durum in Mexico for >18 years  March 2001: BBG/BN overcomes a major gene (LrALTAR*) then protecting, monogenically, most CIMMYT germplasm  >85% CIMMYT elite material became susceptible  *: LrALTAR was assigned the designation Lr72 (Herrera et al., 2013)

Breeding for Leaf Rust Resistance

Addressed primarily from Mexico… Using information of genetic basis

Sybil Herrera (PhD Thesis), Ravi Singh, Julio Huerta

 5 major resistance genes characterized, 4 of them mapped: ■ Lr 27+31, (not mapped) ■ Lr3, 6BL, Xmwg798 ■ LrCamayo, 6BL ■ Lr14a, 7BL, wms344 + wms146 ■ Lr61 (First report), 6BS

Breeding for Leaf Rust Resistance

Successfully mitigated since 2006

Ammar, Espinosa et al. (Unpublished)

Almost all LR susceptible All LR resistant

Breeding for Leaf Rust Resistance

Successful so far since new races are not as devastating

 New race appears in 2008, characterized as BBG/BP, a single mutation from the previous BBG/BN  Defeats Lr 27+31 (Jupare C2001, Banamichi C2004), to date effective anywhere else  Impact on CIMMYT germplasm relatively low:

■ BBG/BN – 2001: >85% germplasm became susceptible ■ BBG/BP – 2008: <20% elite germplasm lost its resistance BBG/BN BBG/BP JUPARE C2001 BANAMICHI C2004

Breeding for Leaf Rust Resistance

Markers raise the “vulnerability” alarm…

 wms344 + wms146, molecular markers diagnostic for Lr14a in durum ■ Positive for 90% of Elite CIMMYT Germplasm in 2009-10 ■ Positive in >80% of ICARDA resistant germplasm ■ Positive in >90% of Italian, French , Spanish cultivars  Genetic vulnerability due to over-reliance on Lr14a ■ Real and present danger ■ Global (all germplasm groups) ■ Lr14a, defeated in France since 2009 (Goyeau et al., 2010), in Spain since 2013 (Solis et al., 2013), in Tunisia since 2012 (Gharbi et al., 2013)

Ammar & Dreisigacker, 2009 (unpublished) Lr14a

wms344 wms146

Marker-Assisted Selection Parent characterization

Breeding for Leaf Rust Resistance

Current strategy at CIMMYT & use of markers

 Avoid crosses where Lr14a is segregating alone: ■ Characterize all parents for the presence of Lr14a (markers are the only practical way) ■ Emphasis on crosses between non Lr14a, but resistant, parents  Combine the maximum number of genes/sources globally effective ■ Conventionally until markers are available  Pyramid known, molecularly-marked, effective genes ■ Lr19, Lr47, Lr37 ( on top of Lr14a)  Aggressively implement a strategy based on minor genes for resistance: ■ To date no markers for minor genes available in durum wheat

Breeding for Leaf Rust Resistance

Minor gene based approach

 Susceptible type infection  Low/intermediate incidence  Non-specific to a race (??)  Quantitative inheritance  Low effect on yield More Durable Widely effective

Breeding for Leaf Rust Resistance

Minor gene based approach… The concept of “slow-rusting”

10 20 30 40 50 60 70 80 90 100 10 20 30 40 50 60 70 Susceptible Minor gene resistance

Days after 1st reading % rust infection

Breeding for Leaf Rust Resistance

Concept: suitable resistance through accumulation of minor genes

Susceptible 1 to 2 minor genes 2 to 3 minor genes 4 to 5 minor genes

% Rust Days data recorded

100 80 60 40 20 10 20 30 40 50

Ravi P. Singh

Breeding for Leaf Rust Resistance

Minor gene based approach… Works in Durum… but….

10 20 30 40 50 60

Herrera & Ammar, 2010 (Unpublished) LSD0.01

2nd Generation 1st Generation Transgressive Segregants

Breeding for Leaf Rust Resistance

Minor gene based approach… Works in Durum… but… Many limitations

 Limited variability in 2nd generation slow-rusters ■ Not highest yielding/agronomically superior lines ■ Marginal-to-average quality profile  Difficult to improve ■ 3-4 genes present, very difficult to recover combination upon crossing with susceptible lines  Need to identify additional sources of minor genes ■ Unrelated to the one from CIMMYT germplasm ■ Can also be used to improve performance and quality

Breeding for Leaf Rust Resistance

Need for more gene discovery & help of markers

 AGER Project: ■ QTL mapping in KOFA x SVEVO and MERIDIANO x CLAUDIO populations ■ QTLs detected in preliminary fashion  APR detected in Association Mapping ■ Regions in 2BL, 3BS, 7BS associated with field resistance

Maccaferri et al., 2009

 Potential APR donors found in Mediterranean Landraces

Loladze & Ammar (CIMMYT), Royo & Villegas (IRTA-Spain), Unpublished

 APR in CIMMYT populations ■ QTL mapping in process ■ Collaboration with N.R.C., Saskatoon, Canada

Threat of Stem Rust

Durum vs. Bread wheat situations

 Ug99+variants: Main problem for bread wheat ■ Present in Kenya, Ethiopia, Yemen, Iran ■ Well characterized ■ Widespread resistance in most durum germplasm groups  Durum-specific Ethiopian races ■ Confined to Ethiopia… but for how long? ■ Not well characterized ■ Highly virulent on durum wheat ■ Very little resistance in all germplasm groups worldwide (<5%)

Threat of Stem Rust

Durum areas at risk

 Durum areas of Central India (1.0 million ha) ■ Through Yemen, most likely path as confirmed by migration of Ug99 ■ Stem rust (less virulent races) already endemic in the region  Middle-East, Turkey, North-Africa (>5 million ha) ■ Less likely dissemination path, but cannot be ignored ■ Durum critical in areas at risk ■ Favorable climatic conditions for the development of stem rust epidemics

David Hodson et al. 2008

 Threat likely to increase with warming temperatures earlier in the cropping seasons as predicted by climate change scenarios

Breeding Stem Rust Resistance

DRRW-CIMMYT: testing site

 Establishment of bi-annual screening program in Ethiopian “hot-spot” ■ Collaboration with Debre Zeit Ag. Res. Center ■ Artificial inoculation with mixture of relevant races ■ Screening of 1000s of lines annually: Resistance sources discovery Genetic studies for resistance characterization

Marker-Assisted Selection

Breeding for Stem Rust Resistance

CIMMYT’s Strategy

 Aggressively inter-cross CIMMYT elite lines found to be reliably resistant in Ethiopia: ■ Higher yield potential, Leaf rust resistance + quality ■ Parallel selection Ethiopia/Mexico in F6  Transfer effective major genes from bread to durum wheat using available molecular markers: ■ Sr25, Sr22, MAS validated in Ethiopia 2010 ■ Sr25+Sr22 pyramided: advanced lines produced, tested for yield, second cycle initiated.  Use of Ethiopian/other resistance sources

Breeding for Stem Rust Resistance

Crossing effort

296 456 268 219 200 400 600 800 1000 1200 2009 2010 2011 2012

Number of Crosses Year

Crosses made for Stem Rust Resistance 2009 - 2012

Stem Rust Crosses

20 – 46% of program’s crossing effort

 Resistance Sources

■ CIMMYT Elite ■ European germplasm ■ North-American germplasm ■ ICARDA germplasm ■ Genetic resources ■ Stocks with marked genes (MAS)

Breeding for Stem Rust Resistance

Selection Scheme

F3 Toluca F2 Obregon F6 PYT Obregon F5 Toluca/Batan F4 Obregon F6 Off season Debre Zeit F7 HR Batan F7 Main season Debre Zeit F8 Rep YT Obregon F8 Off season Debre Zeit Distribution Globally Release Ethiopia

No major selection problem for LR, YR, agronomic type and quality

Breeding for Stem Rust Resistance

Significant progress

Ayele (DZARC), Ammar & Bekele (CIMMYT) Number % Number % Number % Number % Reaction Group*

• f Lines

Total

• f Lines

Total

• f Lines

Total

• f Lines

Total Resistant 20 13.2 5 3.3 17 10.7 26 12.0 Moderately Resistant 5 3.3 17 11.3 44 27.7 60 27.8 R/MR for stem rust 25 16.4 22 14.6 61 38.4 86 39.8 Moderately Susceptible 12 7.9 19 12.7 5 3.1 2 0.9 Susceptible 115 75.7 109 72.7 93 58.5 128 59.3 N = 152 N = 150 N = 159 46 IDYN + IDSN To be distributed 2014 N = 216 43 IDYN + IDSN 44 IDYN + IDSN 45 IDYN + IDSN Distributed 2011 Distributed 2012 Distributed 2013

2009: 3.1% R/MR

Breeding for Stem Rust Resistance

Significant progress… with similar frequency of desirable lines

20 40 60 80 100 120 140 85 90 95 100 105 110 115 120 125 130 135

Number of lines in class Grain Yield as % of Check JUPARE C2001 Yield Distribution under FULL IRRIGATION within germplasm distributed in 2013 and 2014 International Nurseries

ALL (N=304) Stem Rust R/MR (N=124) 20 40 60 80 100 120 85 90 95 100 105 110 115 120 125 130 135

Number of lines in class Grain Yield as % of Check JUPARE C2001 Yield Distribution under DROUGHT within germplasm distributed in 2013 and 2014 International Nurseries

ALL (N=291) Stem Rust R/MR (N=115)

 Stem Rust Resistant lines have similar distribution than other lines ■ Yield Potential ■ Drought Tolerance ■ Quality attributes (gluten strength & yellow color)

Threat of Septoria Tritici

Durum vs. Bread wheat situations

 Bread Wheat: widely spread, many sources of resistance characterized and used (Stb genes)  Durum Wheat: Until recently, epidemics only in Tunisia and Eastern Algeria ■ Main production-limiting factor in durum wheat ■ Could results in massive yield losses (>40%) ■ Very little resistance is available in modern germplasm  Recently became a significant problems in

• ther Mediterranean countries:

■ France ■ Spain ■ Southern Italy ■ Morocco

Breeding for Septoria Tritici Resistance

Tunisian Platform: Very little resistance in CIMMYT germplasm Severity # Lines % Lines 0-1 2 3 0.8 3 4 4 1.0 5 11 2.8 6 20 5.1 7 34 8.7 8 92 23.7 9 225 57.8

38 IDYN, 36 EDUYT, 38 IDSN Screened at INRAT-Béja Station

Level of Tunisian Local Check

M.S. Gharbi, INRAT, (2007)

Breeding for Septoria Tritici Resistance

CIMMYT’s strategy

 Inter-crossing Tunisian + CIMMYT resistance sources ■ Tunisian sources: NASR, MAALI, SELIM ■ CIMMYT sources: 6-7 advanced elite lines

Breeding for Septoria Tritici Resistance

CIMMYT’s strategy

Cross F1, F2, F3 F4, F5 F6

F7, PYT,YT Worldwide Distribution

F6

Data Béja F7, PYT,YT Release Tunisia Mexico Tunisia Several Advanced lines in National Trials + in International Nurseries

Breeding for Septoria Tritici Resistance

Slight overall improvement + some resistant material distributed

10 20 30 40 50 60 70 80 1 2 3 4 5 6 7 8 9

Number of Lines Infection Score

41 IDYN+IDSN - 2010 (N=160) 45 IDYN+IDSN - 2014 (N=159)

Durum Wheat: Sustainability of Global Production

Are genomics / markers helping breeding for enhanced sustainability? The CIMMYT experience so far…

2774 9146 14313 30590 7665 1518 2705 2774 17901 26810 49905 18785 2527 10859 10000 20000 30000 40000 50000 60000 2008 2009 2010 2011 2012 2013 2014

Smaples / Datapoints Year

Marker Use in CIMMYT Durum Wheat Program

DNA Samples Extracted Datapoints Generated

Durum Wheat: Sustainability of Global Production

Yield Potential and Drought Tolerance – Any help from genomics or markers?

 QTLs for Yield or Yield Components ■ Many published, several interesting ■ More sophisticated marker technologies enhances capacity to identify interesting genomic regions ■ NOT used in breeding due to lack of proof of significant/substantial effect in relevant backgrounds  Mutagenesis, TILLING, ... In relation to Yield or Yield Components ■ Some promising events, more to be identified ■ Still under study and need to be evaluated considering wheat plant’s tendency to compensate between yield components  Still in research and/or validation phases!  Genomic Selection ■ ??? No Comments yet! ■ CIMMYT: Proof of concept in bread wheat

Marker-Assisted Selection Parent characterization

Breeding for Leaf & Stem Rust Resistance

Use of markers

 Avoid crosses where Lr14a is segregating alone: ■ Characterize all parents for the presence of Lr14a (markers are the only practical way) ■ Emphasis on crosses between non Lr14a, but resistant, parents  Pyramid known, molecularly-marked, effective genes ■ Lr19, Lr47, Lr37 ( on top of Lr14a)  Transfer effective major genes from bread to durum wheat using available molecular markers: ■ Sr25+Sr22 pyramided: advanced lines produced, tested for yield, second cycle initiated.

Marker-Assisted Selection

Use of Markers for Durum Breeding at CIMMYT

Genes, locations & origins

Gene Location Origin Source Used Trait

Lr14a 7BL Durum Wheat Durum Wheat Leaf Rust Lr47 7AS

• T. speltoides

Durum Wheat1 Leaf Rust Lr37/Cre5 2AS

• T. ventricosum

Bread Wheat Leaf Rust / nematodes Lr19/Sr25 7AL

• L. ponticum

Durum Wheat1 Leaf + Stem Rust Sr22 7AL Bread Wheat Bread Wheat Stem Rust H25 4A

• C. Secale

Durum Wheat2 Hessian Fly FHB-1 3BS Bread Wheat Bread Wheat Fusarium Head Blight FHB-5 5AL Bread Wheat Bread Wheat Fusarium Head Blight GPC-B1 6BS

• T. Dicoccoides

Durum Wheat High Grain Protein

1: Transferred to durum by Dr. Adam Lukashewski, U.C. Riverside 2: Transferred to durum by Freibbe et al. 1999, Kansas State Univ.

Use of Markers for Durum Breeding at CIMMYT

Marker types & use

Gene Marker Type Designation Inheritance Used for

Lr14a

SSR SNP1 wms146/wms344 ubw14 Co-dominant/dominant Co-dominant Parent characterization

Lr47

SSR SNP1 PS10 SNPLr47 dominant Co-dominant MAS, gene pyramiding

Lr37/Cre5

SNP VPM_SNP Co-dominant MAS, gene pyramiding

Lr19/Sr25

SSR PsyA1+PsyER4 Co-dominant MAS, gene pyramiding

Sr22

SSR SSR cfa2123 csKP812 Co-dominant Co-dominant MAS, gene pyramiding

H25

SSR wms610 Co-dominant MAS

FHB-1

SNP umn10_SNP Co-dominant Special studies

FHB-5

SSR Barc180/barc186 Co-dominant Special studies

GPC-B1

SSR SNP UHW89 GPC-B!SNP1 Co-dominant Co-dominant MAS

1: Originally SSR, recently converted to SNP by Dr. Susanne Dreisigacker 2: Recently optimized for high throughput

Use of Markers for Durum Breeding at CIMMYT

Stages of MAS

Parents (Donors + Recipients) F1s (Donor fixed?) Simple Cross F2: Phenotypic + MAS F3: Phenotypic + MAS F4: Phenotypic F5: Phenotypic + MAS F6 (fixed lines): Phenotypic Complex Cross (3/4-way crosses) F1TOP/F1DOB: Phenotypic + MAS F2: Phenotypic + MAS F3: Phenotypic F4: Phenotypic F5: Phenotypic + MAS F6 (fixed lines): Phenotypic Ensure right cross y presence of marker/gene  As soon as segregation starts  Number of MAS cycles depend on: ■ Number of markers monitored ■ Inheritance (dominant/Co-dominant) ■ Reliability of the MAS ■ Resources

Use of Markers for Durum Breeding at CIMMYT

Status for Leaf Rust Resistance breeding

 2-genes stacks: several advanced lines available, many more in the breeding pipeline  3-genes stacks: few fixed lines with Lr14a + Lr19 + Lr47 produced, few more in the breeding pipeline, but questionable yield performance. On hold for now.  4-genes stacks: still in breeding pipeline, on- hold for now.

Use of Markers for Durum Breeding at CIMMYT

Status for Stem Rust Resistance breeding: Linked Sr22+Sr25

Xgpw2242

• 8.2

Xfba243 0.0 Xfba17 Xgpw4130 13.0 Xcfd62 18.7 Xfba231 22.4 XEF1R 33.9 Xfba127 38.9 Xfba109 58.4 Xbcd1438 59.4 Xgpw3201 65.3 Xgpw3234 76.2 Xfbb222 86.8 Xcfa2056 97.8 Xfbb79 98.9 Xfba71 99.5 Xfbb366 106.8 Xgpw3208 125.4 Xcfd6 129.5 Xgpw7313 136.1 Xpsr165 136.6 Xwmc182 137.7 Xpsp3050 138.4 Xcfa2110 147.5 XksuA5 168.5 Xbc9O10 169.6 Xglk478 174.5 XksuG12 178.2 Xcfa2123 193.3 Xfba69 198.7 Xpsp3094 Xgpw2252 210.6 Xtam51 219.9 Xcfa2019 224.0 Xcfa2293 232.4 XksuD2 232.8 Xfba350 244.7 Xwg232.1 253.6 Xwg232.2 253.8 Xcfa2040 256.2 XksuH9 267.5

7AL-1-0.39-0.71 7AL-18-0.9-1

Sr22 (cfa2123, cfa2019) Sr25 (PSY1-EF2_ER4)

• Chr. 7A

(Courtot x C.S.) DWSr22 x Elite 1

F1Sr22

DWSr25 x Elite 2

F1Sr25 X

Double-Cross Population F2 F6 F8 Testing SR Testing SR Yield, Drought Quality MAS

Use of Markers for Durum Breeding at CIMMYT

Status for Stem Rust Resistance breeding: Linked Sr22+Sr25

 Confirmed homozygocity for both genes ■ Markers stably homozygous in F6 – F8 head-rows ■ Stably resistant over 2-3 seasons at Debre Zeit  Improved quality parameters ■ Better gluten strength than most local cultivars ■ Significantly higher yellow color than local cultivars  Variable yield performance and drought tolerance ■ Obregon: Substantial yield penalty due to lower kernel size, especially under drought ■ Ethiopia: bad agronomic type ■ Second round breeding started!!

Breeding for Leaf & Stem Rust Resistance

Currently used marked-genes come with yield and/or quality penalties

* : Developed by Dr. Adam Lukashewski, U.C. Riverside **: ATIL C2000 & RIO COLORADO C97 (Mexico), NASSIRA (Morocco), KOFA (US)

 NILs development: ■ MAS + phenotypic selection in all BC & selfing populations ■ All resulting NILs confirmed homozygous for marker/translocation ■ All resistant to leaf rust

Translocation Recurrent Number NILs Material Source * Parent ** Evaluated Evaluated AG 1-22/2*ACONCHI//2*UC1113 ATIL C2000 10 Lr19/Sr25 RIO COLORADO C97 7 NASSIRA 6 KOFA 7 AG 1-23/2*ACONCHI//2*UC1113 ATIL C2000 8 Lr19/Sr25 RIO COLORADO C97 9 NASSIRA 4 7A.7S-S3/3*ACONCHI ATIL C2000 5 Lr47 RIO COLORADO C97 4 NASSIRA 2 BC4F6 derived lines BC4F6 derived lines BC3F6 derived lines

Breeding for Leaf & Stem Rust Resistance

Lr19/Sr25-ATIL C2000

5.0 5.5 6.0 6.5 7.0 7.5 8.0 Grain Yield FULL IRRIGATION - t/ha 1.5 1.7 1.9 2.1 2.3 2.5 2.7 Grain Yield DROUGHT - t/ha

Donor Ag 1-22 Donor Ag 1-23

• Rec. Parent

ATIL C2000 NILs Ag 1-22 in ATIL C2000 NILs Ag 1-23 in ATIL C2000 Donor Ag 1-22 Donor Ag 1-23

• Rec. Parent

ATIL C2000 NILs Ag 1-22 in ATIL C2000 NILs Ag 1-23 in ATIL C2000 LSD LSD

Values are 2-year averages, 4 reps each

Breeding for Leaf & Stem Rust Resistance

Lr19/Sr25-NASSIRA

2.0 2.2 2.4 2.6 2.8 3.0 Grain Yield DROUGHT - t/ha 5.5 5.7 5.9 6.1 6.3 6.5 6.7 6.9 7.1 7.3 7.5 Grain Yield FULL IRRIGATION - t/ha

Donor Ag 1-22 Donor Ag 1-23

• Rec. Parent

NASSIRA NILs Ag 1-22 in NASSIRA NILs Ag 1-23 in NASSIRA Donor Ag 1-22 Donor Ag 1-23

• Rec. Parent

NASSIRA LSD LSD

Values are 2-year averages, 4 reps each

NILs Ag 1-22 in NASSIRA NILs Ag 1-23 in NASSIRA

Breeding for Leaf & Stem Rust Resistance

Lr47 in 3 lines

1.5 1.7 1.9 2.1 2.3 2.5 2.7 2.9 3.1 Grain Yield DROUGHT - t/ha

Values are 2-year averages, 4 reps each

5.0 5.5 6.0 6.5 7.0 7.5 8.0 Grain Yield FULL IRRIGATION - t/ha LSD LSD Donor Translocation 7A.7S

• Rec. Parent

ATIL C2000

• Rec. Parent

R.COL

• Rec. Parent

NASSIRA NILs 7A.7S in ATIL NILs 7A.7S in R.COL. NILs 7A.7S in NASSIRA Donor Translocation 7A.7S

• Rec. Parent

ATIL C2000

• Rec. Parent

R.COL

• Rec. Parent

NASSIRA NILs 7A.7S in ATIL NILs 7A.7S in R.COL. NILs 7A.7S in NASSIRA

Breeding for Leaf & Stem Rust Resistance

Currently used marked-genes come with yield and/or quality penalties

 Yield penalties variable between/within backgrounds ■ Some NILs with no significant yield penalties under favorable conditions  Yield penalties systematic and more pronounced under drought  Yield penalties in Lr19/Sr25 NILs associated with reduced kernel weight, not biomass ■ Some NILs with no significant kernel weight reduction under either conditions  Yield penalties in Lr47 NILs in spite of generally positive effect

• n kernel weight

 Lr19/Sr25 NILs associated with higher color (additive) ■ Some NILs do not express this improvement under drought stress  Lr47 NILs associated with lower color ■ Except in very low color background

Breeding for Leaf & Stem Rust Resistance

Use of markers for rust resistance: What’s next?

 Gene discovery: Non-penalizing genes ■ “Native” genes in improved germplasm or landraces ■ Ensure “novelty” of gene ■ Ensure wide-effectiveness against most races  Mapping using high-density platforms ■ Get as close to the gene as possible ■ Use of high-throughput platform ■ Ensure mapping-to-breeder friendly marker transition  DURUM-SPECIFIC!!!! ■ Genes from bread wheat do not always work ■ Rust races and septoria strains: very different between species

Breeding for Leaf & Stem Rust Resistance

Use of markers for rust resistance: What’s next?

 Mapping & marker development of “native genes” for LR resistance ■ Earlier identified genes ■ Populations phenotyped at CIMMYT ■ Genotyping, mapping & marker development at USASK – Canada (D. Khtiri & C. Pozniak): Close to completion!

Mapping Phenotyping USASK Marker Source Origin Inheritance1 CIMMYT CANADA Development Gaza Landrace, Middle East 1 major + 1 APR genes F7+F8 6BS + 6BL In process Amria Morocco 1 partially dominant major gene F7+F8 7BS In process Geromtel_3 ICARDA 1 dominant major gene F7+F8 6BL2 In process Tunsyr_2 ICARDA 1 dominant major gene F7+F8 6BL2 In process Byblos France 1 partially dominant major gene F7+F8 7BS In process Arnacoris France 2 recessive genes F7+F8 7BL + 1BL In process Saragolla Italy 2 recessive genes F7+F8 2BS + 3BL In process

1: Inheritance determined in F2 and F3, Loladze et al., 2014 2: Allelic or closely linked to Lr61, Loladze et al., 2014

Breeding for Leaf & Stem Rust Resistance

Use of markers for rust resistance: What’s next?

 Mapping & marker development of “native genes” for LR resistance ■ Populations phenotyped at CIMMYT ■ Genotyping, mapping & marker development at NRC – Canada (Various): Initiating…

Mapping Phenotyping NRC Marker Source Origin Inheritance2 CIMMYT CANADA Development Durum line with T. Dicoccum genes (3 populations) CIMMYT genebank1 2 recessive or complementary genes F6 + F7 6B + 1B Planned Durum line with T. carthlicum genes CIMMYT genebank1 2 recessive or complementary genes F6 + F7 In process Planned Carpio Spain 1 major dominant gene F6 Planned Planned Calero Spain 1 major dominant gene F6 Planned Planned Grecale Italy 2 genes F6 Planned Planned Jennah Khortifa Landrace, Tunisia 2 genes F6 Planned Planned Swabaa Algia Landrace, Tunisia 2 genes F6 Planned Planned INRAT 69 Tunisia 1 major dominant gene F6 Planned Planned PI 61111-GRIN CIMMYT Genebank 2 genes (1 + 1 supressor?) F6 Planned Planned T.DICOCCON, PI 94747 CIMMYT Genebank 2 major dominant genes F6 Planned Planned T.DICOCCON PI 94749-GRIN CIMMYT Genebank 2 genes (1 + 1 supressor?) F6 Planned Planned T.CARTHLICUM PI 94755-GRIN CIMMYT Genebank 2 genes (1 + 1 supressor?) F6 Planned Planned T.CARTHLICUM PI 115817-GRIN CIMMYT Genebank 2 genes (1 + 1 supressor?) F6 Planned Planned T.CARTHLICUM PI 572849-GRIN CIMMYT Genebank 2 genes (1 + 1 supressor?) F6 Planned Planned

1: Identified by Julio Huerta et al., unpublished 2: determined in F2/F3 generations, Loladze & Ammar, unpublishedx

Breeding for Septoria Resistance

Use of markers for rust resistance: What’s next?

 Mapping & marker development of “Selim” resistance ■ 2 strong QTLS identified (Dart) ■ Re-mapped with SNPs (C. Pozniak), markers should be available soon

wPt9532p_6B 0,000 wPt7662p_6B 1,108 wPt7065p_6B 1,366 wPt0245_6B 3,082 wPt6594_6B 21,872 wPt4900_5B|6B 22,044 wPt3376p_6B 24,042 wPt1437p_6B 24,853 wPt1241_6B 30,267 wPt5256p_6B 30,508 tPt3506p_6B 36,054 wmc487_6B 36,318 cfd13_6B 36,390 wPt2111_6B 37,015 wPt7935_6B 37,588 rPt1040_6B 37,957 wPt6651_NA 38,809 wPt5838_NA 39,622 tPt2451bp_NA 50,811 wPt2479p_6B 53,049 wPt8721_6B 60,844 wPt7489_6B 62,783 wPt7945_6B 71,986 gwm193_6B 78,733 wPt6320_7B 88,883 wPt6797p_7A 89,924 wPt2083_7A 90,242 wPt7763p_7A 90,775 wPt8365b_7A 98,104 LR STB

2 4 6 8 10 12 14 16 18 20 22 24 26 28 30

6B

wPt9579a 0,000 wPt7961 1,906 rPt4097p 2,523 wPt9303 3,115 wPt2757 10,790 wPt8480 37,198 wPt0384p 37,941 wPt9577p 39,568 wPt2698p 61,764 barc84 71,393 wPt2491 82,132 tPt3621 83,463 wPt0990p 99,455 wPt2943p 102,698 wPt8559p 111,822 wPt5295 115,667 wPt11691 124,235 wPt3301 127,051 wPt3760p 129,402 rPt0996 130,479 wPt0665 131,406 wPt9488p 134,743 wPt0668 135,060 wPt4412p 143,984 wPt2416 146,093 tPt4541p 147,041 STB

2 4 6 8 10

3B

Berrais, Gharbi et al., to be published

54.5 50.6 32.8 29.6 16.4 7.7 10 20 30 40 50 60 Karim _/_ _/6B 3B/_ 3B/6B Salim Average of DS % QTL combination

3BS: 32.4% 6BS: 23.4%

Durum Wheat: Sustainability of Global Production

Limiting or key factors… How they are addressed at CIMMYT

Sustainability of Global Durum Wheat Production

Primary Breeding Objectives

Continued Progress in Yield Potential (vs. Bread Wheat) Disease Resistance Rusts & Septoria Yield Stability & Drought Tolerance Performance Stability under Heat

Secondary Breeding Objective

Market Access & Industrial Quality

Primary Breeding Objective (Pasta Quality)

Grain “Safeness” FHB Resistance

Not Addressed

Fusarium Head Blight in Durum Wheat

Is there really resistance in durum wheat?

 Already affecting durum production in: ■ North-Dakota, France, Italy ■ Austria, Iran  Some alarming presence in durum- dependent regions: ■ North Africa Durum Wheat FHB resistant Bread Wheat

Fusarium Head Blight in Durum Wheat

Phenotyping platform at CIMMYT

 Transferred from Toluca to El Batan: ■ Drier but better micro-aspersion system ■ Better inoculation capacity and equipment ■ Systematic characterization of virulence and DON production capacity of inoculum ■ Under zero-till after maize ■ Better follow-up of crop / scoring Main contact: Dr. Pawan Singh

Fusarium Head Blight in Durum Wheat

Is there really resistance in durum wheat?

 AGER Project: Massi et al. (PSB), Tuberosa et al. (Univ. Bologna) ■ 92 genotype panel from Italy + CIMMYT, including SUMAI 3 durum derivatives evaluated for two years in Mexico & Italy ■ 256 RILs from population KOFA x SVEVO

Fusarium Head Blight in Durum Wheat

Is there really resistance in durum wheat?

10 20 30 40 50 60 70 80 90

% Infected spikelets Genotype

FHB infection in 92 durum genotype + 4 bread wheat checks

(average of 2 reps, two years)

Resistant bread wheat Durum SUMAI 3 derivatives Best Durum: cv. MOVAS C2010 Other durum AGER project

Durum Wheat: Sustainability of Global Production

Are genomics / markers helping breeding for enhanced sustainability? The CIMMYT experience so far…

2774 9146 14313 30590 7665 1518 2705 2774 17901 26810 49905 18785 2527 10859 10000 20000 30000 40000 50000 60000 2008 2009 2010 2011 2012 2013 2014

Smaples / Datapoints Year

Marker Use in CIMMYT Durum Wheat Program

DNA Samples Extracted Datapoints Generated

 Diagnostics and parental characterization: ■ Key / Critical to our crossing strategy for leaf rust resistance breeding ■ Heavily used.  Marker-Assisted selection for simply inherited traits: ■ Available markers are for genes with problems ■ Still in research / marker development phase for durum specific genes/markers, neutral to yield + quality ■ Durum community need to deliver for its own! ■ Potential for “explosion” of use of gene-based markers