Spring Wheat Breeding for rain-fed areas at CIMMYT

1. Spring Wheat Breeding for rain-fed areas at CIMMYT Yann Manes December 2010

2. Outline of the presentation • Rain-fed areas and drought stress • Program objectives • Methodology: • Yield testing • Early generation selection • Crossing • Use of physiology in rain-fed breeding • Perspectives in marker assisted selection

3. Rainfed spring wheat breeding program • ME4 (ME2): • Low latitude spring wheat. • 20 Millions has • Semidwarf type, photoperiod insensitive • ME6: • High latitude spring wheat • 20 Millions has • Non semidwarf type, photoperiod sensitive

4. Rainfed low latitude (ME4/2) • South America: Argentina,Brazil,Uruguay,Paraguay,Chili • East Africa: Ethiopia, Kenya • North Africa: Morocco, Algeria,Tunisia • West Asia: Iran, Turkey, Afghanistan • South Asia: India,Pakistan,Nepal

5. Drought is a variable phenomenon in space

6. And in time … Moy = 51.5

7. Main objectives ME4 • Yield: drought/heat tolerance and ability to give good yields in the good years • Good grain aspect and size • Resistance to biotic stresses • Common with ME1: • Three rusts (including Ug99) • In high rainfall zones: Septoria Tritici • Depending on rotations: Tan Spot (wheat prevalent in rotation), FHB (wheat-maize rotation) • Specific to low moisture situations: • Root health (Nematodes, Root Rots) • End-user quality

8. Main objectives ME4 • Maintain variability of height: • In environments where high rainfall tend to more frequent: good lodging resistance is needed, avoid tall genotypes • In environments where drought is prevalent: farmers often have also cattle and like to have straw. • In extreme drought situations, semi-dwarf types do not offer an obvious yield advantage

9. Main objectives ME4 • Maintain variability of heading: • Adjustment to rainfall regimes and stress timing: in case of terminal drought & heat stress, earliness is an advantage • Adjustment to late frost risk, with adequate planting dates and earliness. • Adjustment to tillage systems. Zero tillage permits early seeding which allows for longer cycle genotypes

10. Is there contradiction between breeding for yield under favorable conditions and yield under water stress ?

13. Heritability of selection is much lower in rain-fed environments than in irrigated environments: • Large year effects due to high variation of rainfall. • Counfounding effect of phenology (timing of stress)

14. Response to selection can be increased by: • Environment well characterized (soil maps) • Stress monitored and applied at a given phenology stage, with help of irrigation facility or even shelter facility. • For advanced lines testing, it is recommended to have at least two treatments for testing (full and reduced irrigation, rainfed and one irrigation)

15. Drip Irrigation System • Applied in Obregon (desert, no rain), drip allows to monitor stress when desired, at any time of the plant cycle. Possible to get pre-Anthesis Stress and yields < 2 t/ha with drip, impossible with Gravity Irrigation.

16. Yield Testing Scheme (in Mexico) • Parallel testing in low and high yielding conditions in Obregon: • Year 1 (PYT) • Drought Drip, two reps • Full Irrigation, Bed, one rep with replicated checks • Year 2 (Candidates) • Drought, Flat, three reps • Full Irrigation, Beds, three reps • Full Irrigation, Flat, three reps • Heat, Bed, three reps

17. General Breeding Scheme Crosses Shuttle breeding Yield testing Distributing elite lines to National programs Collection and interpretation of multilocation data

18. Early generation selection • Selection made under high-yielding conditions to get the right disease resistance profile and select the right plant type. • And also: • Canopy temperature screen made under drought (one plot with repeated checks) to eliminate drought sensitive bulks at F3 and F4s. • Selection made under zero tillage to improve adaptation to Conservation Agriculture • Use of Marker Assisted Selection for specific traits.

19. Marker Assisted Selection • Markers utilized in routine on CB, F1 Tops and F3 populations, elite lines for confirmation: • Crossing Block characterized for 17 genes: Rh1, Rht2, VrnA/B/D, Ppd-D1, Sr24,25,26,36, Lr37/Yr17, Lr34, 1A1R, 1B1R, Cre1, Cre3, Bo1. • Focus in F1 Top and F3 enrichment put on traits “invisible” in Mexico and important for rainfed environments: • Soil stresses: CCN (Cre1 and Cre3) • Major resistance genes for Ug99 resistance (Sr25, 1A1R, Sr26) • Combination of major resistance genes • MAS limited to markers with very low or null recombination risk. • In 2008, 26000 samples and 39000 datapoints for RFW program.

20. Early Generation Selection • Efficient for heritable and visible traits • MAS helps for simple traits and genes invisible in Mexico fields • BREEDING IS A NUMBER GAME: VERY IMPORTANT TO KEEP VARIATION FOR YIELD AND QUALITY. CONSIDER THEM AS INVISIBLE TO THE EYES: • At the end of early generation phase, need to have enough variation left in advanced lines for yield and quality testing

21. About crossing

22. Crossing block composition • Confirmed elites (from performance in CIMMYT international nurseries) • New CIMMYT elites (good performance in Mexico, composed of new lines selected to international CIMMYT nurseries). • National elites or varieties • Special traits: SR, Soil abiotic stresses, Soil Born Pathogens, Hessian Fly

23. Back-cross or two-way crosses ? • Within elites, there is a range of available information. • Confirmed elites have confirmed value per se • New elites are still to confirm their value, but potentially have higher value than the confirmed elites • Back-cross (confirmed x new) x confirmed is a good secure elite x elite cross • Two-way cross new elite x new elite is more risky but can potentially produce very high yielding lines.

24. Take into account major gene effects (Rht, Ppd and Vrn) in combinations: adapt population size. • Segregation Rht1 x Rht2 decreases by ~ 50% the number of good looking plants in F2. • In spring CIMMYT x winter crosses, segregation for vernalization genes decreases by ~ 50% the number of good looking plants in F2.

25. Crossing Strategy • 60 % CIMMYT elite x CIMMYT elite crosses. Should go towards less crosses and bigger populations. Priority given to top and back-crosses. • 40% “exploratory” crosses: • 15% crosses with Australian cultivars • 15% spring x winter crosses • 10% with primary synthetics/landraces or introduction of specific genes

26. Integration of physiology into the breeding program

27. Water Uptake • Rapid ground cover • protects soil moisture • Access to water by roots • Ψ leaf • cool canopy • (osmotic adjustment) Reynolds M.P. and Tuberosa R., 2008. COPB Physiological breeding: strategic crossing for drought YLD= WU xWUExHI (Passioura, 1979) • Photo-Protection • Leaf morphology • wax/pubescence • posture/rolling • Pigments • chl a:b • carotenoids • Antioxidants • Transpiration Efficiency • WUE of leaf photosynthesis • low 12/13C discrimination • Spike/awn photosynthesis • Partitioning (HI) • Partitioning to stem carbohydrates • Harvest index • Rht alleles

28. Physiological information used for crossing • Each year, 50 to 100 elite lines are given to physiology group for characterization. • Physiology group gives back to RF breeding a “PHY” crossing block with trait information, composed of: • Elite lines • Genetic resources (landraces) • Combined with information on all other traits

29. Stress-Adaptive Traits (Physiological) information on elites and Genetic resources Yield Information from CIMMYT and International trials Crossing plans Disease information from Mexico and CIMMYT hotspots on rusts, Septoria and SBP End-User Quality information DNA marker information (17 to 20 markers)

30. “PT” crosses • PT information is used at the two ends of the breeding program, on the very best germplasm and on new genetic resources (landraces, primary synthetics). • Potentially indicates to the breeder the most promising elite x elite crosses • Landrace or Primary Synthetic introgression by top or back-crosses. PT info can be used to select the best elite background for introgression

31. LSD between Groups = 1.8% • PT lines represent: • 25% of entries in 27th SAWSN • 32% of entries in 17th SAWYT From Reynolds el al, 2009

32. Performance of two PT derived Ug99 resistant lines in South Asia in 2010

33. Breeding strategies to select PT crosses • PT crosses are written to increase genetic progress on yield under stress conditions. • Yield is a quantitative trait relying on many genes. • Two facts have to be taken into account: • Most of the selection is made under favorable conditions. • One has to assume that many of the yield genes are not “visible” before yield testing. • Therefore, it is essential to keep as much variation as possible during the early generation phase.

34. On PT crosses management • Avoid crosses where major segregation will happen for disease resistance, or major genes such as Rht1 and 2. • Increase population size to increase chances to identify high-yielding recombinants. • If possible during the early generation phase, screen F3 or F4 bulks ONCE below stress conditions, provided there is no major variation for phenology and disease resistance in the population. • In selected bulk scheme, select at least 50 plants in F2, 100 to 200 in F3 and F4, and select advanced lines from 100 to 200 head-rows, to maintain as much variation as possible for yield genes. • Objective = getting at least 20 to 30 lines in yield testing.

35. Canopy Temperature Screen • Very good correlation between CT and yield in Obregon conditions under irrigated, drought and heat. • Good correlation between CT and moisture extraction, under Obregon conditions, likely transposable to many residual moisture scenarios in deep soils. • CT is easy and fast to measure, less than 10 seconds per reading

36. On which generation to apply CT in selected bulk scheme ? • Need a small plot to measure CT (at least 2m). • Screening at the “cross” level, of F3 and F4 selected bulks, to eliminate drought susceptible crosses. • We do not apply on individual advanced lines. Then we measure yield directly

37. How to measure it ? Delta of canopy temperature between drought sensitive and tolerant lines is SMALL Variation can be due to the soil, or to the time of the day when reading is made Use a design with a grid of replicated checks, and compare the value of lines or pops to the surrounding checks only. Make several readings during the season (from stem elongation to end of grain filling) and calculate average only from the most discriminatory ones.

38. F3 and F4 CT screening • BEFORE: selection of individual plants in F4/5 pops was made under drought, and CT measured on the bulks. However, no disease pressure for individual plant selection, and no CT checks for comparison and control of soil variation • NOW: • One specific F3 and F4 trial to measure CT with repeated CT checks (one high, one low temp). In 08-09, 1032 entries, two hours for one CT reading. Ten readings were made during the season. • Individual plant selection is made under full irrigation with the right selection pressure for plant height, leaf rust and stem rust.

40. Boot/Heading Grain Filling Diff Res/Susc = 1.15 C Each dot is the mean of 96 values from the experiment

41. Mean DT check = 98% Mean DS check = 102%

42. 500 F2 populations 500 F2 populations 35000 F3 head-rows 35000 F3 head-rows 2000 F4 families of 6 head-rows selected under full irrigation 2000 F4 families of 6 head-rows each 2000 F4 bulks screened for Canopy Temperature under drought (2m plots) 1000 ALs for yield testing 700 ALs for yield testing CT could be applied also in a modified pedigree or pedigree scheme before yield testing

43. Yield and number of lines identified using two breeding methodologies 1. visual selection alone 2. combination of visual selection and canopy temperature depression (CTD), within the progenies of the cross Attila/Babax, under high irrigated conditions, 2004, Obregon, Mexico (from Van Ginkel et al., 2008)

44. Some Perspectives on Marker Assisted Selection

45. On crosses management • Even with a good strategy, probabilities imply that a for a single cross, it will be unlikely to fix more than 5 or 6 segregating yield genes per breeding cycle. • DNA markers can help fixing known favorable alleles. • New breeding schemes would be necessary to accelerate gene fixation: Marker Assisted Recurrent Selection

47. From Manes and al, 2010, poster presented at the 8th IWC

48. Calculation of marker effects for quantitative traits • Bi-parental QTL approach. A x B mapping and model building based on the significant markers. • Genomic selection approach. All markers taken into account, improves prediction. Should be possible to use elite lines panels for model building.

49. From Training populations: • Elite CIMMYT yield trials (SAWYT/ESWYT) • Association Genetic Panels (WAMMI) • Candidates (for stem rust) • Calculation of marker effects and Model Building Genomic Selection applied on new elite x elite crosses New elite lines and new CIMMYT international elite yield trials Training population enriched by new elites, analysis and refinement of genetic prediction models

50. Conclusions (1) • Cimmyt approach is to combine high yield potential and good drought tolerance. • Various tools are used to breed at the same time for high yielding and low yielding environments: • Early generations: CT screen, selection under ZT, Marker-Assisted Selection. • Late generations: trials in moisture controlled environments