1. Physiological Breeding: strategies & genetic gains
Matthew Reynolds (CIMMYT)
Contributions from:
Gemma Molero, Maria Tattaris
Carolina Saint Pierre, Mariano Cossani
Siva Sukumaran, Alistair Pask, Ravi Valluru
Marc Ellis, Yann Manes
Richard Trethowan

2. International Wheat Improvement Network (IWIN)
Coordinated by CIMMYT since 1960s
Latin
America
Africa
Middle East
South &
East Asia
CIMMYT distributes 1,000 new wheat genotypes annually
targeted to a range of environments

3. wheat yield trials from 1994 to 2010.
Average genetic gains at 556 international sites: ~1% per year from
Manes et al Genetic yield gains of CIMMYT international semi-arid
wheat yield trials from 1994 to 2010.
Crop Science 52:

4. Complementary strategies to increase genetic gains
Identify crop characteristics conferring adaptation
Precision and high throughput phenotyping
Exploration of genetic resources for adaptive traits
Inter-specific hybridization to broaden the crop genepool
Genomics to increase breeding efficiency
Strategic crossing to achieve cumulative gene action

5. Complementary strategies to increase genetic gains
Identify crop characteristics conferring adaptation
Precision and high throughput phenotyping
Exploration of genetic resources for adaptive traits
Inter-specific hybridization to broaden the crop genepool
Genomics to increase breeding efficiency
Strategic crossing to achieve cumulative gene action

6. Conceptual Model of Heat-Adaptive Traits
YIELD = LI x RUE x HI
G x E?
Photo-Protection (RUE)
Leaf morphology (display, wax)
Down regulation
Pigment composition
Chl a:b
Carotenoids
Antioxidants
Efficient metabolism (RUE)
CO2 fixation
CO2 conductance
Rubsico (>>)
Canopy photosynthesis
spike photosynthesis
Respiration
G x G?
Light interception (LI)
Rapid ground cover
Functional stay-green
Partitioning (HI)
Spike fertility (meiosis, pollen, etc)
Stress signaling (e.g. ethylene) regulating
senescence rate
floret abortion
Grain filling (starch synthase)
Stem carbohydrate storage & remobilization
Water Use (RUE)
Roots match evaporative demand
Regulation of transpiration (VPD; ABA)
Cossanni & Reynolds, Plant Physiology

7. Complementary Strategies
Identify crop characteristics conferring adaptation
Precision and high throughput phenotyping
Exploration of genetic resources for adaptive traits
Inter-specific hybridization to broaden the crop genepool
Genomics to increase breeding efficiency
Strategic crossing to achieve cumulative gene action

8. Phenotyping is not just about tools!
Design experimental populations to avoid confounding agronomic traits
Seri/Babax population

9. Representative phenotyping platforms (e.g. IWYP-PLAT)
Located at heart of high yield wheat agro-ecosystem (Yaqui Valley NW Mexico)
Production >1 m tons
Farm yields avg 6.5 t/ha
Maximum yields ~10 t/ha
Research and breeding conducted side by side, encouraging maximum accountability of both.

10. Plant selection tools Visual selection ++ Canopy temperature
Spectral reflectance
(Molecular markers)

11. Canopy temperature shows consistent association with yield under drought and heat
From Flintham et al. 1997:
Combined heat and drought stresses after anthesis, which shorten the period of grain-filling, may erode the yield advantages of semi-dwarf lines, to the point where `cross-over' genotype x environment interactions are observed (Brandle & Knott 1986; Hoogendoorn et al. 1988). Drought stress throughout the growing period can reduce both grain number and grain weight to a greater extent in dwarfs (and semi-dwarfs) than in tall controls and these effects have been attributed to reduced water-use efficiency in shorter genotypes (Nizam Uddin & Marshall 1989; Richards 1992b). Genotype x temperature interactions have also been described for Rht effects on plant height, leaf size, ear weight and grain set (Bush & Evans 1988).

12. Deeper roots under drought confer stress adaptation
CT=-0.20x+34.3, R2=0.88
Yield=2.07x+254.9, R2=0.35
Lopes MS and Reynolds MP, Partitioning of assimilates to deeper roots is associated with cooler canopies and increased yield under drought in wheat.
Functional Plant Biology 37:
Pinto & Reynolds, Common genetic basis for canopy temperature depression under heat and drought stress associated with optimized root distribution.
TAG: 128

13. & MEASURE SOIL MOISTURE
GIDDINGS SOIL CORER
TO SAMPLE ROOTS
& MEASURE SOIL MOISTURE

14. Recently featured on BBC Horizons
Aerial remote sensing
Recently featured on BBC Horizons

15. Thermal Imagery: data processing
Removal of outlying pixels
Example of how images are processed..mask is applied to remove soil etc…, then pixels with highest variance removed incase there is any pixel mixing
This is a thermal image

16. Ground v Airborne: UAV & Blimp:
in most cases data from airborne platforms explains genetic
variation in yield etc. better than with ground based readings
NDVI UAV and thermal index UAV against groundbased measurements
HEAT_1 = Cimcog Resto Heat 2012,
HEAT_2=Cimcog Subset Heat 2012
*=normalized by phenology (days to heading)
r_G=genotypic correlation

17. Complementary Strategies
Identify crop characteristics conferring adaptation
Precision and high throughput phenotyping
Exploration of genetic resources for adaptive traits
Inter-specific hybridization to broaden the crop genepool
Genomics to increase breeding efficiency
Strategic crossing to achieve cumulative gene action

18. Genetic resources: ~ 0.5 million Wheat ‘landraces’ in Oaxaca
accessions of
wheat genetic resources
in collections
worldwide
The World Wheat Collection at CIMMYT has ~170,000
Wheat ‘landraces’ in Oaxaca

19. 70,000
wheat genetic resources screened under drought and heat, Sonora, Mexico,

20. FIGS drought set, Sonora, 2013 Focused Identification of Germplasm Strategy ( A

21. FIGS drought set, Sonora, 2013 Focused Identification of Germplasm Strategy ( A B

22. Complementary Strategies
Identify crop characteristics conferring adaptation
Precision and high throughput phenotyping
Exploration of genetic resources for adaptive traits
Inter-specific hybridization to broaden the genepool
Genomics to increase breeding efficiency
Strategic crossing to achieve cumulative gene action

23. Wide crossing with close relatives
e.g. “Synthetics”
Sources of disease resistance
Redistribution of roots to deeper soil profiles under water stress
X =
T. durum
AABB
T. tauschii DD
Hexaploid synthetic
AABBDD 23

24. 1,000 new primary synthetics screened for biomass –heat environment-
# lines
Dry weight (g)
Check

25. Complementary Genetic Strategies
Identify crop characteristics conferring adaptation
Precision and high throughput phenotyping
Exploration of genetic resources for adaptive traits
Inter-specific hybridization to broaden the crop genepool
Genomics to increase breeding efficiency
Strategic crossing to achieve cumulative gene action

26. Canopy temp as a surrogate for root function26

27. CANOPY TEMPERATURE (0C)
CT is robustly associated with performance under heat and drought stress
Drought stress
Heat stress
CANOPY TEMPERATURE (0C) 27 27

28. Common QTL identified for heat and drought adaptation
Pinto et al ,
Heat and drought adaptive QTL in a wheat population designed to minimize confounding agronomic effects.
TAG 121:1001–21
Empty bars: Drought specific QTL
Lined bars: Stress QTL specific for DRT & HOT environments
Solid bars: Robust QTL identified under stress and irrigated environments

29. Root distribution in Seri/Babax ‘iso-QTL’ lines
T-tests for COOL v HOT genotypes:
DROUGHT cm (p=0.002) ; HEAT cm (p=0.0025)
Pinto & Reynolds, TAG

30. Adaptation to plant density

31. Differences between inner and outer rows:

32. GWAS candidate genes: A) ADi Yield, C) ADi KNO
Candidate gene: SET domain protein PI94960 for pollen abortion
Sukumaran et al. Crop Sci. (2015)

33. QTL for spike photosynthesis

34. Complementary Genetic Strategies
Identify crop characteristics conferring adaptation
Precision and high throughput phenotyping
Exploration of genetic resources for adaptive traits
Inter-specific hybridization to broaden the crop genepool
Genomics to increase breeding efficiency
Strategic crossing to achieve cumulative gene action

35. Strategic crossing for cumulative gene action

36. Strategic Crossing to Combine Adaptive Traits
DROUGHT YIELD = WU x WUE x HI
WUE: Transpiration Efficiency
Efficient leaf photosynthesis (CID)
WUE: Photo-Protection
Leaf wax
Pigments
Water Uptake
Ground cover
Access to water by roots
Partitioning (HI)
Stem carbohydrate storage 36

37. First new generation of lines based on physiological crosses & selection, (2007)

38. New lines based on physiological trait (PT) criteria
Check 3.5 t/ha (Vorobey)

39. Yield traits considered in strategic crosses:
YIELD = LI x RUE x HI
SINKS pre-grainfill:
Spike fertility
grain number
kernel weight potential
avoid floret abortion
Development pattern
long juvenile spike phase
SOURCE (grain-filling):
Canopy photosynthesis (RUE/LI)
Leaf conductance
Carbohydrate storage in stem
stay green
SINK (grain-filling)
Harvest Index
tiller survival
grain growth rate
SOURCE (pre-grainfill):
Light interception (LI)
Growth rate
Canopy temperature

40. Abbreviation
Site
Country
BGLD J
BARI Joydebpur
Bangladesh
BGLD D
BARI Dinjpur
BGLD R
BARI Rajshahi
China L
LAOMANCHENG
China
Egypt A
Assiut
Egypt
India D
Delhi
India
India L
Ludhiana
India V
Varanasi
India K
Karnal
India H
Dharwad
India I
Indore
India U
Ugar
Iran D
DARAB-HASSAN-ABAD
Iran
Iran Z
ZARGAN
Iran SP
SPII - KARAJ
Iran S
SAFIABAD AGRIC. RES. CENTER
MEX Bajio
INIFAP-Bajio
Mexico
MEX CM
CIMMYT CENEB
MEX BC
INIFAP-Mexicali Baja California
MEX JAL
INIFAP-Tepatitlan Jalisco
MEX SIN
INIFAP-Valle del Fuerte, Sinaloa
MEX SON
INIFAP_Valle del Yaqui
Nepal B
Bhairahawa
Nepal
PAK I
Islamabad
Pakistan
PAK F
Faisalabad
PAK P
Pirsabak
26 international sites of the 2nd WYCYT 35 new (PT) lines 7 elite checks

41. Mean yield of 7 elite checks: 2nd WYCYT, 2014
Yield g/m2

42. Mean yields of 35 new PT lines v 7 elite checks: (average 7% advantage of new lines)
Yield g/m2

43. Physiological Breeding Pipeline
CROP
DESIGN
GENETIC
RESOURCES
PHENO-
TYPING
ANALYSIS
BREEDING
DELIVERY through IWIN
Strategic crossing
Select best progeny using state-of-the-art phenotyping /molecular tools
Determine traits/genes needed to adapt crops to target environments
Landraces
Wild
relatives
Advanced
lines
Transgenics
High thru-put remote sensing
Precision phenotyping
QTL identified and MAS systems developed
INFORMATICS

44. Standard Phenotyping Protocols

45. Conclusions
Investment in understanding the ‘phenome’ and trade-offs between traits facilitate breeding decisions
Genetic resources represent a vast and largely untapped opportunity for crop improvement, if evaluated using appropriate screens:
Aerial high throughput approaches on large numbers
Precision phenotyping approaches on selected material
Molecular markers (especially for hard to phenotype traits)
Strategic trait-based crossing increases genetic gains compared with crossing the best x best yielding lines
Phenomic and genomic technologies can deliver genetic gains in farmers’ fields; sooner when integrated with proven techniques

47. PT Heat + Parents (late sown Mexico)