Adapting durum wheat to drought and crown rot environments

Abstract

Durum wheat (Triticum turgidum L. ssp. durum) producers can experience significant yield and grain losses due to crown rot (CR) disease, caused primarily by a fungal pathogen Fusarium pseudograminearum. Losses due to CR are exacerbated when disease infection coincides with terminal drought. Durum wheat is very susceptible to CR and resistant germplasm is not currently available in elite breeding pools. Deploying physiological traits for drought adaption (e.g. deeper roots), to reduce stress due to water deficit may, therefore, potentially minimise losses due to CR infection.
The rapid generation advance technology, ‘speed breeding’, was used to rapidly develop recombinant inbred lines (RIL) populations (F6) derived from crosses between Australian cultivars and ICARDA elite breeding lines pre-selected for drought adaptation in Syria and Morocco. Populations were evaluated in the field and under controlled conditions for several physiological traits, including seminal root angle and number and CR severity. This provided the genetic predisposition of lines for rooting behaviour and CR susceptibility in the absence of water stress. Field experiments were established in Queensland, Australia, which allowed an examination of the value of root development traits to improve adaptation to each of the stresses. NDVI measurements were recorded weekly, which enabled modelling of the senescence pattern and calculation of stay-green traits for each genotype. Genome-wide association studies using DArT markers identified key genomic regions underpinning the traits. Our genetic analyses highlighted the genetic relationships between yield as well as above- and below-ground physiological traits.
Through this study, we have provided new insights into the genetic controls and value of these traits, which we anticipate will assist breeders to design improved durum varieties that may mitigate production losses due to water deficit and CR.

Full text

Adapting durum wheat to drought and crown rot
Samir Alahmad, Jack Christopher, Kai Voss-Fels, Jason A. Able, Filippo M. Bassi, Lee T. Hickey
BGRI 2018, Marrakesh, Morocco “Delivering Genetic Gain in Wheat”
@samir_alahmad
s.alahmad@uq.edu.au

Current and future challenges for durum wheat production
(Christensen, et al. 2007)
Future drought hotspots coincide
with durum regions
Drought
Crown rot caused by
Fusarium species
Stubble retention
Crown rot

How does crown rot cause yield loss?
Can we reduce
yield loss?
89%
loss
Improved roots
WUE
TE
Staygreen
Osmotic adjustment
5% yield loss
Infected
crown

Can we reduce
yield loss?
Improved roots
WUE
TE
Staygreen
Osmotic adjustment
89% yield loss
White
heads
Infected
crown
How does crown rot cause yield loss?
5% yield loss
Infected
crown

Can we reduce
yield loss?
Improved roots
WUE
TE
Staygreen
Osmotic adjustment
X
White
heads
Infected
crown
How does crown rot cause yield loss?
5% yield loss
Infected
crown

Can we reduce yield loss?
WUE traits
•TE
•Staygreen
•Osmotic adjustment
Infected
crown
Improve root system
architecture
89% yield loss
Infected
crown
How does crown rot cause yield loss?
5% yield loss
Infected
crown

Crown rot problem! What is the solution?
Abiotic stresses (drought)
Biotic stresses (crown rot)
Can we create populations to
investigate WUE traits?

Establishing populations to fuse ICARDA and Australian germplasm
ICARDA founder lines
Adapted to drought and heat
Tolerance for soil-borne diseases
Low quality
Australian cultivars
High quality
Very susceptible to crown rot
Ideal populations
Combine adaptive traits with quality
Suitable for genetic studies
Australian cultivars
ICARDA elite lines
Dr Filippo Bassi

Durum multi-parent NAM
Oz reference varieties crossed with ICARDA founders
6 selfing generations
Speed breeding to accelerate population development
F6 lines genotyped with DArTseq platform
ICARDA founder lines
Speed breeding facility, University of Queensland
6 generations of selfing
F6 leaves sampled for genotyping

NAM population structure
DBA Aurora and Jandaroi
Reference parents
Founder parents
Fastoz2, Fastoz6,Fastoz10, Kunmiki,
Outrob4,Fastoz3, IC-078, Fadda98
Common founders
Kunmiki and Outrob4
Sub populations
Jandaroi
DBA Aurora

Crown rot problem! What is the solution?
Abiotic stresses (drought)
Biotic stresses (crown rot)
Can we phenotype root
architecture?

Phenotyping root angle
Clear pot
Richard et al. (2015) Plant Methods
Root angle variation
Glasshouse:48.3 -112 (°)
‘Shovelomics’
83°68°
Field: 51.7 -85.8 (°)

●
r
= 0.65
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●
●
●
●
●
●
● ●
●
●
●
●
●
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60 65 70
55
60
65
70
75
80
●
Root angle shovelomics
Root angle clear pot
Kunmiki
Outrob4
IC-078
DBA Aurora
r= 0.65
Clear pot vs shovelomics
Good correlation between glasshouse and field

Crown rot problem! What is the solution?
Abiotic stresses (drought)
Biotic stresses (crown rot)
What are the genomic regions
controlling root architecture?

GWAS for root angle
Subset of 393 NAM lines
2,541 high quality DArTseq SNPs
GenABEL R package
Methods
Results
Major root angle QTL on 6A
Associated markers in high LD
(r2 = 0.46 -0.99)
Bonferroni 4.67

Haplotype analysis for 6A root angle QTL
DBA Aurora
Fastoz-3
Fastoz-8
Fastoz-10
Outrob4
hap1
hap2
hap3
hap4
hap5
hap6
hap7
hap8
75o
55o
10 individuals
1 individual
Hap1 vs hap2 ***
N= 142
N= 120
8°
TCS haplotype network created using PopART
Markers used to
construct haplotype
network

DBA Aurora
Fastoz-3
Fastoz-8
Fastoz-10
Outrob4
hap1
hap2
hap3
hap4
hap5
hap6
hap7
hap8
Hap1 vs hap2 ***
N= 142
N= 120
8°
75o
55o
hap1 hap2

Crown rot problem! What is the solution?
Abiotic stresses (drought)
Biotic stresses (crown rot)
Does root architecture influence
field performance?

Crown rot problem! What is the solution?
Abiotic stresses (drought)
Biotic stresses (crown rot)
Hermitage drought station, Warwick, QLD
Subset of 168 NAM lines
Data collection: weekly NDVI measurements,
flowering time, plant height, yield
Field evaluation under drought conditions
Hermitage research station Measuring plant height Counting storms on harvest day!
Warwick, QLD

Phenotyping rate of senescence
NDVI measurements collected
Logistic curve
Staygreen is a consequence of
saving water early in the season
Senescent type Staygreen type
Christopher et al. (2016)
Flowering time
Harvest
Modelling rate of senescence

Correlation between staygreen and yield
Staygreen traits were significantly
correlated with yield

Area under curve
*
N=35
N=43
hap1 hap2
Flowering
time
Area
under
curve
NDVI (Staygreen)
Staygreen traits were significantly
correlated with yield
Correlation between staygreen and yield
Root angle QTL effects on yield performance

***
Yield t/h
N=35
N=43
hap1 hap2
Flowering
time
Area
under
curve
NDVI (Staygreen)
Staygreen traits were significantly
correlated with yield
Correlation between staygreen and yield
Root angle QTL effects on yield performance

Crown rot problem! What is the solution?
Abiotic stresses (drought)
Biotic stresses (crown rot)
Can WUE traits minimise yield loss
under crown rot?

Crown rot experiment
Similar trial, but high crown rot pressure
Data collection: flowering time, plant height, yield and crown rot
Crown rot assessed as a severity index:
‒White heads % 1st assessment
‒White heads % 2nd assessment
‒Stem browning
Sown on infected stubble Stem scoring 5% white heads 95% white heads

Crown rot problem! What is the solution?
Abiotic stresses (drought)
Biotic stresses (crown rot)
QTL on 6B
Performed haplotype analysis
The region is also associated
with staygreen traits!
GWAS for crown rot Crown rot 6B QTL
Tolerance to crown rot achieved by modulating canopy development
hap1 hap2 hap1 hap2 hap1 hap2
**
Yield t/h
N= 16
N= 21
N=16
N=
21
*
Area under curve
N= 16
N= 21
*
Days to 90% senesced
N= 16
N= 21
*
Days to 50% senesced
N= 16
N= 21
hap1 hap2 hap1 hap2 hap1 hap2 hap1 hap2

Can we combine root and crown rot QTL?
Queensland+CR
Yield t/h
**
Under crown rot
Yield benefit 1.1 t/h
_ _
+ +
Root QTL & Crown rot QTL

Queensland+CR Queensland-CR
Yield t/h
**
.
Under drought yield
benefit 0.41 t/h
Under crown rot
yield benefit 1.1 t/h
_ _
+ +
Root QTL & Crown rot QTL
Can we combine root and crown rot QTL?

South Australia-CR Morocco-CR
Queensland+CR Queensland-CR
Yield t/h
**
Under crown rot
yield benefit 1.1 t/h
Average yield benefit
under drought 0.57 t/h
.
_ _
+ +
Root QTL & Crown rot QTL
Can we combine root and crown rot QTL?

Take home messages
Powerful NAM population for studying WUE traits
Major QTL for root architecture on 6A & crown rot on 6B
‒Opportunity to optimise WUE traits to enhance yield under drought and crown rot
What's next?
Validate trait combinations in a more diverse environmental context
Combine favourable alleles using a genomic selection strategy

Acknowledgments
Lee Hickey
Jason Able
Filippo M. Bassi
Jack Christopher
Eric Dinglasan
Kai Voss-Fels
Steven Simpfendorfer
Hickey lab group
Ian Godwin lab group
Scholarships:
Monsanto's Beachell-Borlaug International
Scholar Program (MBBISP)
University of Queensland Research Scholarship
(UQRS)

Questions?