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Field-based phenotyping for abiotic stresses in maize:
Focus on breeder’s wish-list
P.H. Zaidi*, M.T. Vinayan and K. Seetharam
Asia Regional Maize Program, CIMMYT Int., Hyderabad, India
Breeder’s wish-list (non-exhaustive)...
• Minimize experimental error and improve heritability (≥0.4
under stress and ≥0.7 under optimal condition) .
• Precisely estimate and account for G x E in selection
• Trait(s) are heritable, & genetically (not just phenotypically)
correlated with yield & eventually adding in selection gains
• Dissect complex traits into components; useful in genomic
region discovery.
• Tools for improving precision and efficiency of data collection
on key agronomic traits
Precision Phenotyping Key of success for a genetic improvement program
Feed to breeding
program for
developing
improved products
Diverse germplasm
Phenotype
Genotyping Genotype:phenotype associations
C,C C,T T,T
Sensitive
Tolerant
Association analysis
Promising alleles
breeding program
Conventional breeding
Molecular breeding
RFLP
RAPD
SSR
SNP
GBS-SNPs and
Indels
Full genome re-
sequencing
Epigenome
Methylome
Proteome
Metabolome
RNAi
profiling
GMP Datapoints
(….until 2009)
~ 500,000
>7.0 billion and
growing…!!!
2010-2015
Genomics
evolving
rapidly…!
Source: Raman Babu, CIMMYT
"We are able to study genes and manipulate them but
the study of processes at the level of whole plant has
not been able to keep pace with these advances."
Professor Mark Tester, Univ. Adelaide, Australia
“The growing disparity between (the cost and speed of)
genomics vs. high-quality phenotypes…[is] a major
impediment to functional genomics….”
Harvey JJW, Strauss SH (2008) Towards physiological sculpture of
plants. New Phytol 181:10
Genotype
Environment
Crop management Prevailing weather
Phenotype
“Actual environment” “Noise”
Quantify & Factor G X E in phenotyping!
Phenotyping environment…
(Bruce et al., 2002)
Managed environment
8
Uneven germination
Soil crusting
Uneven thinning
Sources of field variability/error
Differences in soil depth
Differences in soil texture
Termite hills
Bird damage
Uneven weeding
Soil compaction
Nutrient deficiency
Slope
Uneven fertiliser application
Uneven irrigation
Inherent (to be managed) Introduced (to be avoided!)
►Organize trials respecting spatial variability to avoid field gradients & minimize error and use covariate analysis, as needed
(h = >0.4 under stress & >0.7 in optimal conditiins) Precision in phenotyping trials
Fieldm Operations Month Date Day/Week Tmax Tmin
Accumulated GDD (degree C)
2013-14 Planting Nov 26 1 29.3 15.5 12.4
Dec 2 Week-1 27.6 11.4 72.7 Dec 9 Week-2 29.3 13.1 150.4 Dec 16 Week-3 29.4 14.2 229.6 Dec 23 Week-4 28.3 13.5 310.6 Dec 30 Week-5 25.4 17.7 381.5 Jan 6 Week-6 29.3 13.2 456.8 Jan 13 Week-7 28.8 19.6 540.0
Last Irrigation Jan 14 48 25.3 19.4 552.4
2014-15 Planting Nov 30 1 29.3 16.4 12.9
Dec 6 Week-1 27.8 15.6 89.1 Dec 13 Week-2 27.4 12 170.8 Dec 20 Week-3 26.3 6.8 231.1 Dec 27 Week-4 27.7 11.7 290.4 Jan 3 Week-5 27.4 14.3 363.5 Jan 10 Week-6 27.8 7.5 417.7 Jan 17 Week-7 29.2 11.7 479.1 Jan 18 50 28.8 11.3 489.1 Jan 19 51 30.6 12.4 500.6 Jan 20 52 31 12.3 512.3 Jan 21 53 30.3 10.7 522.8 Jan 22 54 29.4 10.2 532.6 Jan 23 55 30.1 10.6 542.9
Last irrigation Jan 24 56 29.7 11.3 553.4
*Site and maturity group specific
(h = >0.5 in stress & >0.7 in optimal trials) Precision in phenotyping trials
►Drought phenotyping trial : When to stop irrigation?
►Drought phenotyping trial : When to resume irrigation?
0.00
10.00
20.00
30.00
40.00
50.00
60.00
70.00
80.00
1 2 3 4 5 6 7 8 9
So
il m
ois
ture
(V
ol.
%)
Observations
10 cm 20 cm30 cm 40 cm60 cm 100 cm
FC-36.7
PWP-16.8
(h = >0.5 in stress & >0.7 in optimal trials) Precision in phenotyping trials
Expression of genotypic variability under managed stress
Early-Feb planting
Mild heat stress Mid-March Planting
Severe heat stress
Managed heat stress by manipulating
planting time & tracking GDD
Hyderabad
Baijenki
Sabor
Ishurdi
Jessor Gazipur
Aurangabad
Ludhiana
Jalandhar
Hoshiarpur
Sahiwal
Faisalabad
Surkhet Nepalgunj
Rampur
Raichur
B’Gudi
Jabalpur
Tmax during Spring
maize flowering
HTMA phenotyping sites
Hyderabad
B’Gudi
Heat stress phenotyping site………
Tem
pera
ture
(oC
) R
H (%
) an
d ra
infa
ll (mm
)
Sabor
Ludhiana
VPD
(kPa) and M
ean G
Y of the trial (t/ha)
Tm
ax (oC
)
Phenotyping sites
400C
350C
Tmax-Reproductive Tmax-Late Veg
Expression of genotypic variability for heat stress
Secondary traits
It is not just sufficient to know a secondary trait is related to stress tolerance
early vigour
VPD
temperature
hormones
deep roots
leaf growth
WUE
stomatal
regulation
grain filling duration
and rate
grain
number
HI
nutrient
acquisition
It is important to know that breeding progress using grain yield & a given secondary trait in selection is greater than using grain yield alone
proven breeding value! √
• Genetically correlated with grain yield (relationship with
yield causal, not casual!)
• Higher heritability than grain yield itself (less G x E than
grain yield).
• Genetic variability for the trait must exist
• The trait should not be associated with poor yields (it
should confer tolerance instead avoidance)
• Measurement - rapid, non-destructive, more
economically than the yield itself and in a reliable way
(updated from….Edmeades et al. 1998)
AN IDEAL SECONDARY TRAIT
0.0
0.5
1.0
1.5
2.0
2.5
0.0 0.2 0.4 0.6 0.8 1.0
Heritab ility o f grain yield
Eff
icie
nc
y o
f in
de
x s
ele
cti
on
Direct selection for yield vs. Index selection (Secondary traits along with grain yield)
(Bänziger and Lafitte, 1997)
Optimal Severe stress
23
Phenotyping root traits:
• Functional traits (water use, utilization pattern and WUE)
• Structural traits (root length, volume, root-length density)
Rooting depth (cm)
Root dry weight (g plant-1)
Drought stress Normal moisture
Rep
rod
uct
ive
per
iod
wat
er u
se (
litre
s)
Tran
spir
atio
n e
ffic
ien
cy (
g lit
re-1
)
S. No. Pedigree WU WUE
1 DTPYC9-F46-3-9-1-2-2-1-3-B*7 27.1 9.0
2 5406-29P24STEC1HC17-4-2-1-1-B*7 26.3 7.2
3 CML-444-BB 25.7 7.8
4 [CL-G2501xCML170]-B-3-1-1-BB-1-B*5 24.5 8.1
5 CML442-B*5 23.3 6.2
6 DTPYC9-F46-3-6-1-2-2-1-1-BB-B1-B2 22.1 7.3
7 POOL 16 BNSEQ.C3 F22 x 1-3-2-2-2 20.4 8.1
8 CLQ-RCYQ41-BB-2-B*5 19.5 8.2
9 (CTS013058/(AMATLC0HS167-1-1-1-2F/R)-B*5/Nei402011)-B*8 19.4 6.4
10 ZM621A-10-1-1-1-2-B*10-1-BBB 18.9 7.1
11 CA00310/AMATLC0HS71-1-1-2-1-1-1-B*14 17.9 9.6
13 EW-DMR-G-C7-HS-(SIB)-9-B-1-B*4 14.6 7.7
14 CML448-BBB 14.3 8.1
15 CL-RCW97-B*4 14.2 7.2
16 90[SPMATC4/P500(SELY)]#-B-48-4-B*7 11.9 5.9
DTPYC9-F46-3-9-1-2-2-1-3-B*7 (right) under DT in a field trial
Thank you
for your
interest!
Photo Credits (top left to bottom right): Julia Cumes/CIMMYT, Awais
Yaqub/CIMMYT, CIMMYT archives, Marcelo Ortiz/CIMMYT, David
Hansen/University of Minnesota, CIMMYT archives, CIMMYT archives (maize),
Ranak Martin/CIMMYT, CIMMYT archives.