Yoseph Beyene (Ph.D)Senor Maize Breeder, CIMMYT-Kenya
Email: [email protected]
Harnessing Agriculture Biotechnology for Resilience to Climate Change: A Lesson from Water Efficient Maize for Africa (WEMA)
Project
Outline• WEMA Project
– Partners – Objectives– Approaches
• Progress by Breeding Approach – Conventional Breeding– Molecular Breeding– Transgenic 4RD
• Highlights of Achievements
Maize is vital for food security in Sub-Saharan Africa
• Over 300 million people depend on maize in SSA
• Example: consumption in Kenya 103 kg/ yr/ person
• Maize yield is low (1.8 t/ha compared to world average of 4.5 t/ha)
• Major constraints:• Drought • Low soil nitrogen • Diseases• Lack of access to quality
seed Recorded droughts between 1971 and 2000, and the number of people affected
Water Efficient Maize for Africa (WEMA)
• A public-private partnership to develop and deploy drought-tolerant and insect-pest protection white maize varieties to smallholder African farmers royalty-free.
Expected Outputs • Under moderate drought, WEMA maize expected to
increase yields by 25% over 2008 hybrids• 15% conventional • 10% transgenic
• Translates into additional 2 million MT maize during drought years to feed about 14 to 21 million people in the long-term.
AATF
African institution mandated to access, develop, & deliver appropriate agricultural technologies to smallholder African farmers royalty-free
Monsanto
World leader in gene discovery and commercialization of Transgenic crops
CIMMYT
World leader for breeding maize for African agro-ecological zones
WEMA Partnership Structure
NARS• Expertise in field trials • Breeding/Test DT maize•Capacity building opportunities
WEMA
KALRO; NARO; ARC; COSTECH; & IIAM
● Rapid development of completely homozygous inbred lines and faster product identification
● Four steps:o F1 is crossed with a haploid inducero Identification of kernels with haploid embryo
using visible anthocyanin markero Artificial genome duplication generation D0
o Selfing generating D1 seed
Accelerating Breeding Gains - Doubled haploids
DH technology is well-integrated in CIMMYT’s product development strategy
• 26, 221 DH lines developed from NARS, Monsanto and CIMMYT bi-parental crosses through WEMA Project
• The DH lines were evaluated for per se, reaction to major leaf diseases in Africa
• Testcross were developed and evaluated in stages 1, 2&3 and regional trials across locations in five countries
• Hybrids were released in Kenya, Uganda, Tanzania, South Africa and nominated in Mozambique
WEMA has strong breeding pipelinesStage Hybrids
Stage I 20, 900Stage II 9, 349Stage III 1, 761WWT 246Total 32, 256
Types of lines TotalDH lines 26, 221Elite lines 1,949Segregating lines 29,308Total 57,478
DH lines compared to pedigree lines under optimum
Pedigree Yield (t/ha)% increase over the best check
Anthesis date
Ear height
Plant height
CKDHL0556 4.7 38.0 66.7 85.0 174.4CKDHL0625 4.6 34.4 65.1 86.5 169.1CKDHL0399 4.0 18.1 63.1 77.0 157.9CKDHL0505 4.0 17.6 68.2 82.1 142.3CKDHL0500 3.7 9.9 73.7 78.7 130.9CML312 3.4 69.5 60.2 159.5CML395 2.4 67.8 93.1 164.3CML442 2.8 70.8 58.9 131.1CML444 3.0 72.7 74.3 126.3CML539 2.2 67.2 66.7 132.9LSD 1.2 2.4 14.7 20.3CV 20.6 1.7 8.9 6.7Heritability 0.9 1.0 0.9 0.9
Date of planting: 6 June 2012Date of last irrigation: 26 July 2012Date of harvesting: 10 Oct 2012
Evaluation of hybrids under managed drought stress
Date of planting: 25 May 2014Date of last irrigation:19 July 2014Date of harvesting: 28 Oct 2014
Accelerating Breeding Gains: Forward breeding
Entry EntryYield (t/ha)
increase over best check (%) AD EA ET
1 (CKDHL0089/CKDHL0333)//CKL14001 8.84 56.0 64.85 1.58 2.002 (CML395/CML444)//CKL14002 8.82 55.6 65.26 1.92 1.753 (CML395/CML444)//CKL14001 8.68 53.2 65.31 1.81 2.004 (CKDHL0159/CKDHL0295)//CKL14003 8.66 52.7 66.06 1.90 2.005 (CKDHL0089/CKDHL0333)//CKL14002 8.62 52.2 66.32 2.25 2.006 (CML395/CML444)//CKL14005 8.55 50.9 65.30 2.16 2.007 (CKDHL0089/CKDHL0295)//CKL14001 8.52 50.3 65.43 1.75 2.008 (CKDHL0089/CML395)//CKL14001 8.39 48.0 65.20 1.74 2.009 (CKDHL0089/CKDHL0295)//CKL14006 8.34 47.2 68.68 1.92 2.00
10 (CKDHL0159/CKDHL0295)//CKL14002 8.28 46.2 65.44 2.34 2.00Pioneer 3253 (Pioneer) 5.67 66.48 3.07 2.25DK8053 (Monsanto) 5.27 65.03 2.75 3.00DH04 (Kenya seed) 5.01 65.77 3.00 2.50
DK8031 (Monsanto) 3.45 65.88 3.84 2.50nlocs 6 6 6 2
Gmean 7.42 65.70 2.35 2.25LSD 1.10 1.32 0.49 0.69CV 7.53 1.02 10.71 15.40
Heritability 0.85 0.89 0.79 0.55
Hybrids Release and Commercialization
Nominating country Hybrid Kenya Uganda TanzaniaWE5101 Yes Yes YesWE5107 Yes Yes YesWE5109 Yes Yes YesWE5103 Yes YesWE5108 Yes YesWE5111 Yes Yes WE5117 Yes Yes
2012 2013 2014 20150
5
10
15
20
25
1
1618
24
Year of release
Num
ber
of h
ybrid
Timeline for delivery pathway of products
13
2013 2014 2015 2016 / 2017
Introduction of first WEMA Hybrid
MON810 application in Kenya
MON810 ApprovalsFor commercialization
MON87460 Approvals (allows
for Stacks with MON810)
Ramp up of WEMA Hybrids
Molecular Breeding
Use of Breeder-friendly Markers for Maize Streak Virus (MSV) Resistance
msv1
GWAS in a panel of 300 lines, genotyped with GBS (~700K SNPs) Validation of SNP markers in 660 DH lines (biparental
populations)
• Three SNP markers identified and validated within the Msv1 region
• MAS for this region increases resistance to MSV by 25% (1.2 units on a 1-5 scale)
Highly r
esista
nt
Resista
nt
Moderatel
y Susce
ptible
Susce
ptible
Highly s
usceptible
0
50
100
150
200
250
Forward breeding: Using markers for MSV resistance at early stage of testcross formation
Sampling leaf tissue in the DH nursery, Sept 2015
SNP Trait Chr SNP RR SS
PZE0186065237 MSV 1 C/T C:C T:T
PZE0186365075 MSV 1 C/A C:C A:A
PZE-10109395MSV
1 A/G A:A G:GPopulation PZE-
101093951PZE0186065237
PZE0186365075
Comment on msv1 data Decision
CML312/INTA-F2-192-2-1-1-1-B*7-2-B-10-B-B-B:@ A:A C:C C:C Homozygous for favorable alleles at 3 loci SelectCML312/INTA-F2-192-2-1-1-1-B*7-2-B-10-B-B-B:@ A:A C:C C:C Homozygous for favorable alleles at 3 loci SelectCML312/LaPostaSeqC7-F18-3-2-1-1-B-B-B:@ A:A C:C C:C Homozygous for favorable alleles at 3 loci SelectCML312/LaPostaSeqC7-F18-3-2-1-1-B-B-B:@ A:A C:C C:C Homozygous for favorable alleles at 3 loci SelectCML312/LaPostaSeqC7-F18-3-2-1-1-B-B-B:@ G:G T:T A:A Homozygous for unfavorable alleles at 3 loci RejectCML312/LaPostaSeqC7-F18-3-2-1-1-B-B-B:@ G:G T:T A:A Homozygous for unfavorable alleles at 3 loci RejectCML312/LaPostaSeqC7-F18-3-2-1-1-B-B-B:@ G:G T:T A:A Homozygous for unfavorable alleles at 3 loci RejectCML312/LaPostaSeqC7-F18-3-2-1-1-B-B-B:@ G:G T:T A:A Homozygous for unfavorable alleles at 3 loci Reject
Large-scale implementation of GS/MARS in Africa
• In 2008, CIMMYT started the largest public GS/MARS projects in SSA
• Over 35 bi-parental maize populations advanced through MARS/GS
• Genetic gain studies completed for 18 populations using two protocols:– using a subset of markers significantly associated
with QTLs for grain yield and ASI– Using all markers distributed across maize genome
without test for association with QTLs
Self selected Plants
Self selected Plants
Self selected Plants
Cycle 1
GenotypeSelf or recombine selected Plants
Cycle 2Genotype Self or
recombine selected PlantsCycle 3
Crossed with Tester
F4
Inbred A x Inbred B
F1
F2
F3 = Cycle 0 F3 x Tester
F5
F6
Evaluate TC under target environments
Phenotypic Selection Cycle 0 Cycle 1 Cycle 2 Cycle 3
Genotype, Select Best
Families Based on Phenotypic and Genotypic
Data and Recombine
Genotyping: All markers or
a subset of significant markers
QC/QA genotyping
Develop DH pop
MARS work flow
Genetic gain studies
Polymorphism screening
Genetic Gain Studies on C0-C3 from MARSCycle Design C0 Made balanced bulk from each F2:3
family within a population
C1 Made balanced bulk from the selected individuals/families
C2 Made balanced bulk from the selected individuals /families
C3 Made balanced bulk from selected individuals /families
Lines from Pedigree
6 random F6 lines from each population selected through pedigree breeding
Reference entries (3)
2 parents and F1
Single cross testerx
+ Best currently available commercial hybrids (checks)
Gain in grain yield using genome-wide SNPs under drought environments in SSA
CML440xCML504
CML441xCML444
CML444xMalawi
6x1008
6x1016
6x1017
6x1020
6x1028
0.0
0.5
1.0
1.5
2.0
2.5
3.0
3.5 Cycle0 Cycle1 Cycle2 Cycle3
Populations
Gra
in y
ield
(Mg/
ha)
Genetic gain from conventional breeding in Africa 18 kg ha-1 yr-1 (Edmeades, 2013)32 kg ha-1 yr-1 (B. Masuka, submitted)
Genetic gain GS is 2- 4 times higher than from conventional breeding reported in sub-Saharan Africa.
Overall gain in GY : 70.5 kg ha-1 year-1
Beyene et al. (2015) Crop Sci. 55:154–163
Performance of hybrids developed from GS-C3-DH lines, founder parents and commercial checks
under optimumYi
eld;
t/ha
Populations
Pop1-GWS Pop2-GWS Pop3-GWS Pop4-GWS Pop5-GWS0
1
2
3
4
5
6
7
8
9 Top 5 hybrids Parents Commercial checks
Phenotyped at 3 optimum locationsGain over the commercial checks= 8.7 to 20.8%Gain over the parents = 9.0 to 91.1%
Gain in grain yield under drought and optimum across 10 MARS pops
Beyene et al. (2016) Crop Sci. 56:1–10
Genetic gain from conventional breeding in Africa 18 kg ha-1 yr-1 (Edmeades, 2013)32 kg ha-1 yr-1 (B. Masuka, submitted)
Genetic gain GS is 1.6- 2.8 times higher than from conventional breeding reported in sub-Saharan Africa.
Overall gain in GY : 51 kg ha-1 year-1
Performance of hybrids developed from individual C1S2 of MARS and pedigree breeding under drought
1008 1015 1016 1017 1018 1019 1020 1021 1023 10280.0
0.5
1.0
1.5
2.0
2.5
3.0
3.5
4.0
Best C1S2PedigreeCheckParents
Populations
Grai
n yi
eld
(t/h
a)
Beyene et al. (2015) Euphytica : online first
Heritability = 0.32 to 0.75
Improved inbred lines and hybrids developed through rapid-cycle GS
Fixed lines
Drought tolerant hybrids
Transgenic R&D
The effect of CspB gene on grain yield of maize under field condition in the USA
Grain yield of 3 hybrids with CspB gene evaluated in yield trials across the western dryland USA - averaged across locations that experienced water-deficit stress during the late vegetative or grain fill periods of theseason.Castiglioni et al., 2008
MON87460 yield differences between positive & negative across locations in South Africa (2008-2014)
• Hybrids showed significant benefit of trait (MON87460) under drought stress in general and under severe, high and moderate drought stress.
• The more severe the stress the higher the differences between positive and negative (up to 360 kg/ha).
**%
Delta
Optimum Stressed Severe High Moderate Low0
1
2
3
4
5
6
7
8
9
*
*Stress N Positive N Negative
Optimum 2472 2593Stressed 7076 7019
Severe 277 279High 3022 2951
Moderate 2383 2348Low 1394 1441
Positive Mean Negative Mean0
2
4
6
8
10
12
Yiel
d [t
/ha]
*24%
• The gene has a positive and significant effect on yield.
• The gene significantly reduced numbers of exit holes and tunnel length after artificial C. partellus infestation.
• The gene significantly reduced B. fusca larvae survival and leaf area consumed.
Prop
ortio
n B.
fusc
a la
rvae
aliv
e
Positive Mean Negative Mean0.00
0.10
0.20
0.30
*-81%
Leaf
Are
a Co
nsum
ed [m
m2 ]
Positive Mean Negative Mean0
10
20
30
40
50
*-73%
Tunn
el le
ngth
[mm
]
Positive Mean Negative Mean0
1
2
3
4
5
*-96%
Positive Mean Negative Mean0
1
2
3
4
Num
ber o
f Exi
t Hol
es *-96%
MON810 Kenya CFT1-3 Executive Summary
Highlights of Achievements• A total of 59 hybrids released in in Kenya, Tanzania, Uganda and
South Africa
• Successfully integrated molecular markers and DH technology into product development
• We have conducted the largest public MARS/GS projects and demonstrated 2-3 fold higher grain yield using MARS and GS than pedigree methods in tropical maize
• • Meta analysis of MON87460 indicated significant benefits of DT
trait under drought stress
• Combined analysis of MON810 in Kenya indicated positive and significant effects on grain yield under artificial infestation
Other contributors to the studies(in alphabetical order)
• Amsal Tarekegne• Barbara Meisel• Bindiganavile S. Vivek• Boddupalli M. Prasanna• Gregorio Alvarado• Jose Crossa• Kassa Semagn• Lewis Machida• Pierre Sehabiague• Raman Babu• Stephen Mugo• Sudha Nair• CIMMYT research assistants at different locations
Acknowledgements
• WEMA Partners• Bill and Melinda Gates Foundation (BMGF)• United States Agency for International
Development (USAID) • Howard G. Buffet Foundation (HGBF)