Asian Maize Drought Tolerance (AMDROUT) Project SP3 PROJECT G4008.56

Principal Investigator: B. S. Vivek

Project Details

Grant Period: (Start: Nov 08) (End: Oct 2013) No cost extension to July 2014

What? Drought tolerant lines using Marker Assisted Recurrent Selection (MARS) based on

genome-wide selection (GWS)

Yellow drought tolerant inbred lines Proof of concept for MARS-GWS Scientists trained in molecular breeding

Principle Outputs

Why?

80% of maize in Asia is grown under rain-fed conditions and prone to drought stress

Drought in Asia …wheat and maize harvests will

be strongly affected by droughts …unless states ..can quickly adapt their agricultural practices

China, Indonesia and Pakistan were relatively well-placed to adapt to climate change. India was found to have one of the lowest capacities to adapt ….its maize production (in C and N India)

2012: The worst drought US witnessed in recent decades

Source: Bob Nielsen (Purdue University)

• Sixth worst departure from yield trend since 1866!

• Yield estimate would be 23% lower than predicted in 2012…

• Drought coupled with heat stress

• Possible global implications in terms of maize prices

Wherever you are, …you need stress resilience to ensure stable performance

Collaboration Dr. B. S. Vivek, CIMMYT-India Girish Kumar Krishna, CIMMYT-India V. Vengadessan , CIMMYT-India P. H. Zaidi, CIMMYT-India Le Quy Kha, NMRI, Vietnam Pichet Grudloyma, NSFCRC, Tak Fa,

Thailand I.S. Singh, Krishidhan Seeds, India R. Babu, CIMMYT-India Eureka Ocampo, Institute of Plant

Breeding, UPLB, Philippines Fan Xingming, YAAS, Kunming, China M. Azrai, ICERI, Maros, Indonesia R.P. Singh, Syngenta, India J. Burgeño, CIMMYT-Mexico J. Crossa, CIMMYT-Mexico

Final irrigation before imposing drought

Drought Phenotyping Optimal Management

Managed Drought

Drought expression at flowering

Typical genotypic variability under drought

Form S2 x tester (CML474)

Evaluate test crosses (At least 3 drought + 3 optimal sites)

Calculate marker effects (MARS-GWS)

Form C1 with best S2 lines based on phenotype data

Genotype S2 families: 350 polymorphic whole genome SNPs: Kbioscience KASPar assay

Form c1F2 (recombine best looking c1 plants)

C2

S6

Genotype-only selection (24 plants with highest GEBVs recombined)

•CML470 •VL1012767 •VL1012764 •CML472

S2

F2 (S1)

F1

P1 P2 x 4 elite yellow Asian lines (lack drought tolerance)

2 African white drought tolerant donors

•CML444 •CML440

Populations •AMDROUT1: CML470/CML444 •AMDROUT2: VL1012767/CML444 •AMDROUT5/6: VL1012764/CML444//CML472xCML440

Genotype C1 plants Calculate Genomic Estimated Breeding Values (GEBVs) using marker effects

How? Genome Wide Selection (GWS)

Mean

Lines developed by pedigree selection

Lines selected for recombination from C0 phenotyping

Cycle 3 MARS lines

Population of random lines extracted from a cross

MARS increases the frequency of favorable alleles

Moves the mean of the selected population beyond the original distribution

MARS / GWS

Sl. No.

AMDROUT Population Number

Population Type

Data from K BioScience

Marker effects available

GEBVs available

No. of individuals in the population

No. of SNPs assayed

1 AMDROUT1 F2:F3 294 340 Yes No

2 AMDROUT1 Cycle-1 242 318 Yes

3 AMDROUT1 Cycle-2 347 278 Yes

4 AMDROUT2 F2:F3 188 376 Yes No

5 AMDROUT2 Cycle-1 258 351 Yes

6 AMDROUT2 Cycle-2 346 271 Yes

7 AMDROUT5 F2:F3 197 421 Yes

8 AMDROUT6 F2:F3 183 340 Yes

9 AMDROUT5/6 Cycle-1 352 425 Yes

10 AMDROUT5/6 Cycle-2 252 399 Yes

@60% gain @40% gain

@80% gain

0.0

1.0

2.0

3.0

4.0

5.0

6.0

0.00

0.50

1.00

1.50

2.00

2.50

3.00

3.50

days

t / h

a

Cycles of selection

GY

ASI

Genetic Gains for Grain Yield under Drought: AMDROUT1 1 location

3 reps 2 row plots H 0.74

c1 c2: Marker-only selection

@ per cent gain over F2

@50% @40%

@60%

0.00

0.50

1.00

1.50

2.00

2.50

3.00

t / h

a

Cycles of selection

GY

GY

Genetic Gains for Grain Yield under Drought: AMDROUT2

1 location 3 reps 2 row plots H 0.74

@ per cent gain over F2

c1 c2: Marker-only selection

AMDROUT1 cycles

AMDROUT1c2 (Phenotypic selection followed by genotype-only selection)

AMDROUT1c1F2 (Two cycles of phenotype-only selection)

Therefore: For grain yield under drought: one cycle of

phenotypic selection followed by one cycle of genotype-only selection gives 50-100% higher genetic gain compared to two cycles of phenotype-only selection

GWS is a useful methodology to improve source (breeding) populations

Moving on….. Nov 2013: Test crosses with cycles of selection May 2014: Drought and well watered trial

information on per se and test cross performance of cycles of selection

August 2014: Draft publication

Meanwhile: Wet season data is being collected Second season of drought screening will be

completed by May 2014

Germplasm Outputs

Cycles of selection from bi-parental crosses between CIMMYT-Asia lines and African DT donors AMDROUT1c3, AMDROUT2c3, AMDROUT(5x6)c3 AMDROUT1c2, AMDROUT2c2, AMDROUT(5x6)c2 AMDROUT1c1F2, AMDROUT1c2F2, AMDROUT2c2F2,

AMDROUT(5x6)c1F2, AMDROUT(5x6)c2F2

Early generation lines from above cycles of selection DH lines from the above cycles?

Genotyping Outputs

1215 SNP data of 175 advanced lines Genetic linkage maps of two populations viz.

AMDROUT1 and 2 Marker effects of SNPs for 4 bi-parental populations

Other Outputs

Proof of Concept publication on MARS-GWS method Trained scientists Cambridge Molecular Breeding Maize breeding Drought phenotyping Data management Visiting scientists On site visits Statistics, molecular breeding course planned

Looking further ahead: Movement of AMDROUT germplasm to farmers’ field

SWOT: What worked? An opportunity to learn and implement new technology

which promises to give higher genetic gain, especially under drought.

Main outputs from this project: yellow drought tolerant selection cycles starting from white African germplasm as donor. Yellow maize covers most of the Asian region, hence having such breeding material on hand again will ensure faster genetic gain. This output will be used in future breeding either as drought tolerant donor or for deriving inbred lines.

Excellent training opportunity (for field evaluation and data analysis) for collaborators.

CIMMYT locations continue to give excellent data, along with couple of other partner sites.

SWOT: What was difficult? There were issues with timely delivery of genotypic

data from KBioscience, UK; but this issue has been taken up and resolved.

Germplasm export to collaborators was slow and timely evaluation of trials was difficult.

Getting good heritability of grain yield was difficult in a lot of partner locations.

SWOT: What was difficult? An unforeseen insect attack by pollen eating blister beetles

(Cylidrothorax tenuicollis), hitherto unseen, almost derailed the recombination of AMDROUT1 and 2

Similar to a locust swarm

SWOT: What was difficult?

Cross selection was a challenge because tropical maize (unlike temperate maize) is very diverse (while temperate maize has a

narrower based and a better defined heterotic behavior)

has a shorter history of genetic improvement has inconsistent pedigree information has poorly maintained historical data

SWOT: What I would do different in the future?

Selection of breeding populations on observed heterosis (evaluation of 3-ways between the target populations and a tester panel) rather than extrapolated heterosis (which was done here through a Design II study); Heterotic partner known before inbreds are developed Direct use of observed heterosis Less reliance on extrapolation and historic information

which is often poorly managed

SWOT: What else could have been different?

Perhaps …….. Using multi-parent synthetics as the breeding

material (as opposed to the bi-parental populations used here). For tropical maize, the onus on selection of the best bi-parental crosses and the right testers is too huge a risk. This risk is magnified by working with few populations (4 in this case). Using multi-parent synthetics would have potentially reduced this risk.