Download Genomic Signatures of Climate and Soil Adaptation in a Widely

2/26/2014
Wide adaptation and diffusion in the cereal
crop sorghum (Sorghum bicolor)
Genomic Signatures of Climate and Soil
Adaptation in a Widely-diffused Crop
Durra: Semiarid climate
Guinea:
Humid
climate
• Extreme differentiation in:
• Architecture
• Phenology
• Secondary metabolites
Geoffrey Morris, Department of Agronomy, Kansas State University
PAG XXII – Population and Conservation Genomics
From diverse germplasm to crop improvement
From diverse germplasm to crop improvement
Diverse Crop Germplasm
Diverse Crop Germplasm
Genotyping-By-Sequencing
(GBS)
Genotype-Phenotype Map for Adaptive Trait
Legend:
Decades and
decades of
painstaking work by
plant breeders
Genome Wide Association
Studies (GWAS)
Genomic
Selection
(GS)
New Crop Varieties Better Adapted to
Current and Future Environments
Genetic Basis of Adaptive Traits
New Crop Varieties Better Adapted to
Current and Future Environments
Genotyping-By-Sequencing based dissection
of agroclimatic traits in sorghum
Functional alleles have striking distributions
Maturity1 (Morris et al. 2013 PNAS)
Inflorescence architecture, plant height, flowering time (Morris et al. 2013 PNAS)
LUG
Determines flowering:
- Photoperiod sensitive in tropics
- Photoperiod insensitive in subtropics
THE1
SP1
DFL2
LOM
3
ID TCP,TLK
CLV1
1 ID
1
BDE1,ID1
GDD
1
APO
1
Functional allele from
Murphy et al. 2011 PNAS
Can we identify functional alleles using geographic distributions?
Tannin1 (Morris et al. 2013 G3)
Inner seed coat tannins, Seed pigmentation, Plant pigmentation (Morris et al. 2013 G3)
Grain tannins defend against:
- Grain mold (wet, warm)
- Pre-harvest sprouting (wet, warm)
Tannin1
Functional allele from
Wu et al. 2011 PNAS
Ibraheem et al. 2010 Genetics
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Can we identify signals of environmental
adaptation directly (without phenotype)?
From diverse germplasm to crop improvement
Diverse Crop Germplasm
•
In wild accessions of Arabidopsis thaliana,
alleles found in a particular environment
GBS
predict fitness in that environment
– Hancock et al. 2011 Science
Genotype-Phenotype
Map for Adaptive Traits
– Fournier-Level et al. 2011 Science
Genome by Environmentof-Origin (GEO)
association map
GEO-GWAS
GWAS
•
What if an environmentally-adaptive trait can’t
GS
be phenotyped?
GEO-GS
Genetic Basis of Adaptive Traits
– Challenge phenotyping in the appropriate
environment
– Genotyping gets easier everyday, field-
New Crop Varieties Better Adapted to
Current and Future Environments
based phenotyping remains very
challenging
ICRISAT, Sudan
Genotyping-by-Sequencing (GBS) of global
source-identified sorghum accessions
Genome by Environment-of-Origin (GEO)
associations to predict adaptation
Neutral:
Adaptive
:
>400,000 SNPs genotyped
in >2,000 source-identified
accessions of African and
Asian origin
GEO-GS
(Identify
adapted
line)
GEO-GWAS
(Identify adaptive allele)
Charlotte Acharya, Katie Hyma, Sharon Mitchell, Ed Buckler (Cornell)
Analogous to the “Common-Disease Common-Variant” hypothesis of GWAS
Punna Ramu, Hari Upadhyaya, Tom Hash, Santosh Deshpande (ICRISAT)
Genebanks: GRIN, ICRISAT. GIS data: WorldClim, Global Agro-Ecological Zones (GAEZ).
GEO-GWAS maps the Tannin1 gene from
“Precipitation in the Warmest Quarter”
How much genotypic variation can be
explained by climate?
Arabidopsis
Sorghum
N accessions = 1819
Space
Climate
N locations = 1468
Space
Jesse Lasky
Columbia
University
Climate
colinear with
Space
Climate
colinear with
Space
Lasky et al. (2012) Molecular Ecology
4th highest peak at Tannin1
Climate
•
•
More variation is explained by
“Climate colinear with Space”
Space diffusion
Climate Ç Space
Climate
Rapid
of sorghum
along similar agroclimatic
zones?
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Is the climate-associated genomic
variation adaptive?
Explained by climate
Explained by climate independent of space
•
Aluminum toxicity is a serious limitation to crop
Al-tolerant
Al-sensitive
1.020
yields on acidic soils worldwide
1.02
•
A major effect Al-tolerance locus (AltSB) is cloned
in sorghum (Magalhaes et al. 2007 Nature
1.01
1.010
Genetics)
1.00
– Does a genome scan for alleles associated
with high-Al soils reveal AltSB (GEO-GWAS)?
0.99
1.000
•
0.98
0.990
Fold enrichment
Can GEO associations with soil Aluminum
predict Aluminum tolerance?
Worldwide sorghum diversity has been
phenotyped for Al-tolerance (Caniato et al. 2011,
PLoS ONE)
Intergenic
Synonymous
n=39,310
n=311,942
– Do alleles from high-Al soils predict observed
Non-synonymous
n=53,375
Al-tolerance phenotypes (GEO-GS)?
Magalhaes et al. 2004, Genetics
Method of Lasky et al. (2012) Molecular Ecology
GEO-GWAS: Does a genome scan for alleles
associated with high-Al soils reveal AltSB?
GEO-GS: Do alleles from high-Al soils predict
observed Al-tolerance phenotypes?
11th SNP is 75kb from AltSB
Aluminum
Tolerance GWAS
•
Relative Net Root
Growth (RNRG) in
Root growth
phenotypes
from Caniato et
al. 2011 (n=166)
Spearman ρ = 0.33
P < 10-5
Al-solution (n=166)
•
Prediction made
without phenotypes,
Observed
Al-Tolerance
or environment-oforigin for
Aluminum Toxicity
GEO-GWAS
phenotyped lines
47th SNP is 120kb from AltSB
GEO-GS prediction
Can GEO associations predict response to
terminal drought stress?
Sudan
India
Terminal Drought Stress
Experiment at UT-Austin
GEO-GS and GEO-GWAS: Flowering time
plasticity under terminal drought stress
Reduced seed set
3200 plants in rain-out
shelter (400 accessions )
Observed
Flowering
Plasticity
•
Spearman ρ = 0.15
P < 0.014
Terminal drought stress is typical for
Well-watered
many sorghum growing regions
•
Adapted varieties may show:
Terminal Drought
Senescence
– Stay-green (non-scenescent)
– Stable grain fill (yield)
Planting
GEO-GS prediction
Flowering Grain Fill Harvest
– Early or delayed flowering
Tom Juenger, Jason Bonnette (UT-Austin)
Stephen Kresovich, Zachary Brenton (Clemson)
Jesse Lasky
GEO-GWAS for
Growing Season
Length
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From diverse germplasm to crop improvement
Project team
Diverse Crop Germplasm
GBS
Genome by Environmentof-Origin (GEO)
association map
Integration
GEO-GWAS
Genotype-Phenotype
Map for Adaptive Traits
GWAS
GS
Stephen Kresovich, Zach Brenton
Ed Buckler, Katie Hyma, Sharon Mitchell, Charlotte Acharya
Punna Ramu, Tom Hash, Hari Upadhyaya, Santosh Deshpande
GEO-GS
Genetic Basis of Adaptive Traits
New Crop Varieties Better Adapted to
Current and Future Environments
Jesse Lasky
Crop
conservation
Tom Juenger, Jason Bonnette
NSF/Gates – Basic Research to Enable Agricultural Development (BREAD)
We’re Hiring,
Come talk to me!
www.MorrisLab.org
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