1. Spatial and temporal variation in selection of
genes associated with varietal quantitative traits
in situ
Yves Vigouroux
Institut de Recherche pour le Développement
Montpellier, France
International Workshop on
“Applied Mathematics and Omics Technologies for Discovering Biodiversity and Genetic Resources for
Climate Change Mitigation and Adaptation to Sustain Agriculture in Drylands”
Rabat - Morocco, 24-27 June 2014

2. Ellis et al. 2010
History Database of the Global
Environment - HYDE

3. Tigo in Niger
1966 : Villages de Tigo et de Katanga (Image
corona)
2004 : Villages de Tigo et de Katanga (Image Spot 5)
Gérard B. Non publié

4. Global temperature changes
Observed changes at the end of the 20 centuries
Walther et al. 2002
Temperature
(°C)
Rainfall
(%)

5. Observations of changes on plants
and animals
• Historic time series:
– Flowering time/nesting time
– Distribution changes of species/populations (&
behavoir changes)

6. Plasticity
Environment
Migration/
Colonization
Adaptation

7. Environment – temporal variation
Neutral allele: variation
associated with demographic
changes
Selected allele: variation
associated with demographic
changes and selection effects
Differentiation
FST

8. Environment
Samples
Field trial in a
common env.
Genetic
analysis
Difference
between
samples?
Differences
between
damples?
Population
demographic
effect?
Selection effect?
Temporal
variation of
climate

9. Pearl millet : landrace settings

10. Study in Niger: stability of varieties
Besançon et al. 2009; Deu et al. 2010

11. Field trial: evolution to earliness
1976 2003
Mariac et al. 2006; Vigouroux et al. 2011
1976
2003
50-55 jours
55-60 jours
60-65 jours
65-70 jours
70-75 jours
75-80 jours
80+ jours

12. 50-55 days
55-60 days
60-65 days
65-70 days
70-75 days
75-80 days
80+ days
Flowering time
1976
2003
Plant height
170-185 cm
185-200 cm
200-215 cm
215-230 cm
230-245 cm
245+ cm
Spike lenght
20-35 cm
35-50 cm
50-65 cm
65-80 cm
80-95 cm
95+ cm
P<0.001 P<0.001 P<0.001
Vigouroux et al. 2011

13. A change associated with climate
variation1976 2003
1976
2003
50-55 days
55-60 days
60-65 days
65-70 days
70-75 days
75-80 days
80+ days
40
50
60
70
80
200 400 600 800 1000
Annual rainfall
Floweringtime
1976
2003
Rainfall 1950 to 1976
Rainfall 1977 to 2003
Mariac et al. 2006; Vigouroux et al. 2011

14. Study of genes associated with
phenotypic variations
• PHYTOCHROME C gene
-7,105 bp
Sb01g007830
0 bp
Sb01g007850
(PHYC)
-5,373 bp
Sb01g007840
25,828 bp
Sb01g007870
54,317 bp
Sb01g007878
Sorghum
bicolor
90,839 bp
Sb01g007870
-log(P-value)
Flowering time
Spike length
Basal spike diameter
Saïdou et al. 2009; Mariac et al. 2011, Saïdou et al. 2014

15. Selection for precocity
Saïdou et al. 2009; Mariac et al. 2011, Vigouroux et al. 2011
Selection for precocity
FST

16. Global scal approach at the scale of a
whole country
Complex effect: environ. & human
Is there a local selection annually?
Could we considered environ. effect
alone?

17. Sampling
13.00
13.20
13.40
13.60
13.80
14.00
14.20
2.00 2.20 2.40 2.60 2.80 3.00 3.20
Latitude
Longitude
GO
TO
DE
GU
IHJ
GAR
KA
BI
WA
YI
TI
GAs
DI
SA
AL
GAm
AT
17 fields, over two years
100 seedlings+100 seeds /site/an
~7000 individuals
seedsleaves

18. We know: strong annual
variability
1.8 2 2.2 2.4 2.6 2.8 3 3.2
12.8
13
13.2
13.4
13.6
13.8
14
14.2
12.8
13
13.2
13.4
13.6
13.8
14
14.2
1.8 2 2.2 2.4 2.6 2.8 3 3.2
Alkama
Ataloga
Billingol
DeberiGati
Diribangou
fandoubery2 GassanKournie
Gamonzon
GardamaKouaraGorougoussa
Guilahel
IHJachere
Kare
Kouresud
Sandideye
TiloaKaina
TondibiaGorou Wankama
Yillade
340
370
400
430
460
490
520
550
580
610
640
670
700
7402008 2009
Rainfall in mm

19. • Genotyping of PHYC allele & PgMADS11
gene
• Allele frequency variations?
Rainfall
isohyete
Longitude
0 2 4 6 8 10 12 14
12
14
16
18
20
22
Latitude
Genotype frequency
0 2 4 6 8 10 12 14
12
14
16
18
20
22
Latitude
Longitude

20. 13.00
13.20
13.40
13.60
13.80
14.00
14.20
2.00 2.20 2.40 2.60 2.80 3.00 3.20
13.00
13.20
13.40
13.60
13.80
14.00
14.20
2.00 2.20 2.40 2.60 2.80 3.00 3.20
Latitude
Longitude
GO
TO
DE
GU
IHJ
GAR
KA
BI
WA
YI
TI
GAs
DI
SA
AL
GAm
AT
Evolution de la fréquence de l’allée de
précocité de PHYC

21. Maximum likelihood estimation
of effective size
• Microsatellite loci
• Estimate demographic effect
• Develop a simulation of neutral drift
differentiation distribution

22. 0.0025 0.0125 0.0225 0.0325 0.0425 0.0525 0.0625 0.0725
Histogram of simulated and empirical Fst : Diribangou 2008 Ne = 378
Fst Values
Frequency
0.00.20.40.60.8
Fst emp
Fst sim.
FST
Selection effect suggest
on this gene

23. Assessment of selection
• Use of approximate bayesian approaches
• AA (1-q)2/(2hsq(q-1)+1-sq2)
• Aa 2q(1-q) /(2hsq(q-1)+1-sq2)
• aa q2/(2hsq(q-1)+1-sq2)
• Effect of drift (Ne), sampling (n) and
selection (s) with q allele frequency of a

24. Simulation

25. Estimation
• Selection estimated ~0.40

26. Results suggest a strong variability of selection spatially and
between years
Evenif strong selection : might concern few fields a given
year
Effect of seed flow from other fields = human effect
Effect of human selection on panicles

27. Conclusion
• Results suggest a genetic basis of
adaptation/evolution in situ
• Results suggest a strong variability of
selection on a year to year basis but also
spatially

28. Thanks