Spatial and temporal variation in selection of
genes associated with varietal quantitative traits
in situ
Yves Vigouroux
I...
Ellis et al. 2010
History Database of the Global
Environment - HYDE
Tigo in Niger
1966 : Villages de Tigo et de Katanga (Image
corona)
2004 : Villages de Tigo et de Katanga (Image Spot 5)
Gé...
Global temperature changes
Observed changes at the end of the 20 centuries
Walther et al. 2002
Temperature
(°C)
Rainfall
(...
Observations of changes on plants
and animals
• Historic time series:
– Flowering time/nesting time
– Distribution changes...
Plasticity
Environment
Migration/
Colonization
Adaptation
Environment – temporal variation
Neutral allele: variation
associated with demographic
changes
Selected allele: variation
...
Environment
Samples
Field trial in a
common env.
Genetic
analysis
Difference
between
samples?
Differences
between
damples?...
Pearl millet : landrace settings
Study in Niger: stability of varieties
Besançon et al. 2009; Deu et al. 2010
Field trial: evolution to earliness
1976 2003
Mariac et al. 2006; Vigouroux et al. 2011
1976
2003
50-55 jours
55-60 jours
...
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 c...
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...
Study of genes associated with
phenotypic variations
• PHYTOCHROME C gene
-7,105 bp
Sb01g007830
0 bp
Sb01g007850
(PHYC)
-5...
Selection for precocity
Saïdou et al. 2009; Mariac et al. 2011, Vigouroux et al. 2011
Selection for precocity
FST
Global scal approach at the scale of a
whole country
Complex effect: environ. & human
Is there a local selection annually?...
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
G...
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
...
• Genotyping of PHYC allele & PgMADS11
gene
• Allele frequency variations?
Rainfall
isohyete
Longitude
0 2 4 6 8 10 12 14
...
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
2.0...
Maximum likelihood estimation
of effective size
• Microsatellite loci
• Estimate demographic effect
• Develop a simulation...
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 = 37...
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-...
Simulation
Estimation
• Selection estimated ~0.40
Results suggest a strong variability of selection spatially and
between years
Evenif strong selection : might concern few ...
Conclusion
• Results suggest a genetic basis of
adaptation/evolution in situ
• Results suggest a strong variability of
sel...
Thanks
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THEME – 4 Spatial and temporal variation in selection of genes associated with varietal quantitative traits in situ

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THEME – 4 Spatial and temporal variation in selection of genes associated with varietal quantitative traits in situ

  1. 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. 2. Ellis et al. 2010 History Database of the Global Environment - HYDE
  3. 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. 4. Global temperature changes Observed changes at the end of the 20 centuries Walther et al. 2002 Temperature (°C) Rainfall (%)
  5. 5. Observations of changes on plants and animals • Historic time series: – Flowering time/nesting time – Distribution changes of species/populations (& behavoir changes)
  6. 6. Plasticity Environment Migration/ Colonization Adaptation
  7. 7. Environment – temporal variation Neutral allele: variation associated with demographic changes Selected allele: variation associated with demographic changes and selection effects Differentiation FST
  8. 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. 9. Pearl millet : landrace settings
  10. 10. Study in Niger: stability of varieties Besançon et al. 2009; Deu et al. 2010
  11. 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. 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. 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. 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. 15. Selection for precocity Saïdou et al. 2009; Mariac et al. 2011, Vigouroux et al. 2011 Selection for precocity FST
  16. 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. 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. 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. 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. 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. 21. Maximum likelihood estimation of effective size • Microsatellite loci • Estimate demographic effect • Develop a simulation of neutral drift differentiation distribution
  22. 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. 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. 24. Simulation
  25. 25. Estimation • Selection estimated ~0.40
  26. 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. 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. 28. Thanks
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