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

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)

Gérard B. Non publié

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 of species/populations (&

behavoir changes)

Plasticity

Environment

Migration/ Colonization

Adaptation

Environment – temporal variation

Neutral allele: variation associated with demographic changes

Selected allele: variation associated with demographic changes and selection effects

Differentiation FST

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

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 60-65 jours

65-70 jours

70-75 jours

75-80 jours

80+ 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 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

A change associated with climate

variation 1976 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

Flo

weri

ng t

ime

1976 2003

Rainfall 1950 to 1976

Rainfall 1977 to 2003

Mariac et al. 2006; Vigouroux et al. 2011

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

-lo

g (

P-v

alu

e)

Flowering time

Spike length

Basal spike diameter

Saïdou et al. 2009; Mariac et al. 2011, Saïdou et al. 2014

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?

Could we considered environ. effect

alone?

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

Lo

ng

itu

de

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

seeds leaves

We know: strong annual

variability

1.8 2 2.2 2.4 2.6 2.8 3 3.212.8

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

KouresudSandideye

TiloaKaina

TondibiaGorou Wankama

Yillade

340

370

400

430

460

490

520

550

580

610

640

670

700

7402008 2009

Rainfall in mm

• 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

Latitu

de

Genotype frequency

0 2 4 6 8 10 12 14

12

14

16

18

20

22

Latitu

de

Longitude

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

Lo

ng

itu

de

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

Maximum likelihood estimation

of effective size • Microsatellite loci

• Estimate demographic effect

• Develop a simulation of neutral drift

differentiation distribution

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

Fre

qu

en

cy

0.0

0.2

0.4

0.6

0.8

Fst emp

Fst sim.

FST

Selection effect suggest on this gene

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

Simulation

Estimation

• Selection estimated ~0.40

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

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

Thanks