Rhoné, Bénédicte (2008) Genetic mechanisms involved in climatic adaptation of experimentally evolving populations of bread wheat. PhD thesis Science de la vie, UMR INRA/Univ. Paris-Sud/CNRS/AgroParisTech, AgroParistech 2008AGPT0018 p.230.

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Abstract

Local adaptation resulting from selection pressure acts on heritable characters and is a major

force shaping the phenotypic diversity of natural populations. Currently, numerous questions

exist surrounding the impact of selection on the evolution of genes involved in the structure of

adaptive traits, which are often complex characters involving many interacting genes.

The objective of this thesis is to identify certain genetic mechanisms which are activated

during the adaptation of experimental wheat populations to different climactic contexts. The

adaptive trait studied was flowering time, which permits the plant to synchronize reproduction

with favorable seasonal conditions. The experimental populations considered had a common

genetic origin and have evolved independently since 1984 in different sites in France, without

conscious human selection or migration, but subject to the influence of natural selection and

genetic drift. Using a base of knowledge on genes implicated in flowering in Arabidopsis

thaliana and rice, and recent publications on wheat, the evolution of nucleotide

polymorphisms in candidate genes was followed during 12 generations (2, 7 and 12) in three

experimental populations (Vervins in the north of France, Le Moulon in the Parisian region

and Tolouse in the South). These populations were also characterized for precocity of

flowering time measured under different day length and vernalization regimes (duration of

exposure to low temperatures) and for diversity of microsatellite loci sampled from

throughout the genome. The comparison of levels of genetic differentiation among

populations for these three measures of genetic diversity showed that precocity was subject to

divergent selection from the first generations. However, it appears that this selection was not

directly for flowering time, but instead achieved through indirect selection on correlated traits

in the different environments, such as plant height or grain weight. Selection for precocity

can be related to climactic characteristics of the experimental locations, with the northern

populations flowering later than the southern population. This rapid evolution of the trait

accompanied significant changes in allele frequencies for major genes involved in flowering

time, and the development of specific multi-locus allelic combinations in the different

climatic contexts considered. This evolution did not diminish the existing within-population

genetic diversity because multiple combinations were favored in the different populations.

The work presented in this thesis is an important contribution to our understanding of the

maintenance of evolutionary potential in cultivated species.

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Table of content

CHAPITRE I : INTRODUCTION 4

I-1 L'adaptation comme moteur de l'évolution 4

I-1.1 Définitions et exemples 4

I-1.2 Intérêt d'étudier l'adaptation 5

I-2 Comprendre les mécanismes génétiques de l'adaptation 6

I-2.1 Dissection des bases génétiques de l'adaptation 6

I-2.1.1 Architecture des caractères quantitatifs adaptatifs 7

I-2.1.2 Détection de la sélection 9

I-2.1.3 Combinaisons de plusieurs informations 11

I-2.2 Des avancées, mais encore de nombreuses questions 11

I-2.2.1 Nombre et effets des gènes impliqués dans l’adaptation 12

I-2.2.2 « Standing genetic variation » ou nouvelles mutations ? 13

I-2.2.3 Rôle de la pléiotropie 15

I-2.2.4 Rôle de l’épistasie 15

I-2.2.5 Type des mutations préférentiellement sélectionnées 16

I-2.2.6 Conclusions 16

I-3 Etude de l'adaptation locale dans des populations expérimentales de blé héxaploïde : exemple de la précocité de floraison 17

I-3.1 Présentation des populations expérimentales de gestion dynamique 17

I-3.1.1 Principe des populations 17

I-3.1.2 Principaux résultats 18

I-3.3 Pourquoi s’intéresser à la précocité de floraison en particulier ? 20

I-3.3.1 La précocité de floraison, un caractère adaptatif majeur. 20

I-3.3.2 L’architecture du caractère chez le blé 21

I-3.3.3 Déterminisme bien connu pour des espèces modèles tels le riz ou Arabidopsis thaliana 21

I-4 Objectifs et plan de la thèse 24

CHAPITRE II : MATERIEL ET METHODES 26

II-1. Matériel végétal 26

II-1.1 Conduite des populations de gestion dynamique 26

II-1.2 Echantillonnage 27

II-1.3 Constitution du matériel d'étude 27

II-2. Dispositif expérimental pour la caractérisation phénotypique des populations 28

II-2.1 Estimation de la précocité de floraison au champ et sous différentes conditions de vernalisation en pépinière 28

II-2.2 Estimation des composantes de la précocité à partir des différents traitements 32

II-2.3 Estimation des composantes de la valeur sélective 33

II-3. Marquage microsatellite des populations de GD 34

II-3.1 Extraction 34

II-3.2 Choix des marqueurs 34

II-3.3 Génotypage et acquisition des résultats 36

II-4 Génotypage des gènes candidats 36

II-4.1 Révélation du polymorphisme de VRN-1 36

II-4.2 Révélation du polymorphisme de Ppd-1 37

II-4.3 Génotypage de FT 38

II-4.4 Génotypage de LD, CO et GI 38

CHAPITRE III : SUIVI DE L'EVOLUTION DES MARQUEURS NEUTRES DU GENOME DANS LES POPULATIONS DE GESTION DYNAMIQUE 41

III-1 Introduction 41

III-2. Méthodes 45

III-2.1 Diversité 45

III-2.2 Taux d'allo-fécondation 45

III-2.3 Structuration spatiale et temporelle 47

III-2.4 Variations de fréquences alléliques et effectifs efficaces 47

III-2.5 Déséquilibre de liaison 49

III-2.6 Reconstruction d'haplotypes multilocus 50

III-3 Résultats 52

III-3.1 Diversité génétique, apparition de nouveaux allèles 52

III-3.2 Différenciation spatiale 54

III-3.3 Variations temporelles des fréquences alléliques et effectifs efficaces 55

III-3.4 Régime de reproduction 56

III-3.5 Evolution du DL et génotype multilocus 57

III-4. Discussion 65

III-4.1 Régime de reproduction 65

III-4.2 Régime de reproduction et effectif efficace 68

III-4.3 Régime de reproduction et déséquilibre de liaison 69

III-4.4 Nouveaux allèles : mutation ou migration ? 71

III-4.5 Cas particulier de la population de Vervins 73

III-5 Conclusions 75

CHAPITRE IV: EVOLUTION DES CARACTERES QUANTITATIFS: PRECOCITE DE FLORAISON ET COMPOSANTES DE LA VALEUR SELECTIVE 77

IV-1 Introduction 77

IV-2 Méthodes 80

IV-2.1 Estimation des variances environnementales 81

IV-2.2 Evolution des caractères au cours des générations dans chaque population 84

IV-2.2.1 Evolution phénotypique des caractères 84

IV-2.2.2 Caractérisation de la variabilité génétique intra population des caractères 85

IV-2.3 Caractérisation de la variabilité génétique inter populations des caractères : mise en évidence de la sélection. 86

IV-2.4 Estimation de la sélection directionnelle directe et indirecte : approche multivariée 87

IV-2.4.1 Estimation des gradients de sélection directionnelle observés dans les conditions "champ" au Moulon. 87

IV-2.4.2 Estimation des gradients de sélection attendus dans des contextes variant pour les besoins en vernalisation 89

IV-3. Résultats 91

IV-3.1 Evolution phénotypique de la précocité et des composantes de la valeur sélective au champ 91

IV-3.2 Evolution de la variabilité intra population pour les caractères mesurés au champ 93

IV-3.3 Détection de la sélection 95

IV-3.4 Corrélations entre précocité et composantes de la valeur sélective : estimation des gradients de sélection. 96

IV-3.5 Estimation des gradients de sélection attendus en conditions différentes pour la durée de vernalisation. 97

IV-3.6. Evolution des composantes de la précocité de floraison 99

IV-3.6.1 Evolution des composantes de la précocité dans les populations 99

IV-3.6.2 Evolution des corrélations entre mesures de précocité 102

IV-4 Discussion 105

IV-4.1 Evolution de la précocité: mise en évidence de la sélection divergente 105

IV-4.2 Les forces de sélection agissant sur la précocité en relation avec les composantes de la valeur sélective 108

IV-4.3. La précocité évolue en fonction des caractéristiques climatiques de chaque site 110

IV-5 Conclusions 115

CHAPITRE V: EVOLUTION CONJOINTE DES CARACTERES QUANTITATIFS, DES MARQUEURS MICROSATELLITES ET DES GENES CANDIDATS DE PRECOCITE 116

V-1 Introduction 116

V-2 Relations entre l’évolution du gène majeur de la voie de la vernalisation et l’évolution de la sensibilité à la vernalisation 117

V-3 Détection de la sélection des gènes candidats pour la précocité de floraison 135

V-4 Conclusions 178

CHAPITRE VI : CONCLUSIONS ET PERSPECTIVES 179

VI-1 Etude de l’évolution conjointe des marqueurs microsatellites, de la précocité de floraison et des gènes candidats : synthèse des principaux résultats 179

VI-2 Apports et limites de l’étude dans la compréhension des bases génétiques de l’adaptation 181

VI-2.1 Les apports de l’étude 181

VI-2.1.1 Effets des gènes sélectionnés 181

VI-2.1.2 Standing genetic variation vs. mutation 181

VI-2.1.3 Pléiotropie 182

VI-2.1.4 Rôle de l’épistasie 182

VI-2.1.5 Type de mutations 183

VI-2.2 Les limites 184

VI-2.3 Les nouvelles interrogations 185

VI-2.3.1 Allogamie 185

VI-2.3.2 Polyploïdie 186

VI-3 Implications pour la conservation dynamique des ressources génétiques du blé 187

BIBLIOGRAPHIE 188

ANNEXES 199

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