Analysis Of Developmental Plasticity Of Rice Panicle In Response To Plant C Source Sink Balance Case Study Of Qtsn Isolines

DEWI ERIKA ADRIANI

ANALYSIS OF DEVELOPMENTAL PLASTICITY OF RICE

PANICLE IN RESPONSE TO PLANT C SOURCE-SINK

BALANCE: CASE STUDY OF

QTSN

ISOLINES

GRADUATE SCHOOL

BOGOR AGRICULTURAL UNIVERSITY BOGOR

MONTPELLIER SUPAGRO

2 PLACE VIALA, 34060 MONTPELLIER CEDEX 1 FRANCE

ATTESTATION OF ORIGINALITY, PROPER CITATION

AND COPYRIGHT DELEGATION*

I declare that the PhD thesis entitled ―Analysis of Developmental Plasticity of Rice Panicle in response to plant C source-sink balance. Case study of qTSN isolines‖ is the result of my own work under the supervision of a supervisor committee and is not being concurrently submitted in candidature for any degree. All sources have been cited from published or unpublished works by other authors have acknowledged by means of text citation and complete references.

Herewith I delegate copyright of my manuscript to Bogor Agricultural University, Indonesia and Montpellier SupAgro, France.

Bogor, January 2016 Dewi Erika Adriani Registration number A262107061

RINGKASAN

Perkembangan malai padi meliputi pembentukan percabangan, elongasi cabang dan penyebaran gabah. Proses-proses penting tersebut dibentuk selama fase reproduktif, yaitu periode antara inisiasi malai dan pembungaan. Proses ini merupakan fokus utama yang sedang diteliti dan menjadi pusat perhatian para pemulia tanaman dengan tujuan untuk memperbaiki potensi hasil dengan cara memperbesar ukuran malai. perkembangan malai padi tidak hanya memiliki sumber keragaman yang besar, proses ini juga peka terhadap interaksi antara genotipe dan lingkungan. Penelitian untuk menganalisis kontrol genetik dan lingkungan terhadap morfologi tanaman telah banyak dilakukan, namun demikian plastisitas yang berhubungan dengan arsitektur malai dan ―trade-offs‖ antar karakter dalam responnya terhadap ukuran malai masih sedikit dipahami.

Penelitian ini membahas respon komponen malai padi terhadap akses tanaman terhadap cahaya yang kontras dari Near Isogenic Lines (NILs) pada kultivar IR64 dan IRRI146, pembawa QTL qTSN4 atau qTSN12 untuk ukuran malai besar beserta tetuanya. Sebelumya telah dilaporkan bahwa QTL qTSN4 (gen SPIKE) menunjukkan ukuran daun bendera yang lebih besar dan jumlah gabah per malai yang lebih banyak, dengan semacam ―trade-off‖ terrhadap jumlah malai, dan secara konsisten terkait dengan hasil gabah lebih tinggi dalam kondisi lingkungan yang menguntungkan. Meskipun QTL ini terlihat menjanjikan dalam arti dapat meningkatkan kapasitas source dan sink tanaman padi, pengaruhnya terhadap fungsi seluruh tanaman belum diteliti dan dapat membawa ke penemuan-penemuan yang relatif menarik terhadap kontrol plastisitas malai.

Tujuan penelitian ini adalah untuk menganalisis plastisitas morfologi malai padi dalam hal dimensi, jumlah gabah, jumlah cabang dan panjang cabang serta determinasinya dengan mmpertimbangkan morfogenesis dan laju pertumbuhan tanaman keseluruhan yang menghasilkan interaksi source-sink. Akses tanaman terhadap cahaya yang kontras diimplementasikan dalam penelitian ini untuk mengatur kondisi pertumbuhan yang berpengaruh kuat terhadap ukuran malai. Hal ini dilakukan melalui pemberian kondisi cahaya penuh (kontrol) dan naungan di rumah kaca yang dilakukan di Montpellier, Prancis dan perlakuan populasi tanaman yang berbeda di lapangan (kerapatan normal dan kerapatan tinggi) dan di rumah kaca (kerapatan normal dan renggang) dilakukan di IRRI, Filipina. Luaran dari penelitian ini adalah informasi yang dapat memberikan pemahaman yang lebih mendalam terhadap karakter-karakter yang membatasi produktivitas , yaitu i) variasi genetik, dan ii) plastisitas fenotipik dalam respon terhadap hubungan C source-sink tanaman.

Pengaruh qTSN terhadap ukuran malai dikonfirmasi dalam penelitian ini melalui peningkatan panjang cabang total dan jumlah cabang serta gabah. Peningkatan ini terkait dengan meningkatnya ukuran organ yang berada di posisi bagian atas dari batang, yaitu luas tiga hingga empat daun teratas dan juga diameter potongan melintang tiga hingga empat ruas teratas. Hasil penelitian juga menunjukkan bahwa tidak hanya luas individu daun, tapi juga laju fotosintesis, cadangan pati dan kandungan N daun lebih tinggi sedangkan Specific Leaf Area (SLA) lebih rendah. Penelitian ini menunjukkan bahwa penghentian pembentukan anakan terjadi lebih awal sebelum inisiasi malai sebagai akibat adanya QTL, yang berhubungan dengan meningkatnya laju pertumbuhan batang utama, dan

mengindikasikan sebagai pengendali dari lebih tingginya keragaan batang utama yang terdeskripsi lebih awal.

Namun demikian, keseluruhan tampilan alel qTSN pada tingkat batang utama tidak serta merta dapat diamati pada tingkat tanaman, karena adanya pengaruh terhadap karakter morfologi tanaman lainnya, seperti trade-off antara ukuran dan jumlah malai, dan ukuran malai bukan resipien fenotifik utama dari QTL ini. Kenyataannya, variasi dalam ukuran malai tampaknya berhubungan dengan laju pertumbuhan batang sebelum pembungaan, yang menjelaskan adanya beberapa interaksi GxE terhadap ukuran malai. Sebagaimana yang dapat diamati dalam penelitian ini dan dilaporkan dalam literatur, nilai tambah qTSN juga tergantung pada praktek budidaya (radiasi matahari, ketersediaan N, kedalaman solum tanah). Dengan demikian, qTSN4 dan qTSN12 tidak berdiri sendiri sebagai sumber perbaikan potensi hasil karena interaksi GxE dan kompensasi peningkatan ukuran malai oleh plastisitas adaptif dari karakter morfologi lainnya.

Kata kunci: qTSN4, qTSN12, plastisitas malai, kontras akses terhadap cahaya, vigor batang sebelum pembungaan, interaksi GxE

SUMMARY

Rice panicle development consists of branching, branch elongation and spikelet deployment. These elemental processes are established during the reproductive phase, between panicle initiation and heading. They are actually under-going major focus as they are the center of attention of breeders who aim at improving yield potential through larger panicles. Indeed, they are source of great diversity but are also prone to Genotype x Environment interactions. Numerous studies analyzed genetic and environment control of plant morphology, however the associated plasticity of panicle architecture and trade-offs between traits in response to larger panicles are less well understood.

This study addressed the response of rice panicle components to contrasted plant access to light of near isogenic lines (NILs) of IR64 and IRRI146 backgrounds, carrying QTL qTSN4 or qTSN12 for large panicle, and their parental lines. The QTL qTSN4 (SPIKE gene) had been reported in the IRRI farm, Philippines, exhibiting larger flag leaf and greater spikelet number, with a likely trade-off on panicle number, and consistently associated with higher grain yield under favorable environments. Although this QTL seems promising in terms of increasing source and sink capacity of the rice plant, its effect on the whole plant functioning has not been investigated and should lead to interesting findings relative to the control of panicle plasticity.

The present work aimed at analyzing the plasticity of the rice panicle morphology in terms of dimension, spikelet and branch number, and branch length, and its determinants with respect of the whole plant morphogenesis and growth rate, and the resulting C source-sink interactions. In order to set up growing conditions having a strong effect on the panicle size, contrasted plant access to light was implemented through full light and shading conditions in the greenhouse in Montpellier, France, and distinct plant populations in the field (normal and high plant density) and in the greenhouse (normal plant population and isolated plants) at IRRI, Philippines. The outputs of this PhD thesis expect to provide further insights on the traits subtending i) genetic variation and , ii) phenotypic plasticity in response to plant C source-sink relationships.

The effect of qTSN on panicle size was confirmed here through higher total branch length, and branch and spikelet number. This enhancement was associated with the increase of the size of organs located at the upper positions on the stem, i.e. the area of the top three-to-four leaves but also the cross-section of the top three-to-four internodes. It was also demonstrated that, not only individual leaf area, but also the photosynthetic rate, the starch reserves and the leaf N content were higher, and the SLA lower. Interestingly, an early tiller cessation was observed before panicle initiation (PI) in the presence of QTL which was correlated with higher main stem growth rate and which is likely the driver of the higher performance of the main stem described earlier.

Ultimately, however, the overall performance of the qTSN allele at main tiller level was not consistently reported at crop level as effects on other plant morphological traits, like trade-offs between panicle size and number, were observed, and panicle size was not the primary phenotypic recipient of these QTLs. In fact, the variation in panicle size appeared to be related to pre-floral stem growth rate, explaining some of the G x E interactions on panicle size. As

observed in this study and reported in the literature, the added value of qTSN also depends on the cultural practices (radiation, N supply, soil depth). Therefore, the qTSN4 and qTSN12 do not appear as a standing-alone source of yield potential improvement because of G x E interactions and compensation of the increased panicle size by the adaptive plasticity of other morphological traits.

Key words: qTSN4, qTSN12, panicle plasticity, contrasted access to light, pre-floral stem vigor, GxE interactions

RESUME

Le développement de la panicule de riz inclut l‘initiation des branches, leur allongement et le développement des épillets. Ces processus élémentaires ont lieu pendant la phase reproductives, entre l‘initiation paniculaire et l‘épiaison. Ils sont actuellement le centre d‘attention des programmes de sélection qui visent à augmenter le potentiel de rendement grâce à des panicules plus grosses. De fait, les caractéristiques de la panicule sont caractérisées par une large diversité phénotypique mais sont aussi sujettes aux interactions Génotype x Environnement. Bien que de nombreuses études se soient intéressées au contrôle génétique et environnemental de la morphologie de la plante, la plasticité de l‘architecture paniculaire et les compensations entre caractères en réponse à l‘accroissement de la panicule ont été peu analysées.

Cette étude a analysé la réponse des caractères décrivant la panicule à des conditions d‘accès à la lumière contrastées de lignées isogéniques (NILs) de fond génétique IR64 et IRRI146 enrichies des QTLs qTSN4 ou qTSN12 codant pour une panicule plus grosse, et de leurs lignées parentales. Le QTL qTSN4 (gène SPIKE) a été associé, au cours d‘essais à l‘IRRI, Philippines, à une feuille drapeau plus large et un nombre de grains plus important, mais aussi à une éventuelle compensation sur le nombre de panicules, pour un rendement plus élevé en conditions favorables (Fujita et al, 2012, 2013). Bien que ce QTL soit prometteur en termes d‘augmentation des capacités source et puits, son effet n‘a pas été étudié à l‘échelle de la plante entière et devrait pourtant conduire à des résultats intéressants concernant le contrôle de la plasticité de la panicule.

Ce travail vise à analyser la plasticité de la morphologie de la panicule de riz en termes de dimension, de nombre d‘épillets et de branches, et de la longueur des branches, et de ses déterminants en lien avec la morphogénèse, le taux de croissance et les interactions source:puits de la plante entière. Dans le but d‘analyser la plasticité de la panicule en réponse à l‘environnement, les plantes ont été cultivées en conditions contrastées d‘accès à la lumière soit par de l‘ombrage, en serre à Montpellier, soit par des densités de plantes différentes au champ (normales et élevées) et en serre (normales et faibles) à l‘IRRI, aux Philippines. Les sorties de ce travail visent à fournir une meilleure compréhension des caractères expliquant la diversité génétique et la plasticité phénotypique en réponse aux relations source:puits en C dans la plante.

L‘effet du qTSN sur la taille de panicule a été confirmé sur la base de la longueur totale de branches, et du nombre de branches et d‘épillets. Cet accroissement a été associé avec l‘augmentation de la taille des organes situés aux positions supérieures de la tige, c.a.d la surface des 3-4 feuilles supérieures mais aussi la section des 3-4 entre-nœuds supérieurs. Il a été démontré que, non seulement la taille de la feuille individuelle, mais aussi le taux de photosynthèse, les réserves en amidon et la teneur en N de la feuille étaient plus élevées, et la surface foliaire spécifique plus faible. Il est à noter qu‘un arrêt précoce du tallage a été observé avant l‘initiation de la panicule en présence du QTL, qu‘il a été corrélé au taux de croissance de la tige principale, et qu‘il est suggéré être le moteur de la performance supérieure de la tige principale comme décrite plus haut.

De manière plus intégrée, la performance globale de l‘allèle qTSN à l‘échelle de la tige principale n‘a pas été confirmée de manière constante à l‘échelle de la plante entière puisque des effets sur d‘autres caractères morphologiques de la plante, comme la compensation entre la taille de la panicule et leur nombre, ont été observés et que la taille de la panicule n‘a pas été la cible phénotypique première de ce QTL. En fait, la variation de la taille de la panicule apparaît comme la conséquence du taux de croissance de la tige pendant la phase reproductive, expliquant ainsi les interactions G x E observées sur la taille de panicule. Comme montré au cours de cette étude, et publié dans la litérature, la valeur ajoutée du qTSN dépend aussi des pratiques culturales (rayonnement, fertilisation, profondeur de sol). De fait, le qTSN4 et qTSN12 n‘apparaissent pas comme une source directe d‘augmentation du potentiel de rendement car les interactions G x E et la compensation de la taille de la panicule par la plasticité d‘autres caractères morphologiques.

Mots clés : qTSN4, qTSN12, plasticité paniculaire, accès à la lumière contrasté, vigueur pré-florale de la tige, interactions G x E

ANALYSIS OF DEVELOPMENTAL PLASTICITY OF RICE

PANICLE IN RESPONSE TO PLANT C SOURCE-SINK

BALANCE: CASE STUDY OF

QTSN

ISOLINES

DEWI ERIKA ADRIANI

DISSERTATION For obtaining the degree of

DOCTOR at

Study Program Agronomy and Horticulture Biologie Intégrative des Plantes

GRADUATE SCHOOL

BOGOR AGRICULTURAL UNIVERSITY BOGOR

MONTPELLIER SUPAGRO

2 PLACE VIALA, 34060 MONTPELLIER CEDEX 1 FRANCE

Examiners at close defense : 1. Dr Bruno Andrieu

INRA, Agro ParisTech, France 2. Dr Suwarno

Indonesia Rice Research Center 3. Dr Nobuya Kobayashi

Japan International Research Center for Agricultural Sciences

4. Dr Buang Abdullah

Indonesia Rice Research Center

Examiners at promotion : 1. Prof Dr Didy Sopandie

Department of Agronomy and Horticulture, Bogor Agricultural University

2. Dr Suwarno

© Bogor Agricultural University and Montpellier SupAgro,

2016

Copyright is protected by law

Citing and quoting this manuscript in part or in whole is prohibited without proper referencing. Citation is strictly limited for academic purposes, scientific research and report paper, or critical review, and inflict no intellectual property loss for Bogor Agricultural University and Montpellier SupAgro.

Publication and multiplication of this manuscript in part or in whole in any form is prohibited without written permission from Bogor Agricultural University and Montpellier SupAgro.

PREFACE

Syukur Alhamdulillahirabbilalamin, grateful to Allah Subhanahu Wa Ta `ala for His blessing so that this manuscript could be done. Research topic choosen is a promising subject for agronomy, physiology, genetics and breeding studies. As the rice panicle development is a key in yield improvement which its morphogenesis does not much addressed and thus the relationship to pre-floral stage, in particular under sub optimal conditions those mainly become a problem in paddy field in the tropics and sub tropics.

This work could not be accomplished without support from the supervisors, research team, colleagues, friends and family members. The author would like to gratitude to:

1. Prof Dr Sudirman Yahya, Dr Sudradjat, Dr Suwarto as supervisors committee from IPB for the suggestions, advices, support during a long period of PhD. 2. Dr Delphine Luquet and Dr Tanguy Lafarge as supervisors committee from

Montpellier SupAgro, for counted me in PAM (Phenotypic and Adaptation of Monocots) team, CIRAD, for the advices, assist, understanding and support during ―not easy-three years period‖ in France.

3. All jury members who evaluated and approved my manuscript. Thank you for the external examiners: Dr Suwarno, Dr Bruno Andrieu, Dr Buang Abdullah, Dr Nobuya Kobayashi and Prof Dr Didy Sopandie for the suggestions and corrections.

4. Dr Michael Dingkuhn and all phenotyping team members in CESD (Crop and Environment Science Division), IRRI, Philippines for the advices, support and courage to pass my ―collapsed-period‖ in IRRI.

5. Dr Tsutomu Ishimaru in PBGB (Plant Breeding and Genetics and Biotechnology), IRRI, who provided the seed materials for all my experiments and as collaborator in field experiment.

6. Dr Stefan Jouannic (IRD, France), Prof Dr Xinyou Yin (Wageningen University) and Dr Dominique This (Montpellier SupAgro) for advices and suggestions as thesis committee members in Montpellier SupAgro.

7. Dr Naresworo, Prof Dr Nahrowi and Dr Irwan Katili as PiC of double degree program and Dr Didier Pillot from Agreenium for help and mediation for this program since the beginning until the end of my PhD.

8. Prof Dr Munif Ghulamahdi and Dr Maya Melati as head of study program of Agronomy and Horticulture, Bogor Agricultural University and the staff. 9. Faculty of Agriculture, University of Lambung Mangkurat for

recommendation and support the PhD.

10. Directorate General of Higher Education of Indonesia, Campus France, Agreenium and CIRAD for PhD scholarships.

11. My office-mates in PAM team, who already became a ―Dr‖, Sébastien Peraudeau for help, discussion and sharing knowledge about rice; and Lisa Perrier for help and sympathy.

12. PAM team: Audrey, Béatrice, Sandrine, Denis, Anne, Sylfie, Alain and all of you who I cannot mention one by one. Thank you for always be there and give your hand.

13. Friends: graduate students of Agronomy and Horticulture (Forsca AGH) and double degree group 2010, thank you for the support and togetherness for the first two years in IPB; Indonesian student association in Montpellier (Perhimpunan Pelajar Indonesia di Montpellier = PPIM), thank you for becoming a family, sharing the happiness and sadness as we are all away from home; around the world-friends in IRRI, thank you for the support, cheerful and discussion about lab/field work at dinner time in cafeteria. All of you had colored my days and enriched my experience in every phase of my PhD.

14. Finally my beloved husband RM Cahyo Wiryanto, my kids Annisa Yorikasyifa Maharani and M Indra Arrafi Adn, my beloved parents and all families for everlasting support, the understanding, patience and sincerity during my PhD

Hopefully this PhD work would be benefits to the science particularly in agronomy, physiology and breeding.

Bogor, January 2016 Dewi Erika Adriani

TABLE OF CONTENTS

1 INTRODUCTION 1

2 PROBLEMATIC AND STATE OF THE ART 3

Rice Development and Growth Cycle 3

Vegetative Phase 3

Reproductive Phase 4

Ripening Phase 5

Rice Panicle Development 5

Phenotypic Plasticity of Rice 6

Phenotypic Plasticity of Ppanicle Development and Architecture 7

Challenges in Breeding for Panicle Size 8

3 OBJECTIVES, OVERVIEW OF THE CHAPTERS AND THE METHODOLOGY 9 Methodological overview 10 References 13 4 RICE PANICLE PLASTICITY IN NEAR ISOGENIC LINES CARRYING A QTL FOR LARGER PANICLE IS GENOTYPE AND ENVIRONMENT DEPENDENT 17 Abstract 17

Background 17

Materials and Methods 19

Results 24

Discussion 34

Conclusion 38

References 38

Supplementary material 42

5 THE QTSN POSITIVE EFFECT ON PANICLE AND FLAG LEAF SIZE IS ASSOCIATED WITH AN EARLY DOWN-REGULATION OF TILLERING 44 Abstract 44

Introduction 44

Materials and Methods 46

Results 52

Discussion 66

Conclusion 68

References 68

Supplementary material 72

6 QTSN4 EFFECT ON FLAG LEAF SIZE, PHOTOSYNTHESIS AND PANICLE SIZE, BENEFITS TO PLANT GRAIN PRODUCTION DEPENDING ON ITS ACCESS TO LIGHT 76 Abstract 76

Introduction 76

Materials and Methods 78

Discussion 88

References 91

Supplementary material 95

7 SYNTHESIS, GENERAL DISCUSSION AND PERSPECTIVE 99

Synthesis 99

General Discussion 100

Perspectives 105

References 106

CURRICULUM VITAE 108

LIST OF TABLES

OBJECTIVES, OVERVIEW OF THE CHAPTERS AND THE METHODOLOGY

1. Environmental characteristics of three experiments in greenhouse

(GH) Montpellier, field and GH IRRI 11

RICE PANICLE PLASTICITY IN NEAR ISOGENIC LINES CARRYING A QTL FOR LARGER PANICLE IS GENOTYPE AND ENVIRONMENT DEPENDENT

1. Description of parameters with the unit of measurement 22 2. Effect of QTL (Q) and treatment (T) on single tiller of green house

experiment (mean ± standard deviation) ns, *, **, *** not significant, significantly different at 5%, 1% and 0.1% levels, respectively for

each pair of genotype (n = 5) 25

3. Effect of QTL (Q) and treatment (T) on single tiller of field experiment (mean ± standard deviation) ns, *, **, *** not significant, significantly different at 5%, 1% and 0.1% levels, respectively for

each pair of genotype (n = 4) 26

4. Effect of QTL (Q) and treatment (T) on single tiller of greenhouse experiment (mean±standard deviation) ns, *, **, *** not significant, significantly different at 5%, 1% and 0.1% levels, respectively for

each pair of genotype (n=5) 28

5. Effect of QTL (Q) and treatment (T) on single tiller of field experiment (mean ± standard deviation) ns, *, **, *** not significant, significantly different at 5%, 1% and 0.1% levels, respectively for

each pair of genotype (n = 4) 28

S1. P-values as result of three-stages ANOVA of yield component in GH

and field experiments 42

S2. The increase (positive values) and reduction (negative values) of panicle architecture traits as the result of the qTSN4 and treatment (light or density) effects. Values in bold are significantly different at P<0.05 according to Duncan test for multiple comparisons of each genotype (n=5 for GH-CNRS, n=8 for field-IRRI) 43

THE QTSN POSITIVE EFFECT ON PANICLE AND FLAG LEAF SIZE IS ASSOCIATED WITH AN EARLY DOWN-REGULATION OF TILLERING

1. Details of plant materials 47

2. ANOVA of flag leaf area, tiller number at PI (Panicle Initiation), FLO (flowering) (heading in GH-CNRS), MAT (grain physiological maturity), biomass related traits (DW, Dry Weight) at plant and main stem level at FLO and MAT for vegetative DW and at MAT only for

panicle DW and FGDW (FG: Filled Grain) 53

3. Response rate of traits to QTLs introgression in each pair of isoline in a given treatment (in the field-IRRI, LD is for Low Density, HD is for high density) and genetic background (IR64 and IRRI146) (A), to low access to light in each trial (field-IRRI, GH-CNRS) (B), for each genotype (parent, NIL, NIL1). Grey columns indicate no treatment effect as shading in GH-CNRS just imposed at PI 54 QTSN4 EFFECT ON FLAG LEAF SIZE, PHOTOSYNTHESIS AND PANICLE SIZE, BENEFITS TO PLANT GRAIN PRODUCTION DEPENDING ON ITS ACCESS TO LIGHT

1. Plant material description 78

2. Description of the trials used for a multi-environment analysis of qTSN4 effect on plant grain production, flag leaf dimension and spikelet number per panicle on the mains stem 79 S1. ANOVA of flag leaf area (FLA) in GH-CNRS 2013 and field 2014 95 S2. ANOVA of flag leaf width (FLW) in GH-CNRS 2013 and field 2014 95 S3. ANOVA of spikelet number per panicle (SPN) in GH-CNRS 2013

and field 2014 96

S4. ANOVA of plant grain dry weight (PGDW) in GH-CNRS 2013 and

field 2014 96

S5. ANOVA of photosynthetic parameters (CO2 assimilation and

Vcmax) in GH-CNRS 2013 97

S6. ANOVA of SLA and N content in GH-CNRS 2013 97

S7. ANOVA of leaf and internode starch in GH-CNRS 2013 98

LIST OF FIGURES

PROBLEMATIC AND STATE OF THE ART

1. The crop cycle of rice plant. PI: panicle initiation, FLO: flowering, MAT: maturity Description of parameters with the unit of

measurement 4

2. Differentiation of panicle architexctural components as provided by P-TRAP software: main axis length (A), primary branch length (B) and secondary branch length (C). Scale bar 5 cm (Adriani et al,

OBJECTIVES, OVERVIEW OF THE CHAPTERS AND THE METHODOLOGY

1. Control and shading treatment in greenhouse experiment, Montpellier 12 2. Field and greenhouse experiments in IRRI, Philippines 12 RICE PANICLE PLASTICITY IN NEAR ISOGENIC LINES CARRYING A QTL FOR LARGER PANICLE IS GENOTYPE AND ENVIRONMENT DEPENDENT

1. P-TRAP analysis resulting panicle structure with the rachis length (A), primary branch length (B) and secondary branch length (C). Scale bar

5 cm 23

2. Panicle architecture analysis by P-TRAP of IR64 parent line and its NIL. A Greenhouse – control. B Greenhouse – shading. C Field – low density. D Field – High density. Scale bar 5 cm 30 3. Panicle architecture traits of main tiller by PTRAP in the greenhouse

under control and shading treatments (A – D), and in the field under low density (LD) and high density (HD) treatments (E – H). A and E Spikelet number per panicle. B and F Total length of branches (cm). C and G Rachis and primary branch length (cm). D and H Primary and secondary branches number. The values are mean ± SE. Different letters indicate significant differences at P<0.05 according to Duncan test for multiple comparisons of each genotype (n = 5 for GH-CNRS,

n = 8 for field-IRRI) 32

4. Relationships between panicle total length (cm) and spikelet number of main tiller across treatments and experiments. Regression curves are associated with confidence interval at P = 0.05 (n = 5 for

GH-CNRS, n = 8 for field-IRRI) 33

5. Relationships between main stem growth rate and spikelet number (SN) of main tiller. A IR64 background in both experiments. B IRRI146 background in both experiments. C Green house experiment in both backgrounds. D Field experiment in both backgrounds. Regression curves are associated with confidence interval at P = 0.05

(n = 16) 34

THE QTSN POSITIVE EFFECT ON PANICLE AND FLAG LEAF SIZE IS ASSOCIATED WITH AN EARLY DOWN-REGULATION OF TILLERING

1. Plant tiller number (A, D), leaf number on the main tiller (B, E) and stem length of the main tiller (C, E) of parent (black) and NIL (grey) in IR64 (A – C) and IRRI146 (D – F) background, under control (C) and shading (S) in GH-CNRS trial. The valies are mean ± SE. n = 3 55 2. Plant tiller number (A, D), leaf number on the main tiller (B, E) and

stem length of the main tiller (C, E) of parent (black) and NIL (grey) in IR64 (A – C) and IRRI146 (D – F) background, under low density (LD) and high density (HD) in field trial. The values are mean ± SE. n

= 4 57

3. Individual leaf area of main tiller (FL: flag leaf, FL-1to FL-5: one to five leaves below the flag leaf) at flowering (FLO) of parent (black),

NIL (grey) and NIL1 (white) in IR64 background (A) and IRRI146 background (B) in GH-CNRS under control and shading, in IR64 background (C) and IRRI146 background (D) in the field under low density (LD) and high density (HD), in IRRI146 background (E) in GH-IRRI under crowded and isolated plants. The values are mean ± SE. Results of Duncan test for multiple comparisons of each genotype per treatment at 5% level are shown in the letters above the bars. n = 4 in GH-CNRS and filed-IRRI, n = 3 in GH-IRRI. 58 4. Plant filled grain dry weight (A, E), main stem panicle dry weight at

maturity (B, F), plant shoot biomass at maturity (C, G), plant green leaf area at flowering (D, H) under control (C) and shading (S) in GH-CNRS (A – D), under low density (LD) and high density (HD) in field-IRRI (E – J). The values are mean ± SE. Results of Duncan test for multiple comparisons of each genotype per treatment at 5% level are shown by the letters above error bars. n = 5 at maturity and n = 4

at flowering in GH-CNRS, n = 4 in field-IRRI 61

5. Relationship between tillering rate from initial measurement to panicle initiation (PI) and main stem growth rate from PI to flowering (FLO) of the parent (black symbol) and the NIL (grey symbol), in IR64 background in GH-CNRS and field trials (A), in IRRI146 background in GH-CNRS and field trials (B), in GH-CNRS in IR64 and IRRI146 backgrounds (C), in field-IRRI experiment in IR64 and IRRI146 backgrounds (D). The values are mean ± SE. Regression curves are associated with confidence interval at P = 0.05. n = 40 for IR64 background and field-IRRI trial, n = 32 for IRRI146 background and GH-CNRS trial for regression curve 62 6. Relationship between main stem growth rate from panicle initiation

(PI) to flowering (FLO) and main stem panicle dry weight at maturity of the parent (black symbol) and the NIL (grey symbol), in IR64 background in GH-CNRS and field trials (A), in IRRI146 background in GH-CNRS and field trials (B), in GH-CNRS in IR64 and IRRI146 backgrounds (C), in fild-IRRI experiment in IR64 and IRRI146 backgrounds (D). The values are mean ± SE. Regression curves are associated with confidence interval at P = 0.05. n = 40 for IR64 background and field-IRRI trial, n = 32 for IRRI146 background and GH-CNRS trial for regression curve 63 7. Relationship between plant shoot growth rate from panicle initiation

(PI) to flowering (FLO) and plant panicle dry weight at maturity of the parent (black symbol) and the NIL (grey symbol), in IR64 background in GH-CNRS and field trials (A), in IRRI146 background in GH-CNRS and field trials (B), in GH-CNRS in IR64 and IRRI146 backgrounds (C), in field-IRRI experiment in IR64 and IRRI146 backgrounds (D). The values are mean ± SE. Regression curves are associated with confidence interval at P = 0.05. n = 42 for IR64 background and field-IRRI trial, n = 34 for IRRI146 background and GH-CNRS trial for regression curve 64 8. Carbon assimilation (A, B) and internode starch concentration during

(white) under control (C) and shading (S) in GH-CNRS (A, C), under low density (LD) and high density (HD) in field-IRRI (B, D). The values are mean ± SE. Results of Duncan test for multiple comparisons of each genotype per treatment at 5% level are shown in the letters above the bars. n = 3 in GH-CNRS, n = 4 in field-IRRI 65 S1. The relative (NIL-P) of IRRI146 background in GH-CNRS under

control. Leaf number on the main tiller (A) Tiller number per plant (B) Stem length of the main tiller (C) Individual leaf area at flowering and spikelet number per panicle at maturity (D) Peduncle and internode length at maturity (E) Peduncle and internode thickness at maturity (F) 72 S2. The relative (NIL1-P) of IR64 background in field-IRRI under low

density. Leaf number on the main tiller (A) Tiller number per plant (B) Stem length of the main tiller (C) Individual leaf area at flowering and spikelet number per panicle at maturity (D) Peduncle and internode length at maturity (E) Peduncle and internode thickness at maturity (F) 73 S3. Relationship between plant shoot growth rate from panicle initiation

(PI) to flowering (FLO) and plant grain dry weight at maturity of the parent (black symbol) and the NIL (grey symbol), in IR64 background in GH-CNRS and field trials (A) in IRRI146 background in GH-CNRS and field trials (B) in GH-CNRS in IR64 and IRRI146 backgrounds (C) in field-IRRI experiment in IR64 and IRRI146 backgrounds (D). The values are mean ± SE. Regression curves are associated with confidence interval at P = 0.05. n = 42 for IR64 background and field-IRRI trial, n = 34 for field-IRRI146 background and GH-CNRS trial for

regression curve 74

S4. Carbon assimilation (A) and internode starch concentration during panicle development (B) of parent (black), NIL (grey) under isolated and crowded population in GH-IRRI. The values are mean ± SE. Results of Duncan test for multiple comparisons of each genotype per treatment at 5% level are shown in the letters above the bars. n = 3 75 QTSN4 EFFECT ON FLAG LEAF SIZE, PHOTOSYNTHESIS AND PANICLE SIZE, BENEFITS TO PLANT GRAIN PRODUCTION DEPENDING ON ITS ACCESS TO LIGHT

1. Morphological characteristics measured at heading and grain physiological maturity in four trials detailed in Table 6.2.

C: control; S: shading at 58% from panicle initiation to heading; LD: low planting density, HD: high planting density; Cr: Crowded plants from panicle initiation to heading; Is: Isolated plants during this period. Letters indicate the level of significance of qTSN4 effect between parent and NIL at p<0.05 in each treatment (Tukey HSD test). Each bar represents mean ± s.e. (A) Flag leaf area (excepted for GH-IRRI 2012) (B) Flag leaf width on the main stem (C) Spikelet number per panicle on the main stem (D) Plant grain dry weight 83 2. Physiological leaf characteristics measured at three weeks after

panicle initiation in greenhouse experiment (GH-CNRS 2013) with two light treatments. C: Control; S: Shading. Different letters indicate

significant difference at p<0.05 (Tukey HSD test) among values in a given experiment. Each bar represents mean ± s.e. (n=3)

(A)Photosynthetic rate (B) Maximum carboxylation rate (Vcmax) 85 3. Leaf anatomical characteristics and N status measured at three weeks

after paicle initiation in greenhouse experiment (GH-CNRS 2013) with two light treatments. C: Control; S: Shading. Different letters indicate significant difference at p<0.05 (Tukey HSD test) among values in a given experiment. Each bar represents mean ± s.e. (n=3) (A) Specific leaf area (SLA) (B) Dry weight based leaf nitrogen

content (Nm) 86

4. Relationship between photosynthetic rate at PAR saturation (A) and the leaf area N content (Na) for control and shade-acclimated plants in experiment GH-CNRS 2013. Presence or absence of qTSN4 is

indicated by +/- QTL 87

5. Starch content measured at three weeks after panicle initiation in greenhouse experiment (GH-CNRS 2013) with two light treatments. C: Control; S: Shading. Different letters indicate significant difference at p<0.05 (Tukey HSD test) among values in a given experiment. Each bar represents mean ± s.e. (n=5)

(A) Leaf starch (B) Internode starch 88

SYNTHESIS, GENERAL DISCUSSION AND PERSPECTIVE

1. Schematic hierarchisation of qTSN effect-trait heritability and the level of QTL x E interactions on the observed main traits 100 2. Conceptual scheme the synthesis of qTSN effect on sink and source

1 INTRODUCTION

This PhD work takes place within the context of the international consortium GRiSP (Global Rice Science Partnership) and more particularly in the project "Yield Potential Breeding‖ coordinated by International Rice Research Institute (IRRI) (http://www.cgiar.org/our-strategy/cgiar-research-programs/rice-grisp/). The challenge of this project is to improve yield potential of rice, i.e. grain production to meet the demand of the growing population by genomic and physiological approaches targeting source related traits. The present PhD thesis tackles this challenge through an ecophysiological approach.

Since the 1960‘s breeders in IRRI developed varieties those have been distributed globally and as important parental varieties in breeding program. In 1966, one of the breeding lines became a new cultivar, IR8, a semi-dwarf rice variety that could produce more grains of rice per plant when grown with certain fertilizers and irrigation, triggered the green revolution in the Asia tropical countries (Hossain, 1995). De data et al. (1968) reported his findings that IR8 rice yielded about 5 tons per hectare with no fertilizer, and almost 10 tons per hectare under optimal conditions. This was 10 times the yield of traditional rice. IR8 was a success throughout Asia, and followed by indica inbred cultivars such as IR36, IR64 and IR72 (Peng and Khush, 2003).

However, until today, using conventional breeding and selection, breeders have not been able to break yield ceiling in rice since the release of IR8 (Peng et al. 1999). As a result, yield stagnation of newly developed rice varieties has been observed in the tropics (GRiSP 2010). This led rice breeders in the late 1980s to select for genotypes with larger panicles (Dingkuhn et al. 1991; Peng et al. 1994, 2008; Li et al. 2014) by developing a new plant type (NPT) with the goal of increasing yield potential under tropical environments. Unlike IR64, the NPT varieties have several agronomic traits inherited from tropical japonica-type varieties: low tiller number, low number of unproductive tillers, large panicle, thick culm, lodging resistance and large, dark green flag leaves (Khush 1995).

With this respect, these NPT varieties had been backcrossed against high yield indica cultivars (IR64 and IRRI146) to develop Introgression Lines (ILs). Using these ILs, Fujita et al. (2009, 2012) identified QTLs for yield components, in particular spikelet number, panicle number and grain weight. Among some agronomic traits for grain yield which had evaluated (days to heading, culm length, panicle length, leaf width, leaf length, panicle number, total spikelet number per panicle and 100-grain weight), QTL for high total spikelet number (TSN) was detected in long arm of chromosome 4 by using simple sequence repeat (SSR) markers (Fujita et al. 2012). This QTL (qTSN4) is colocated with Nal1 (Narrow Leaf1) gene that has been reported to affect leaf vein pattern and carboxylation capacity (Qi et al. 2008). With this respect, some Near Isogenic Lines (NILs) with larger leaf and panicle size compared to recipient lines were developed (Fujita et al. 2009; 2012; 2013) and had been evaluated in the IRRI field over four seasons. The positive effect of qTSN was proved but modulated by the trade-off it implies between panicle size and number, potentially reducing the benefits of qTSN on crop grain yield. Such a trade-off was shown to vary with the cropping

environment (Okami et al. 2014); suggesting qTSN is prone to QTL x environment interactions. The added value of qTSN for future breeding programmes implies to better understand such interactions.

Accordingly, from an ecophysiological point of view, these NILs, when compared to their recipient lines, represent a relevant genetic material, to study the way (i) panicle size is elaborated with respect to tiller vigor and physiological performances and is described in function of branch and spikelet size and number, and (ii) yield components compensate depending on the environment i.e. to which extent they are plastic and compete for a given resource within the plant. Elaboration of panicle architecture and sizing was, however, poorly addressed by physiologists, as it develops mainly in hidden parts of the plants, i.e. encapsulated within the sheaths of leaves previously developed on a given tiller. This PhD work addresses the phenotypic plasticity of panicle development in response to limitation of carbohydrates due to incoming light restriction. It aimed at understanding rice panicle morphogenesis from initiation to flowering in terms of dimension, growth and developmental rate, panicle architecture and its relations with the whole plant morphogenetic pattern and resulting C source-sink relationships.

Once presented the problematic and the state of the art, this PhD work will be presented in three chapters that were submitted (and accepted for one of them) as article in international journals. Chapters will be articulated based on an intermediate, short summary and finally discussed and opened on perspective in a global discussion.

2 PROBLEMATIC AND STATE OF THE ART

Rice (Oryza sativa L.) is the first of the three most important cereal crop species (before wheat and maize) and forms the staple diet of about half of the world's population. The global production of rice in the world has been recorded at the level of 741 million tones in 165 million hectares of harvested area (FAOSTAT, 2013). Asia is the leader in rice production accounting for about 90% of the world's production. Over 75% of the world supply is consumed by people in Asian countries and thus rice is of immense importance to food security in Asia. The demand for rice is expected to increase further in view of expected

increase in the population (Tripathi et al. 2011).

Rice Development and Growth Cycle

Rice is grown throughout a wide range of climates. It is a C3 plant that can grow in thermal conditions ranging from 15 to 35°C, although the range 20 – 30°C seems optimal, and that can express consistent tolerance under transient drought (Luquet et al. 2008; Pallas et al. 2013) and submergence (Septiningsih et al. 2015), and even in saline conditions (Kizhakkedath et al. 2015) and problem soils (Haefele et al. 2014).

Generally, rice plant growth is divided into three phases: vegetative (from germination to panicle initiation), reproductive (from panicle initiation to heading) and grain filling or ripening (from heading to maturity) (Li 1979).

Vegetative Phase

During vegetative growth, plant leaf area increase is composed of individual leaf size as well as leaf and tiller emergence rate. It determines the capacity of the plant to intercept radiation and produce biomass, which impacts on yield later on during the reproductive and grain filling phases (Figure 1). The vegetative stage is characterized by active tillering, gradual increase in plant height, and leaf emergence at regular intervals. All contribute to increasing the leaf area that receives sunlight. Tillering may start when the main culm develops the 5th or 6th leaf (if including the prophylle and coleoptile that are unshaped leaves already present in the embryo). Active tillering refers to a stage when tillering rate – the increase in tiller number per unit of time — is high. The maximum tiller number stage follows active tillering. It is a stage when tiller number per plant or per square meter is maximum - before or after the initiation of panicle primordia - depending on a variety growth duration (Yoshida 1981).

Figure 1 The crop cycle of rice plant. PI: panicle initiation, FLO: flowering, MAT: maturity

Reproductive Phase

Tillers continuously develop as the plant enters into the next step which is stem (internode) elongation that coincides with the reproductive phase (Figure 1). This stage may indeed begin most generally with panicle initiation (PI). During this period, tillers continue to increase in number and height, with no appreciable

senescence of leaves noticeable (Tripathi et al. 2011). Internode elongation

usually begins around the initiation of panicle primordia and continues until heading. The top five internodes may be elongated at heading. For this reason, the reproductive growth stage is sometimes called the internode elongation stage (Yoshida 1981).

The reproductive phase thus characterized by culm elongation (which increases plant height), plateau in tiller number, emergence of the flag leaf (the last leaf), booting, heading, and flowering. The initiation of panicle primordium starts about 30 days before heading; it corresponds to the time when the fourth leaf from the top begins to elongate. Before heading a considerable amount of starch and sugar accumulates in the culms and leaf sheaths, thus to be translocated to the grains during ripening. Panicle development and growth start with the neck-node differentiation and end when the pollen is fully matured. The total duration of panicle development varies with variety and weather and ranges from 27 to 46 days (Yoshida 1981).

As the panicle continues to develop, the spikelet becomes distinguishable (Figure 1). The young panicle increases in size and its upward extension inside the flag leaf sheath causes the leaf sheath bulge. This bulging of the flag leaf sheath is called booting. Booting is most likely to occur first in the main culm. At booting, senescing (aging and dying) leaves and juvenile tillers are noticeable at the base of

the plant (Tripathi et al. 2011).

Heading means panicle exertion and is marked by the emergence of the

panicle tip from the flag leaf sheath. The panicle continues to emerge until it

partially or completely protrudes from the sheath. Spikelet anthesis (or flowering)

Vegetative phase Reproductive phase Ripening phase

PI

begins with panicle exertion, or on the following day. Consequently, heading is considered a synonym for anthesis in terms of calendar days in the life history of rice. It takes 10 –14 days for a crop to complete heading because of variation in panicle exertion between tillers of the same plant and between plants in the same field. From an agronomic point of view, heading is usually defined as the time when 50% of the panicles have exerted (Tripathi et al. 2011; Yoshida 1981). Ripening Phase

The ripening period is characterized by grain growth — increase in size and weight, changes in grain color, and senescence of leaves. At the early stages of ripening, the grains are green, then turn yellow as they mature. The texture of the grains changes from a milky, semifluid state to a hard solid. On the basis of such changes the ripening period is subdivided into milky, dough, yellow ripe, and maturity stages. Leaf senescence starts from the lower leaves and extends upward as the plant matures. Leaf senescence is faster in indica than in japonica rices and in warm regions than in cool regions. In cool regions, some leaves remain green even at maturity (Yoshida 1981).

Agronomically, the duration of ripening is from the date of heading to the time when the maximum grain weight is attained. The time of harvest is usually determined by past experience, grain color, and leaf senescence. The length of ripening and thus filled grain predominantly affected by temperature (Ahmed et al. 2015), solar radiation (Okawa et al. 2003; Restrepo and Garcés 2013), water requirement (Boonjung and Fukai 1996).

Rice Panicle Development

The term panicle is synonymous with the inflorescence of angiosperms, and is a proper appellation used for Graminae (Takeoka et al. 1993). The rice panicle is composed of rachis and spikelets. Rachis has peduncle (panicle base axis), main axis (distance from panicle neck node up to the tip node), primary, secondary or tertiary branches according to branching stages and pedicel (Takeoka et al. 1993; Yoshida 1981). Architectural components of the panicle are presented in Figure 2. Pedicels come out from each node at the tip of branches curve around their edge where spikelets are set. Spikelets are composed of glumes (which alternately develop on the rachis), lemma and paleae laterally developing on the floral axis, and floral organs (two lodicules, six stamens and one pistil) (Takeoka et al. 1993).

There are several hypotheses regarding panicle development stage (Ikeda et al. 2004; Yamagishi et al. 2004; Itoh et al. 2005; Wang and Li 2005). Practically it can be divided into two main stages; the early stage is the establishment of rachis followed by the formation of primary branches on successive nodes of the rachis (5 – 14 days after PI when the panicle is less than 4 mm in length), and the late stage is the onset of elongation of primary branches and differentiation of higher order branches, followed by floret formation (14 or 16 days after PI up to heading). When the inflorescence becomes 40 mm long and all organ primordia are formed, rachis and branches start their rapid elongation.

Figure 2 Differentiation of panicle architexctural components as provided by P-TRAP software: main axis length (A), primary branch length (B) and secondary branch length (C). Scale bar 5 cm

Phenotypic Plasticity of Rice

The dynamic responses of plant morphogenesis to its environment constitute is phenotypic plasticity. Phenotypic plasticity enables the plant to adjust its morphology and phenology to variable environments (Sultan 2000, Dingkuhn et al. 2005; Luquet et al. 2005).

From a physiological angle, phenotypic plasticity is the environment-induced diversity of phenotypes a given genotype can generate, brought about by the responsiveness of the plant‘s metabolic, growth and developmental processes to external and internal signals. This responsiveness may or may not involve changes in the expression patterns of genes, depending on whether the response is actively induced or inherent (constitutive) to the physiological apparatus. Phenotypic plasticity rarely affects the body plan (or basic structure) of the phenotype, but can strongly affect morphology, histology and phenology of a plant (Dingkuhn et al. 2006).

Plasticity phenomena can be classified in different ways, e.g. based on the nature of the involved traits (e.g. morphological, physiological and behavioral), the nature of the environmental signal (low access of light, population density) interpreted by the plastic developmental system or the relevant organism‘s performance (escape or avoidance) in the ecological context (Fusco and Minelli 2012).

The architecture of the plant is modified through the allocation of assimilate, which determines the growth rates of different organs. At the same time, the plant is subjected to external mechanical stresses, such as gravity or

B

C A

wind forces, and must adapt its shape and develop support structures. In order to adapt their shape to the constantly changing environment, and in response to competition from nearby plants, individual plants gradually develop their architecture according to source – sink activities and endogenous signals (Guo et al. 2011).

The plasticity of rice as induced by phosphorus (P) deficiency corresponds to a reduction of shoot growth and thus assimilates demand, while root growth is not inhibited or even triggered. It was suggested that morphogenetic effects of P deficiency are the result of modified relationships among sinks, and specifically, inhibition of leaf expansion (Luquet et al. 2005).

Under suboptimal cropping conditions (no abiotic stress), rice plant morphology is strongly affected, amongst others, by planting density, a major characteristic of cultural practices (Zhang and Yamagishi 2010; Oghalo 2011). Depending on planting density, plant-plant competition for light and asasociated reduction in plant internal availability of C assimilates resources, will occur more or less rapidly during crop cycle , resulting in a variable regulation of plant morphogenesis in timing and intensity (tillering, organ size, starch remobilization, senescence) (Lafarge et al. 2010). With respect to yield potential and its optimization by the genotype and the cultural practices, it is thus crucial to understand the Genotype X Environment interactions (GxE), i.e. the level of phenotypic plasticity of yield component traits, panicle number and morphology in first place. While many studies addressed the phenotypic plasticity of rice at the vegetative stage (Luquet et al. 2005) under phosphorus deficiency, Luquet et al. (2008) under drought, Lafarge et al. (2010) under shading), that of panicle formation was much less explored.

Phenotypic Plasticity of Panicle Development and Architecture

Panicle development is a key developmental stage in rice because at this stage plant switches from vegetative to reproductive development and source-sink relations change to allocate a part of photoassimilates to reproductive sinks, namely growing spikelets and kernels (Streck et al. 2009), in addition to elongating culms and accumulating C reserves.

The stages of panicle development are strongly influenced by G x E interactions. For instances, it was shown that elevated CO2 can compensate the

negative impact of low plant access to light on panicle morphogenesis on japonica rice (Choi et al. 2013). N application at panicle formation stage was shown to contribute to panicle morphogenetic processes (Kobayashi and Horie 1994) and enhance spikelet density (Hasegawa et al. 1994). Spikelet number per panicle was shown to depend on the interaction between shoot C accumulation and flowering time, and its effect on the number of primary branches per panicle (Endo-Higashi and Izawa 2011). Low planting density was shown to increase panicle number per plant but decrease panicle number per unit area, which was associated to higher differentiated spikelet number per panicle compared to higher planting density (Zhang and Yamagishi 2010).

Challenges in Breeding for Panicle Size

In order to raise the yield ceiling, different breeding strategies had conducted with a key focus on large panicle, in terms of many fertile spikelets, since the conception of new plant types with varieties having limited tillering ability (New Plant Type, NPT: Dingkuhn 1991; Peng et al. 1994; Super Hybrid Rice: Peng et al. 2008; Li et al. 2014). These large panicles raised, however, questions on the adequate panicle structure and size for efficient grain filling and the trade-off between panicle size and number. Indeed the QTL qTSN4 which was recently developed by Fujita et al. (2009), exhibited such physiological trade-offs between panicle size and panicle number (Fujita et al. 2013), leading instability in grain production under different culture practice (Okami et al. 2014). The qTSN then becomes an interesting material of understanding this trade-off and the plasticity of the panicle.

Therefore the hypotheses should be confirmed are: i) Panicle sizing and its contribution to grain production in plant and crop level depends on the whole plant nutritional status and resulting competition for resources among sinks, in particular panicle size and number, ii) Panicle size specifically depends on plant C source-sink relationships as a main driver of plant phenotypic plasticity under sub optimal conditions, in particular under limited access of light.

3 OBJECTIVES, OVERVIEW OF THE CHAPTERS AND THE METHODOLOGY

The GRiSP, (Global Rice Science Partnership, WEBSITE) and more particularly Yield Potential project aims at Increasing the yield potential in rice using genomic and physiological approaches. In this context and with respect to abovementioned challenge and hypothesis, the goal of this PhD project is to provide further insight on the traits explaining i) genetic variation and , ii) phenotypic plasticity in response to plant C source-sink relationships. For this purpose, original genetic, of current interest for breeders at IRRI, was used consisting of isolines carrying qTSN4 (or qTSN12), a QTL enhancing flag leaf and panicle size. This material was studied in contrasting situations of plant access to light as a factor affecting plant C source-sink relationships. The fourth chapter entitled ―Rice panicle plasticity in near-isogenic lines carrying QTL for larger panicle is genotype and environment dependent” addresses abovementioned hypotheses under contrasted situations of plant access to light and thus to C assimilates. It discusses the way panicle architecture is related to genotypic and C assimilation differences and its association with organ vigor in morphogenetic development traits in 2 pairs of contrasted genotypes (NILs vs parents), under full light and low light conditions in greenhouse Montpelier, and low vs high density in field IRRI trials.

The chapter 5 aims at understanding the response of rice panicle morphogenesis to whole plant and local (stem, leaf) non-structural carbohydrates availability and source to sink balance. In the second chapter ”The qTSN positive effect on panicle and flag leaf size of rice is associated with an early down-regulation of tillering” explores the role of plant morphogenesis (tillering, leaf appearance, stem elongation), biomass accumulation in organ and the whole plant, conjointly with C assimilation and sugar related traits. The data collected in Montpellier in a greenhouse in 2013; in IRRI, Philippines in the field and in greenhouse (2014) on two high yielding genotypes (IR64 and IRRI146) those were compared to their Near Isogenic Lines (NIL) carrying QTL qTSN4 and QTL qTSN12 were described in this chapter.

The sixth chapter ―qTSN4 effect on flag leaf size, photosynthesis and panicle size, benefits to plant grain production depending on its access to light” explores physiological traits are related to enlarged of sink size. It is aim at challenging qTSN4 expression with different environmental conditions while observing the morphological and physiological phenotype. It describes the genotypes‘ photosynthetic characteristics at the leaf level when adapted to differential shading conditions, backed by information on leaf nitrogen status and non-structural carbohydrate (NSC) levels in the leaf and the stem internode located next to the leaf. In this chapter, another data set acquired in a greenhouse experiment at IRRI in 2012 on the same genetic backgrounds (NIL vs parent) is used to increase data resources, with in-depth focused on greenhouse experiment in Montpellier.

Finally, the last chapter is a general discussion of this work. Considering the results of Montpellier and IRRI experiments in chapters 4, 5, 6. It addresses the opportunities and limits of the present work regarding the plasticity of panicle and its response to the introgression of QTLs carrying larger leaf and panicle size, and low access of light; the yield component related traits as well as the consequences for physiological and genetic studies. Future physiological and genetic studies are suggested to better understand genotype and environment dependent that limit the panicle size and thus grain yield under full and low access of light.

Methodological Overview

To date, many QTLs were identified in rice to increase panicle size with the final goal of increasing grain yield. Recently, Fujita et al. (2009, 2012, 2013) revealed, by using simple sequence repeat (SSR) markers, a QTL, qTSN4, that enhances panicle size through higher total spikelet number (TSN) per panicle and that is located on the long arm of chromosome 4. This QTL was confirmed to increase grain yield, through larger flag leaf and panicle size, under non-limiting environment in the IRRI farm, Philippines, across 3 distinct growing seasons (Fujita et al. 2013). Recently, it was reported that this QTL leads to fewer but larger tillers under well-watered and drought-rewatering treatments (Okami et al. 2015). However,higher grain yield associated with this QTL was reported only under given culture practices as observed under flooded and aerobic culture in summer field experiments in Japan (Okami et al. 2014).

To evaluate the advantage of qTSN4 on panicle size, we tested some developed NILs and their parental backgrounds, IR64 and IRRI146 (NSIC Rc158), under C limitation in term of light access variability as shading (58% of light attenuation) in the greenhouse (GH) in Montpellier, France, and high planting density in the field at IRRI, Philippines, to represent common C-limited situations observed in farmers‘ fields like cloudiness or high cropping density. In the field, another QTL, qTSN12 (a QTL that also enhances panicle size and that is located on chromosome 12) was used within IR64 genetic background to re-inforce, if confirmed, the results reported with qTSN4. An additional experiment was conducted in the greenhouse at IRRI with crowded and isolated plants, using a pair of rice genotypes, i.e. IRRI146 recipient line and its NIL, to evaluate the plasticity of plant morphogenesis under an excess of light resources at plant level. These three experiments are summarized in Table 1.

Table 1 Environmental characteristic of three experiments in greenhouse (GH) Montpellier, field and GH IRRI

Experiment Growing

period

Genotype Design Temperature

(min – max)

PPFD (mean) Soil

management GH,

Montpellier

May –

September 2013

IR64 + qTSN4 ; IRRI146 + qTSN4

3 replicates, two treatments (full light and shading at 58% of light attenuation from PI to heading)

27 – 32oC 10.3 mol.m-2.d-1

(shading); 24.7

mol.m-2.d-1

(control)

EGOT 140 media (17N-10P-14K, pH of 5)

Total N supply : 0.66 g per 3 liter pot Field,

IRRI

December

2013 –

April 2014

IR64 + qTSN4 + qTSN12; IRRI146 + qTSN4 4 replicates, two treatments (High density: 100

plants m-²,

low density:

25 plants m-²)

22 – 29oC 31.0 mol.m-2.d-1 Andaqueptic

Haplaquoll with a topsoil of 61% clay, 32% silt, 7% sand pH of 6.2

Total N supply : 160

kg ha-1 (i.e.

0.16g (HD) and 0.64g (LD) per plant

GH, IRRI August –

November 2014

IRRI146 + qTSN4 3 replicates, two treatments (isolated vs. crowded plants from PI to flowering)

24 – 31oC 29.8 mol.m-2.d-1 Andaqueptic

Haplaquoll with a topsoil of 61% clay, 32% silt, 7% sand pH of 6.2

Total N supply: 1.26 g per 6 liter pot

Before the first experiment, a pre-trial was conducted (January – April 2013) in the greenhouse, Montpellier, to clarify the protocol for panicle observation and morphogenetic related traits measurements and to determine the appropriate material to setup shading. The plant materials used in this pre-trial were two pairs of isogenic lines vs. their parents (IR64 and IRRI146), and two newly-developed plant types (IR65 and IR68), which were grown under control, intermediate (38%) and deep shading (58%) from PI up to heading. From this trial, we extracted main conclusions those were used as reference for the next trials; (1) it was observed that two genetic backgrounds have different PI time, which is after 11 leaves appeared on the main stem for IR64 background, and 12 leaves for IRRI146 background, (2) Only deep shading (58% of light attenuation) from PI up to heading was significantly different from control (full light), and (3) only two

pairs of genotype (NIL vs parent), will be used for the next trials as we observed the lowest growth and development of two NPT lines.

In the first experiment, that was conducted in GH-Montpellier, accordingly, only two pairs of genotypes (NIL vs. parent), were grown under deep shading (58% of light attenuation) from panicle initiation (PI) up to heading. The shading set up and the GH conditions are presented in Figure 1.

Figure 1 Control and shading treatment in greenhouse experiment, Montpellier In IRRI, the same two genetic backgrounds as in GH Montpellier, with an additional pair of P/NIL that is IR64 and NIL1 carrying qTSN12, were grown in the field during the dry season under two planting densities, 25 and 100 plants m-2, and continuous flooding and appropriate N application for high yield. The two densities included the common situation as used in breeding fields, 25 plants m-2, and a situation where plants were confronted to high inter-plant competition for access to light (Figure 2).

A small experiment was also conducted at IRRI with plants in pots in the greenhouse during the wet season with a pair of P/NIL that is IRRI146 and its NIL (qTSN4). under two plant spacing from PI up to flowering, one as the common density within farmers‘ fields (Crowded, 25 plants m-2), the other close to isolated plants, 60 cm x 60 cm (2.78 plants m-2) (Figure 2).

In all trials, panicle development was observed weekly during the first two weeks after PI time by meristem dissection, panicle fixation and microscopic analysis provided by Histalim, an independent laboratory in food histology in Montpellier. At flowering and maturity, panicle architecture was then characterized by analysing its picture with help of a Java-based stand-alone software, P TRAP. This software enables to automatize the extraction of parameters such as individual axis length and number, and spikelet number (Figure 1 Chapter 2). Due to difficulties in interpreting microscopic images (the first two weeks after PI) and P TRAP analyses at flowering (because of non-fully developed panicles), only images at maturity have been exploited in this study. To correlate panicle architecture to the individual plant status and growth rate, measurements of plant height (distance from the base of the plant to the highest collar), green tiller number, green and dead leaf number on the main stem, organ dry weight (leaves, stems, sheath, and panicle for the main stem, for two extra tillers and for the whole plant) were collected at each developmental stage, i.e. at PI, flowering and maturity. In addition, photosynthesis and sugar content were measured to enlarge the understanding of the control of panicle architecture to the interaction of source-sink activities.

The following chapter dedicated to research paper submitted in RICE journal. This chapter highlighted the increase of panicle size in the presence of qTSN4 through greater architecture in terms of panicle branching and spikelet number. Variation in panicle size was related to pre-floral stem dry-weight growth suggesting qTSN4 increases primarily assimilate resources available at tiller level, followed by the trade-offs between panicle size and number. The effect of qTSN4 on grain production cannot be confirmed at crop level explaining some of genetic background, treatment and environment effects.

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Figure 2 Conceptual scheme the synthesis of qTSN effect on sink and source size

Is the qTSN a promising allele to improve yield potential under sub optimal

conditions?

A consistent increase in the size of the source organs (flag leaf area), of the storage and translocating organs (internodes and peduncles), and of the sink organs (spikelet number in the panicle) was confirmed in the presence of qTSN under a combination of three independent experiments consisting in various treatments limiting plant C resources through reduction of the access to light per plant (shading and population density). As already mentioned, the increase of the size of source and sink organs produced soon before PI was accompanied by an earlier cessation of tillering. This trade-off was more pronounced under non-limiting rather than limit access to light condition. This is in line with Fujita et al. (2013) who observed the same trade-off at the latter stage, i.e. at maturity under favorable condition in IRRI field. However, the gain in grain production was not confirmed within all experiments, as grain production was enhanced only in GH-Montpellier, while the qTSN effect was weaker or even non-significant in the field and in GH-IRRI.

Our study confirmed that the positive qTSN effect on panicle size and spikelet number per panicle was stable across environments in IRRI146 background. However, in IR64 background, the qTSN4 effect was observed only in GH-Montpellier whereas in the field-IRRI, the QTL effect was only from qTSN12. Panicle architecture analyzed by P-TRAP software as addressed in chapter 4, highlights the plasticity of panicle size (spikelet number) and structure (branch length and number) when analyzing contrasted genotypes under various environments (greenhouse vs field) and treatments (full light vs low light). Indeed we observed the variation in panicle sink size, thus variation in grain yield, which was related to pre-floral stem dry-weight growth, explaining some of the qTSN, treatment and environment effects.

Pre-floral main stem vigor

Flag leaf size Internode size

Better assimilation Thicker leaf &

higher N content Greater starch storage

in internodes Main tiller panicle size

Greater architecture (branch, spikelet number) Trade-off between panicle size

and panicle number Earlier cessation of tiller

production

Impact on grain production at plant level is genotype and

environment dependent

Enhanced organ (internode, leaf) size on main stem expressed from panicle initiation

R e m o b il iz a ti o n C-stora ge H ig h e r e a rl y a p ic a l d o m in a n c e Enhanced by low access to light

This variation was also characterized by the differences of photosynthetic rate between environments, in particular under direct light limitation (shading in GH-CNRS) vs indirect light limitation by canopy closure (plant population density in the field and GH-IRRI), as addressed in chapter 6. Therefore the benefits of qTSN may be expressed depending on the cropping culture, where sub optimal environment (low light, low N, low soil exploration as in pots in greenhouse) was exposed. These suggest that the phenotype of qTSN is plastic and prone to different environment.

Therefore this QTL alone is not necessarily a sufficient input to improve yield potential because single-panicle or single-culm traits are usually compensated by the adaptive plasticity of other morphological traits. Complex pleiotropic effects of qTSN may thus have a common physiological basis, although a more direct genetic control of several traits by the QTL cannot be

excluded. The QTL‘s primary effects shall be related to resource availability per

tiller or to more upstream processes, thereby affecting panicle size and, in some cases, yield. This pleiotropic effect was also reported for other QTLs or genes affecting the panicle, e.g., WFP (gene OsSPL14) affecting shoot branching at vegetative stage and final tiller number (Miura et al. 2010), and gene APO1 increasing leaf number, panicle primary branch number and harvest index (Ikeda et al. 2007; Terao et al. 2010).

Perspectives

The results obtained in this study make qTSN4 and qTSN12 alleles as interesting research components for further physiological studies, regarding the understanding of the regulation of this allele on plant functioning and on the effect on given cultural practices like the planting date (through contrasted radiation or N fertilization. As such kind of trade-offs was observed early through an earlier cessation of tiller production due to qTSN introgression, nevertheless we were not able to further interpret if this early effect impacts directly tillering rate or organ dimensioning at meristem level, as we did not observe hormonal signaling that may be involved in this regulation. It would be interesting to look at meristem size of the NILs compared to the parental lines along plant development and also to have a more comprehensive analysis of qTSN impact on plant C assimilation and starch storage, i.e. other organs on the main stem and on other tillers depending on their fertility.

To our knowledge, this is the first physiological study to evaluate the effect of qTSN during panicle development stage under stressing light condition. The results will certainly trigger further physiological and genetic studies on whole plant functioning due to qTSN introgression for rice grain yield improvement, in particular under different environments, as our results in the field cannot confirm the enhance of grain yield due to qTSN which was observed in the greenhouse.

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CURRICULUM VITAE

Dewi Erika Adriani. The author was born in Banjarbaru on April 13, 1976 as the oldest child of three siblings of M. Adriansyah Umar and Ernie Hasniati. Recently the writer lives at Jl. Unlam II No. 9, Banjarbaru, Kalimantan Selatan. She got Bachelor degree of Agriculture in 1999 at Faculty of Agriculture, University of Lambung Mangkurat. Since 2000, the author devoted herself on the almamater as the lecturer. In 2005 the author got her Master degree of Agriculture at the same university.

Starting PhD program in 2010, the author got a scholarship of Double-Degree program between Indonesia and France, funded by Indonesian Directorate General of Higher Education, Campus France and Agreenium. Bogor Agricultural University is the host university collaborated with Montpellier SupAgro as the partner university, under joint supervision of Prof. Dr. Sudirman Yahya, Dr Suwarto, Dr Sudradjat, Dr Delphine Luquet and Dr Tanguy Lafarge.

Two years spent by the author in Bogor Agricultural University for taking courses those supported thesis research at Agronomy and Horticulture department. In 2012 up to 2015 the author started research activities in ecophysiology domain, entitled:‖Analysis of Developmental Plasticity of Rice Panicle in response to plant C source-sink balance. Case study of qTSN isolines‖, in Agricultural Research Center for Development (CIRAD) as research host in France and conducted two experiments in International Rice Research Institute (IRRI), Philippines as collaborator research host.

Report papers those were submitted, presented and published during the PhD:

1. Adriani DE, Dardou A, Adam H, Yahya S, Ishimaru T, Dingkuhn M, Lafarge

T, and Luquet D. 2014. Analysis of the developmental plasticity of the rice panicle and its control by plant sugar status in near-isogenic lines differing at QTL TSN 4 and 12. Poster presentation at The 4th International Rice Congress, 27 October - 1 November 2014, BITEC, Bangkok, Thailand. IRC14-1192. 2. Dingkuhn M, Luquet D, Laza R, Kumar U, Adriani DE, Peraudeau S, Lafarge

T. 2014. Rice yield potential : can integration of ‗omics‘ and ideotype modeling break new ground ? Invited paper presented at the Symposium

―Increasing yield potential: from physiological processes to ideotyping‖. The 4th International Rice Congress, 27 October - 1 November 2014, BITEC, Bangkok, Thailand. IRC14-1192.

3. Dewi E. Adriani, Michael Dingkuhn, Audrey Dardou, Hélène Adam, Delphine

Luquet, Tanguy Lafarge. Rice panicle plasticity in near isogenic lines carrying a QTL for larger panicle is genotype and environment dependent. Revised submission to RICE 1st February 2016.

4. Dewi E. Adriani, Tanguy Lafarge, Audrey Dardou, Aubrey Fabro, Anne

Clément-Vidal, Sudirman Yahya, Michael Dingkuhn, Delphine Luquet. 2016. The qTSN positive effect on panicle and flag leaf size of rice is associated with an early down-regulation of tillering. Frontiers in Plant Science. 6(1197): 17pp. doi: 10.3389/fpls.2015.01197.

5. Denis Fabre, Dewi E. Adriani, Michael Dingkuhn, Tsutomu Ishimaru, Bermenito Punzalan, Tanguy Lafarge, Anne Clément-Vidal, Delphine Luquet. qTSN4 effect on flag leaf size, photosynthesis and panicle size, benefits to plant grain production depending on its access to light. Submitted to Frontiers in Plant Science 14 January 2016.