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This thesis examines the growth response and inter-relationships between shoots and roots of plants grown in compact soil. In the field, two topsoil and two subsoil conditions were created with five vegetable crops sequentially grown. Between 6 and 12% of the root system grew in the compact subsoil, which had a soil strength of 3.1 c.f. 1.9 MPa in the loosened subsoil. Both the root length density (Lv) and the specific root length were lower in the compact subsoil (80% and 30%, respectively). This had no effect on shoot growth when water and nutrients were well supplied. Compensatory root growth in the lose soil above the compact subsoil occurred in broccoli plants. As a result plants grown in soil with or without a compact subsoil had a similar total root length but with altered root distribution. When the water and nitrogen supplied to the soil was reduced, the lower subsoil Lv in the compact subsoil did not restrict water or N acquisition. This was possibly due to a large increase in the specific uptake per unit length of root, by the fewer roots in the compact subsoil. Compared to the subsoil treatments, only small changes in topsoil physical properties occurred when tillage was ceased. From the field trials the proportion and time of root growth into compact soil appeared important in determining the plant response. In a series of split-root experiments (horizontal and vertical arrangements of compact and loose soil) compensatory root growth in the loose soil only occurred when the root system was exposed to horizontally compact soil When compensatory root growth did not occur shoot growth was reduced. This resulted in there being a close relationship between total root length and leaf area. Further test results support a direct effect of mechanical impedance on shoot growth with a rapid (within 10 minutes) and large (50%) reduction in leaf elongation occurring when roots were mechanically impeded. In the field only plants whose roots were totally exposed to compact soil had reduced shoot growth with very compact subsoil having no effect. / Doctor of Philosophy (PhD)

Genotypes adapted to contrasting environments are expected to behave differently when placed in common controlled conditions, if their sensitivity to environmental cues or intrinsic growth behaviour are set to different thresholds, or are limited at distinct levels. This allows natural variation to be exploited as an unlimited source of new alleles or genes for the study of the genetic basis of quantitative trait variation. My doctoral work focuses on analysing natural variation for shoot growth and response to the environment in A. thaliana. Natural variation analyses aim at understanding how molecular genetic or epigenetic diversity controls phenotypic variation at different scales and times of plant development and under different environmental conditions, and how selection or demographic processes influence the frequency of those molecular variants in populations for them to get adapted to their local environment. As such, the analysis of A. thaliana natural variation can be addressed using a variety of approaches, from genetics and molecular methods to ecology and evolutionary questions. During my PhD, I got the chance to tackle several of those aspects through my contributions to three independent projects which have in common to exploit A. thaliana natural variation. The first one is the analysis of the pattern of polymorphism from a set of 102 A. thaliana accessions at the MOT1 gene coding for a molybdate transporter (an essential micronutrient) and responsible for contrasted growth and fitness among accessions in response to Mo availability in the soil. I showed at different geographical scales that MOT1 pattern of polymorphisms is not consistent with neutral evolution and shows signs of diversifying selection. This work helped reinforce the hypothesis that in some populations, mutations in MOT1 have been selected to face soils rich in Mo and potentially deleterious despite their negative effect on Mo-limiting soils. The second project consists in the characterisation and functional analysis of two putative receptor-like kinases (RLKs) identified from their effect on shoot growth specifically under mannitol-supplemented media and not in response to other osmotic constraints. The function of such RLKs in A. thaliana, which is not known to synthesize mannitol was intriguing at first but, through different experiments, we built the hypothesis that those RLKs could be activated by the mannitol produced by some pathogens such as fungi and participate to plant defensive response. The third project, in collaboration with Michel Vincentz's team from CBMEG (Brasil) and Vincent Colot (IBENS, Paris), consists in the analysis of the occurrence of natural epigenetic variants of the QQS gene in different populations from Central Asia and their possible phenotypic and adaptive consequences. Overall, these analyses of the genetic and epigenetic molecular variation leading to the biomass phenotype(s) in interaction with the environment provide clues as to how and where in the pathways adaptation is shaping natural variation.

Thesis (MscAgric (Horticulture))--University of Stellenbosch, 2010. / ENGLISH ABSTRACT: Commercial fig production with popular European cultivars, Bourjasotte Noire, Col de Damme Noire and Noire de Caromb, is new to the Western Cape. Little research on fig production has been conducted in South Africa and producers are struggling to implement effective commercial practices. In order to establish practices that will maximise yield of quality fruit, the most productive one-year-old shoot lengths were identified in a phenological study. All shoot length categories evaluated in ‘Bourjasotte Noire’ (10 – 15 cm, 25 – 40 cm, 50 – 65 cm, 75+ cm) yielded fruit and will probably yield well the following season. In ‘Col de Damme Noire’, shoots longer than 60 cm seem to be suited to reproduction, yet they might produce a poor yield the following season. Shoots 10 – 20 cm long in ‘Noire de Caromb’ are productive relative to their length, while shoots 30 – 50 cm and 60 – 80 cm long are also fairly productive. Shoots longer than 100 cm produced suitable shoot lengths for yield the following season. Two experiments were conducted on ‘Bourjasotte Noire’ and ‘Col de Damme Noire’ to establish the type (Experiment 1, different intensity heading cuts) and timing (Experiment 2) of pruning cuts required to stimulate the growth of shoots of the same length as the shoots selected to be optimal for yield in the phenology study, and to reduce the expression of distal branching. In ‘Bourjasotte Noire’, removing one third of the total length of one-year-old shoots on 21 July by heading stimulated the development of more growth and longer current season shoots compared to other treatments, while reducing yield slightly. Heading back to three nodes in ‘Col de Damme Noire’ stimulated the growth of current season shoots of the optimal length established in the phenology study, while heading cuts on 30 June produced the longest average current season shoot length in ‘Col de Damme Noire’. To further address the effects of distal branching (acrotony), an experiment was conducted to establish whether rest breaking agents (RBA’s) in combination with tip-pruning can increase tree complexity by improving bud break, and whether increased complexity would increase yield in all three cultivars. A second experiment was conducted to evaluate the effects of timing RBA applications on bud break and harvest scheduling. Lift® increased the number of buds breaking in ‘Bourjasotte Noire’, while in ‘Noire de Caromb’ Dormex® and oil increased bud break. Tip-pruning increased the average shoot length in ‘Bourjasotte Noire’ and ‘Col de Damme Noire’, while causing a reduction in the amount of new growth in ‘Noire de Caromb’. Lift® applied 3 August and Dormex® applied 30 June shortened the number of days to 50% bud break in ‘Bourjasotte Noire’ and ‘Col de Damme Noire’. Both Lift® and Dormex® applied on 30 June decreased the number of days to 50% bud break and 50% harvest of the breba crop in ‘Noire de Caromb’. These treatments increased the number of fruit in both the breba and main crop of ‘Noire de Caromb’, but reduced fruit size. In conclusion, different approaches with regards to pruning needs to be followed for each cultivar to establish or maintain the optimal shoots for reproduction, while RBA’s can be used to force earlier, increased- bud break and harvest of breba fruit. / AFRIKAANSE OPSOMMING: Kommersiele verbouing van drie Europese vykultivars, Bourjasotte Noire, Col de Damme Noire en Noire de Caromb is nuut tot die Wes-Kaap. Baie min navorsing oor die verbouing van vye is al in Suid-Afrika gedoen, met die gevolg dat produsente sukkel om effektiewe kommersiële verbouingspraktyke te implementeer. ‘n Fenologiese studie van die drie kultivars is uitgevoer om vas te stel wat die mees produktiewe een-jaar-oue lootlengte is, met die doel om die opbrengs van kwaliteit vrugte te maksimeer. Al vier kategorieë wat ge-evalueer is in ‘Bourjasotte Noire’ (10 – 15 cm, 25 – 40 cm, 50 – 65 cm, 75+ cm) is gevind om geskik te wees vir huidige en volgende seisoen opbrengs. Lote langer as 60 cm is geskik vir opbrengs in ‘Col de Damme Noire’ in die huidige seisoen, maar mag in die volgende seisoen swak presteer a.g.v. die gebrekkige lengte van nuwe lote wat daarop ontwikkel. In ‘Noire de Caromb’ is gevind dat lote 10 – 20 cm lank baie produktief is relatief tot hul lengte en dat lote 20 – 50 cm en 60 – 80 cm lank ook relatief produktief is. Lote langer as 100 cm was minder produktief, maar het nuwe lote gelewer wat geskik is vir opbrengs die volgende seisoen. Twee snoei eskperimente is uitgevoer op ‘Bourjasotte Noire’ en ‘Col de Damme Noire’ om vas te stel wat die mees geskikte tipe snoeisnit (Eksperiment 1, verskillende dieptes van topsnitte) en tydstip om te snoei (Eksperiment 2) is met die doel om lote te produseer soortgelyk in lengte aan die wat in die fenologie studie uitgewys is as die produktiefste, en om moontlik die voorkoms van “kaalnekke” te verminder. In ‘Bourjasotte Noire’ is gevind dat die wegsnoei van ‘n derde van die loot op 21 Julie aanleiding gee tot meer groei, langer een-jaar-oue lote en ‘n effense afname in opbrengs. Geskikte lote langer as 60 cm kan in ‘Col de Damme Noire’ verkry word deur lote te top sodat net drie nodes oorbly. Die uitvoer van topsnitte op 30 Junie het langer gemiddelde lootlengtes tot gevolg gehad. Om die probleem van “kaalnekke” (apikale dominansie) verder aan te spreek, is ‘n eksperiment uitgevoer om vas te stel of rusbreekmiddels gekombineerd met tip-snoei gebruik kan word om kompleksiteit te vermeerder deur knopbreek te verhoog, en indien wel, of dit sal aanleiding gee tot verhoogde opbrengs in al drie kultivars. ‘n Tweede eksperiment met verskillende toedieningstye van rusbreekmiddels is uitgevoer om vas te stel of oeste geskeduleer kan word. Lift® het knopbreek verhoog in ‘Bourjasotte Noire’, terwyl Dormex® en olie knopbreek verhoog het in ‘Noire de Caromb’. Tip-snoei het die gemiddelde lootlengtes verhoog in ‘Bourjasotte Noire’ en ‘Col de Damme Noire’, terwyl dit groei verminder het in ‘Noire de Caromb’. Lift® toediening op 3 Augustus en Dormex® toediening op 30 Junie het die aanvang van 50% knopbreek vervroeg in ‘Boujasotte Noire’ en ‘Col de Damme Noire’. Beide Lift® en Dormex® toediening op 30 Junie het die bereiking van 50% knopbreek- en 50% oes vervroeg in ‘Noire de Caromb’. Hierdie behandeling het ook die aantal vrugte van die breba- en hoofoes vermeerder, maar vruggrootte verminder. Verskillende snoeibenaderings behoort dus gevolg te word om vir elke kultivar die regte lootlengtes te genereer of te onderhou, terwyl rusbreekmiddels gebruik kan word om knopbreek te vervroeg en verhoog, en om die breba oes te vervroeg.

Made available in DSpace on 2014-08-20T14:22:03Z (GMT). No. of bitstreams: 1 tese_mateus_silveira_pasa.pdf: 859976 bytes, checksum: f2ff90aef57af32f1bbedd20e9ba4218 (MD5) Previous issue date: 2014-01-17 / Excessive vegetative growth is a major concern among pear growers because it results in serious negative effects in the orchard, such as increased pruning costs, shading of the inner parts of the canopy, poor fruit quality and difficult pest control. The use of plant growth regulators [e.g. Prohexadione calcium (PCa)] is one of the most promising techniques currently available to manage vegetative growth in pears. PCa reduces shoot growth by blocking the biosynthesis of the plant hormone gibberellin, which regulates longitudinal shoot growth. The aim of this study was, therefore, to evaluate the productive and vegetative responses of various pear cultivars to PCa. Three trials were carried out: Trial 1) PCa was applied to d Anjou pear trees in the lower and upper Hood River Valley, Oregon, USA to determine its effectiveness for managing the excessive vigor of d Anjou under different growing climates, with PCa rates ranging from 125 to 250 mg L-1. Ethephon was also applied (150 and 300 mg L-1) as an attempt to improve flower bud differentiation; Trial 2) PCa was selectively applied to dormant-headed (1/3rd removed) and unpruned shoots in a high-density d Anjou pear orchard in Oregon, USA. Both sets of shoots were treated with 250 mg L-1 P-Ca in either a single or double application; Trial 3) PCa was applied to Carrick , Packham s and William s pear in the experimental field of Federal University of Pelotas, RS, Brazil. Trees were treated with 750 g ha-1 i.a. PCa, which was split in four (187.5 g ha-1 a.i. each) and three timings (250 g ha-1 a.i. each) in the 2011 and 2012 growing seasons, respectively. The most important results are presented separated for each trial. Trial 1) P-Ca was effective for reducing shoot elongation at multiple sites over several growing seasons. In one case, the added benefits of increased fruit set and yield were also observed. However, the consistent reduction in return bloom and its translation to lower return yields, not previously documented for d Anjou , counteracts these benefits. Ethephon showed potential to ameliorate the activity of P-Ca on return bloom and production but it requires further investigation. Trial 2) At the end of the season, unpruned shoot length was decreased by 28% and 41% for shoots treated with P-Ca once and twice, respectively, while headed shoots were 37% shorter than their controls (treated only once). The number of nodes and average internode length were significantly reduced for P-Ca-treated shoots, irrespective of pruning level, conferring a higher node density relative to control shoots. These results implicate P-Ca as a powerful tool for precision-management of tree vigor in intensive pear plantings via selective treatment to areas of high vigor. Trial 3) The application of PCa at 750 g. ha-1 a.i satisfactorily controls shoot growth through the reduction of internode length of Carrick , Packham s and William s pears. Besides, it was observed that return bloom is not negatively affected by PCa. So, this plant growth regulator is a promissing management tool to reduce shoot growth and the need for pruning in pear orchards. / O excesso de crescimento vegetativo é uma das principais preocupações dos produtores de pera porque resulta em sérios efeitos negativos no pomar, como alto custo de poda, sombreamento da parte interna da copa, baixa qualidade de frutas e dificuldade no manejo de pragas e doenças. A utilização de fitorreguladores [e.g. Prohexadiona cálcio (PCa)] é uma das alternativas mais promissoras para manejar o crescimento vegetativo de pereiras. PCa reduz o crescimento de ramos através do bloqueio da biossíntese do hormônio vegetal giberelina, a qual regula o crescimento longitudinal dos ramos. O objetivo do presente estudo foi, portanto, de avaliar as respostas produtivas e vegetativas de várias cultivares de pereira em função da PCa. Três experimentos foram conduzidos: Experimento 1) PCa foi aplicado em pereiras d Anjou localizadas em regiões de baixa e alta altitude do Hood River Valley, Oregon, USA, para determinar a sua efetividade no manejo do crescimento vegetativo excessivo em diferentes condições climáticas, com doses de PCa variando de 125 a 250 mg L-1. O fitorregulador Etefon também foi aplicado (150 e 300 mg L-1) como uma tentativa de melhorar a diferenciação floral; Experimento 2) PCa foi seletivamente aplicado em ramos despontados no período de dormência (1/3 removido) e não podados em um pomar em alta densidade de pereiras d Anjou em Oregon, USA. Ambos os conjuntos de ramos foram tratados com 250 mg L-1 i.a. P-Ca, o qual foi aplicado uma ou duas vezes; Experimento 3) PCa foi aplicado em pereiras Carrick , Packham s e William s no campo experimental da Universidade Federal de Pelotas, RS, Brasil. As plantas foram tratadas com 750 g ha-1 a.i. PCa, o qual foi parcelado em quatro (187,5 g ha-1 i.a. cada) e três vezes (250 g ha-1 i.a. cada) nas safras de 2011 e 2012, respectivamente. Os resultados mais importantes são apresentados separadamente para cada experimento. Experimento 1) P-Ca foi eficiente na redução do crescimento de ramos nos diferentes locais e em diferentes safras. Em uma das safras, também foi observado aumento na frutificação efetiva e produtividade. No entanto, a consistente redução no retorno da floração, que resultou em menores retornos de produtividade, a qual não foi relatada anteriormente para d Anjou , neutraliza esses benefícios. Etefon mostrou potencial para melhorar os efeitos do PCa no retorno da floração e produção, mas isso requer estudos adicionais. Experimento 2) No final da estação de crescimento, o comprimento dos ramos não despontados foi reduzido em 28% e 41%, quando tratados com PCa uma e duas vezes, respectivamente, enquanto que os ramos despontados foram 37% menores (tratados apenas uma vez com PCa) do que o controle. O número de entrenós e comprimento médio dos entrenós foram significativamente reduzidos nos ramos tratados com PCa, independentemente do tipo de poda, conferindo uma maior densidade de entrenós em relação aos ramos controle. Esses resultados mostram que o PCa é uma potente ferramenta para o manejo preciso do vigor das plantas em pomares conduzidos em alta densidade através do tratamento seletivo de áreas com vigor excessivo. Experimento 3) A aplicação de PCa na dose de 750 g. ha-1 i.a. controla satisfatoriamente o crescimento de ramos das pereiras Carrick , Packham s e William s , através da redução no comprimento médio dos entrenós. Além disso, foi observado que o retorno da floração não é negativamente afetado pela aplicação do PCa. Dessa forma, esse fitorregulador é uma ferramenta de manejo promissora para reduzir o crescimento de ramos e a necessidade de poda de pomares de pereira.

Des génotypes adaptés à des environnements contrastés ont de grandes chances de se comporter différemment lorsqu’ils sont placés dans des conditions similaires et contrôlées, notamment si leur sensibilité aux signaux environnementaux et/ou leur croissance intrinsèque sont limitées à différents niveaux. De ce fait, la variabilité observée dans les populations naturelles peut être utilisée comme une source illimitée de nouveaux allèles ou gènes pour l’étude des bases génétiques de la variation des traits quantitatifs. Mon travail de doctorat a consisté en l’analyse de la variabilité naturelle pour la croissance et la réponse à l’environnement chez Arabidopsis thaliana. Le but des approches de génétique quantitative est de comprendre comment la diversité génétique et épigénétique contrôle la variabilité phénotypique observée dans les populations à différentes échelles, au cours du développement et sous différentes contraintes environnementales. De plus, ces analyses ont pour objectif de comprendre comment les processus adaptatifs et démographiques influencent la fréquence de ces variants dans les populations en fonction de leur environnement local. Ainsi, l’étude de la variabilité naturelle peut être appréhendée en utilisant diverses approches, de la génétique et des méthodes de biologie moléculaire aux études écologiques et évolutives. Au cours de mon doctorat, j’ai eu la chance de travailler sur plusieurs de ces aspects au travers de trois projets indépendants qui exploitent tous la variabilité naturelle d’A. thaliana.Le premier projet a consisté en l’analyse du pattern de polymorphisme observé dans des populations d’A. thaliana au gène MOT1 qui code pour un transporteur de molybdate (la forme assimilable du molybdène (Mo), un micro-élément essentiel) et qui est responsable d’une partie des variations de croissance et de fitness observées à l’échelle de l’espèce en fonction de la disponibilité en Mo des sols. J’ai montré à différentes échelles géographiques que le pattern de polymorphisme à MOT1 ne reflète pas une évolution neutre mais présente plutôt des traces de sélection diversifiante. Ce travail a contribué à renforcer l’hypothèse selon laquelle des mutations au niveau du gène MOT1 pourraient avoir été sélectionnées dans certaines populations pour faire face aux niveaux élevés de Mo observés dans certains sols et potentiellement délétères malgré leur effet négatif sur des milieux pauvres en Mo.Le deuxième projet portait sur la caractérisation et l’analyse fonctionnelle de deux récepteur-kinase putatifs (RLK) identifiés de part leurs effets sur la croissance foliaire spécifiquement en réponse à un stress induit par du mannitol mais pas sous d’autres contraintes osmotiques. La fonction de ces récepteurs chez A. thaliana -qui n’est pas connu pour produire du mannitol- peut paraître intrigante. Les différentes expériences réalisées au cours de cette thèse nous ont cependant permis de construire un modèle selon lequel ces récepteurs pourraient être activés par le mannitol produit par certains pathogènes tel que les champignons et participer aux réponses de défense de la plante.Le troisième projet a été réalisé en collaboration avec l’équipe de Michel Vincentz (CBMEG, Brésil) et de Vincent Colot (IBENS, Paris) et consiste en l’analyse de l’occurrence de variants épigénétiques naturels au gène QQS dans différentes populations d’Asie Centrale et de leurs possibles conséquences phénotypique et adaptative.En conclusion, l’analyse des variants génétiques et épigénétiques naturels à l’origine des variations de biomasse en interaction avec l’environnement permet de comprendre comment l’évolution façonne la variabilité naturelle. / Genotypes adapted to contrasting environments are expected to behave differently when placed in common controlled conditions, if their sensitivity to environmental cues or intrinsic growth behaviour are set to different thresholds, or are limited at distinct levels. This allows natural variation to be exploited as an unlimited source of new alleles or genes for the study of the genetic basis of quantitative trait variation. My doctoral work focuses on analysing natural variation for shoot growth and response to the environment in A. thaliana. Natural variation analyses aim at understanding how molecular genetic or epigenetic diversity controls phenotypic variation at different scales and times of plant development and under different environmental conditions, and how selection or demographic processes influence the frequency of those molecular variants in populations for them to get adapted to their local environment. As such, the analysis of A. thaliana natural variation can be addressed using a variety of approaches, from genetics and molecular methods to ecology and evolutionary questions. During my PhD, I got the chance to tackle several of those aspects through my contributions to three independent projects which have in common to exploit A. thaliana natural variation. The first one is the analysis of the pattern of polymorphism from a set of 102 A. thaliana accessions at the MOT1 gene coding for a molybdate transporter (an essential micronutrient) and responsible for contrasted growth and fitness among accessions in response to Mo availability in the soil. I showed at different geographical scales that MOT1 pattern of polymorphisms is not consistent with neutral evolution and shows signs of diversifying selection. This work helped reinforce the hypothesis that in some populations, mutations in MOT1 have been selected to face soils rich in Mo and potentially deleterious despite their negative effect on Mo-limiting soils. The second project consists in the characterisation and functional analysis of two putative receptor-like kinases (RLKs) identified from their effect on shoot growth specifically under mannitol-supplemented media and not in response to other osmotic constraints. The function of such RLKs in A. thaliana, which is not known to synthesize mannitol was intriguing at first but, through different experiments, we built the hypothesis that those RLKs could be activated by the mannitol produced by some pathogens such as fungi and participate to plant defensive response. The third project, in collaboration with Michel Vincentz’s team from CBMEG (Brasil) and Vincent Colot (IBENS, Paris), consists in the analysis of the occurrence of natural epigenetic variants of the QQS gene in different populations from Central Asia and their possible phenotypic and adaptive consequences. Overall, these analyses of the genetic and epigenetic molecular variation leading to the biomass phenotype(s) in interaction with the environment provide clues as to how and where in the pathways adaptation is shaping natural variation.