Genetic diversity and population structure of Musa accessions in ex situ conservation

Abstract Background Banana cultivars are mostly derived from hybridization between wild diploid subspecies of Musa acuminata (A genome) and M. balbisiana (B genome), and they exhibit various levels of ploidy and genomic constitution. The Embrapa ex situ Musa collection contains over 220 accessions, of which only a few have been genetically characterized. Knowledge regarding the genetic relationships and diversity between modern cultivars and wild relatives would assist in conservation and breeding strategies. Our objectives were to determine the genomic constitution based on Internal Transcribed Spacer (ITS) regions polymorphism and the ploidy of all accessions by flow cytometry and to investigate the population structure of the collection using Simple Sequence Repeat (SSR) loci as co-dominant markers based on Structure software, not previously performed in Musa. Results From the 221 accessions analyzed by flow cytometry, the correct ploidy was confirmed or established for 212 (95.9%), whereas digestion of the ITS region confirmed the genomic constitution of 209 (94.6%). Neighbor-joining clustering analysis derived from SSR binary data allowed the detection of two major groups, essentially distinguished by the presence or absence of the B genome, while subgroups were formed according to the genomic composition and commercial classification. The co-dominant nature of SSR was explored to analyze the structure of the population based on a Bayesian approach, detecting 21 subpopulations. Most of the subpopulations were in agreement with the clustering analysis. Conclusions The data generated by flow cytometry, ITS and SSR supported the hypothesis about the occurrence of homeologue recombination between A and B genomes, leading to discrepancies in the number of sets or portions from each parental genome. These phenomenons have been largely disregarded in the evolution of banana, as the “single-step domestication” hypothesis had long predominated. These findings will have an impact in future breeding approaches. Structure analysis enabled the efficient detection of ancestry of recently developed tetraploid hybrids by breeding programs, and for some triploids. However, for the main commercial subgroups, Structure appeared to be less efficient to detect the ancestry in diploid groups, possibly due to sampling restrictions. The possibility of inferring the membership among accessions to correct the effects of genetic structure opens possibilities for its use in marker-assisted selection by association mapping.

Implementation of a non ground meta interpreter for defeasible logic

Human reasoning is a fascinating and complex cognitive process that can be applied in different research areas such as philosophy, psychology, laws and financial. Unfortunately, developing supporting software (to those different areas) able to cope such as complex reasoning it’s difficult and requires a suitable logic abstract formalism. In this thesis we aim to develop a program, that has the job to evaluate a theory (a set of rules) w.r.t. a Goal, and provide some results such as “The Goal is derivable from the KB5 (of the theory)”. In order to achieve this goal we need to analyse different logics and choose the one that best meets our needs. In logic, usually, we try to determine if a given conclusion is logically implied by a set of assumptions T (theory). However, when we deal with programming logic we need an efficient algorithm in order to find such implications. In this work we use a logic rather similar to human logic. Indeed, human reasoning requires an extension of the first order logic able to reach a conclusion depending on not definitely true6 premises belonging to a incomplete set of knowledge. Thus, we implemented a defeasible logic7 framework able to manipulate defeasible rules. Defeasible logic is a non-monotonic logic designed for efficient defeasible reasoning by Nute (see Chapter 2). Those kind of applications are useful in laws area especially if they offer an implementation of an argumentation framework that provides a formal modelling of game. Roughly speaking, let the theory is the set of laws, a keyclaim is the conclusion that one of the party wants to prove (and the other one wants to defeat) and adding dynamic assertion of rules, namely, facts putted forward by the parties, then, we can play an argumentative challenge between two players and decide if the conclusion is provable or not depending on the different strategies performed by the players. Implementing a game model requires one more meta-interpreter able to evaluate the defeasible logic framework; indeed, according to Göedel theorem (see on page 127), we cannot evaluate the meaning of a language using the tools provided by the language itself, but we need a meta-language able to manipulate the object language8. Thus, rather than a simple meta-interpreter, we propose a Meta-level containing different Meta-evaluators. The former has been explained above, the second one is needed to perform the game model, and the last one will be used to change game execution and tree derivation strategies.

Genetische Kartierung und QTL-Analyse agronomischer Eigenschaften der Weinrebe unter besonderer Berücksichtigung der Pilzresistenz

153 Nachkommen einer Kreuzung aus der pilzresistenten Rebsorte ‘Regent‘ und ‘Lemberger‘ als klassischer pilzsensitiver Sorte zeigen quantitative Merkmalsvariation bezüglich der Resistenz gegen Plasmopara viticola und Uncinula necator sowie für weitere Eigenschaften, die z.B. das Eintreten der Beerenreife betreffen. Auf dem Weg über die genetische Kartierung mit molekularen Markern und der Lokalisierung von QTL-Effekten konnten Hinweise auf weinbaulich relevante Genomregionen gewonnen werden; dies liefert z.B. die Basis für markergestützte Selektion bei Zuchtvorhaben mit dem Resistenzträger ‘Regent’ (vgl. auch FISCHER et al., 2004). Ein Major-QTL für die Resistenz gegen den Echten Mehltau Uncinula necator sowie zwei Major QTL für die Resistenz gegen den Erreger des Falschen Mehltau, Plasmopara viticola, traten mit hoher Signifikanz auf drei verschiedenen Kopplungsgruppen von ‘Regent‘ auf. Auch Regionen mit Relevanz für das Eintreten der Beerenreife wurden beschrieben. Über die Isolierung, Sequenzierung und anschließende Analyse einzelner Markerfragmente mit Methoden der Bioinformatik ist es gelungen, ein putatives T10P12.4-Ortholog der Weinrebe (ein thioredoxinähnliches Protein) in enger Kopplung zu einem Major-QTL-Maximum für Plasmopara viticola-Resistenz zu identifizieren, das als Kandidat für die Beteiligung an der Pathogenantwort in Frage kommt. Es konnte exemplarisch gezeigt werden, dass die eingesetzten Methoden der Kartierung und QTL-Analyse unter Verwendung PCR-basierter Markertypen wie SSR und AFLP und einer beschleunigten Analyse über computergestützte Kapillargelelektrophorese in vertretbarem Zeitrahmen bis zur Isolation potentieller Schlüsselgene führen können. Die grundsätzliche Eignung der QTL-Analyse als effizientes Werkzeug gezielter Züchtungsplanung für den Weinbau bestätigte sich. Ihre Anwendung im Rahmen der vorliegenden Dissertation hat die Basis für die Nutzung von QTL-Information bei dem Vergleich etablierter und der Entwicklung neuer Sorten gelegt und zum Verständnis von Prozessen beigetragen, die den betrachteten Eigenschaften wie der Pilzresistenz möglicherweise zu Grunde liegen. Ein großer Teil der gewonnenen Daten bringt auch die Untersuchungen anderer Kultivare voran und ist intervarietal übertragbar. Darüber hinaus haben sich Chancen für vergleichende Studien zwischen der Weinrebe einerseits und der Modellpflanze Arabidopsis thaliana sowie weiteren Kulturpflanzen andererseits abgezeichnet. Die Hinweise auf die zentrale Rolle und universelle Natur des Redox-Signalling haben interessante Perspektiven zum Verständnis organismenübergreifender physiologischer Zusammenhänge eröffnet. Dies betrifft z.B. auch die Reaktion auf Verwundung oder die Pathogenantwort.

Synergies and trade-offs between insect and pathogen resistance in maize leaves and roots

Determining links between plant defence strategies is important to understand plant evolution and to optimize crop breeding strategies. Although several examples of synergies and trade-offs between defence traits are known for plants that are under attack by multiple organisms, few studies have attempted to measure correlations of defensive strategies using specific single attackers. Such links are hard to detect in natural populations because they are inherently confounded by the evolutionary history of different ecotypes. We therefore used a range of 20 maize inbred lines with considerable differences in resistance traits to determine if correlations exist between leaf and root resistance against pathogens and insects. Aboveground resistance against insects was positively correlated with the plant's capacity to produce volatiles in response to insect attack. Resistance to herbivores and resistance to a pathogen, on the other hand, were negatively correlated. Our results also give first insights into the intraspecific variability of root volatiles release in maize and its positive correlation with leaf volatile production. We show that the breeding history of the different genotypes (dent versus flint) has influenced several defensive parameters. Taken together, our study demonstrates the importance of genetically determined synergies and trade-offs for plant resistance against insects and pathogens.

Quantitative trait loci and metabolic pathways

The interpretation of quantitative trait locus (QTL) studies is limited by the lack of information on metabolic pathways leading to most economic traits. Inferences about the roles of the underlying genes with a pathway or the nature of their interaction with other loci are generally not possible. An exception is resistance to the corn earworm Helicoverpa zea (Boddie) in maize (Zea mays L.) because of maysin, a C-glycosyl flavone synthesized in silks via a branch of the well characterized flavonoid pathway. Our results using flavone synthesis as a model QTL system indicate: (i) the importance of regulatory loci as QTLs, (ii) the importance of interconnecting biochemical pathways on product levels, (iii) evidence for “channeling” of intermediates, allowing independent synthesis of related compounds, (iv) the utility of QTL analysis in clarifying the role of specific genes in a biochemical pathway, and (v) identification of a previously unknown locus on chromosome 9S affecting flavone level. A greater understanding of the genetic basis of maysin synthesis and associated corn earworm resistance should lead to improved breeding strategies. More broadly, the insights gained in relating a defined genetic and biochemical pathway affecting a quantitative trait should enhance interpretation of the biological basis of variation for other quantitative traits.

Interactions between quantitative trait loci in soybean in which trait variation at one locus is conditional upon a specific allele at another.

A large recombinant inbred population of soybean has been characterized for 220 restriction fragment-length polymorphism (RFLP) markers. Values for agronomic traits also have been measured. Quantitative trait loci (QTL) for height, yield, and maturity were located by their linkage to RFLP markers. QTL controlling large amounts of trait variation were analyzed for the dependence of trait variation on particular alleles at a second locus by comparing cumulative distributions of the trait for each genotype (four genotypes per pair of loci). Interesting pairs of loci were analyzed statistically with maximum likelihood and Monte Carlo comparison of additive and epistatic models. For each locus affecting height, variation was conditional upon the presence of a particular allele at a second unlinked locus that itself explained little or no trait variation. The results show that interactions between QTL are frequent and control large effects. Interactions distinguished between different QTL in a single linkage group and between QTL that affect different traits closely linked to one RFLP marker--i.e., distinguished between pleiotropy and closely linked genes. The implications for the evolution of inbreeding plants and for the construction of agronomic breeding strategies are discussed.

Trait physiology and crop modelling as a framework to link phenotypic complexity to underlying genetic systems

New tools derived from advances in molecular biology have not been widely adopted in plant breeding for complex traits because of the inability to connect information at gene level to the phenotype in a manner that is useful for selection. In this study, we explored whether physiological dissection and integrative modelling of complex traits could link phenotype complexity to underlying genetic systems in a way that enhanced the power of molecular breeding strategies. A crop and breeding system simulation study on sorghum, which involved variation in 4 key adaptive traits-phenology, osmotic adjustment, transpiration efficiency, stay-green-and a broad range of production environments in north-eastern Australia, was used. The full matrix of simulated phenotypes, which consisted of 547 location-season combinations and 4235 genotypic expression states, was analysed for genetic and environmental effects. The analysis was conducted in stages assuming gradually increased understanding of gene-to-phenotype relationships, which would arise from physiological dissection and modelling. It was found that environmental characterisation and physiological knowledge helped to explain and unravel gene and environment context dependencies in the data. Based on the analyses of gene effects, a range of marker-assisted selection breeding strategies was simulated. It was shown that the inclusion of knowledge resulting from trait physiology and modelling generated an enhanced rate of yield advance over cycles of selection. This occurred because the knowledge associated with component trait physiology and extrapolation to the target population of environments by modelling removed confounding effects associated with environment and gene context dependencies for the markers used. Developing and implementing this gene-to-phenotype capability in crop improvement requires enhanced attention to phenotyping, ecophysiological modelling, and validation studies to test the stability of candidate genetic regions.

Improving drought tolerance in rainfed lowland rice: An example from Thailand

A large portion of the world's poor farm in rainfed systems where the water supply is unpredictable and droughts are common. In Thailand there are approximately 6.2 million ha of rain fed lowland rice, which account for 67% of the country's total rice-growing area. This rice system is often characterised by too much and too little water in the same season. Farmers' estimates of their annual losses to drought are as high as 45% in the upper parts of the toposequence. In contrast to irrigated rice systems, gains from crop improvement of rainfed rice have been modest, in part because there has been little effort to breed and select for drought tolerance for the target rainfed environments. The crop improvement strategy being used in Thailand considers three mechanisms that influence yield in the drought prone targets: yield potential as an important mechanism for mild drought (where yield loss is less than 50%), drought escape (appropriate phenology) and drought tolerance traits of leaf water potential, sterility, flower delay and drought response index for more severe drought conditions. Genotypes are exposed to managed drought environments for selection of drought tolerant genotypes. A marker assisted selection (MAS) scheme has been developed and applied for selection of progenies in the backcrossing program. The plant breeding program uses rapid generation advance techniques that enable early yield testing in the target population of environments (TPE) through inter-station (multi-location yield testing) and on-farm trials. A farmer participatory approach has been used to identify the TPE for the breeding program. Four terrace paddy levels have been identified, upper (drought), middle (drought prone to favorable) and lower (flooded). This paper reports the change in the breeding program for the drought prone tainted lowland rice environments of North and Northeast Thailand by incorporating our knowledge on adaptation and on response of rice to drought. (c) 2005 Elsevier B.V. All rights reserved.

Trait physiology and crop modelling to link phenotypic complexity to underlying genetic systems

New tools derived from advances in molecular biology have not been widely adopted in plant breeding because of the inability to connect information at gene level to the phenotype in a manner that is useful for selection. We explore whether a crop growth and development modelling framework can link phenotype complexity to underlying genetic systems in a way that strengthens molecular breeding strategies. We use gene-to-phenotype simulation studies on sorghum to consider the value to marker-assisted selection of intrinsically stable QTLs that might be generated by physiological dissection of complex traits. The consequences on grain yield of genetic variation in four key adaptive traits – phenology, osmotic adjustment, transpiration efficiency, and staygreen – were simulated for a diverse set of environments by placing the known extent of genetic variation in the context of the physiological determinants framework of a crop growth and development model. It was assumed that the three to five genes associated with each trait, had two alleles per locus acting in an additive manner. The effects on average simulated yield, generated by differing combinations of positive alleles for the traits incorporated, varied with environment type. The full matrix of simulated phenotypes, which consisted of 547 location-season combinations and 4235 genotypic expression states, was analysed for genetic and environmental effects. The analysis was conducted in stages with gradually increased understanding of gene-to-phenotype relationships, which would arise from physiological dissection and modelling. It was found that environmental characterisation and physiological knowledge helped to explain and unravel gene and environment context dependencies. We simulated a marker-assisted selection (MAS) breeding strategy based on the analyses of gene effects. When marker scores were allocated based on the contribution of gene effects to yield in a single environment, there was a wide divergence in rate of yield gain over all environments with breeding cycle depending on the environment chosen for the QTL analysis. It was suggested that knowledge resulting from trait physiology and modelling would overcome this dependency by identifying stable QTLs. The improved predictive power would increase the utility of the QTLs in MAS. Developing and implementing this gene-to-phenotype capability in crop improvement requires enhanced attention to phenotyping, ecophysiological modelling, and validation studies to test the stability of candidate QTLs.

Isotopic composition of diet and tissues, and isotope discrimination factors for pink-footed and barnacle geese, Svalbard

Breeding in the high Arctic is time constrained and animals should therefore start with their annual reproduction as early as possible. To allow for such early reproduction in migratory birds, females arrive at the breeding grounds either with body stores or they try to rapidly develop their eggs after arrival using local resources. Svalbard breeding barnacle geese Branta leucopsis have to fly non-stop for about 1100 km from their last continental staging site to the archipelago making the transport of body stores costly. However, environmental conditions at the breeding grounds are highly unpredictable favouring residual body stores allowing for egg production after arrival on the breeding grounds. We estimated the reliance on southern continental resources, i.e. body stores for egg formation, in barnacle geese using stable isotope ratios in the geese's forage along the flyway and in their eggs. Females adopted mixed breeding strategies by using southern resources as well as local resources to varying extents for egg formation. Southern capital in lipid-free yolk averaged 41% (range: 23-65%), early laid eggs containing more southern capital than eggs laid late in the season. Yolk lipids and albumen did not vary over time and averaged a southern capital proportion of 54% (range: 32-73%) and 47% (range: 25-88%), respectively. Our findings indicate that female geese vary the use of southern resources when synthesizing their eggs and this allocation also varies among egg tissues. Their mixed and flexible use of distant and local resources potentially allows for adaptive adjustments to environmental conditions encountered at the archipelago just before breeding.

Genetic variation of temperature-regulated curd induction in cauliflower: elucidation of floral transition by genome-wide association mapping and gene expression analysis

Cauliflower (Brassica oleracea var. botrytis) is a vernalization-responsive crop. High ambient temperatures delay harvest time. The elucidation of the genetic regulation of floral transition is highly interesting for a precise harvest scheduling and to ensure stable market supply. This study aims at genetic dissection of temperature-dependent curd induction in cauliflower by genome-wide association studies and gene expression analysis. To assess temperature dependent curd induction, two greenhouse trials under distinct temperature regimes were conducted on a diversity panel consisting of 111 cauliflower commercial parent lines, genotyped with 14,385 SNPs. Broad phenotypic variation and high heritability (0.93) were observed for temperature-related curd induction within the cauliflower population. GWA mapping identified a total of 18 QTL localized on chromosomes O1, O2, O3, O4, O6, O8, and O9 for curding time under two distinct temperature regimes. Among those, several QTL are localized within regions of promising candidate flowering genes. Inferring population structure and genetic relatedness among the diversity set assigned three main genetic clusters. Linkage disequilibrium (LD) patterns estimated global LD extent of r(2) = 0.06 and a maximum physical distance of 400 kb for genetic linkage. Transcriptional profiling of flowering genes FLOWERING LOCUS C (BoFLC) and VERNALIZATION 2 (BoVRN2) was performed, showing increased expression levels of BoVRN2 in genotypes with faster curding. However, functional relevance of BoVRN2 and BoFLC2 could not consistently be supported, which probably suggests to act facultative and/or might evidence for BoVRN2/BoFLC-independent mechanisms in temperature regulated floral transition in cauliflower. Genetic insights in temperature-regulated curd induction can underpin genetically informed phenology models and benefit molecular breeding strategies toward the development of thermo-tolerant cultivars.

Plano estratégico de melhoramento nos ovinos Serra da Estrela

A ovelha Serra da Estrela é a principal raça ovina leiteira do país, com 2 variedades: branca (em maior número) e preta. Os principais produtos resultantes da exploração destes animais são o leite (através da sua transformação em Queijo Serra da Estrela) e a carne (através da comercialização de borregos com 30 a 40 dias de idade), ambos de Denominação de Origem Protegida (DOP). Tem sido através da intervenção, a vários níveis, da Associação Nacional de Criadores de Ovinos Serra da Estrela (ANCOSE), que esta raça se tem mantido, nomeadamente, através das acções reprodutivas nas explorações (IA, sincronização de cios, utilização de machos seleccionados) e da recolha e organização da informação genealógica e produtiva (através dos contrastes funcionais de lactação). A informatização integrada e mais racional desta informação, realizada nos últimos anos, tornou possível a execução de outras atividades, nomeadamente, a caracterização genética por análise demográfica e avaliação genética da raça. Com este trabalho pretende-se, através da análise da informação disponível no Livro Genealógico da raça, cedida pela ANCOSE, estudar vários parâmetros que contribuem para a caracterização demográfica da raça Serra da Estrela e a sua avaliação genética. Foram considerados 302911 animais, 401177 partos de 144024 ovelhas, para estimação dos valores genéticos da PROL e 351720 registos de lactações de 131760 ovelhas, para estimação dos valores genéticos da PL150 obtidos em 844 explorações e registados entre 1986 e 2012. Estes resultados auxiliarão na definição das estratégias futuras para a gestão destas populações e à sua utilização em esquemas de selecção desta raça, propondo-se um plano estratégico, com actuações a vários níveis. Nos últimos anos as estratégias de melhoramento genético dos animais por selecção evoluiu consideravelmente. Através das estimativas dos valores genéticos dos animais, obtidas a partir das suas performances e dos seus parentes, pretende-se seleccionar os animais geneticamente superiores para as características mais importantes.

Sustainable deployment of QTLs conferring quantitative resistance to crops: first lessons from a stochastic model

International audience

Seven Ulmus minor clones tolerant to Ophiostoma novo-ulmi registered as forest reproductive material in Spain

The Spanish elm programme began in 1986 in response to the devastating impact of Dutch elm disease on natural elm stands and urban trees. Its main objectives were to conserve remaining genetic resources and select and breed tolerant native elm genotypes. After 27 years of work conducting susceptibility trials on thousands of elm genotypes, the first seven tolerant Ulmus minor trees are now being registered by the Spanish Environmental Administration. This paper presents the results of the susceptibility tests on these clones and their distinctive genetic, morphological and phenological features. In all susceptibility trials the commercial ?Sapporo Autumn Gold? clone, which is highly tolerant to O. novo-ulmi, was used as a control. The registered clones were named ?Ademuz?, ?Dehesa de la Villa?, ?Majadahonda?, ?Toledo?, ?Dehesa de Amaniel?, ?Retiro? and ?Fuente Umbría?. The most tolerant clone was ?Dehesa de Amaniel?, as its wilting values were below 5% during the two consecutive inoculation trials performed in Madrid. ?Fuente Umbría?, tested over four consecutive years in Guadalajara and Palencia, was the Spanish clone with the most reliable tolerance level to O. novo-ulmi. The ?Ademuz? and ?Majadahonda? clones had the highest ornamental scores and are promising trees for use in urban environments and tree breeding for ornamental quality. These two genotypes showed a later bud burst phenology than the other U. minor clones, demonstrating suitability to areas with late frost events. The Spanish programme aims to substantially increase the range of tolerant native elms through new selections and crossings to gain a better understanding of the genetic basis of resistance.

Enhancing legume ecosystem services through an understanding of plant–pollinator interplay

Legumes are bee-pollinated, but to a different extent. The importance of the plant– pollinator interplay (PPI), in flowering crops such as legumes lies in a combination of the importance of pollination for the production service and breeding strategies, plus the increasing urgency in mitigating the decline of pollinators through the development and implementation of conservation measures. To realize the full potential of the PPI, a multidisciplinary approach is required. This article assembles an international team of genebank managers, geneticists, plant breeders, experts on environmental governance and agro-ecology, and comprises several sections. The contributions in these sections outline both the state of the art of knowledge in the field and the novel aspects under development, and encompass a range of reviews, opinions and perspectives. The first three sections explore the role of PPI in legume breeding strategies. PPI based approaches to crop improvement can make it possible to adapt and re-design breeding strategies to meet both goals of: (1) optimal productivity, based on an efficient use of pollinators, and (2) biodiversity conservation. The next section deals with entomological aspects and focuses on the protection of the “pest control service” and pollinators in legume crops. The final section addresses general approaches to encourage the synergybetweenfoodproductionandpollinationservicesatfarmerfieldlevel.Twobasic approaches are proposed: (a) Farming with Alternative Pollinators and (b) Crop Design System.