Genetic diversity of potato for nitrogen use efficiency under low input conditions in Ethiopia
Getahun, Baye Berihun - \ 2017
Wageningen University. Promotor(en): R.G.F. Visser, co-promotor(en): C.G. van der Linden. - Wageningen : Wageningen University - ISBN 9789463436595 - 219
solanum tuberosum - potatoes - genetic diversity - nitrogen - plant breeding - ethiopia - nutrient use efficiency - solanum tuberosum - aardappelen - genetische diversiteit - stikstof - plantenveredeling - ethiopië - nutriëntengebruiksefficiëntie
Potato is a prime food security crop for smallholder farmers in the highland part of North western Ethiopia. In this region, nutrient availability, especially nitrogen (N) is a major constraint for crop productivity. To obtain insight in the possibility of improving potato for growth under low N input conditions in Ethiopia, we evaluated CxE diploid back cross population, modern European and Ethiopian potato cultivars and local Ethiopian cultivars for their ability to grow and produce tubers under low and high N input conditions. The experiments were conducted under rainfed and irrigation conditions. Eighty-eight Dutch cultivars and 9 Ethiopian cultivars were evaluated in three locations in North-western Ethiopia, in 2013 and in 2015. The two years represent two different growth seasons: rain-fed (June-October 2013) and irrigated cultivation (February-June 2015). Similarly 100 CxE diploid back cross potato genotypes were evaluated in both rainfed and irrigation production seasons in 2014. The Growth of the plants was monitored throughout the growth cycle using canopy cover measurements, with modelled canopy characteristics, and other agronomic traits were measured as per the description. The effect of season and location was further investigated by a GGE Biplot genotype-by-environment interaction analysis, and genetic factors determining phenotypic traits and yield were identified through QTL mapping and association mapping. Ethiopian cultivars showed a remarkable, environment-dependent difference in utilisation of the canopy for tuber production. While total photosynthetic capacity was higher in Ethiopian cultivars than in Dutch cultivars in rainfed production season at Injibara, tuber production was higher in Dutch cultivars. This low radiation use efficiency was not observed in the other rain-fed location (Debre-Tabor). A Genotype by Environment analysis using GGE biplots demonstrates that, Irrespective of the N levels and locations, rainfed production season test environments were grouped as one mega environment and irrigation production season test environments as the other mega environment, indicating most of the variation for yield and nitrogen use efficiency (NUE) in the dataset may be caused by the effect of rain-fed vs irrigation season. Further trials are needed to confirm this result. The QTL mapping with the CxE diploid population and GWAS analysis with the Dutch cultivars discovered both season-environment and N-specific QTL as well as constitutive QTLs. Overall, N availability affects Dutch and Ethiopian cultivars differentially, with strong environmental interaction on canopy and yield traits. Rainfed and irrigated seasons in Ethiopia may require different breeding programs for improved yield under varying fertilizer levels. Both constitutive and environment-specific QTLs were identified that may be targets for breeding prorgams towards improved yield under Ethiopian cultivation conditions.
From species to trait evolution in Aethionema (Brassicaceae)
Mohammadin, Setareh - \ 2017
Wageningen University. Promotor(en): M.E. Schranz. - Wageningen : Wageningen University - ISBN 9789463431385 - 125
brassicaceae - evolution - rna - genomes - genetic diversity - phytogeography - glucosinolates - quantitative trait loci - next generation sequencing - brassicaceae - evolutie - rna - genomen - genetische diversiteit - plantengeografie - glucosinolaten - loci voor kwantitatief kenmerk - next generation sequencing
The plant family Brassicaceae (or crucifers) is an economically important group that includes many food crops (e.g. cabbages and radishes), horticultural species (e.g. Draba, Iberis, Lunaria), and model plant species (particularly Arabidopsis thaliana). Because of the fundamental importance of A. thaliana to plant biology, it makes the Brassicaceae an ideal system for comparative genomics and to test wider evolutionary, ecological and speciation hypotheses. One such hypothesis is the ‘Whole Genome Duplication Radiation Lag Time’ (WGD-RLT) model for the role of polyploidy on the evolution of important plant families such as the Brassicaceae. The WGD-RLT model indicates a higher rate of diversification of a core-group compared to its sister group, due to a lag time after a whole genome duplication event that made it possible for novel traits or geo- or ecological events to increase the core groups diversification rate.
Aethionema is the species-poor sister genus of the core Brassicaceae and hence is at an important comparative position to analyse trait and genomic evolution of the species-rich core group. Aethionema species occur mainly in the western Irano-Turanian region, which is concordantly the biodiversity hotspot of the Brassicaceae family. Moreover comparing Aethionema to the Brassicaceae core group can help us to understand and test the ‘WGD-RLT’ model. However to be able to do so we first need to know more about Aethionema. In this thesis, I investigated various levels of evolutionary change (from macro, to micro to trait evolution) within the genus Aethionema, with a major focus the emerging model species Aethionema arabicum.
Next generation sequencing has made it possible to use the genomes of many species in a comparative framework. However, the formation of proteins and enzymes, and in the end the phenotype of the whole plant, relies on transcription from particular regions of the genome including genes. Hence, the transcriptome makes it possible to assess the functional parts of the genome. However, the functional part of the genome not only relies on the protein coding genes. Gene regulatory elements like promoters and long non-coding RNAs function as regulators of gene expression and hence are involved in increasing or decreasing transcription. In Chapter 2 I used the transcriptome of four different Aethionema species to understand the lineage specificity of these long non-coding RNAs. Moreover in a comparison with the Brassicaceae core group and Brassicaceae’s sister family the Cleomaceae I show that although the position of long non-coding RNAs can be conserved, their sequences do not have to be.
Most of the Aethionema species occur in the Irano-Turanian region, a politically instable region, making it hard for scientist to collect from. However the natural history collections made throughout the last centuries are a great resource. Combing these collections with the newest sequencing techniques, e.g. next generation sequencing, have allowed me to infer the phylogeny of ~75% of the known Aethionema species in a time calibrated and historical biogeographical framework. Hence, I was able to establish that Aethionema species likely originated from the Anatolian Diagonal and that major geological events like the uplift of the Turkish and Iranian plateau have had a hand in their speciation (Chapter 3).
To examine species-level processes I sequenced and analysed transcriptomes of eight Ae. arabicum accessions coming from Cyprus, Iran and Turkey to investigate population structure, genetic diversity and local adaptation (Chapter 4). The most prominent finding was a ploidy difference between the Iranian and Turkish/Cypriotic lines, whereby the former were (allo)tetraploid and the latter diploid. The tetraploid Iranian lines seem to have one set of alleles from the Turkish/Cypriotic gene-pool. However we do not know where the other alleles come from. In addition to the differences in ploidy level there are also differences in glucosinolate defence compounds between these two populations (Iranian vs Turkish/Cypriotic), with the Iranian lines lacking the diversity and concentration of indolic glucosinolates that the Turkish/Cypriotic lines have. This chapter serves as a good resource and starting point for future research in the region, maybe by using the natural history collections that are at hand.
Glucosinolates (i.e. mustard oils) are mainly made by Brassicales species, with their highest structural diversity in the Brassicaceae. In Chapter 5, I examined two Ae. arabicum lines (CYP and TUR) and their recombinant inbred lines to assess glucosinolate composition in different tissues and throughout the plants development. The levels of glucosinolates in the leaves changed when Ae. arabicum went from vegetative to a reproductive state. Moreover, a major difference in glucosinolate content (up to 10-fold) between CYP and TUR indicates a likely regulatory pathway outside of the main glucosinolate biosynthesis pathway. Multi-trait and multi-environment QTL analyses based on leaves, reproductive tissues and seeds identified a single major QTL. Fine mapping this region reduced the interval to only fifteen protein coding genes, including the two most intriguing candidates: FLOWERING LOCUS C (FLC) and the sulphate transporter SULTR2;1. These findings show an interesting correlation between development and defence.
Finally, Chapter 6 gives a final discussion of this thesis and its results. It brings the different topics together, put them in a bigger picture and look forward to new research possibilities.
Genetics of equine insect bite hypersensitivity and genetic diversity in horses
Shrestha, Merina - \ 2017
Wageningen University. Promotor(en): Henk Bovenhuis; D.J. de Koning, co-promotor(en): Bart Ducro; A.M. Johansson. - Wageningen : Wageningen University - ISBN 9789463430166
paarden - equus - insectenbeten - overgevoeligheid - diergenetica - genetische diversiteit - genetische variatie - allergische reacties - horses - equus - insect bites - hypersensitivity - animal genetics - genetic diversity - genetic variation - allergic reactions
Genetic variation contributing to the phenotypic variation was utilized in this thesis to understand the genetic background of a complex trait IBH, and to understand genetic diversity and relationships between various horse populations.
IBH is the most common skin allergic disorder in horses, caused by bites of midges, predominantly Culicoides species. It affects various horse breeds worldwide. With no effective treatment, IBH degrades horse health and causes economic loss. In this thesis, we used genome-wide SNPs to identify regions contributing to genetic variance of IBH susceptibility. We also investigated influence of increased number of horses and dense SNPs on identification of genomic regions associated to IBH susceptibility. Multiple genomic regions with small effects were observed in Studies I-III. Interesting genomic regions in the Icelandic horse population across the studies I and II, was observed on chromosomes 1, 7, 10, 15 and 17. The percentage of the genetic variance explained by top ten windows increased from 3.07% (Study I) to 6.56% (Study II). Novel genomic regions were identified when number of Icelandic horses was increased in Study II. Using dense SNPs on the Exmoor pony population we identified novel genomic regions, on chr 8, associated to IBH susceptibility, though with borderline significance.
In Study IV, pre-conceived understanding about evolutionary history of horse populations matched obtained results from investigation of genetic relationships within Dutch warmblood populations (pairwise mean FST ≤ 0.070), and within pony-like populations (pairwise mean FST ≤ 0.078). Horse populations with similar genetic background might share similar genetic components for IBH susceptibility. The Friesian horse population had lowest diversity (mean inbreeding coefficients: fi: 30.4%, fiROH= 22.2%) in Study IV and was genetically distinct (FST ranged from 0.13 to 0.17). This might be a result of a history of several population bottlenecks and selection on a closed breeding scheme. Low diversity in immunity related genes, observed in the Friesian horse population, might have led to increased prevalence of IBH. Similarly, low susceptibility of IBH in a warmblood population, KWPN sport horse population might be due to high genetic diversity ( =-6.9%). High genetic diversity in KWPN sport horse population might be a result of an open breeding scheme and interbreeding with other warmblood populations.
Werken aan diversiteit in tarwe en groenten : voor meer variatie op het veld, in het winkelschap en op het bord
Nuijten, Edwin ; Lammerts van Bueren, Edith - \ 2016
Driebergen : Louis Bolk Instituut (Publicatie / Louis Bolk Instituut 2016-030 LbP) - 20
kwekers - biologische landbouw - rassen (planten) - tarwe - zaden - plantenveredeling - groenten - genetische diversiteit - diversiteit - biologische plantenveredeling - growers - organic farming - varieties - wheat - seeds - plant breeding - vegetables - genetic diversity - diversity - organic plant breeding
Van 2014 tot 2016 heeft het Louis Bolk Instituut onderzoek gedaan naar de mogelijkheden van een breder assortiment in gewassen voor de teler (op het veld) en voor de consument (op het bord). Aanleiding voor het onderzoek is dat het aantal rassen dat aangepast is aan biologische teeltomstandigheden (rassen die dus zonder gebruik van kunstmest en bestrijdingsmiddelen kunnen) beperkt is en blijft. Veel veredelingsbedrijven kunnen vanwege de ontwikkelingskosten geen aparte rassen ontwikkelen voor een kleine markt. Meestal worden rassen uit het bestaande (gangbare) assortiment geselecteerd voor biologische vermeerdering. Bovendien zijn biologische telers en handelaren meegegaan in de huidige eisen voor hoge opbrengst en uniforme eindproducten. Het aanbieden van zaadvaste rassen in plaats van bijvoorbeeld hybride rassen is daarmee commercieel niet meteen vanzelfsprekend. Divers en Dichtbij Van 2014 tot 2016 heeft het Louis Bolk Instituut onderzoek gedaan naar de mogelijkheden van een breder assortiment in gewassen voor de teler (op het veld) en voor de consument (op het bord). Dit onderzoek is samen met Estafette Odin BV en de biologische dynamische telers GAOS in Swifterbant, De Groenen Hof in Esbeek en de Maatschap Dames en Heren Vos in Kraggenburg uitgevoerd. Het doel van dit project Divers en Dichtbij was de diversiteit op het veld en op het bord te vergroten. Daarmee bedoelen we niet alleen meer verschillende rassen, maar vooral andere type rassen of populaties die zelf meer genetische variatie bezitten. Dat kan door te kiezen voor zaadvaste rassen bij groentegewassen en populaties bij granen. Tot nu toe is populatieveredeling alleen toegepast bij granen en nog niet of nauwelijks bij groentegewassen (zie voor definities Box 1 op pagina 7). Dit betekent ook een keuze voor andere manieren van veredelen en selecteren. Aanleiding voor het onderzoek is dat het aantal rassen dat aangepast is aan biologische teeltomstandigheden (rassen die dus zonder gebruik van kunstmest en bestrijdingsmiddelen kunnen) beperkt is en blijft. Veel veredelingsbedrijven kunnen vanwege de ontwikkelingskosten geen aparte rassen ontwikkelen voor een kleine markt. Meestal worden rassen uit het bestaande (gangbare) assortiment geselecteerd voor biologische vermeerdering. Bovendien zijn biologische telers en handelaren meegegaan in de huidige eisen voor hoge opbrengst en uniforme eindproducten. Het aanbieden van zaadvaste rassen in plaats van bijvoorbeeld hybride rassen is daarmee commercieel niet meteen vanzelfsprekend. En toch heeft ons brede speurwerk in dit project wel degelijk een aantal interessante zaadvaste rassen opgeleverd! Want gelukkig zijn er in Europa en Amerika diverse biologische veredelaars actief in het veredelen van zaadvaste rassen en populaties. De informatie in deze brochure is bedoeld voor telers en andere ketenpartijen om meer te leren over de mogelijkheden van zaadvaste rassen bij groenten en populaties bij tarwe.
The origin, versatility and distribution of azole fungicide resistance in the banana black Sigatoka pathogen Pseudocercospora fijiensis
Chong Aguirre, Pablo A. - \ 2016
Wageningen University. Promotor(en): Gert Kema; Pedro Crous. - Wageningen : Wageningen University - ISBN 9789462578791 - 289
pseudocercospora - plant pathogenic fungi - fungicides - pesticide resistance - defence mechanisms - genetic diversity - genetic mapping - sensitivity - musa - bananas - fungal diseases - disease control - pseudocercospora - plantenziekteverwekkende schimmels - fungiciden - resistentie tegen pesticiden - verdedigingsmechanismen - genetische diversiteit - genetische kartering - gevoeligheid - musa - bananen - schimmelziekten - ziektebestrijding
Pseudocercospora fijiensis causes black Sigatoka disease of banana. It is one of the most damaging threats of the crop requiring excessive fungicide applications for disease control as the major export “Cavendish” clones are highly susceptible. The consequence of this practice is the reduced efficacy of disease management strategies due to increasing levels of fungicide resistance. In this thesis the history and current practices of black Sigatoka disease management as well as the underlying mechanisms of fungicide resistance to a major group of fungicides are described. We discovered that both target site mutations and promotor insertions are crucial for modulating sensitivity. The more insertions, the higher the expression of the gene and the more resistant the strain. Using this information, we advocate modern monitoring techniques and improved disease control strategies as well as the urgent need for innovative banana breeding to develop resistant varieties for a sustainable global banana production.
Targets and tools for optimizing lignocellulosic biomass quality of miscanthus
Weijde, R.T. van der - \ 2016
Wageningen University. Promotor(en): Richard Visser, co-promotor(en): Luisa Trindade; Oene Dolstra. - Wageningen : Wageningen University - ISBN 9789462578388 - 231
miscanthus - bioethanol - biomass - biofuels - lignocellulose - fuel crops - plant breeding - cell walls - cell wall components - genetic diversity - genetic variation - biomass conversion - biobased economy - miscanthus - bioethanol - biomassa - biobrandstoffen - lignocellulose - brandstofgewassen - plantenveredeling - celwanden - celwandstoffen - genetische diversiteit - genetische variatie - biomassaconversie - biobased economy
Miscanthus is a perennial energy grass characterized by a high productivity and resource-use efficiency, making it an ideal biomass feedstock for the production of cellulosic biofuels and a wide range of other biobased value-chains. However, the large-scale commercialization of converting biomass into cellulosic biofuel is hindered by our inability to efficiently deconstruct the plant cell wall. The plant cell wall is a complex and dynamic structure and its components are extensively cross-linked into an unyielding matrix. The production of biofuel depends on the extraction, hydrolysis and fermentation of cell wall polysaccharides, which currently requires energetically and chemically intensive processing operations that negatively affect the economic viability and sustainability of the industry. To address this challenge it is envisioned that the bioenergy feedstocks can be compositionally tailored to increase the accessibility and extractability of cell wall polysaccharides, which would allow a more efficient conversion of biomass into biofuel under milder processing conditions.
Extensive phenotypic and genetic diversity in cell wall composition and conversion efficiency was observed in different miscanthus species, including M. sinensis, M. sacchariflorus and interspecific hybrids between these two species. In multiple experiments a twofold increase in the release of fermentable sugars was observed in ‘high quality’ accessions compared to ‘low quality’ accessions. The exhaustive characterization of eight highly diverse M. sinensis genotypes revealed novel and distinct breeding targets for different bioenergy conversion routes. The key traits that contributed favourably to the conversion efficiency of biomass into biofuel were a high content of hemicellulosic polysaccharides, extensive cross-linking of hemicellulosic polysaccharides (revealed by a high content of trans-ferulic acids and a high ratio of arabinose-to-xylose), a low lignin content and extensive incorporation of para-coumaric acid into the lignin polymer.
Lignin is widely recognized as one of the key factors conveying recalcitrance against enzymatic deconstruction of the cell wall. The incorporation of para-coumaric acid into the lignin polymer is hypothesized to make lignin more easily degradable during alkaline pretreatment, one of the most widely applied processing methods that is used to pretreat biomass prior to enzymatic hydrolysis. Previous studies have shown that reducing lignin content is often implicated in reduced resistance of plants to lodging. We hypothesize that extensively cross-linked hemicellulosic polysaccharides may fulfil a similar function in supporting cell wall structural rigidity and increasing the content of hemicellulosic polysaccharides may be a way to reduce lignin content without adversely affecting cell wall rigidity. This strategy can be used to improve biomass quality for biobased applications, as hemicellulosic polysaccharides are more easily degradable during industrial processing than lignin. Furthermore, hemicellulosic polysaccharides adhere to cellulose, which negatively affects the level of cellulose crystallinity. Crystalline cellulose is harder to degrade than its more amorphous form. Therefore the reduction of cellulose crystallinity is another mechanism through which increasing the content of hemicellulosic polysaccharides positively contributes to cell wall degradability. These results provided new insights into the traits that may be targeted to improve the quality of lignocellulose feedstocks.
However, evaluation of complex biochemical traits for selection purposes is hindered by the fact that their accurate quantification is a costly, lengthy and laborious procedure. To overcome these limitations an accurate and high-throughput method was developed based on near-infrared spectroscopy. Through extensive calibration we developed accurate prediction models for a wide range of biomass quality characteristics, which may be readily implemented as a phenotyping tool for selection purposes.
Additionally, progress through breeding may substantially be improved by marker-assisted selection, which will reduce the need for the evaluation of genotype performance in multi-year field trials. To this end, a biparental M. sinensis mapping population of 186 individuals was developed and genotyped using a genotyping-by-sequencing approach. A total of 564 short-sequence markers were used to construct a new M. sinensis genetic map. Cell wall composition and conversion efficiency were observed to be highly heritable and quantitatively inherited properties. This is the first genetic study in miscanthus to map quantitative trait loci (QTLs) for biomass quality properties and is a first step towards the application of marker-assisted selection for biomass quality properties.
Through the evaluation of a diverse set of miscanthus genotypes in multiple locations we demonstrated that in addition to genotypic variation, growing conditions may have a substantial influence on cell wall composition and conversion efficiency. While further research is needed to identify which specific environmental parameters are responsible for the observed effects, these results clearly indicate that the environmental influence on biomass quality needs to be taken into account in order to match genotype, location and end-use of miscanthus as a lignocellulose feedstock. Moreover, significant genotype-by-environment interaction effects were observed for cell wall composition and conversion efficiency, indicating variation in environmental sensitivity across genotypes. Although the magnitude of the genotypic differences was small in comparison to genotype and environmental main effects, this affected the ranking of accession across environments. Stability analysis indicated some stable accessions performed relatively across diverse locations.
In addition to trialing miscanthus in diverse locations, we also evaluated miscanthus biomass quality under drought conditions for a number of reasons: 1) drought stress is linked to a differential expression of cell wall biosynthesis genes, 2) incidence of drought events is increasing due to climate change, 3) irrigation is likely to be uneconomical during the cultivation of miscanthus and 4) miscanthus has many characteristics that make it a crop with a good potential for cultivation on marginal soils, where abiotic stresses such as drought may prevail. Drought stress was shown to result in a large reduction in cell wall and cellulose content and a substantial increase in hemicellulosic polysaccharides and cellulose conversion rates. We hypothesized that the reduction in cellulose content was due to an increase in the production of osmolytes, which are well-known for their role in plant protection against drought. The results indicated that drought stress had a positive effect on the cell wall degradability of miscanthus biomass.
Overall the compendium of knowledge generated within the framework of this thesis provided insights into the variation in biomass quality properties in miscanthus, increased our understanding of the molecular, genetic and environmental factors influencing its conversion efficiency into biofuel and provided tools to exploit these factors to expand the use of miscanthus as a lignocellulose feedstock.
Flinke uitbreiding genenbank voor Nederlandse paardenrassen
Hoving, A.H. ; Wit, A.A.C. de; Sulkers, H. - \ 2016
Zeldzaam huisdier 41 (2016)1. - ISSN 0929-905X - p. 20 - 21.
genenbanken - paardenrassen - genetische diversiteit - zeldzame rassen - gene banks - horse breeds - genetic diversity - rare breeds
Het Centrum voor Genetische Bronnen Nederland (CGN) bewaart sperma
van Nederlandse paardenrassen in de genenbank voor landbouwhuisdieren.
Doel is het veiligstellen van de genetische diversiteit binnen
Potato breeding in the Netherlands: successful collaboration between farmers and commercial breeders
Almekinders, C.J.M. ; Mertens, L. ; Loon, Jan van; Lammerts Van Bueren, E. - \ 2016
Farming Matters 32 (2016)Special Issue April. - ISSN 2210-6499 - p. 34 - 37.
potatoes - table potatoes - plant breeding - netherlands - cooperation - farmers - genetic diversity - firms - agricultural law - new variety - organic farming - aardappelen - consumptieaardappelen - plantenveredeling - nederland - samenwerking - boeren - genetische diversiteit - firma's - agrarisch recht - nieuwe variëteit - biologische landbouw
The Dutch potato breeding model, which involves a partnership between farmers and commercial breeding companies in a modern, Western context, is unique. While there are other examples of collaborative relationships between farmers and breeders in Europe, the Dutch potato breeding model stands out in terms of its long track record, the involvement of the private sector, and the institutional integration of the relationship which up to today facilitates access to genetic materials and financial benefit sharing.
Development of a breeding strategy for nitrogen use efficiency in spinach (Spinacia oleracea L.)
Chan Navarrete, J.R. - \ 2016
Wageningen University. Promotor(en): Edith Lammerts van Bueren, co-promotor(en): Oene Dolstra; Gerard van der Linden. - Wageningen : Wageningen University - ISBN 9789462577961 - 161
spinacia oleracea - spinach - plant breeding - nitrogen - nutrient use efficiency - genetic mapping - nitrogen fertilizers - fertilizer application - genetic diversity - nitrogen response - spinacia oleracea - spinazie - plantenveredeling - stikstof - nutriëntengebruiksefficiëntie - genetische kartering - stikstofmeststoffen - bemesting - genetische diversiteit - stikstofrespons
Spinach (Spinacia oleracea L.) is one of the most consumed leafy vegetables worldwide and it is considered to be highly nutritious. Spinach is a short-cycle leafy crop that has a high demand for nitrogen in order to rapidly come to a harvestable product that has the required dark green colour within a reasonable harvest window. In commercial production of spinach the recovery of N is poor, which may result in environmental pollution. To increase sustainability of both organic and conventional spinach cultivation there is a need to reduce the dependency on high levels of nitrogen. Growers therefore urgently need cultivars with a satisfactory yield under reduced N input conditions. Nitrogen use efficiency (NUE), defined as the ability to produce high biomass per unit N applied, is low in spinach. The present study aims to evaluate spinach genotypes for selectable traits under varying N supply and provide tools and knowledge to facilitate the development of varieties with good yield, quality and stability under low N input. To minimise environmental variation affecting the identification of traits related to NUE a screening method was developed using a hydroponics system. The genetic diversity for NUE related traits was first studied with 24 commercial cultivars under contrasting levels of N supply based on the Ingestad model with a steady-state N application. This demonstrated that the hydroponics screening strategy as a pre-screening tool enabled reliable detection of heritable variation among cultivars for NUE-related traits under optimal as well as suboptimal N input. Shoot dry weight and leaf area were preferred selectable traits for the detection of heritable differences contributing to NUE in spinach. The effect of N application strategy was examined in seven cultivars grown under hydroponics conditions with low and high N levels supplied either as a single bulk N application resembling N fertilization in field cultivation, or a steady-state N application according to Ingestad. The latter application strategy provided more stable and reproducible conditions for determination of genetic differences in NUE under low N conditions for a short-cycle leafy vegetable crop. Several tools for molecular genetic evaluation of NUE in spinach were provided as well, including a SNP marker set for marker-assisted breeding, a genetic mapping population with a corresponding genetic map, and the identification of two major QTL regions contributing to growth under low N conditions. With these tools, an efficient strategy for breeding for NUE efficiency in spinach would include screening under controlled conditions at high and low N using leaf area, biomass and root to shoot ratio as selectable traits, and QTL identification of genetic factors that can be targeted and combined using marker-assisted selection. An in depth genotype by environment interaction analysis using six field trials showed that environmental factors like temperature, soil, and management strongly influence nitrogen availability in the soil in a short cycle crop like spinach. This severely complicates selection and breeding for NUE of spinach under field conditions, and emphasizes the importance of performing trials under better controllable conditions for genetic dissection of NUE and discovery of genetic factors contributing to NUE. It also underscores the importance of validating these findings in various field trials. Multi-environment field trials with different levels of N fertilization will then allow selection of cultivars that combine stable performance under various low input growing conditions with high yields under more favorable conditions.
Conservation genetics of the frankincense tree
Bekele, A.A. - \ 2016
Wageningen University. Promotor(en): Frans Bongers, co-promotor(en): Rene Smulders; K. Tesfaye Geletu. - Wageningen : Wageningen University - ISBN 9789462576865 - 158
boswellia - genomes - dna sequencing - tropical forests - genetic diversity - genetic variation - genetics - forest management - plant breeding - boswellia - genomen - dna-sequencing - tropische bossen - genetische diversiteit - genetische variatie - genetica - bosbedrijfsvoering - plantenveredeling
Boswellia papyrifera is an important tree species of the extensive Combretum-Terminalia dry tropical forests and woodlands in Africa. The species produces a frankincense which is internationally traded because of its value as ingredient in cosmetic, detergent, food flavor and perfumes productions, and because of its extensive use as incense during religious and cultural ceremonies in many parts of the world. The forests in which B. papyrifera grows are increasingly overexploited at the expense of the economic benefit and the wealth of ecological services they provide. Populations of B. papyrifera have declined in size and are increasingly fragmented. Regeneration has been blocked for the last 50 years in most areas and adult productive trees are dying. Projections showed a 90% loss of B. papyrifera trees in the coming 50 years and a 50% loss of frankincense production in 15 years time.
This study addressed the conservation genetics of B. papyrifera. Forty six microsatellite (SSR) markers were developed for this species, and these genetic markers were applied to characterize the genetic diversity pattern of 12 B. papyrifera populations in Ethiopia. Next to this, also the generational change in genetic diversity and the within-population genetic structure (FSGS) of two cohort groups (adults and seedlings) were studied in two populations from Western Ethiopia. In these populations seedlings and saplings were found and natural regeneration still takes place, a discovery that is important for the conservation of the species.
Despite the threats the populations are experiencing, ample genetic variation was present in the adult trees of the populations, including the most degraded populations. Low levels of population differentiation and isolation-by-distance patterns were detected. Populations could be grouped into four genetic clusters: the North eastern (NE), Western (W), North western (NW) and Northern (N) part of Ethiopia. The clusters corresponded to environmentally different conditions in terms of temperature, rainfall and soil conditions. We detected a low FSGS and found that individuals are significantly related up to a distance of 60-130 m.
Conservation of the B. papyrifera populations is urgently needed. The regeneration bottlenecks in most existing populations are an urgent prevailing problem that needs to be solved to ensure the continuity of the genetic diversity, species survival and sustainable production of frankincense. Local communities living in and around the forests should be involved in the use and management of the forests. In situ conservation activities will promote gene flow among fragmented populations and scattered remnant trees, so that the existing level of genetic diversity may be preserved. Geographical distance among populations is the main factor to be considered in sampling for ex situ conservation. A minimum of four conservation sites for B. papyrifera is recommended, representing each of the genetic clusters. Based on the findings of FSGS analyses, seed collection for ex situ conservation and plantation programmes should come from trees at least 100 m, but preferably 150 m apart.
Genetische diversiteit van de door essentaksterfte geplaagde gewone es
Copini, P. ; Kopinga, J. ; Laros, I. ; Bovenschen, J. ; Buiteveld, J. - \ 2016
Vakblad Natuur Bos Landschap (2016)april. - ISSN 1572-7610 - p. 14 - 17.
chalara fraxinea - fraxinus excelsior - schimmelziekten - resistentie van variëteiten - genetische diversiteit - rassenlijsten - genenbanken - bosbeheer - chalara fraxinea - fraxinus excelsior - fungal diseases - varietal resistance - genetic diversity - descriptive list of varieties - gene banks - forest administration
Essenzaadbronnen op de Rassenlijst Bomen hebben een hoge genetische diversiteit. Dat is een belangrijk kwaliteitsaspect van teeltmateriaal en speelt een cruciale rol in het aanpassingsvermogen van soorten aan een veranderend klimaat en nieuwe ziekten en plagen. De huidige generatie essenbossen heeft te kampen met de veelal desastreuze gevolgen van essentaksterfte. Uit onderzoek blijkt dat resistentie tegen deze ziekte genetisch bepaald is, en dat een klein deel van de essen goed bestand is tegen de ziekte. Deze genetische basis biedt hoop om een
nieuwe generatie essen te selecteren die bestand is tegen de ziekte, met behoud van de genetische diversiteit.
Genetic diversity and evolution in Lactuca L. (Asteraceae) : from phylogeny to molecular breeding
Wei, Z. - \ 2016
Wageningen University. Promotor(en): Eric Schranz. - Wageningen : Wageningen University - ISBN 9789462576148 - 210
lactuca sativa - leafy vegetables - phylogeny - genetic diversity - domestication - molecular breeding - genomes - dna - quantitative trait loci - evolution - lactuca sativa - bladgroenten - fylogenie - genetische diversiteit - domesticatie - moleculaire veredeling - genomen - dna - loci voor kwantitatief kenmerk - evolutie
Cultivated lettuce (Lactuca sativa L.) is an important leafy vegetable worldwide. However, the phylogenetic relationships between domesticated lettuce and its wild relatives are still not clear. In this thesis, I focus on the phylogenetic relationships within Lactuca L., including an analysis of the wild Lactuca species that are endemic to Africa for the first time. The genetic variation of responses to salinity in a recombinant inbred line population, derived from a cross between the lettuce crop (L. sativa ‘Salinas’) and wild species (L. serriola), was investigated and the candidate gene in the identified QTL regions was further studied.
In Chapter 1, I introduce and discuss topics related to genetic diversity and evolution in Lactuca, including an overview of lettuce cultivars and uses, its hypothesized domestication history, the taxonomic position of Lactuca, current status of molecular breeding in lettuce and mechanisms of salinity tolerance in plants, especially the High-affinity K+ Transporter (HKT) gene family.
In Chapter 2, the most extensive molecular phylogenetic analysis of Lactuca was constructed based on two chloroplast genes (ndhF and trnL-F), including endemic African species for the first time. This taxon sampling covers nearly 40% of the total Lactuca species endemic to Africa and 34% of all Lactuca species. DNA sequences from all the subfamilies of Asteraceae in Genbank and those generated from Lactuca herbarium samples were used to elucidate the monophyly of Lactuca and the affiliation of Lactuca within Asteracaeae. Based on the subfamily tree, 33 ndhF sequences from 30 species and 79 trnL-F sequences from 48 species were selected to infer phylogenetic relationships within Lactuca using Randomized Axelerated Maximum Likelihood (RAxML) and Bayesian Inference (BI) analyses. In addition, biogeographical, chromosomal and morphological character states were analysed based on the Bayesian tree topology. The results showed that Lactuca contains two distinct phylogenetic clades - the crop clade and the Pterocypsela clade. Other North American, Asian and widespread species either form smaller clades or mix with the Melanoseris species in an unresolved polytomy. The newly sampled African endemic species probably should be excluded from Lactuca and treated as a new genus.
In Chapter 3, twenty-seven wild Lactuca species and four outgroup species were sequenced using next generation sequencing (NGS) technology. The sampling covers 36% of total Lactuca species and all the important geographical groups in the genus. Thirty chloroplast genomes, including one complete (partial) large single copy region (LSC), one small single copy region (SSC), one inverted repeat (IR) region, and twenty-nine nuclear ribosomal DNA sequences (containing the internal transcribed spacer region ) were successfully assembled and analysed. A methodology paper for which I am co-author, but is not included in this thesis, of the sequencing pipeline was published: ‘Herbarium genomics: plastome sequence assembly from a range of herbarium specimens using an Iterative Organelle Genome Assembly (IOGA) pipeline’. These NGS data helped resolve deeper nodes in the phylogeny within Lactuca and resolved the polytomy from Chapter 2. The results showed that there are at least four main groups within Lactuca: the crop group, the Pterocypsela group, the North American group and the group containing widely-distributed species. I also confirmed that the endemic African species should be removed and treated as a new genus.
In Chapter 4, quantitative trait loci (QTLs) related to salt-induced changes in Root System Architecture (RSA) and ion accumulation were determined using a recombinant inbred line population derived from a cross between cultivated lettuce and wild lettuce. I measured the components of RSA by replicated lettuce seedlings grown on vertical agar plates with different NaCl concentrations in a controlled growth chamber environment. I also quantified the concentration of sodium and potassium in replicates of greenhouse-grown plants watered with 100 mM NaCl. The results identified a total of fourteen QTLs using multi-trait linkage analysis, including three major QTLs associated with general root development (qRC9.1), root growth in salt stress condition (qRS2.1), and ion accumulation (qLS7.2).
In Chapter 5, one of the identified QTL regions (qLS7.2) reported in Chapter 4 was found to contain a homolog of the HKT1 from Arabidopsis thaliana. I did a phylogenetic analysis of Lactuca HKT1-like protein sequences with other published HKT protein sequences and determined transmembrane and pore segments of lettuce HKT1;1 alleles, according to the model proposed for AtHKT1;1. Gene expression pattern and level of LsaHKT1;1 (L. sativa ‘Salinas’) and LseHKT1;1 (L. serriola) in root and shoot were investigated in plants growing hydroponically over a time-course. The measurements of Na+ and K+ contents were sampled at the same time as the samples used for gene expression test. In addition, I examined the 5’ promoter regions of the two genotypes. The results showed low expression levels of both HKT1;1 alleles in Lactuca root and relatively higher expression in shoot, probably due to the negative cis-regulatory elements of HKT1 alleles found in Lactuca promoter regions. Significant allelic differences were found in HKT1;1 expression in early stage (0-24 hours) shoots in and in late stage (2-6 days) roots. shoot HKT1;1 expression/root HKT1;1 expression was generally consistent with the ratios of Na+/K+ balance in the relevant tissues (shoot Na+/K+ divided by root Na+/K+).
In Chapter 6, I summarize and discuss the results from previous chapters briefly. The implications of Chapter 2 and 3 for Lactuca phylogenetics are discussed, including some key characters for the diagnosis of species within Lactuca, the use of herbarium DNA for NGS technology, and perspectives into Lactuca phylogeny. Future perspectives of genome-wide association mapping for lettuce breeding were also discussed. Lastly, I propose to integrate phylogenetic approaches into investigations of allelic differences in lettuce, not just associated with salinity stress but also with other stressed and beneficial characters, both within and between species.
Chocola maken van een Meloen
Peters, Sander - \ 2015
Meloen - Sequencing - veredeling - genetische diversiteit - Genomics
Sneller veredelen dankzij slimme combinatie van technieken. Veredelingsprogramma’s kunnen spectaculair worden versneld. Het ontwikkelen van een nieuw ras kost straks misschien nog maar twee jaar in plaats van vijf tot tien. Dat is te danken aan nieuwe slimme combinaties van state of the art moleculaire technieken.
Approaches to the conservation of forest genetic resources in Europe in the context of climate change
Kelleher, Colin T. ; Vries, S.M.G. de; Baliuckas, Virgilijus - \ 2015
Rome : Biodiversity International - ISBN 9789292550325 - 46
forest trees - genetic diversity - genetic resources - plant genetic resources - forest resources - climatic change - forest policy - bosbomen - genetische diversiteit - genetische bronnen - genetische bronnen van plantensoorten - bosbestanden - klimaatverandering - bosbeleid
In Europe, forests have been expanding in terms of area and timber stock over the past 50 years and subsequently they have acted as a carbon sink while they have been recovering from previous eras of deforestation. National adaptation strategies to climate change and other policies have been formulated in many European countries to harness the potential of forests and the forestry sector for mitigating climate change. However, the impacts of climate change on forests, and especially on their genetic diversity have not been given a proper consideration in these policies. For these reasons, the EUFORGEN Steering Committee established a working group on climate change and the conservation of forest genetic resources that made several recommendations for action presented in this report
Pan-European strategy for genetic conservation of forest trees and establishment of a core network of dynamic conservation units
Vries, S.M.G. de; Alan, Murat ; Bozzano, Michele ; Burianek, Vaclav - \ 2015
Rome : EUFORGEN - ISBN 9789292550295 - 40
forest administration - forests - forest trees - genetic diversity - trees - nature conservation - bosbeheer - bossen - bosbomen - genetische diversiteit - bomen - natuurbescherming
The diversity of forests, at the level of species and at the level of genetic diversity within species, is an important resource for Europe. Over the past several decades European countries have made considerable efforts to conserve the genetic diversity of tree species. According to the EUFGIS portal, there are more than 3200 genetic conservation units which harbour more than 4000 populations of about 100 tree species. An earlier analysis of the EUFGIS information revealed significant gaps in the conservation efforts in terms of the species covered and the geographical distribution of the units within the species’ ranges. Subsequently, the EUFORGEN Steering Committee established a working group to develop the pan-European genetic conservation strategy for forest trees. The process followed by the working group and its results are presented in this report
Worse comes to worst: bananas and Panama disease—when plant and pathogen clones meet
Ordonez Roman, N.I. ; Seidl, M.F. ; Waalwijk, C. ; Drenth, A. ; Kilian, A. ; Thomma, B.P.H.J. ; Ploetz, R.C. ; Kema, G.H.J. - \ 2015
PLoS Pathogens 11 (2015)11. - ISSN 1553-7366 - 7
bananas - tropical small fruits - agricultural research - fungal diseases - fusarium oxysporum f.sp. cubense - soil fungi - pathogenicity - food production - genetic diversity - plant protection - bananen - tropisch kleinfruit - landbouwkundig onderzoek - schimmelziekten - fusarium oxysporum f.sp. cubense - bodemschimmels - pathogeniteit - voedselproductie - genetische diversiteit - gewasbescherming
This article deals with: Bananas: their origin and global rollout; genetic diversity of Fusarium oxysporum f.sp. cubense, the causal agent of Panama Disease; Panama Disease: history repeats itself; tropical race 4, a single pathogen clone, threatens global banana production; strategies for sustainable Panama Disease management.
Monitoring van de Nederlandse otterpopulatie
Groot, G.A. de - \ 2015
otters - populatie-ecologie - monitoring - genetische diversiteit - verwantschap - inteelt - natuurbeheer - wildbeheer - otters - population ecology - monitoring - genetic diversity - kinship - inbreeding - nature management - wildlife management
Sinds in 2002 een nieuwe populatie otters (Lutra lutra) in ons land werd uitgezet, heeft Alterra de status van deze populatie nauwgezet gevolgd. Nadat de eerste dieren waren gevolgd met behulp van zenders, werd overgestapt op non-invasive genetische monitoring via spraints (otteruitwerpselen). Op deze manier kunnen de dieren langer worden gevolgd en kunnen meer dieren tegelijk worden gevolgd met beperkte kosten. Sinds juli 2002 werden meer dan vijfduizend spraints verzameld en geanalyseerd in het lab, ter bepaling van een genetisch profiel. Op basis daarvan kon een stamboom worden gemaakt, die uitwees dat slechts een klein deel van de aanwezige mannen verantwoordelijk was voor een groot deel van het nageslacht (sterke dominantie). De verwantschap tussen dieren, en daarmee het inteelt-niveau, loopt op. Dit is een belangrijk signaal dat voor de Nederlandse populatie ‘vers bloed’ nodig is, ofwel via aanvullende introducties, of door uitwisseling tussen populaties tot stand te brengen.
Inauguratie Koen Kramer
Kramer, K. - \ 2015
adaptatie - genetische diversiteit - bossen - modelleren - klimaatverandering - bosbescherming - bosproducten - bosecologie - adaptation - genetic diversity - forests - modeling - climatic change - protection of forests - forest products - forest ecology
Nieuwe en bestaande bossen kunnen door gebruik te maken van de genetische diversiteit van bomen hun functionaliteit behouden bij klimaatverandering. Dat stelt prof. dr. Koen Kramer bij zijn oratie als buitengewoon hoogleraar Kwantitatieve bosgenetica aan Wageningen University op donderdag 8 oktober
The conservation and use of crop genetic resources for food security
Khoury, C.K. - \ 2015
Wageningen University. Promotor(en): Paul Struik, co-promotor(en): A. Jarvis. - Wageningen : Wageningen University - ISBN 9789462574427 - 302
genetische bronnen van plantensoorten - genetische diversiteit - germplasm - landbouwontwikkeling - klimaatadaptatie - wilde verwanten - ex-situ conservering - voedselzekerheid - plant genetic resources - genetic diversity - germplasm - agricultural development - climate adaptation - wild relatives - ex situ conservation - food security - cum laude
Cum laude graduation
Among the factors hindering the conservation of crop genetic resources is a lack of essential information regarding this diversity. Questions include: (a) what is the status of diversity in our food systems, and where are the greatest vulnerabilities?, (b) where can genetic diversity be found that can be useful in increasing productivity and mitigating these vulnerabilities?, (c) is this genetic diversity available in the present and in the long term?, and (d) what steps are needed to improve the ability for researchers to access genetic resources critical for present and future crop improvement? This thesis aims to contribute to the knowledge required to answer these questions through an exploration of the need for, potential of, challenges and constraints regarding, and necessary steps to enhance the conservation and use of crop genetic diversity.
Breeding program for indigenous chicken in Kenya
Ngeno, K. - \ 2015
Wageningen University. Promotor(en): Johan van Arendonk, co-promotor(en): Liesbeth van der Waaij; A.K. Kahi. - Wageningen : Wageningen University - ISBN 9789462572775 - 154
kippen - pluimvee - inheems vee - dierveredeling - veredelingsprogramma's - genetische diversiteit - ecotypen - genomen - genetische verbetering - kenya - fowls - poultry - native livestock - animal breeding - breeding programmes - genetic diversity - ecotypes - genomes - genetic improvement - kenya
Ngeno, K. (2015). Breeding program for indigenous chicken in Kenya. Analysis of diversity in indigenous chicken populations. PhD thesis, Wageningen University, the Netherlands
The objective of this research was to generate knowledge required for the development of an indigenous chicken (IC) breeding program for enhanced productivity and improved human livelihood in Kenya. The initial step was to review five questions; what, why and how should we conserve IC in an effective and sustainable way, who are the stakeholders and what are their roles in the IC breeding program. The next step of the research focused on detecting distinctive IC ecotypes through morphological and genomic characterization. Indigenous chicken ecotypes were found to be populations with huge variability in the morphological features. Molecular characterization was carried out using microsatellite markers and whole genome re-sequenced data. The studied IC ecotypes are genetically distinct groups. The MHC-linked microsatellite markers divided the eight IC ecotypes studied into three mixed clusters, composing of individuals from the different ecotypes whereas non-MHC markers grouped ICs into two groups. Analysis revealed high genetic variation within the ecotype with highly diverse MHC-linked alleles which are known to be involved in disease resistance. Whole genome re-sequencing revealed genomic variability, regions affected by selection, candidate genes and mutations that can explain partially the phenotypic divergence between IC and commercial layers. Unlike commercial chickens, IC preserved a high genomic variability that may be important in addressing present and future challenges associated with environmental adaptation and farmers’ breeding goals. Lastly, this study showed that there is an opportunity to improve IC through selection within the population. Genetic improvement utilizing within IC selection requires setting up a breeding program. The study described the systematic and logical steps in designing a breeding program by focusing on farmers’ need, how to improve IC to fit the farming conditions, and management regimes.