Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Recognition of Verticillium effector Ave1 by tomato immune receptor Ve1 mediates Verticillium resistance in diverse plant species
Song, Yin - \ 2017
University. Promotor(en): Bart Thomma; Pierre de Wit. - Wageningen : Wageningen University - ISBN 9789463437950 - 231
disease resistance - defence mechanisms - immunity - plant-microbe interactions - plant pathogens - verticillium dahliae - verticillium - tomatoes - solanum lycopersicum - receptors - genes - tobacco - nicotiana glutinosa - potatoes - solanum tuberosum - solanum torvum - humulus lupulus - cotton - gossypium hirsutum - transgenic plants - arabidopsis thaliana - ziekteresistentie - verdedigingsmechanismen - immuniteit - plant-microbe interacties - plantenziekteverwekkers - tomaten - receptoren - genen - tabak - aardappelen - katoen - transgene planten

Plant-pathogenic microbes secrete effector molecules to establish disease on their hosts, whereas plants in turn employ immune receptors to try and intercept such effectors in order to prevent pathogen colonization. Based on structure and subcellular location, immune receptors fall into two major classes; cell surface-localized receptors that comprise receptor kinases (RKs) and receptor-like proteins (RLPs) that monitor the extracellular space, and cytoplasm-localized nucleotide-binding domain leucine-rich repeat receptors (NLRs) that survey the intracellular environment. Race-specific resistance to Verticillium wilt in tomato (Solanum lycopersicum) is governed by the tomato extracellular leucine-rich repeat (eLRR)-containing RLP-type cell surface receptor Ve1 upon recognition of the effector protein Ave1 that is secreted by race 1 strains of the soil-borne vascular wilt Verticillium dahliae. Homologues of V. dahliae Ave1 (VdAve1) are found in plants and in a number of plant pathogenic microbes, and some of these VdAve1 homologues are recognized by tomato Ve1. The research presented in this thesis aims to characterize the role of the tomato cell surface-localized immune receptor Ve1, and its homologues in other diverse plant species, in Verticillium wilt resistance.

Making interventions work on the farm : Unravelling the gap between technology-oriented potato interventions and livelihood building in Southern Ethiopia
Tadesse, Yenenesh - \ 2017
University. Promotor(en): Paul Struik, co-promotor(en): Conny Almekinders; Rogier Schulte. - Wageningen : Wageningen University - ISBN 9789463436847 - 120
potatoes - crop production - crop physiology - technology - intervention - livelihood strategies - livelihoods - ethiopia - east africa - aardappelen - gewasproductie - gewasfysiologie - technologie - interventie - strategieën voor levensonderhoud - middelen van bestaan - ethiopië - oost-afrika

Poor adoption of modern technologies in sub-Saharan Africa is one of the major factors that limit food production and thereby threaten food security of smallholder farmers. This is despite the potential and emerging success stories of new technologies in increasing productivity of smallholder agriculture. Explanations for low uptake of technologies are diverse. Some studies associated it with characteristics of the farmers and their farm; others attributed it to poor access to information about a particular technology, while some others recognize the importance of technology attributes. Farmers’ adoption decision is shaped socially and the farming practices are changing, not only because of the technical changes introduced, but also because of changes in social circumstances among smallholders. All these possible reasons did, however, miss largely important insights on how local complexities influence adoption. The research presented in this thesis analyses the social dynamics of technology-oriented interventions. More specifically, the study assessed the influence of technology introduction strategies, social networks and social differentiation on the adoption, dissemination and effects of potato technologies. As a case, it used interventions introducing improved potato technologies in Chencha, Southern Ethiopia. The field work combined individual and group in-depth interviews, household surveys and field observation for data collection.

Results show that the efforts to introduce technologies for improved potato production to progressive farmers with the assumption that farmers will eventually adopt, once they become familiar with the technology is a distant prospect. Some of the production practices - agronomic field and storage practices - failed to spread to poor farmers as expected, while the majority of agronomic practices fitted well with wealthy farmers. This resulted in diverse outcomes and strategies for livelihood improvement at household level. Access to the technologies and the necessary resources and diverse needs for technology were important factors in explaining variation in adoption and effects of technology across wealth categories. Tracing the seed diffusion through farmers’ networks showed that not all households had equal access to improved seed potatoes, mainly because of social barriers formed by differences in wealth, gender and religion, and because the type of personal relationship (relatives, neighbours, friends and acquaintance) between seed providers and seed recipients affected farmer to farmer seed sharing. In addition, the set-up of farmer-group based seed production demands resources and faces contextual challenges, which could be addressed through a long-term approach that engages continually in diagnosis and responding to the emerging social as well as material challenges. Development practitioners, however, took organizing group initiatives as a one-time process of design and start-up activity. Thus, clean seed potato production and dissemination through farmers’ organizations could not be sustainable. In conclusion, the present study has indicated that through providing special attention to the social dynamics researchers can arrive at better understanding of constraints affecting technology adoption. This implies effective interventions for a range of farm contexts involve not only finding technical solutions but also integrated understanding of farmers’ production conditions and existing social dynamics.

Agronomic and socioeconomic sustainability of farming systems : A case in Chencha, South Ethiopia
Dersseh, Waga Mazengia - \ 2017
University. Promotor(en): Paul Struik, co-promotor(en): Rogier Schulte. - Wageningen : Wageningen University - ISBN 9789463436830 - 157
potatoes - solanum tuberosum - ethiopia - food security - farming systems - mixed farming - sustainability - optimization - efficiency - farm surveys - household surveys - socioeconomics - self sufficiency - profits - training - agronomic characteristics - productivity - soil fertility - rotation - animal feeding - improved varieties - inorganic fertilizers - aardappelen - ethiopië - voedselzekerheid - bedrijfssystemen - gemengde landbouw - duurzaamheid (sustainability) - optimalisatie - efficiëntie - bedrijfsonderzoeken - huishoudonderzoeken - sociale economie - zelfvoorziening - winsten - opleiding - agronomische kenmerken - productiviteit - bodemvruchtbaarheid - rotatie - diervoedering - veredelde rassen - anorganische meststoffen

Potato has multiple benefits and thus can play a vital role in ensuring food security in Ethiopia. However, for diverse reasons, its productivity is low. The farming systems in Ethiopia in which potato is grown, are predominantly mixed farming systems.

Most of the research in Ethiopia is focused on crop-specific constraints and thus there is limited research in which the interrelations between crop and livestock management practices are investigated. There is also not enough research focused on combined analysis of soil nutrient and animal feed balances and agronomic and socioeconomic efficiencies at farm level.

This study assessed production constraints and agronomic and socioeconomic sustainability of the farming systems in South Ethiopia and explored the possible synergetic options to alleviate major constraints. More specifically, the study intended to quantify the variation in input and output among farms, to identify constraints hindering expansion of potato production, to evaluate the sustainability of the farming systems at farm level, to identify constraints of sustainable intensification, and to explore synergetic solutions for the major constraints. Different research approaches were used ranging from lab analysis, household surveys, group discussions, to farm surveys.

Results showed that constraints related to input and product use in potato production vary across households indicating a need for a pluriform advisory model recognizing (and building upon alleviation of) the diversity of constraints identified in this analysis. The sustainability of the farming system is constrained by low agricultural productivity, low soil fertility, poor labour efficiency and limited economic return associated with improper crop rotation, inappropriate soil fertility management practices, shortage of animal feed, labour- and economically inefficient farm practices and labour shortage. However, there is ample scope to overcome the major constraints and simultaneously to optimize farm management.

The core messages of the study can be summarized as follows:

1) the current potato production is characterized by low productivity and economic returns due to various socioeconomic, agronomic and biological factors;

2) the soil fertility is low and there is uneven distribution of nutrients over plots with relatively high fertility levels in the homestead areas;

3) the current labour shortage can be attributed to mainly inefficiency of agricultural management practices and labour migration to towns for economic reasons indicating that the farming system is not sustainable in terms of labour;

4) considering the direct return from animal production, most of the farms had very low gross margin with the current management system and this reduced the overall operating profit of farms. The low return from animal rearing was offset by the relatively high profit from crop production indicating the benefit of mixed farming system in sustaining agricultural production; and

5) each farm can have a wide range of optimized solutions mainly through introduction of improved technologies and subsequent redesigning of the farm managements.

In general, the findings of the current study indicate that it is worthwhile to assess the sustainability of agricultural production in different farming systems and agro-ecologies of Ethiopia. In addition, the combined effect of introducing improved agricultural technologies and subsequent reconfiguring the farm management is very crucial to increase and sustain agricultural production.

Genetic diversity of potato for nitrogen use efficiency under low input conditions in Ethiopia
Getahun, Baye Berihun - \ 2017
University. Promotor(en): Richard Visser, co-promotor(en): Gerard van der Linden. - Wageningen : Wageningen University - ISBN 9789463436595 - 219
solanum tuberosum - potatoes - genetic diversity - nitrogen - plant breeding - ethiopia - nutrient use efficiency - 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.

Strokenteelt klaar voor de praktijk : aardappel drie tot tien dagen later branden
Apeldoorn, D.F. van; Rossing, W.A.H. ; Oomen, Gerard - \ 2017
Ekoland (2017)5. - ISSN 0926-9142 - p. 10 - 11.
strokenteelt - aardappelen - akkerbouw - phytophthora - zomertarwe - teeltsystemen - landbouw - biologische landbouw - teelt - strip cropping - potatoes - arable farming - spring wheat - cropping systems - agriculture - organic farming - cultivation
Na de eerste verkenningen met het telen in stroken zijn onderzoeken naar de effecten ervan verder uitgebreid. Inmiddels zijn er meerdere strokenproeven verdeeld over vier locaties – Droevendaal, ERF, De Graanrepubliek en NZ27 – en zijn de verwachte voordelen van dit teeltsysteem bevestigd. Afhankelijk van de inrichting van het bedrijf en aansluitende mechanisatie lijkt strokenteelt klaar voor de praktijk.
Duurzame beheersing van phytophthora : Resistentiemanagement blijft noodzakelijk
Pacilly, F.C.A. - \ 2017
Ekoland (2017)5. - ISSN 0926-9142 - p. 22 - 23.
aardappelen - resistentie van variëteiten - gewasbescherming - phytophthora - akkerbouw - teelt - biologische landbouw - potatoes - varietal resistance - plant protection - arable farming - cultivation - organic farming
De Wageningse promovenda Francine Pacilly doet onderzoek naar phytophthorabeheersing. Ze ontwikkelt een computermodel waarmee je kan onderzoeken wat het effect is van bepaalde maatregelen. Afgelopen winter is het model getest met hulp van biologische en gangbare aardappeltelers. In dit artikel meer achtergronden over het model en de ervaringen uit de workshops met de telers.
Genetic studies towards elucidation of drought tolerance of potato
Tessema, Biructa Bekele - \ 2017
University. Promotor(en): Richard Visser, co-promotor(en): Gerard van der Linden. - Wageningen : Wageningen University - ISBN 9789463431958 - 195
solanum tuberosum - potatoes - drought resistance - plant breeding - genetic analysis - quantitative trait loci - aardappelen - droogteresistentie - plantenveredeling - genetische analyse - loci voor kwantitatief kenmerk

Drought is a major threat to agricultural production, which makes drought tolerance a prime target for breeding approaches towards crop improvement. Drought is a complex polygenic trait and poses a challenge for drought tolerance breeding. Improving crops for drought tolerance at least requires the knowledge of the physiological mechanisms of the contributing traits and their genetic control. Thus, identification of genetic variation for drought tolerance is the first step towards drought tolerance breeding. The effect of drought stress on potato tuber yield and quality is very significant as potato is considered sensitive to water shortage. To understand the genetic factors underlying drought tolerance in potato, we performed drought stress experiments under green house and field conditions with moderate drought and severe drought stress conditions, respectively. In the field, potato genotypes were exposed to severe drought stress for two consecutive years starting from tuber initiation, which progressed to severe drought stress. In addition, we examined potato cultivars for moderate drought tolerance under greenhouse conditions where water application was reduced 50-60% from optimum amount starting from stolon formation. Morphological and physiological trait data were collected that allowed precise monitoring of the drought response of potato. Phenotypic data collected under severe drought stress conditions which includes traits like shoot and root biomass (fresh and dry), yield and chlorophyll content were used for QTL mapping while data collected under moderate drought stress conditions was used for genome wide association mapping. With QTL mapping, 60 QTLs were identified controlling those traits both under well-watered and drought stress conditions. In the drought tolerance evaluation of the potato cultivars under greenhouse conditions we identified significant marker trait associations for both above- and belowground traits. Many of the QTLs detected for drought tolerance traits were specific to either moderate or severe drought tolerance conditions. However, a few QTLs showed an overlap between these drought stress environments. This demonstrates the presence of common genomic regions controlling drought tolerance traits under moderate and severe drought stress conditions. In addition, from the two years of field drought stress experiments we selected a subset of genotypes that showed contrasting responses to drought stress. We used these genotypes to further examine the relationship between canopy development and tuber yield under severe drought stress conditions. Canopy development was measured for several time points and the data were used for curve fitting. From the curve-fit, parameters related to the different developmental phase of canopy were extracted. We observed that there is positive correlation between canopy parameters and tuber yield under drought stress conditions. The evaluation of potato for drought tolerance under field and greenhouse conditions has resulted in the identification of several QTLs that can be interesting to be used for enhancing drought tolerance in potato. Furthermore, the use of model derived parameters gave a better insight into the relationship between canopy development and tuber yield under water stress conditions.

Potatoes, pathogens and pests : effects of genetic modifi cation for plant resistance on non-target arthropods
Lazebnik, Jenny - \ 2017
University. Promotor(en): Joop van Loon; Marcel Dicke. - Wageningen : Wageningen University - ISBN 9789463431620 - 151
solanum tuberosum - potatoes - oomycetes - phytophthora infestans - genetic engineering - transgenic plants - disease resistance - risk assessment - nontarget organisms - arthropods - insect pests - herbivores - trophic levels - ecological risk assessment - greenhouse experiments - field experimentation - aardappelen - oömyceten - genetische modificatie - transgene planten - ziekteresistentie - risicoschatting - niet-doelorganismen - geleedpotigen - insectenplagen - herbivoren - trofische graden - ecologische risicoschatting - kasproeven - experimenteel veldonderzoek

Currently, fungicides are necessary to protect potato crops against late blight, Phytophthora infestans, one of the world’s most damaging crop pathogens. The introgression of plant resistance genes from wild potato species targeted specifically to the late blight pathogen into susceptible potato varieties may alleviate the environmental impact of chemical control. Genetically modified plants are subject to an environmental risk assessment, and this includes testing for risks to the non-target arthropod community associated with the crop. The thesis begins with a review about the main plant defense responses and their role in influencing sequential interactions between herbivores and plant pathogens. The experimental chapters each focus on different aspects of the interaction between potato plants (both resistant and susceptible), the target pathogen (P. infestans) and several non-target insects. With each chapter, the scope widens: from the molecular gene expression in potato leaves in response to sequential attacks, to field scale biodiversity analyses. At the molecular level, one of the main findings was that the genomic position of the Rpi-vnt1 insertion conferring resistance to P. infestans influenced potato gene expression measured in leaves, when interacting with the non-target insect pests Myzus persicae (Green peach aphid) and Leptinotarsa decemlineata (Colorado potato beetle). Insect performance differed between the resistant GM and susceptible non-GM comparator. In the following chapter, the differences in insect performance were tested across a range of conventionally bred cultivars varying in resistance to P. infestans. Differences in M. persicae performance between several cultivars greatly outweighed the differences previously detected between the GM and non-GM comparator. These results are crucial in shaping the way risk is assessed in the context of GM crops, and these results are supported in our experiments assessing effects on biodiversity with pitfall traps in the field. The third trophic level was also addressed by comparing the performance of the parasitoid Aphidius colemani reared on GM and non-GM fed aphids, both with an without exposure to P. infestans. Differences in parasitoid performance were only found on the susceptible cultivar when inoculated with P. infestans. In the last experimental chapter the risk assessment is taken to the field comparing pitfall trap catches over two years and in two countries. Different methods for statistical analysis of biodiversity data were compared to arrive at recommendations for such analysis in the framework of environmental risk assessments. Drawing on these lessons, the discussion ends with ideas for the development of protocols for environmental risk assessments in the light of expected scientific progress in agricultural biotechnology.

Aardappel: knolgewas van wereldformaat : De oorsprong van de aardappel (herziene versie)
Pistorius, R. ; Hoekstra, R. - \ 2017
Wageningen : Centrum voor Genetische Bronnen Nederland - 20 p.
aardappelen - herkomst - verspreiding - genetische bronnen van plantensoorten - rassen (planten) - potatoes - provenance - dispersal - plant genetic resources - varieties
In vier eeuwen tijd is de aardappel uitgegroeid van een lokaal voedselgewas tot het op drie na grootste bulkvoedselgewas ter wereld. Nederland is in de laatste eeuw uitgegroeid tot 's werelds grootste exporteur van pootaardappelen. De aardappelteelt en -export liggen diep verankerd in onze landbouwgeschiedenis.
Susceptibility genes : an additional source for improved resistance
Sun, Kaile - \ 2017
University. Promotor(en): Richard Visser, co-promotor(en): Evert Jacobsen; Yuling Bai. - Wageningen : Wageningen University - ISBN 9789463431415 - 174
solanum tuberosum - potatoes - solanum lycopersicum - tomatoes - genes - susceptibility - plant pathogenic fungi - phytophthora infestans - disease resistance - plant breeding - aardappelen - tomaten - genen - vatbaarheid - plantenziekteverwekkende schimmels - ziekteresistentie - plantenveredeling

Potato is affected by several diseases. Although, resistance can be obtained by introgression of major resistance genes from wild species, this has rarely been durable. Hence, other sources of resistance are highly needed. New research with a focus on loss of function mutations has led to the identification of disease susceptibility (S) genes in plants. The research in this thesis was aimed at the identification and characterization of potato S genes involved in the interaction with Phytophthora infestans and Botrytis cinerea. We selected 11 Arabidopsis thaliana S genes and silenced their potato orthologs by RNAi in the potato cultivar Desiree. The silencing of six genes resulted in resistance to P. infestans. Moreover, silencing of StDND1 reduced the infection of B. cinerea. Microscopic analysis showed that spore attachment and/or germination of P. infestans and B. cinerea was hampered on the leaf surface of StDND1-silenced potato plants. On StDMR1- and StDMR6-silenced potato plants, hyphal growth of P. infestans was arrested by the hypersensitive response-like cell death. Our results demonstrate that impairment of plant S genes may open a new way for breeding potatoes with resistance to pathogens like P. infestans and B. cinerea.

Resultaat tot nu toe op biologisch proefveld: veelbelovende resistente tafelaardappelrassen
Balen, D.J.M. van; Janmaat, L. - \ 2017
Ekoland 37 (2017)1. - ISSN 0926-9142 - p. 17 - 17.
biologische landbouw - aardappelen - rassen (planten) - consumptieaardappelen - rassenproeven - veldproeven - akkerbouw - organic farming - potatoes - varieties - table potatoes - variety trials - field tests - arable farming
De biologische agf-keten heeft de ambitie om bio-aardappelen te produceren en het winkelschap te vullen met goede kwaliteit biologische consumptieaardappelen. Dat vergt de komende jaren de nodige inspanning. Kwekers werken aan verruiming van het assortiment resistente rassen. Telers zorgen voor goed resistentiemanagement. Winkels gaan het aanbod aanpassen en kiezen voor sterke rassen. Jaarlijks worden de aardappelrassen getest op vatbaarheid, productie en kwaliteit. De infectiedruk was afgelopen jaar hoog. Hoe hebben de rassen gepresteerd?
Beoordeling van mogelijk gebruik van N-bijmestsystemen voor aardappelen als equivalente maatregel
Ruijter, F.J. de; Schröder, J.J. ; Geel, W.C.A. van; Postma, R. - \ 2016
Wageningen : Wageningen Plant Research (Wageningen Plant Research rapport 672) - 37
solanum tuberosum - aardappelen - akkerbouw - bemesting - maatregelen - stikstofmeststoffen - nederland - potatoes - arable farming - fertilizer application - measures - nitrogen fertilizers - netherlands
Het vijfde Nederlandse Actieprogramma Nitraatrichtlijn biedt ruimte voor zgn. equivalente maatregelen: maatregelen waarbij gebruiksnormen verhoogd kunnen worden zonder dat de milieukwaliteit verslechtert. Dit onderzoek richt zich op evaluatie van N-bijmestsystemen voor aardappel en gebruik als equivalente maatregel. Een theoretische verkenning laat zien dat ideale N-bijmestsystemen die voor verschillende groeiomstandigheden de juiste N-gift geven een iets lager N-overschot geven ten opzichte van bemesting volgens een vaste totale gift. Evaluatie van proeven liet zien dat N-bijmestsystemen mogelijke besparingen ten opzichte van de N-bemestingsrichtlijn veelal goed konden aangeven, maar situaties met een hogere optimale N-gift niet. Daarmee heeft gebruik van N-bijmestsystemen als equivalente maatregel momenteel onvoldoende perspectief.
Fungicide evaluation to rate efficacy to control leaf late blight for the EuroBlight table Results 2006-2015
Evenhuis, A. ; Bain, R. ; Hausladen, H. ; Nielsen, B.J. ; Berg, W. van den; Schepers, H.T.A.M. - \ 2016
Lelystad : Applied Plant Research - 46 p.
solanum tuberosum - potatoes - plant pathogenic fungi - oomycetes - phytophthora infestans - fungicides - protocols - field experimentation - europe - aardappelen - plantenziekteverwekkende schimmels - oömyceten - fungiciden - protocollen - experimenteel veldonderzoek - europa
Hevige phytophthora-uitbraak 2016 benadrukt noodzaak resistente rassen
Lammerts Van Bueren, E. ; Hutten, R.C.B. ; Engelen, C.J.M. - \ 2016
Aardappelwereld 2016 (2016)9. - ISSN 0169-653X - p. 32 - 33.
phytophthora infestans - aardappelen - biologische landbouw - ziekteresistentie - resistentie van variëteiten - rassen (planten) - plantenveredeling - potatoes - organic farming - disease resistance - varietal resistance - varieties - plant breeding
De biologische aardappelteelt heeft het in 2016 weer zwaar te verduren gehad met de hevige uitbraak van Phytophtora infestans. Door aanhoudende regenval in juni en juli waren veel telers genoodzaakt om hun percelen met aangetaste aardappelen al vroeg in het seizoen te branden. Gecombineerd met de late pootdatum hebben velen een (te) lage opbrengst van hun vatbare rassen dit jaar. "DIt bevestigt nog maar weer eens de noodzaak van resistente rassen", zo stellen Edith Lammerts van Bueren, Ronald Hutten en Christel Engelen, van het project Bioimpuls waar de deelnemers hard aan nieuwe resistente rassen werken.
Aardappelwereld (Journal)
Lammerts van Bueren, Edith - \ 2016
Aardappelwereld (2016). - ISSN 0169-653X
potatoes - growers - plant breeding - arable farming - varieties - cooperation - organic farming
Kweekspecial 2016 - Deze productie is een uitgave van BioImpuls i.s.m. met Aardappelwereld BV.
Development and application of a 20K SNP array in potato
Vos, Peter - \ 2016
University. Promotor(en): Richard Visser; Fred van Eeuwijk, co-promotor(en): Herman van Eck. - Wageningen : Wageningen University - ISBN 9789462579569 - 166
solanum tuberosum - potatoes - genotypes - single nucleotide polymorphism - data analysis - plant breeding - linkage disequilibrium - genome analysis - tetraploidy - aardappelen - genotypen - gegevensanalyse - plantenveredeling - verstoord koppelingsevenwicht - genoomanalyse - tetraploïdie

In this thesis the results are described of investigations of various application of genome wide SNP (single nucleotide polymorphism) markers. The set of SNP markers was identified by GBS (genotyping by sequencing) strategy. The resulting dataset of 129,156 SNPs across 83 tetraploid varieties was used directly to map traits, but also as a basis for the development of a 20K SNP array in Potato (Solanum tuberosum L.). Subsequently this array, named SolSTW, was used to collect genotypic data from 569 potato genotypes. This dataset offered insight in the breeding history of potato, population structure, linkage disequilibrium (LD) and the potential of GWAS (genome wide association studies) in potato.

In Chapter 2 we describe to development of the SolSTW 20K Infinium SNP array. One third of the SNPs on this array originate from the well-known SolCAP 8303 SNP array. The other SNPs are a subset from a targeted re-sequencing project of 83 tetraploid potato varieties. Because of the high SNP density in potato only a limited number of SNPs is suitable for assay development on a SNP array. An obvious outcome is that flanking SNPs contribute to assay failure, particularly for assays with SNPs located in introns. We used fitTetra software to cluster the distribution of captured signals of each marker into the expected five genotypic classes (nulliplex, simplex, duplex, triplex, quadruplex), resulting in a dataset with 14,530 SNP markers. Subsequently the genotypic data obtained with the SolSTW array was used to characterize a set of 569 potato varieties, advanced breeding clones and progenitors. This resulted in the identification of several footprints of potato breeding. Firstly SNPs were dated i.e. the year of market release of the first variety showing polymorphism for a SNP locus is an indication of the ancestry of a SNP. In such a way we identified SNPs with an ancestry tracing back to heirloom varieties, and SNPs (post-1945 SNPs) tracing back to wild species used in modern introgression breeding. Secondly, the changes in allele frequency were calculated over time. Most SNPs show a relative stable allele frequency over time, and very limited genetic variation is removed from the gene-pool of potato i.e genetic erosion is almost absent. Therefore we conclude that 100 years of breeding has not been able to get rid of non-beneficial genetic variation. Only a limited number of SNPs show a rapid increased in allele frequency, which can be explained by positive selection for disease resistance by breeders, or the more frequent use of several founders.

Better understanding of the genome wide decay of Linkage Disequilibrium (LD) and population structure offers relevant knowledge to perform and interpret the results of a genome wide association study (GWAS) (Chapter 3). Linkage disequilibrium (LD) is a complex phenomenon, and the influence of the factors shaping LD in tetraploids is hardly studied. Therefore we used simulated data to disentangle and therewith understand often-confounded factors underlying LD-decay. We simulated datasets differing in number of haplotypes in a population, and differing in percentage of haplotype specific SNPs. In these simulations we observed that the choice of an estimator of LD-decay has a major effect on the outcome of an LD-decay estimate, while the true LD-decay remains the same. Based on the simulation we conclude that a 90% percentile and a so-called D1/2 (the distance where 50% of the initial LD is decayed) performed best to estimate and compare LD-decay in potato. To understand the various aspects of LD-decay in the variety panel of 537 varieties, the panel was subdivided in several groups based on the age of a variety and the population structure groups. This resulted in the identification of LD-decay over time, i.e in relatively young varieties the average size of the LD-blocks is smaller. The differences between subpopulations were smaller and are most likely the effect of the population structure. We also observed that there are very long LD-blocks caused by introgression breeding and that different a priori MAF-thresholds also can influence the outcome of LD-decay estimation.

Having both LD-decay and population structure defined a genome wide association study (GWAS) was conducted (Chapter 4). For this purpose α-solanine and α-chaconine were measured in potato tubers. Subsequently the sum of both (total SGA) and the ratio between the two were used to discover QTLs for these traits in a GWAS. Additionally we used three bi-parental populations to validate the GWAS results. Total SGA content was confounded with population structure and therefore it was difficult to explain all phenotypic variation with SNP markers. Two QTLs (Sgt1.1 and Sgt11.1) were identified which could be validated in one of the segregating populations. The ratio between α-solanine and α-chaconine was not confounded with population structure, resulted in the identification of two major-effect QTLs (Sgr7.1 & Sgr8.1) located near the candidate genes SGT1 and SGT2, which are known for being responsible in the final steps towards either α-solanine or α-chaconine. The QTL Sgr8.1 could be validated, however similar phenotypes were explained by different haplotypes in two populations. We show that population structure, low frequent alleles and genetic heterogeneity may explain to some degree the missing heritability in GWAS in potato.

In Chapter 5 we describe how the method of graphical genotyping, which is widely used in diploid bi-parental populations, can be applied in a variety panel of tetraploid varieties. We show that a few discrete filtering steps in Excel can be used to display patterns that are visual representations of introgression segments and the locations of historical recombination events. Using this method we identified introgression segments from Solanum vernei including the Gpa5 locus on chromosome 5 and Solanum stoloniferum introgression segment including a gene involved in resistance to Potato Virus Y on chromosome 11. This method requires that the haplotypes that cause the phenotypic effect have to be identical by descent (IBD).

In the final chapter 6 the results of chapter 2 to 5 are discussed. We look forward on how our results can be used in future research and applied in marker-assisted breeding. Additionally some new GWAS results are presented for tuber flesh colour, foliage maturity and resistance to Globodera pallida pathotype 3.

Starch meets biotechnology : in planta modification of starch composition and functionalities
Xu, Xuan - \ 2016
University. Promotor(en): Richard Visser, co-promotor(en): Luisa Trindade. - Wageningen : Wageningen University - ISBN 9789462579200 - 169
starch - potato starch - potatoes - solanum tuberosum - plant biotechnology - biotechnology - genetic engineering - transgenic plants - modified starches - phosphate - arabidopsis thaliana - plant breeding - zetmeel - aardappelzetmeel - aardappelen - plantenbiotechnologie - biotechnologie - genetische modificatie - transgene planten - gemodificeerd zetmeel - fosfaat - plantenveredeling

Storage starch is an energy reservoir for plants and the major source of calories in the human diet. Starch is used in a broad range of industrial applications, as a cheap, abundant, renewable and biodegradable biopolymer. However, starch needs to be modified before it can fulfill the required properties for specific industrial applications. Genetic modification of starch, as a green technology with environmental and economic advantages, has attracted increasingly attention. Many achievements obtained from earlier studies have demonstrated the feasibility and potential of using this approach to produce starches with novel properties (Chapter 2).

The main objective of this research was to produce novel starches with enhanced functionalities through genetic modification, while gaining a better understanding of storage starch biosynthesis. A focus on potato was warranted as it represents a superior model system for storage starch biosynthesis studies and for the production of starches with novel properties. To this end, a number of enzymes from various sources have been expressed in potato tubers to modify starch phosphate content and polysaccharide structure, since these two characteristics have long been recognized as key features in starch properties.

To modify starch phosphate content and explore starch (de)phosphorylation, a human phosphatase enzyme named laforin, and modifications of it, were introduced into potato (Chapter 3). Interestingly, modified starches exhibited a significantly higher phosphate content rather than the expected lower phosphate content. Transcriptome analysis showed that the increase in phosphate content was a result of upregulation of starch phosphorylating genes, which revealed a compensatory response to the loss of phosphate content in potato starch. Furthermore, the increase of phosphate content in potato starch was reached to a threshold level. This was in line with the observations in the modified starches from overexpressed- Glucan water dikinase (GWD1) transgenic plants (Chapter 4). Furthermore, overexpression of two starch dikinases from Arabidopsis thaliana, glucan water dikinase 2 and 3 (AtGWD2 and AtGWD3), did not result in a significant increase in phosphate content of potato starch (Chapter 5). Taken together, these results indicated that phosphate content of potato starch is under strict control.

Morphological analysis of starch granules containing different levels of phosphate content confirmed the indispensible role of phosphate content in the normal formation of starch granules, since cracked granules were observed in the starches containing low phosphate content, while irregular bumpy shaped granules were observed in the tubers from plants containing high phosphate content. Interestingly, further analyses on the expression level of genes involved in starch metabolism and sugar-starch conversion suggested that starch phosphorylation might affect starch synthesis by controlling the carbon flux into starch while simultaneously modulating starch-synthesizing genes. Further studies are needed to confirm this finding (Chapter 4).

To produce starches with novel structures, an (engineered) 4, 6-α-glucanotransferase (GTFB) from Lactobacillus reuteri 121 was introduced into potato tubers (Chapter 6). The resulting starches showed severe changes in granule morphology, but not in starch fine structure. Transcriptome analysis revealed the existence of a self-repair mechanism to restore the regular packing of double helices in starch granules, which possibly resulted in the removal of novel glucose chains potentially introduced by the (engineered) GTFB.

This research successfully generated starches with various functionalities, including altered gelatinization characteristics (Chapter 3 and 4), improved freeze-thaw stability (Chapter 4) and higher digestibility (Chapter 6). The exploitation of relationships between starch characteristics and starch properties revealed that starch properties represent the outcome of the combined effect of many factors and are highly dependent on the genetic background in which the modification has been performed.

In conclusion, the research described in this thesis demonstrates the great potential of genetic modification in producing starches with novel properties. Meanwhile, these results revealed the presence of complex and exquisite molecular regulation mechanisms for starch biosynthesis in potato. In future research, these regulations need to be taken into account for the relational design of starch in planta. Certainly, a better understanding of the process of starch metabolism in storage organs would be a great step forward towards tailoring starch in an economically important crop such as potato.

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.
Nitrogen use efficiency in potato : an integrated agronomic, physiological and genetic approach
Ospina Nieto, C.A. - \ 2016
University. Promotor(en): Paul Struik; Edith Lammerts van Bueren, co-promotor(en): Gerard van der Linden. - Wageningen : Wageningen University - ISBN 9789462576469 - 177 p.
solanum tuberosum - potatoes - nitrogen - nutrient use efficiency - plant breeding - crop physiology - plant physiology - quantitative trait loci - cultivars - aardappelen - stikstof - nutriëntengebruiksefficiëntie - plantenveredeling - gewasfysiologie - plantenfysiologie - loci voor kwantitatief kenmerk

Nitrogen (N) fertilizers increased food production over the last 60 years, but also contributed significantly to the use of fossil energy and the total amount of reactive N in the environment. Agriculture needs to reduce N input and increase nitrogen use efficiency (NUE). Legislation like the Nitrate Directive (91/767/EEC) and the Water Framework Directive (2000/60/EC) forces a reduction in N supply in crop production. The effects of this constraint on yield and quality of potato are expected to be significant since N plays an important role in the vegetative development and production of potato. Considerable amounts of N are needed as N recovery is notoriously low due to the small and shallow roots. The overall aim of this thesis is to improve the nitrogen use efficiency of potato under low nitrogen supply. Specific aims are i) to understand the N effects on potato performance, especially under low N input, ii) to quantify the genotypic variation under contrasting N inputs, iii) to identify quantitative trait loci associated with the crop’s response to nitrogen. We used ecophysiological models to dissect the canopy development into biological meaningful parameters as phenotyping tools. Two potato populations (a set of tetraploid cultivars and a biparental diploid population) were phenotyped in the field under two contrasting N levels. Additionally, a set of 6 cultivars from three maturity groups (early, middle and late) were phenotyped in more detail under 5 nitrogen conditions combining two input levels and two fertilizers types plus a control without nitrogen fertilisation. The curve-fit parameters were, together with other agronomical traits, used in the agronomic and genetic analysis. Our approach using the ecophysiological models captured the phenotypic response to N, enhancing the interpretation of the nitrogen effects and of the differences among maturity types. The nitrogen effects on canopy development resulted in large differences in light interception, tuber yield, tuber size distribution and nitrogen uptake. There were differences in the response to nitrogen between the diploid biparental population and the set of tetraploid cultivars. In general, in the diploid population, having less vigour and therefore less potential to respond to the extra nitrogen, the time required to complete each phase of the canopy development was longer than in the set of tetraploids. In the set of cultivars the rate of early vegetative growth was higher, the onset of the phase with maximum canopy cover was earlier, and the duration of maximum canopy was longer than for the diploid population. However, in both the diploid and the tetraploid population maturity was the major factor accounting for genetic variation in canopy development and tuber development traits. The genotypic differences were reflected in quantitative trait loci that were either N dependent or N independent, with pleiotropic regions affecting most of the maturity-related traits. Few traits showed quantitative trait loci on common regions that were not maturity related like those on chromosomes 2 and 6 (association mapping) or linkage groups ma_VI, pa_VIII pa_XI. Maturity obscures other genotype-dependent physiological traits; therefore it is imperative to find traits that are responsible for genotypic variation, but not related to maturity type. Moreover the results showed that nitrogen use efficiency under low nitrogen input is higher than under high nitrogen input, and higher for late cultivars than for early cultivars. Therefore, breeding for nitrogen use efficiency under low input requires direct selection combined with good response to extra nitrogen and should be done within each maturity group. Finally in a broader context we discussed the need of high-throughput phenotyping in breeding for complex traits, like those involving efficiency, to make the most of the large amount of genetic data, all possible based on advances in technology in remote sensing and images analysis.

Keywords: Association mapping, Breeding for low input, Canopy development, Maturity type, Nitrogen use efficiency, Potato, Solanum tuberosum, Quantitative trait loci.

Effect of adjuvant and spray volume on mancozeb residue on potato and onion leaves and on Phythophthora infestans in potato and Peronospora destructor in onion
Putter, H. de; Schepers, H.T.A.M. ; Topper, C.G. ; Evenhuis, A. - \ 2016
Wageningen : Wageningen UR (vegIMPACT Report 21) - 21 p.
arable farming - vegetable growing - outdoor cropping - potatoes - onions - laboratory tests - solanum tuberosum - allium cepa - plant protection - pesticides - akkerbouw - groenteteelt - vollegrondsteelt - aardappelen - uien - laboratoriumproeven - gewasbescherming - pesticiden
As part of the vegIMPACT project a laboratory test in the Netherlands was done with potato (Solanum tuberosum) var. Bintje and onion (Allium cepa) var. Sturon. In both crops mancozeb was sprayed with and without the adjuvants Bond and Indostick. In both crops these three treatments were applied with high and low spray volumes. After spraying, rain was simulated (0.5, 3 or 6 hours after spraying and a control without rain) to test the sticker properties. After five days, plant leaves were analysed on mancozeb residue. Five days after spraying the potato plants were inoculated with Phytophthora infestans and onions with Peronospora destructor. Subsequently, disease symptoms were observed and visually rated as percentage of infected leaves. In potato lower mancozeb residue levels were measured at high spray volumes. Under dry conditions the effect of adjuvant on mancozeb residue in potato was limited. In onion the spreader characteristics of the adjuvants resulted in higher mancozeb residue concentrations than without adjuvant. The impact of rain simulation was much bigger than the impact of adjuvant on mancozeb residue and late blight incidence. Therefore, it is not recommended to spray when rain is expected within the same day as spraying. With rain simulation in both onion and potato more mancozeb residue was present when using the adjuvant Bond than when spraying mancozeb without an adjuvant. However, also with Bond after rain simulation high amounts of mancozeb were washed off. Mancozeb with Bond in potato resulted in less late blight incidence than with spraying mancozeb without adjuvants. Overall the adjuvant Bond performed better than Indostick in terms of mancozeb retention on both potato and onion leaves . Indostick had good spreading properties that under dry conditions resulted in higher mancozeb residue levels in onion. Under rainy conditions the effect of Indostick on mancozeb residues was not or only slightly better than mancozeb without adjuvant.
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