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.

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Corrigendum : Factors affecting quality and health promoting compounds during growth and postharvest life of sweet cherry (Prunus avium L.) (Front. Plant Sci (2017) 8, (2166), 10.3389/fpls.2017.02166)
Correia, Sofia ; Schouten, Rob ; Silva, Ana P. ; Gonçalves, Berta - \ 2018
Frontiers in Plant Science 9 (2018). - ISSN 1664-462X

There is an error in the Funding statement. The correct Name for the Funder is INTERACT project—Integrative Research in Environment, Agro-Chains and Technology, no. NORTE-01-0145-FEDER-000017, in its line of research entitled ISAC-P2, co-financed by the European Regional Development Fund (ERDF) through NORTE 2020 (North Regional Operational Program 2014/2020). The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. Authors acknowledge the support provided by European Investment Funds by FEDER/COMPETE/POCI-Operational Competitiveness and Internationalization Programme, under the Project POCI-01-0145-FEDER-006958 and National Funds by FCT-Portuguese Foundation for Science and Technology, under the project UID/AGR/04033/2013. SC acknowledge the support provided by the FCT-Portuguese Foundation for Science and Technology (SFRH/BD/52541/2014), under the Doctoral Programme Agricultural Production Chains—from fork to farm (PD/00122/2012).

Sweet cherry fruit cracking mechanisms and prevention strategies : A review
Correia, Sofia ; Schouten, Rob ; Silva, Ana Paula ; Gonçalves, Berta - \ 2018
Scientia Horticulturae 240 (2018). - ISSN 0304-4238 - p. 369 - 377.
Biostimulants - Candidate compounds - Cracking markers - Cracking mechanisms - Prunus avium L. - Rainfall

Sweet cherry (Prunus avium L.) is highly perishable and is greatly affected by orchard management and environmental conditions, such as excess rainfall before harvest. Rain-induced cracking is the major cause of crop loss in sweet cherry in most production areas of the world. Advances in understanding the physiological and molecular mechanisms involved in cracking physiology in combination with orchard management strategies to limit cherry cracking are discussed. The current opinions to explain fruit cracking is that the process initiates with water uptake by the fruit surface that results in localised bursting of cells that release malic acid into the apoplast. This results in swelling of the epidermis and weakening of the epidermal and hypodermal cells until macroscopic fruit cracking. This review focusses on management strategies such as rain cover protection, mineral sprays, anti-transpirants and growth regulators. Tree responses to growth regulators and biostimulants vary with cultivar, application frequency, concentration and type, making it hard to generalize their effects. New approaches to limit cracking are presented, including the development of tolerant cultivars, candidate mineral sprays, biostimulants and technologies for rainwater removal such as orchard air-blast sprayers or creating downwash by helicopters.

Sensory analysis of characterising flavours : Evaluating tobacco product odours using an expert panel
Krüsemann, Erna J.Z. ; Lasschuijt, Marlou P. ; Graaf, C. de; Wijk, René A. de; Punter, Pieter H. ; Tiel, Loes van; Cremers, Johannes W.J.M. ; Nobelen, Suzanne van de; Boesveldt, Sanne ; Talhout, Reinskje - \ 2018
Tobacco Control (2018). - ISSN 0964-4563
advertising and promotion - prevention - public policy

Objectives: Tobacco flavours are an important regulatory concept in several jurisdictions, for example in the USA, Canada and Europe. The European Tobacco Products Directive 2014/40/EU prohibits cigarettes and roll-your-own tobacco having a characterising flavour. This directive defines characterising flavour as 'a clearly noticeable smell or taste other than one of tobacco [⋯]'. To distinguish between products with and without a characterising flavour, we trained an expert panel to identify characterising flavours by smelling. Methods: An expert panel (n=18) evaluated the smell of 20 tobacco products using self-defined odour attributes, following Quantitative Descriptive Analysis. The panel was trained during 14 attribute training, consensus training and performance monitoring sessions. Products were assessed during six test sessions. Principal component analysis, hierarchical clustering (four and six clusters) and Hotelling's T-tests (95% and 99% CIs) were used to determine differences and similarities between tobacco products based on odour attributes. Results: The final attribute list contained 13 odour descriptors. Panel performance was sufficient after 14 training sessions. Products marketed as unflavoured that formed a cluster were considered reference products. A four-cluster method distinguished cherry-flavoured, vanilla-flavoured and menthol-flavoured products from reference products. Six clusters subdivided reference products into tobacco leaves, roll-your-own and commercial products. Conclusions: An expert panel was successfully trained to assess characterising odours in cigarettes and roll-your-own tobacco. This method could be applied to other product types such as e-cigarettes. Regulatory decisions on the choice of reference products and significance level are needed which directly influences the products being assessed as having a characterising odour.

HEx : A heterologous expression platform for the discovery of fungal natural products
Harvey, Colin J.B. ; Tang, Mancheng ; Schlecht, Ulrich ; Horecka, Joe ; Fischer, Curt R. ; Lin, Hsiao Ching ; Li, Jian ; Naughton, Brian ; Cherry, James ; Miranda, Molly ; Li, Yong Fuga ; Chu, Angela M. ; Hennessy, James R. ; Vandova, Gergana A. ; Inglis, Diane ; Aiyar, Raeka S. ; Steinmetz, Lars M. ; Davis, Ronald W. ; Medema, Marnix H. ; Sattely, Elizabeth ; Khosla, Chaitan ; Onge, Robert P.S. ; Tang, Yi ; Hillenmeyer, Maureen E. - \ 2018
Science Advances 4 (2018)4. - ISSN 2375-2548
For decades, fungi have been a source of U.S. Food and Drug Administration-approved natural products such as penicillin, cyclosporine, and the statins. Recent breakthroughs in DNA sequencing suggest that millions of fungal species exist on Earth, with each genome encoding pathways capable of generating as many as dozens of natural products. However, the majority of encoded molecules are difficult or impossible to access because the organisms are uncultivable or the genes are transcriptionally silent. To overcome this bottleneck in natural product discovery, we developed the HEx (Heterologous EXpression) synthetic biology platform for rapid, scalable expression of fungal biosynthetic genes and their encoded metabolites in Saccharomyces cerevisiae. We applied this platform to 41 fungal biosynthetic gene clusters from diverse fungal species from around the world, 22 of which produced detectable compounds. These included novel compounds with unexpected biosynthetic origins, particularly from poorly studied species. This result establishes the HEx platform for rapid discovery of natural products from any fungal species, even those that are uncultivable, and opens the door to discovery of the next generation of natural products.
Short-term salt stress strongly affects dynamic photosynthesis, but not steady-state photosynthesis, in tomato (Solanum lycopersicum)
Zhang, Yuqi ; Kaiser, Elias ; Zhang, Yating ; Yang, Qichang ; Li, Tao - \ 2018
Environmental and Experimental Botany 149 (2018). - ISSN 0098-8472 - p. 109 - 119.
Dynamic photosynthesis - Fluctuating light - Salt stress - Solanum lycopersicum - Stomatal conductance - Tomato
Salt stress occurs worldwide due to widespread soil salinization. Also, plants are often subjected to rapidly alternating periods of sun and shade (sunflecks). Despite this combined occurrence of salt stress and sunflecks, dynamic photosynthetic responses to sunflecks under salt stress remain unknown. This study addresses this discrepancy by exploring photosynthetic gas exchange and chlorophyll fluorescence, both after dark-light transitions and during artificial light fluctuations (lightflecks and shadeflecks), in salt stressed leaves. Three weeks old growth-chamber grown tomato (Solanum lycopersicum Mill ‘Beijing Cherry Tomato’) plants were exposed to 0, 70 or 140 mM of sodium chloride (NaCl), for 7–9 days. Photosynthetic induction after dark-light transitions was strongly inhibited in salt-stressed leaves, due to increased transient stomatal limitation and slower apparent Rubisco activation. During photosynthetic induction, non-photochemical quenching (NPQ) and intrinsic water use efficiency (WUEi) were positively correlated with [NaCl]. Under periods of low light (shadeflecks), the longer the shadefleck lasted, the more strongly photosynthesis after re-illumination was downregulated by salt stress, and this downregulation in photosynthesis was positively correlated with the severity of salt stress. Under regularly applied lightflecks, salt stress decreased photosynthesis by 12–42%, which was mainly caused by decreased stomatal conductance. Salt-stressed leaves also displayed significantly lower stomatal pore area and stomatal index. Crucially, salt stress did not affect steady-state photosynthetic capacity as indicated by similar light and CO2 response curves of photosynthesis. We conclude that a short-term salt stress strongly affects dynamic leaf photosynthesis in tomato while its effect on steady state photosynthesis is negligible.
Identification of bloom date QTLs and haplotype analysis in tetraploid sour cherry (Prunus cerasus)
Cai, Lichun ; Stegmeir, Travis ; Sebolt, Audrey ; Zheng, Chaozhi ; Bink, Marco C.A.M. ; Iezzoni, Amy - \ 2018
Tree Genetics and Genomes 14 (2018)2. - ISSN 1614-2942
Bloom date - Haplotype - Marker-assisted breeding - QTL - Sour cherry
Bloom date is an important production trait in sour cherry (Prunus cerasus L.) as the risk of crop loss to floral freeze injury increases with early bloom time. Knowledge of the major loci controlling bloom date would enable breeders to design crosses and select seedlings with late bloom date. As sour cherry is a segmental allotetraploid, quantitative trait locus (QTL) analysis for bloom date was performed based on haplotype reconstruction by identifying the parental origins of marker alleles in sour cherry. A total of 338 sour cherry individuals from five F1 populations were genotyped using the cherry 6K Illumina Infinium® SNP array and phenotyped for bloom date in 3 years. A total of four QTLs were identified on linkage group (G)1, G2, G4, and G5, respectively. For these QTLs, 14 haplotypes constructed for the QTL regions were significantly associated with bloom date, accounting for 10.1–27.9% of the bloom date variation within individual populations. The three most significant haplotypes, which were identified for the G4 (G4-k), G2 (G2-j), and G1 (G1-c) QTLs, were associated with 2.8, 1.8, and 1.0 days bloom delay, respectively. These three haplotypes were also demonstrated to have additive effects on delaying bloom date for both individual and multiple QTLs. These results demonstrate that bloom date is under polygenic control in sour cherry; yet, pyramiding late blooming haplotypes for single and multiple QTLs would be an effective strategy to obtain later blooming offspring.
Factors affecting quality and health promoting compounds during growth and postharvest life of sweet cherry (Prunus avium L.)
Correia, Sofia ; Schouten, Rob ; Silva, Ana P. ; Gonçalves, Berta - \ 2017
Frontiers in Plant Science 8 (2017). - ISSN 1664-462X
Breeding for quality - Growth conditions - New preservation technologies - Phenolic compounds - Quality indicators
Sweet cherries are attractive fruits due to their taste, color, nutritional value, and beneficial health effects. Sweet cherry is a highly perishable fruit and all quality attributes and the level of health promoting compounds are affected by growth conditions, picking, packing, transport, and storage. During production, the correct combination of scion × rootstock will produce fruits with higher firmness, weight, sugars, vitamins, and phenolic compounds that boost the fruit antioxidant activity. Orchard management, such as applying drip irrigation and summer pruning, will increase fruit sugar levels and total phenolic content, while application of growth regulators can result in improved storability, increased red coloring, increased fruit size, and reduced cracking. Salicylic acid, oxalic acid, acetylsalicylic acid, and methyl salicylate are promising growth regulators as they also increase total phenolics, anthocyanins, and induce higher activity of antioxidant enzymes. These growth regulators are now also applied as fruit coatings that improve shelf-life with higher antioxidant enzyme activities and total phenolics. Optimizing storage and transport conditions, such as hydro cooling with added CaCl2, chain temperature and relative humidity control, are crucial for slowing down decay of quality attributes and increasing the antioxidant capacity. Application of controlled atmosphere during storage is successful in delaying quality attributes, but lowers ascorbic acid levels. The combination of low temperature storage in combination with modified atmosphere packaging (MAP) is successful in reducing the incidence of fruit decay, while preserving taste attributes and stem color with a higher antioxidant capacity. A new trend in MAP is the use of biodegradable films such as micro-perforated polylactic acid film that combine significant retention of quality attributes, high consumer acceptability, and a reduced environmental footprint. Another trend is to replace MAP with fruit edible coatings. Edible coatings, such as various lipid composite coatings, have advantages in retaining quality attributes and increasing the antioxidant activity (chitosan) and are regarded as approved food additives, although studies regarding consumer acceptance are needed. The recent publication of the sweet cherry genome will likely increase the identification of more candidate genes involved in growing and maintaining health related compounds and quality attributes.
Prunus fruit juices
Toydemir, Gamze ; Boyacioglu, Dilek ; Hall, R.D. ; Beekwilder, M.J. ; Capanoglu, Esra - \ 2017
In: Innovative Technologies in Beverage Processing / Aguiló-Aguayo, I., Plaza, L., Chichester UK : Wiley - ISBN 9781118929377 - p. 59 - 77.
The juice drinks obtained from Prunus fruit species, apricot (Prunus armeniaca), cherry (sweet cherry (Prunus avium) and sour cherry (Prunus cerasus)), peach (Prunus persica), and plum (Prunus domestica), are gaining increasing interest as a convenient alternative to fresh fruits. The conventional thermal pasteurization of fruit juices may cause some quality deterioration, such as nonenzymatic browning, losses of essential nutrients, and changes in physicochemical and organoleptic properties. Recently, novel nonthermal technologies are being extensively explored as promising alternatives to avoid the negative effects of heat pasteurization. The most studied nonthermal processing methods in Prunus fruit juices are pulsed electric fields and high-pressure processing, which are reviewed in detail in the scope of this chapter by describing the aim and the basic concepts, and highlighting their effects on microbial quality, enzymatic activity, and physical, chemical, and sensory properties of Prunus fruit juices.
Erratum to : Genetic structure of a QTL hotspot on chromosome 2 in sweet cherry indicates positive selection for favorable haplotypes (Molecular Breeding, (2017), 37, 7, (85), 10.1007/s11032-017-0689-6)
Cai, Lichun ; Voorrips, Roeland E. ; Weg, Eric van de; Peace, Cameron ; Iezzoni, Amy - \ 2017
Molecular Breeding 37 (2017)8. - ISSN 1380-3743
In the original publication, the numbers assigned to each haplotype in Fig. 2 and its expanded version (Supplementary Fig. S2) are not consistent with the numbers used in the article. The haplotype numbers are corrected and the haplotypes are reordered according to these new numbers in the attached revised Fig. 2 and Supplementary Fig. S2. Fig. 2Marker allele composition of each haplotype across the five haploblocks for the sweet cherry QTL hotspot on chromosome 2 illustrated using the smallest number of markers needed to differentiate the haplotypes. SSR alleles are recorded as fragment sizes in base pairs. Haplotypes were assigned by the PediHaplotyper software (Voorrips et al. 2016). Haplotypes containing missing marker scores were omitted from the table. The complete marker composition is in Supplementary Fig. S2 Supplementary Fig. S2 Marker allele composition of each haplotype across five haploblocks for the sweet cherry QTL hotspot on chromosome 2. SSR alleles are recorded as fragment sizes in base pairs. The smallest subset of markers needed to differentiate the haplotypes within each haploblock are highlighted in red font. Haplotypes were assigned by the PediHaplotyper software (Voorrips et al., 2016). Haplotypes containing missing marker scores were omitted from the table.
Genetic structure of a QTL hotspot on chromosome 2 in sweet cherry indicates positive selection for favorable haplotypes
Cai, Lichun ; Voorrips, Roeland E. ; Weg, Eric van de; Peace, Cameron ; Iezzoni, Amy - \ 2017
Molecular Breeding 37 (2017)7. - ISSN 1380-3743 - 10 p.
Haplotype - Prunus avium - QTL hotspot - SNP

A genomic region of particular interest for sweet cherry (Prunus avium L.) breeding is a quantitative trait locus (QTL) “hotspot” on chromosome 2. QTLs for fruit size, firmness, sweetness, and flowering time are reported to map to this region. An understanding of genetic diversity, allele sources, linkage relationships, and historical recombinations is critical to enable the combining of favorable alleles at multiple loci. The objectives of this study were to characterize, visualize, and interpret the genetic structure of this previously identified QTL hotspot within North American sweet cherry breeding germplasm, using a pedigree-based haploblocking approach. Across the 29.4 cM (6.3 Mbp) region defined by single nucleotide polymorphism (SNP) information from the RosBREED cherry 6K SNP array v1, a total of 12 recombination events falling into six inter-marker regions were traced within the pedigree of elite and wild germplasm (n = 55). These recombinations defined five haploblocks containing 5–15 markers and exhibiting 7–11 haplotypes each. Over the entire QTL hotspot, 30 extended haplotypes were identified for which parental gametes could be determined. When the haploblocks and their haplotypes were used to explore genetic diversity, ancestry, and recombination patterns, and then integrated with previous QTL results for fruit size, the results indicated that favorable alleles at this QTL hotspot are under positive selection in breeding. The genetic framework provided by a haploblock approach and knowledge of haplotype-level diversity sets the stage for assigning breeding utility to these haplotypes.

Biology and control of bacterial diseases and Drosophila suzukii in cherry growing in the Netherlands
Wenneker, M. ; Helsen, H.H.M. - \ 2016
In: Book of Abstracts COST FA1104 Ziti publications - p. 59 - 59.
Biology and control of bacterial diseases and Drosophila suzukii in cherry growing in the Netherlands
Wenneker, M. ; Helsen, H.H.M. - \ 2016
Susceptibility pays off: insights into the mlo-based powdery mildew resistance
Appiano, Michela - \ 2016
University. Promotor(en): Richard Visser, co-promotor(en): Yuling Bai; Anne-Marie Wolters. - Wageningen : Wageningen University - ISBN 9789462579484 - 265
solanum lycopersicum - tomatoes - disease resistance - susceptibility - oidium neolycopersici - genes - gene expression - genomics - molecular breeding - plant breeding - tomaten - ziekteresistentie - vatbaarheid - genen - genexpressie - genomica - moleculaire veredeling - plantenveredeling

Powdery mildew (PM) is a worldwide-occurring plant disease caused by ascomycete fungi of the order Erysiphales. A conspicuous number of plant species are susceptible to this disease, the occurrence of which is increasing due to the influence of climate change. Symptoms are easy to recognize by the powdery whitish fungal structures growing on the surface of plant organs. Severe infections cause significant losses in crops, such as tomato, cucumber and wheat, as well as in ornamentals, like rose and petunia. Accordingly, breeding crops with a robust immunity to this disease is of great economic importance.

A significant step in this direction was the discovery of mlo (mildew locus o) mutant alleles of the barley HvMlo gene, which are responsible for the non-race specific resistance to the barley PM pathogen, Blumeria graminis f.sp. hordei (Bgh). During the years, this recessively inherited resistance was observed to be durable, contrary to the short life-span of resistances conferred by dominant resistance (R-) genes used in barley breeding programs. Studies on the histological mechanisms of the mlo-based resistance showed that the PM pathogen was stopped during penetration of the cell wall by the formation of a papilla. This structure prevents the formation of the feeding structure of the pathogen, called a haustorium.

After sequencing many plant genomes, we are discovering that MLO genes are not only typical of this cereal, but are ubiquitously present in higher plant species in multiple copies per species, forming a gene family. The impairment of some members of a number of ever increasing plant species lead to broad-spectrum resistance towards their adapted PM pathogens. For example, in tomato the ol-2 gene, naturally harbored by the cherry tomato Solanum lycopersicum var. cerasiforme, represents the loss-of-function allele of the SlMLO1 gene, conferring resistance to the PM pathogen Oidium neolycopersici (On). Consequently, the use of mlo mutants represents a suitable alternative to the classical use of R-genes in breeding programs.

In Chapter 2, we describe the in silico identification of the complete tomato SlMLO gene family using the available information in the SOL genomic network database. In total, 16 tomato SlMLO members were cloned from leaf, root, flower and fruit of the susceptible tomato cv. Moneymaker to confirm the sequences retrieved from the database and to verify their actual expression in these tissues. We observed the presence of various types of splicing variants, although their possible functional meaning has not been investigated. Motif analyses of each of the translated protein sequences and phylogenetic studies highlighted, on one hand, amino acid stretches that characterize the whole MLO family, and, on the other hand, stretches conserved in MLO homologs that are phylogenetically related. Following a gene expression study upon On inoculation, we identified members of the SlMLO family that are upregulated few hours after pathogen challenge. Except SlMLO1, none of the three newly identified homologs in clade V, thus phylogenetically close to SlMLO1, are induced. Interestingly, two homologs, each found in different clades, are upregulated similarly to SlMLO1. Using an RNAi approach, we silenced the additional clade V-SlMLO homologs, namely SlMLO3, SlMLO5 and SlMLO8, to investigate their possible role in PM resistance. We observed that none of these homologs if individually silenced, leads to PM resistance. However, if SlMLO5 and SlMLO8 are silenced together with SlMLO1, a significantly higher level of resistance is achieved compared to plants carrying the ol-2 allele. The role of SlMLO3 could not be verified. We, therefore, concluded that there are three SlMLO genes in tomato unevenly contributing to the PM disease, of which SlMLO1 has a major role.

Chapter 3 focuses on the components of the tomato mlo-based resistance. In Arabidopsis, it is known that four members of the SNARE protein family, involved in membrane fusion, are involved in mlo-based resistance. In this chapter, we focused on the identification of tomato homologs of the Arabidopsis syntaxin PEN1 (AtSYP121). Among the group of syntaxins identified in tomato, two were closely related to each other and also to AtPEN1, denominated SlPEN1a and SlPEN1b. Another Arabidopsis syntaxin that shows a high level of homology with PEN1, called SYP122, was also found to group together with the newly identified SlPEN1 genes. However, the role of SYP122 in plant immunity was not shown in literature. After obtaining individual silencing RNAi constructs, we transformed the resistant ol-2 line, and we challenged the obtained transformants with the adapted PM On, and the non-adapted Bgh. Interestingly, we observed a significant On growth and an enhanced Bgh cell entry only in SlPEN1a silenced plants but not in SlPEN1b silenced ones. We performed a protein alignment of tomato and Arabidopsis functional and non-functional PEN sequences. The presence of three differently conserved non-synonymous amino-acid substitutions is hypothesised to be responsible for the specialization in plant immune function.

In Chapter 4 and Chapter 5, we build up a body of evidence pointing to the fact that the function of the MLO susceptibility genes is highly conserved between monocot and dicot plant species.

In Chapter 4 we started by identifying and functionally characterizing two new MLO genes of Solanaceous crops affected by the PM disease, tobacco (Nicotiana tabacum) and eggplant (Solanum melongena). We named them NtMLO1 and SmMLO1 in the respective species, as they are the closest homologs to tomato SlMLO1. By overexpressing these genes in the resistant ol-2 line, we obtained transgenic plants that were susceptible to the PM pathogen On. This finding demonstrates that both heterologous MLO proteins can rescue the function of the impaired ol-2 allele in tomato. In addition, we found in tobacco NtMLO1 an amino acid (Q198) of critical importance for the susceptibility function of this protein.

In Chapter 5, we used the same approach adopted in Chapter 4 to show that other MLO proteins of more distant dicot species, like pea PsMLO1, can rescue the loss-of-function of the tomato ol-2 allele. And finally, we stretched this concept also to monocot MLO proteins, using barley HvMlo. While performing these experiments, we could verify that the function of the monocot and dicot susceptibility MLO proteins does not rely on the presence of class-specific conservation. The latter can be the reason for the phylogenetic divergence, placing monocot MLO proteins in clade IV and dicot MLO proteins in clade V of the phylogenetic MLO tree. However, functional conservation might depend on crucial shared amino acids of clade IV and V MLO proteins. Therefore, we also conducted a codon-based evolutionary analysis that resulted in the identification of 130 codons under negative selection, thus strongly maintained during evolution.

In Chapter 6 we introduce the PM disease in cucumber caused by Podosphaera xanthii (Px). We cloned the candidate susceptibility gene for PM in cucumber, CsaMLO8, from susceptible and resistant genotypes. The latter was described as an advanced cucumber breeding line characterized by hypocotyl resistance. In this line, we found the presence of aberrant splicing variants of the CsaMLO8 mRNA due to the insertion in its corresponding genomic region of a Class LTR retrotransposon. Heterologous expression of the wild-type cucumber allele in the tomato ol-2 line restored its PM susceptibility, while the heterologous expression of the aberrant protein variant failed to do so. This finding confirms that the resistance of the advanced cucumber breeding line is due to the disruption of the coding region of this gene. We also showed that the expression of CsaMLO8 in the susceptible genotype is induced by Px in hypocotyl tissue, but not in cotyledon or leaf. Finally, by examination of the resequencing data of a collection of 115 cucumber accessions, we found the presence of the TE-containing allele in 31 of them among which a wild cucumber accession that might have been used in breeding programs to obtain resistance to the PM disease in cucumber.

In Chapter 7 a novel loss-of-function allele of the SlMLO1 gene is described, designated m200. This allele was found in a resistant plant (M200) from a mutagenized tomato Micro-Tom (MT) population obtained with the chemical mutagen ethyl methanesulfonate (EMS). The m200 mutation corresponds to a nucleotide transversion (T à A) which results in a premature stop codon. The length of the predicted SlMLO1 protein in the M200 plant is only 21 amino acids, thus much shorter than the predicted protein of the previously described ol-2 allele, consisting of 200 amino acids. Thanks to the development of a High-Resolution Melting (HRM) marker designed to detect the m200 mutation, we observed that this allele confers recessively inherited resistance in backcross populations of the resistant M200 plant with MT and Moneymaker. Histological study showed that the resistance of the m200 mutant is associated with papilla formation. Finally, we compared the rate of On penetration in epidermal cells of m200 plants with the one of plants carrying the ol-2 allele and the transgenic plants in which multiple SlMLO homologs were silenced, generated in Chapter 2.

Ultimately, in Chapter 8 the results of the previous chapters are discussed in the context of 1) practical applications in breeding programs aimed at introducing the mlo-based resistance in new crops, 2) possible research aimed at unraveling the function of the MLO protein and 3) the role of other SNARE proteins.

Integrating black cherry in forest management in the Netherlands and Belgium
Nyssen, B. ; Ouden, J. den; Verheyen, K. ; Vanhellemont, M. - \ 2016
In: Introduced tree species in European forests: opportunities and challenges / Krumm, Frank, Vítková, Lucie, European Forest Institute - ISBN 9789525980318 - p. 362 - 372.
Cherry Juice
Toydemir, Gamze ; Boyacioglu, D. ; Beekwilder, M.J. ; Hall, R.D. ; Capanoglu, E. - \ 2016
In: Handbook of Functional Beverages and Human Health CRC Press - ISBN 9781466596412 - p. 175 - 185.
Where are we now as we merge genomics into plant breeding and what are our limitations? Experiences from RosBREED
Iezzoni, A. ; Weebadde, C. ; Peace, C. ; Main, D. ; Bassil, N.V. ; Coe, M. ; Fazio, G. ; Gallardo, K. ; Gasic, K. ; Luby, J. ; McFerson, J. ; De Weg, E. Van; Yue, C. - \ 2016
In: 29th International Horticultural Congress on Horticulture: Sustaining Lives, Livelihoods and Landscapes (IHC 2014): 2nd International Berry Fruit Symposium: Interactions! Local and Global Berry Research and Innovation International Society for Horticultural Science (Acta Horticulturae ) - ISBN 9789462611139 - p. 1 - 5.
Apple - Cherry - Genetic improvement - Marker-assisted breeding - Peach - Strawberry

The complete genome sequences of apple, peach, and diploid strawberry - one member of each of the three main fruit-producing branches of the Rosaceae tree - were available in 2010. Despite this achievement, virtually none of this genomics knowledge was being used to assist breeding efforts of these crops. Four years later, this gap has been bridged, with genetic information routinely used in many US apple, peach, and cherry breeding programs. For example, DNA tests predict apple crispness, peach maturity date, and cherry fruit size, enabling breeders to determine the best parents to combine and the best seedlings to advance. This application significantly reduces the wasted effort to eliminate entirely poor families and reduces the costs to grow and evaluate thousands of seedlings genetically destined to have unacceptable fruit quality or maturity date. This achievement was enabled by international community efforts, including the RosBREED project, funded by the USDA-National Institute of Food and Agriculture Specialty Crop Research Initiative (SCRI). DNA tests are now applied for high-value attributes where the targeted loci explain a large proportion of the trait variation. However, limitations to widespread adoption of these predictive tests still exist. Some limitations are due to lack of knowledge, such as an understanding of genotype by environment (G×E) interactions and loci associated with variation for other valuable attributes. Technical limitations include streamlined phasing of alleles from multiple families of pedigree-connected breeding germplasm and access to suitable commercial service providers.

Predicting the potential establishment of two insect species using the simulation environment INSIM (INsect SIMulation)
Hemerik, Lia ; Nes, Egbert H. van - \ 2016
Entomologia Experimentalis et Applicata 159 (2016)2. - ISSN 0013-8703 - p. 222 - 229.
Podisus maculiventris - Biological control - Degree-day model - Development - Drosophila suzukii - Invasive species - Life history - Mortality - Reproduction - Temperature-dependent

Degree-day models have long been used to predict events in the life cycle of insects and therewith the timing of outbreaks of insect pests and their natural enemies. This approach assumes, however, that the effect of temperature is linear, whereas developmental rates of insects are non-linearly related to temperature. Therefore, we have developed the simulation tool INSIM (INsect SIMulation) that can easily handle non-linear temperature relationships, because the program interpolates between measured growth, mortality, and reproduction parameter values given at two subsequent ambient temperatures. We use the tool for predicting the establishment of two insect species. For the application of the biological control agent Podisus maculiventris (Say) (Hemiptera: Pentatomidae) in The Netherlands, we compare a linear and a non-linear function for the development. The number of adult females increases six-fold in the course of a year for the non-linear case, suggesting that the Dutch climate might be warm enough for this beneficial insect to settle. The implementation of a linear development rate shows approximately the same increase. For the invasive pest Drosophila suzukii (Matsumura) (Diptera: Drosophilidae) in The Netherlands, we assessed that it is probably well-adapted to the current Dutch climate: it is predicted to establish easily in most of the simulated scenarios. However, if it were only to attack blueberries (and not cherries), its invasion success is predicted to be limited, because the reproduction in blueberries is low. The implementation of a linear development rate gives rise to 50% fewer adult females (on cherry) or even 95% fewer (on blueberry) after a year. More data are needed for both systems, specifically on overwintering survival for P. maculiventris and for D. suzukii on lifetime reproduction at various temperatures and in different fruit hosts. From the implementation of the linear rate model we can see that, depending on how well the linear approximation is, the results may differ considerably. We have demonstrated that the INSIM program is a useful tool that can easily be adapted to predict the success and individual variation for different insect species.

FEM growth and yield data monocultures - other species
Goudzwaard, L. ; Jansen, J.J. ; Oosterbaan, A. ; Oldenburger, J.F. ; Mohren, G.M.J. ; Ouden, J. den - \ 2016
growth and yield - even-aged monoculture forest - tree diameter - tree height - crown class - coordinates stem positions - age - top height - dominant height - dominant diameter - monitoring - Black alder (Alnus glutinosa) - Black locust (Robinia pseudocacia - European hornbeam (Carpinus betulus) - European larch (Larix decidua) - Elm (Ulmus species) - Eastern white pine (Pinus strobus) - Lodgepole pine (Pinus contorta) - Maritime pine ( Pinus maritima) - Port Orford cedar (Chamaecyparis lawsoniana) - Sweet chestnut (Castanea sativa) - Serbian spruce (Picea omorika) - Silver fir (Abies alba) - Western hemlock (Tsuga hetrophylla) - Western red ceder (Thuja plicata) - Wild cherry (Prunus avium)
The current database is part of the FEM growth and yield database, a collection of growth and yield data from even-aged monocultures (douglas fir, common oak, poplar, Japanese Larch, Norway spruce, Scots pine, Corsican pine, Austrian pine, red oak and several other species, with only a few plots, even-aged mixed species forest plots, uneven-aged natural forest, uneven-aged selection forest and roadside plantattions of poplar. The FEM growth and yield data base is currently supervised by Jan den Ouden and Frits Mohren.
Sugar and acid interconversion in tomato fruits based on biopsy sampling of locule gel and pericarp tissue
Schouten, R.E. ; Woltering, E.J. ; Tijskens, L.M.M. - \ 2016
Postharvest Biology and Technology 111 (2016). - ISSN 0925-5214 - p. 83 - 92.
This study deals with quantifying sugar and acids levels important for the perceived taste of tomatoes (Solanum lycopersicum). Sugar and acids levels were measured repeatedly on the same tomato using tissue samples obtained with a biopsy needle in combination with HPLC protocols. Biopsies of pericarp and locular gel tissue from tomatoes differing in position in the truss, from mature green to ripe red, were taken from a beef- (‘Licorossa’), a cocktail- (‘Lucino’) and a cherry type (‘Petit Sweet’) cultivar. Tomatoes were stored up to three weeks at three temperatures (12, 19 and 24.5 °C) and biopsy samples were taken every few days. A model regarding the most important processes that interconvert sugars and acids (glycolysis, TCA cycle and gluconeogenesis (GNG)) is proposed. Results of the model calibration showed more breakdown of hexoses in red tomatoes and more conversion of malate into hexoses in green tomatoes. More hexose turnover was found in locular gel than in pericarp tissue. GNG was more important in the cherry type cultivar due to faster hexose and malate breakdown. In the round type cultivar malate levels were higher due to faster citrate breakdown and slower malate breakdown. Starch and sucrose levels did not significantly affect postharvest sugar and acid development. Molecular markers that quantify the kinetic parameters of the model might be important to develop genotypes with better taste performance.
QTL mapping of pomological traits in peach and related species breeding germplasm
Fresnedo-Ramírez, J. ; Bink, M.C.A.M. ; Weg, W.E. van de; Famula, T.R. ; Crisosto, C.H. ; Frett, T. ; Gasic, K. ; Peace, C.P. ; Gradziel, T.M. - \ 2015
Molecular Breeding 35 (2015). - ISSN 1380-3743 - 19 p.
persica l. batsch - prunus-persica - linkage disequilibrium - fruit size - population-structure - candidate genes - genome database - sweet cherry - almond - cultivars
Peach is an economically important fruit tree crop that exhibits high phenotypic variability yet suffers from diversity-limited gene pool. Genetic introgression of novel alleles from related species is being pursued to expand genetic diversity. This process is, however, challenging and requires the incorporation of innovative genomic and statistical tools to facilitate efficient transfer of these exotic alleles across the multiple generations required for introgression. In this study, pedigree-based analysis (PBA) in a Bayesian QTL mapping framework was applied to a diverse peach pedigree introgressed with almond and other related Prunus species. The aim was to investigate the genetic control of eight commercially important fruit productivity and fruit quality traits over two subsequent years. Fifty-two QTLs with at least positive evidence explaining up to 98 % of the phenotypic variance across all trait/year combinations were mapped separately per trait and year. Several QTLs exhibited variable association with traits between years. By using the peach genome sequence as a reference, the intrachromosomal positions for several QTLs were shown to differ from those previously reported in peach. The inclusion of introgressed germplasm and the explicit declaration of the genetic structure of the pedigree as covariate in PBA enhanced the mapping and interpretation of QTLs. This study serves as a model study for PBA in a diverse peach breeding program, and the results highlight the ability of this strategy to identify genomic resources for direct utilization in marker-assisted breeding.
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