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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On the use of the observation-wise k-fold operation in PCA cross-validation
Saccenti, E. ; Camacho, J. - \ 2015
Journal of Chemometrics 29 (2015)8. - ISSN 0886-9383 - p. 467 - 478.
principal component analysis - missing data - models - number - spectroscopy - mspc - pls
Cross-validation (CV) is a common approach for determining the optimal number of components in a principal component analysis model. To guarantee the independence between model testing and calibration, the observationwise k-fold operation is commonly implemented in each cross-validation step. This operation renders the CV algorithm computationally intensive, and it is the main limitation to apply CV on very large data sets. In this paper, we carry out an empirical and theoretical investigation of the use of this operation in the element-wise k-fold (ekf) algorithm, the state-of-the-art CV algorithm. We show that when very large data sets need to be cross-validated and the computational time is a matter of concern, the observation-wise k-fold operation can be skipped. The theoretical properties of the resulting modified algorithm, referred to as column-wise k-fold (ckf) algorithm, are derived. Also, its performance is evaluated with several artificial and real data sets. We suggest the ckf algorithm to be a valid alternative to the standard ekf to reduce the computational time needed to cross-validate a data set
Maternal allocation in cooperative breeders: Should mothers match or compensate for expected helper contributions?
Savage, J.L. ; Russell, A.F. ; Johnstone, R.A. - \ 2015
Animal Behaviour 102 (2015). - ISSN 0003-3472 - p. 189 - 197.
egg size - clutch size - trade-off - parental investment - male attractiveness - offspring quality - breeding birds - body-size - number - growth
Among species with variable numbers of individuals contributing to offspring care, an individual's investment strategy should depend upon both the size of the breeding group and the relative contributions of each carer. Existing theoretical work on carer investment rules has, however, largely focused on biparental care, and on modelling offspring provisioning in isolation from other stages of investment. Consequently, there has been little exploration of how maternal investment prior to birth might be expected to influence carer provisioning decisions after birth, and how these should be modified by the number of carers present. In particular, it is unclear whether mothers should increase or decrease their investment in each offspring under favourable rearing conditions, and whether this differs under alternative assumptions about the consequences of being ‘high quality’ at birth. We develop a game-theoretical model of cooperative care that incorporates female control of prebirth investment, and allow increased maternal investment to either substitute for later investment (giving offspring a ‘head start’) or raise the value of later investment (a ‘silver spoon’). We show that mothers reduce prebirth investment under better rearing conditions (more helpers) when investment is substitutable, leading to concealed helper effects. In contrast, when maternal prebirth investment primes offspring to benefit more from postbirth care, mothers should take advantage of good care environments by investing more in offspring both before and after birth. These results provide novel mechanisms to explain contrasting patterns of maternal investment across cooperative breeders.
Evaluation of ecosystem-based marine management strategies based on risk assessment
Piet, G.J. ; Jongbloed, R.H. ; Knights, A.M. ; Tamis, J.E. ; Paijmans, A.J. ; Sluis, M.T. van der; Vries, P. de; Robinson, L.A. - \ 2015
Biological Conservation 186 (2015). - ISSN 0006-3207 - p. 158 - 166.
fisheries management - new-zealand - vulnerability - support - areas - south - pressure - context - threats - number
This study presents a comprehensive and generic framework that provides a typology for the identification and selection of consistently defined ecosystem-based management measures and allows a coherent evaluation of these measures based on their performance to achieve policy objectives. The performance is expressed in terms of their reduction of risk of an adverse impact on the marine ecosystem. This typology consists of two interlinked aspects of a measure, i.e. the “Focus” and the “Type”. The “Focus” is determined by the part of the impact chain (Driver–Pressure–State) the measure is supposed to mitigate or counteract. The “Type” represents the physical measure itself in terms of how it affects the impact chain directly; we distinguish Spatio-temporal distribution controls, Input and Output controls, Remediation and Restoration measures. The performance of these measures in terms of their reduction in risk of adverse impacts was assessed based on an explicit consideration of three time horizons: past, present and future. Application of the framework in an integrated management strategy evaluation of a suite of measures, shows that depending on the time horizon, different measures perform best. “Past” points to measures targeting persistent pressures (e.g. marine litter) from past activities. “Present” favors measures targeting a driver (e.g. fisheries) that has a high likelihood of causing adverse impacts. “Future” involves impacts that both have a high likelihood of an adverse impact, as well as a long time to return to pre-impacted condition after the implementation of appropriate management, e.g. those caused by permanent infrastructure or persistent pressures such as marine litter or specific types of pollution.
Neandertal Admixture in Eurasia Confirmed by Maximum-Likelihood Analysis of Three Genomes
Lohse, K. ; Frantz, L.A.F. - \ 2014
Genetics 196 (2014)4. - ISSN 0016-6731 - p. 1241 - 1251.
ancestral population sizes - dna-sequences - divergence - speciation - history - number - recombination - coalescent - migration - inference
Although there has been much interest in estimating histories of divergence and admixture from genomic data, it has proved difficult to distinguish recent admixture from long-term structure in the ancestral population. Thus, recent genome-wide analyses based on summary statistics have sparked controversy about the possibility of interbreeding between Neandertals and modern humans in Eurasia. Here we derive the probability of full mutational configurations in nonrecombining sequence blocks under both admixture and ancestral structure scenarios. Dividing the genome into short blocks gives an efficient way to compute maximum-likelihood estimates of parameters. We apply this likelihood scheme to triplets of human and Neandertal genomes and compare the relative support for a model of admixture from Neandertals into Eurasian populations after their expansion out of Africa against a history of persistent structure in their common ancestral population in Africa. Our analysis allows us to conclusively reject a model of ancestral structure in Africa and instead reveals strong support for Neandertal admixture in Eurasia at a higher rate (3.4-7.3%) than suggested previously. Using analysis and simulations we show that our inference is more powerful than previous summary statistics and robust to realistic levels of recombination.
The presence of a below-ground neighbour alters within-plant seed size distribution in Phaseolus vulgaris
Chen, B. ; During, H.J. ; Vermeulen, P.J. ; Anten, N.P.R. - \ 2014
Annals of Botany 114 (2014). - ISSN 0305-7364 - p. 937 - 943.
root competition - variable environments - optimal balance - number - recognition - germination - growth - consequences - adaptation - plasticity
* Background and Aims Considerable variation in seed size commonly exists within plants, and is believed to be favoured under natural selection. This study aims to examine the extent to which seed size distribution depends on the presence of competing neighbour plants. * Methods Phaseolus vulgaris plants rooting with or without a conspecific neighbourwere grown in soil with high or low nutrient availability. Seeds were harvested at the end of the growth cycle, the total nitrogen and phosphorus invested in seed production were measured and within-plant seed size distribution was quantified using a set of statistical descriptors. * Key Results Exposure to neighbours’ roots induced significant changes in seed size distribution. Plants produced proportionally more large seeds and fewer small ones, as reflected by significant increases in minimal seed size, mean seed size, skewness and Lorenz asymmetry coefficient. These effects were different from, and in several cases opposite to, the responses when the soil nutrient level was reduced, and were significant after correction for the amount of resources invested in seed production. * Conclusions Below-ground neighbour presence affects within-plant seed size distribution in P. vulgaris. This effect appears to be non-resource-mediated, i.e. to be independent of neighbour-induced effects on resource availability. It implies that, based on current environmental cues, plants can make an anticipatory adjustment of their investment strategy in offspring as an adaptation to the local environment in the future. Key words: Anticipatory maternal effect, bet-hedging, game theory, neighbour detection, Phaseolus vulgaris, kidney bean, root competition, seed-setting, seed size variation, size inequality, skewness. INTRODUCTION A considerable degree of variation in seed size within plants is commonly observed (Michaels et al., 1988; Silvertown, 1989; Ruiz de Clavijo, 2002; Vo¨ller et al., 2012). Such variation is often interpreted as an adaptive bet-hedging strategy (Harper et al., 1970; McGinley et al., 1987; McGinley and Charnov, 1988; Venable and Brown, 1988; Geritz, 1995). Many studies also reveal that plants modify the pattern of variation (i.e. distribution) to cope with their abiotic environmental conditions (e.g. temperature, Wulff, 1986; light, Galloway, 2001; nutrients, Galloway, 2001;water, Parciak, 2002). Herewe demonstrate that seed size distribution may also be modified in response to the presence of a below-ground neighbour. Within a species, seed size (following common practice, seed size refers to seedweight in this paper) often correlates positively with the competitiveness of the offspring (e.g. Houssard and Escarre´, 1991; Eriksson, 1999; Lehtila¨ and Ehrle´n, 2005; Dubois and Cheptou, 2012). Based on the trade-off, induced by resource limitation in plants, between competition (favours large seeds) and colonization (favours a large number of small seeds), Geritz (1995) extended an optimal offspring size model (Smith and Fretwell, 1974) by considering seedling competition and using
Automatic fruit recognition and counting from multiple images
Song, Y. ; Glasbey, C.A. ; Horgan, G.W. ; Polder, G. ; Dieleman, J.A. ; Heijden, G.W.A.M. van der - \ 2014
Biosystems Engineering 118 (2014). - ISSN 1537-5110 - p. 203 - 215.
harvesting robot - orchard - vision - pepper - apples - number
In our post-genomic world, where we are deluged with genetic information, the bottleneck to scientific progress is often phenotyping, i.e. measuring the observable characteristics of living organisms, such as counting the number of fruits on a plant. Image analysis is one route to automation. In this paper we present a method for recognising and counting fruits from images in cluttered greenhouses. The plants are 3-m high peppers with fruits of complex shapes and varying colours similar to the plant canopy. Our calibration and validation datasets each consist of over 28,000 colour images of over 1000 experimental plants. We describe a new two-step method to locate and count pepper fruits: the first step is to find fruits in a single image using a bag-of-words model, and the second is to aggregate estimates from multiple images using a novel statistical approach to cluster repeated, incomplete observations. We demonstrate that image analysis can potentially yield a good correlation with manual measurement (94.6%) and our proposed method achieves a correlation of 74.2% without any linear adjustment for a large dataset.
Less is more: The effect of multiple implementation intentions targeting unhealthy snacking habits
Verhoeven, A.A.C. ; Adriaanse, M.A. ; Ridder, D.T.D. de; Vet, E.W.M.L. de; Fennis, B.M. - \ 2013
European Journal of Social Psychology 43 (2013)5. - ISSN 0046-2772 - p. 344 - 354.
behavior-change - goal achievement - personal goals - past behavior - strength - plans - metaanalysis - breaking - number - power
Implementation intentions have been shown to effectively change counter-intentional habits. Research has, however, almost solely been concerned with the effectiveness of a single plan. In the present research, we investigated the behavioral and cognitive implications of making multiple implementation intentions targeting unhealthy snacking habits and its underlying processes, linking multiple habitual snacking cues to healthy alternatives. Study 1 revealed that formulating multiple implementation intentions was not effective in decreasing unhealthy snacking, whereas formulating a single plan successfully induced behavior change. By using a lexical decision task in Study 2, it was found that when making a single plan, but not multiple plans, the healthy alternative became cognitively more accessible in response to a critical cue prime than the habitual response. However, when making additional plans in an unrelated domain, the negative effects of making multiple plans were absent. In sum, the current findings suggest that formulating multiple implementation intentions is ineffective when changing unwanted behavior. These reduced effects of multiple implementation intentions do not occur when making the plan but are rather due to interference in the enacting phase of the planning process.
Histological and molecular investigation of the basis for variation in tomato fruit size in response to fruit load and genotype
Fanwoua, J. ; Visser, P.H.B. de; Heuvelink, E. ; Angenent, G.C. ; Yin, X. ; Marcelis, L.F.M. ; Struik, P.C. - \ 2012
Functional Plant Biology 39 (2012)9. - ISSN 1445-4408 - p. 754 - 763.
plant-cell cycle - dna endoreduplication - carbon availability - gene-expression - hormone levels - growth - number - proliferation - carbohydrate - metabolism
Understanding the molecular mechanisms and cellular dynamics that cause variation in fruit size is critical for the control of fruit growth. The aim of this study was to investigate how both genotypic factors and carbohydrate limitation cause variation in fruit size. We grew a parental line (Solanum lycopersicum L.) and two inbred lines from Solanum chmielewskii (C.M.Rick et al.; D.M.Spooner et al.) producing small or large fruits under three fruit loads (FL): continuously two fruits/truss (2&2F) or five fruits/truss (5&5F) and a switch from five to two fruits/truss (5&2F) 7 days after anthesis (DAA). Final fruit size, sugar content and cell phenotypes were measured. The expression of major cell cycle genes 7 DAA was investigated using quantitative PCR. The 5&5F treatment resulted in significantly smaller fruits than the 5&2F and 2&2F treatments. In the 5&5F treatment, cell number and cell volume contributed equally to the genotypic variation in final fruit size. In the 5&2F and 2&2F treatment, cell number contributed twice as much to the genotypic variation in final fruit size than cell volume did. FL treatments resulted in only subtle variations in gene expression. Genotypic differences were detected in transcript levels of CycD3 (cyclin) and CDKB1 (cyclin-dependent-kinase), but not CycB2. Genotypic variation in fruit FW, pericarp volume and cell volume was linked to pericarp glucose and fructose content (R2 = 0.41, R2 = 0.48, R2 = 0.11 respectively). Genotypic variation in cell number was positively correlated with pericarp fructose content (R2 = 0.28). These results emphasise the role of sugar content and of the timing of assimilate supply in the variation of cell and fruit phenotypes
Banking risk and regulation: Does one size fit all?
Klomp, J.G. ; Haan, J. de - \ 2012
Journal of Banking and Finance 36 (2012)12. - ISSN 0378-4266 - p. 3197 - 3212.
basel core principles - quantile regression - crises - soundness - inference - growth - models - system - number
Using data for more than 200 banks from 21 OECD countries for the period 2002–2008, we examine the impact of bank regulation and supervision on banking risk using quantile regressions. In contrast to most previous research, we find that banking regulation and supervision has an effect on the risks of high-risk banks. However, most measures for bank regulation and supervision do not have a significant effect on low-risk banks. As banking risk and bank regulation and supervision are multi-faceted concepts, our measures for both concepts are constructed using factor analysis
Effects of shoot tipping on development and yield of the tuber crop Plectranthus edulis
Taye, M. ; Lommen, W.J.M. ; Struik, P.C. - \ 2012
The Journal of Agricultural Science 150 (2012)4. - ISSN 0021-8596 - p. 484 - 494.
potato crops - growth - number
Plectranthus edulis (Vatke) Agnew is one of the tuber crops of the genus Plectranthus that is widely cultivated in Africa and Asia. P. edulis produces below-ground tubers on stolons originating from the stems, comparable to the potato (Solanum tuberosum L.). Farmers apply several laborious cultural practices to enhance shoot growth and yield, among which shoot tipping is very common. Tipping (pinching) is the removal of the shoot apex with one or two pairs of leaves from the main stems and branches. The rationale of this practice, especially when repeated more than once during one cropping season, is not fully understood. One similar experiment with two cultivars was carried out at two locations (Awassa and Wondogenet) in Ethiopia to assess and analyse the effects of shoot tipping and its frequency on crop development and tuber production. Tipping treatments included zero tipping, tipping once, tipping twice and tipping thrice, with the first tipping taking place 68 days after planting (DAP), a stage at which most of the stems reached a height of about 0·15 m, and the remainder following at intervals of 44–46 days. Tipping stimulated stem branching; it significantly increased the number of primary, secondary and tertiary stems in both experiments. Soil cover increased with an increase in the frequency of the tipping in Awassa, because of the tipping effects on the different canopy development variables. Tipping also enhanced the soil cover in Wondogenet, but the crop did not gain any extra benefit from a third tipping. Tipping enhanced early stolon formation, but did not consistently affect the number of stolons per hole later in the growing season. The number of tubers increased with an increase in the frequency of tipping in both cultivars in Wondogenet and in one cultivar in Awassa. Tuber dry matter yield increased with an increase in the frequency of tipping at both sites. Fresh tuber yield in the final harvest at 208 DAP was c. 1·9 kg/m2. Tipping on average increased fresh tuber yield by 17% in Wondogenet, whereas the difference was not detectable in Awassa. Because senescence was delayed slightly by tipping, yield effects of tipping might be larger when harvesting later. In general, there was a positive effect of tipping on canopy development and tuber yield.
Simplivariate Models: Uncovering the Underlying Biology in Functional Genomics Data
Saccenti, E. ; Westerhuis, J.A. ; Smilde, A.K. ; Werf, M.J. van der; Hageman, J.A. ; Hendriks, M.M.W.B. - \ 2011
PLoS ONE 6 (2011)6. - ISSN 1932-6203
metabolomics data - multiple-regression - genetic algorithms - escherichia-coli - microarray data - decomposition - number - indole
One of the first steps in analyzing high-dimensional functional genomics data is an exploratory analysis of such data. Cluster Analysis and Principal Component Analysis are then usually the method of choice. Despite their versatility they also have a severe drawback: they do not always generate simple and interpretable solutions. On the basis of the observation that functional genomics data often contain both informative and non-informative variation, we propose a method that finds sets of variables containing informative variation. This informative variation is subsequently expressed in easily interpretable simplivariate components. We present a new implementation of the recently introduced simplivariate models. In this implementation, the informative variation is described by multiplicative models that can adequately represent the relations between functional genomics data. Both a simulated and two real-life metabolomics data sets show good performance of the method.
Attitudes, perceptions, and trust. Insights from a consumer survey regarding genetically modified banana in Uganda
Kikulwe, E.M. ; Wesseler, J.H.H. ; Falck-Zepeda, J. - \ 2011
Appetite 57 (2011). - ISSN 0195-6663 - p. 401 - 413.
modified food - gm foods - acceptance - benefits - number - crop - pay
Genetically modified (GM) crops and food are still controversial. This paper analyzes consumers’ perceptions and institutional awareness and trust toward GM banana regulation in Uganda. Results are based on a study conducted among 421 banana-consuming households between July and August 2007. Results show a high willingness to purchase GM banana among consumers. An explanatory factor analysis is conducted to identify the perceptions toward genetic modification. The identified factors are used in a cluster analysis that grouped consumers into segments of GM skepticism, government trust, health safety concern, and food and environmental safety concern. Socioeconomic characteristics differed significantly across segments. Consumer characteristics and perception factors influence consumers’ willingness to purchase GM banana. The institutional awareness and trust varied significantly across segments as well. The findings would be essential to policy makers when designing risk-communication strategies targeting different consumer segments to ensure proper discussion and addressing potential concerns about GM technology.
Determinants of barley grain yield in a wide range of Mediterranean environments
Francia, E. ; Tondelli, A. ; Rizza, F. ; Badeck, F.W. ; Li Destri Nicosia, O. ; Akar, T. ; Grando, S. ; Al-Yassin, A. ; Benkelkacim, A. ; Thomas, W.T.B. ; Eeuwijk, F.A. van; Romagosa, I. ; Stanca, A.M. ; Pechionni, N. - \ 2011
Field Crops Research 120 (2011)1. - ISSN 0378-4290 - p. 169 - 178.
carbon-isotope discrimination - drought tolerance - stress tolerance - number - genes - wheat - improvement - adaptation - temperature - photoperiod
Barley grain yield in rainfed Mediterranean regions can be largely influenced by terminal drought events. In this study the ecophysiological performance of the ‘Nure’ (winter) × ‘Tremois’ (spring) barley mapping population (118 Doubled Haploids, DHs) was evaluated in a multi-environment trial of eighteen site–year combinations across the Mediterranean Basin during two consecutive harvest years (2004 and 2005). Mean grain yield of sites ranged from 0.07 to 5.43 t ha-1, clearly dependent upon both the total water input (rainfall plus irrigation) and the water stress index (WSI) accumulated during the growing season. All DHs were characterized for possessing molecular marker alleles tagging four genes that regulate barley cycle, i.e. Vrn-H1, Vrn-H2, Ppd-H2 and Eam6. Grain yield differences were initially interpreted in terms of mean differences between genotypes (G), environments (E), and for each combination of genotype and environment (GE) through a “full interaction” ANOVA model. Variance components estimates clearly showed the greater importance of GE over G, although both were much lower than E. Alternative linear and bilinear models of increasing complexity were used to describe GE. A linear model fitting allelic variation at the four genes explained genotype main effect and genotype × environment interaction much better than growth habit itself. Adaptation was primarily driven by the allelic constitution at three out of the four segregating major genes, i.e. Vrn-H1, Ppd-H2 and Eam6. In fact, the three genes together explained 47.2% of G and 26.3% of GE sum of squares. Grain yield performance was more determined by the number of grains per unit area than by the grain weight (phenotypic correlation across all genotypic values: r = 0.948 and 0.559, respectively). The inter-relationships among a series of characters defining grain yield and its components were also explored as a function of the length of the different barley developmental phases, i.e. vegetative, reproductive, and grain filling stages. In most environments, the best performing (adapted) genotypes were those with faster development until early occurrence of anthesis. This confirmed the crucial role of the period defining the number of grains per unit area in grain yield determination under Mediterranean environments
A single nucleotide polymorphism set for paternal identification to reduce the costs of trait recording in commercial pig breeding
Harlizius, B. ; Lopes, M.S. ; Duijvesteijn, N. ; Goor, L.H.P.V. van der; Haeringen, W.A. van; Panneman, H. ; Guimaraes, S.E.F. ; Merks, J.W.M. ; Knol, E.F. - \ 2011
Journal of Animal Science 89 (2011)6. - ISSN 0021-8812 - p. 1661 - 1668.
parentage exclusion - beef-cattle - snp markers - traceability - probability - population - selection - pedigree - number - impact
In animal breeding, recording of correct pedigrees is essential to achieve genetic progress. Markers on DNA are useful to verify the on-farm pedigree records (parental verification) but can also be used to assign parents retrospectively (parental identification). This approach could reduce the costs of recording for traits with low incidence, such as those related to diseases or mortality. In this study, SNP were used to assign the true sires of 368 purebred animals from a Duroc-based sire line and 140 crossbred offspring from a commercial pig population. Some of the sires were closely related. There were 3 full sibs and 17 half sibs among the true fathers and 4 full sibs and 35 half sibs among all putative fathers. To define the number of SNP necessary, 5 SNP panels (40, 60, 80, 100, and 120 SNP) were assembled from the Illumina PorcineSNP60 Beadchip (Illumina, San Diego, CA) based on minor allele frequency (>0.3), high genotyping call rate (=90%), and equal spacing across the genome. For paternal identification considering only the 66 true sires in the data set, 60 SNP resulted in 100% correct assignment of the sire. By including additional putative sires (n = 304), 80 SNP were sufficient for 100% correct assignment of the sire. The following criteria were derived to identify the correct sire for the current data set: the logarithm of odds (LOD) score for assigning the correct sire was =5, the number of mismatches was =1, and the difference in the LOD score between the first and the second most likely sire was >5. If the correct sire was not present among all putative sires, the mean LOD for the most likely sire was close to zero or negative when using 100 SNP. More SNP would be needed for paternal identification if the number of putative sires increased and the degree of relatedness was greater than in the data set used here. The threshold for the number of mismatches can be adjusted according to the practical situation to account for the trade-off between false negatives and false positives. The latter can be avoided efficiently, ensuring that the correct father is being sampled. Nevertheless, a restriction on the number of putative sires is advisable to reduce the risk of assigning close relatives.
Determination of genetic structure of germplasm collections: are traditional hierarchical clustering methods appropriate for molecular marker data?
Odong, T.L. ; Heerwaarden, J. van; Jansen, J. ; Hintum, T.J.L. van; Eeuwijk, F.A. van - \ 2011
Theoretical and Applied Genetics 123 (2011)2. - ISSN 0040-5752 - p. 195 - 205.
multilocus genotype data - genome-wide association - forming core subsets - population-structure - data set - linkage disequilibrium - f-statistics - number - inference - diversity
Despite the availability of newer approaches, traditional hierarchical clustering remains very popular in genetic diversity studies in plants. However, little is known about its suitability for molecular marker data. We studied the performance of traditional hierarchical clustering techniques using real and simulated molecular marker data. Our study also compared the performance of traditional hierarchical clustering with model-based clustering (STRUCTURE). We showed that the cophenetic correlation coefficient is directly related to subgroup differentiation and can thus be used as an indicator of the presence of genetically distinct subgroups in germplasm collections. Whereas UPGMA performed well in preserving distances between accessions, Ward excelled in recovering groups. Our results also showed a close similarity between clusters obtained by Ward and by STRUCTURE. Traditional cluster analysis can provide an easy and effective way of determining structure in germplasm collections using molecular marker data, and, the output can be used for sampling core collections or for association studies.
China's one-child policy and "the mystery of missing women": Ethnic minorities and male-biased sex ratios
Bulte, E.H. ; Zhang, X. ; Heerink, N. - \ 2011
Oxford Bulletin of Economics and Statistics 73 (2011)1. - ISSN 0305-9049 - p. 21 - 39.
rural china - gender bias - health-care - hepatitis-b - mortality - number - birth - fertility - account - poverty
Recent estimates suggest that as many as 40 million women are ‘missing’ in China. We exploit a special provision in the Chinese one-child policy (OCP; allowing for preferential treatment of ethnic minority groups) to revisit the mystery of these missing women, and in particular to explore the contribution of China's OCP in distorting sex ratios. Our results imply that preference for boys is the main driver of the gender gap, and that the OCP is responsible for about half of it. This is true even before ultrasound technologies for prenatal gender determination were available. Not surprisingly, interaction between the OCP and ultrasound technologies has contributed to the gender gap
Analysis of SSRs uncovers hierarchial structure and genetic diversity in Chinese soybean landraces
Li, Y.H. ; Smulders, M.J.M. ; Chang, R.Z. ; Qiu, L.J. - \ 2010
Agricultural Sciences in China 9 (2010)12. - ISSN 1671-2927 - p. 1739 - 1748.
population-structure - differentiation - assignment - software - number
For clarifying the hierarchical patterns of population structure of soybean landraces in China, the seven clusters previously identified using Bayesian clustering of 1 504 soybean landraces based on SSR markers genotyping data were further analyzed. Using the largest value of ¿K, these landraces could be split into 20 sub-clusters, which was supported by highly significant pairwise Fst-values and generally in accordance with the geographic origin and sowing types. The autumn-sowing types ended up in one distinct sub-cluster from the otherwise summer-sowing type, where the autumn-sowing types are most likely derived from. The division into 20 sub-clusters explained 7.3% of the genetic variation, next to 9.7% present among the seven clusters, 81.1% residing among landraces within sub-clusters, and 1.9% within the landraces. The distribution pattern of genetic diversity among the sub-clusters of each cluster was uneven, with two HSuM sub-clusters (Central China) and some South China sub-clusters showing significantly higher level of genetic diversity.
Can VNTRs be used to study genetic variation within white spot syndrome virus isolates?
Bui Thi Minh Dieu, ; Zwart, M.P. ; Vlak, J.M. - \ 2010
Journal of Fish Diseases 33 (2010)8. - ISSN 0140-7775 - p. 689 - 693.
nuclear polyhedrosis-virus - tandem repeats - shrimp - sequence - number
Seed transmission of Pepino mosaic virus in tomato
Hanssen, I.M. ; Mumford, R. ; Blystad, D.R. ; Cortez, I. ; Hasiów-AJaroszewska, B. ; Hristova, D. ; Pagán, I. ; Pereira, A.M. ; Peters, J. ; Pospieszny, H. ; Ravnikar, M. ; Stijger, I. ; Tomassoli, L. ; Varveri, C. ; Vlugt, R.A.A. van der; Nielsen, S.L. - \ 2010
European Journal of Plant Pathology 126 (2010)2. - ISSN 0929-1873 - p. 145 - 152.
genomic rna - greenhouse tomatoes - sequence - isolate - population - infection - protein - number - crops - uk
In this manuscript we provide evidence for the seed transmission of Pepino mosaic virus (PepMV) in tomato. Fruit was harvested from a tomato crop artificially infected with both European and CH2 genotypes of PepMV and more than 100,000 seeds were extracted and cleaned using an enzymatic treatment without disinfection. Infection assays using indicator plants confirmed the presence of viable virus on the seeds. Seeds were distributed to ten different laboratories in three separate batches, where they were germinated and the young plants tested by ELISA. In total over 87,000 plants were tested and 23 positives detected, indicating an overall transmission rate of 0.026%. However, the observed seed transmission rates varied from 0.005% to 0.057%, depending on the seed batch used. Results clearly showed that PepMV can be transmitted from seeds contaminated with virus to seedlings, highlighting the risk of using seeds from PepMV-infected plants and the potential for seed transmission to contribute to the further spread of PepMV
Effect of excessive, hormonally induced intrauterine crowding in the gilt on fetal development on day 40 of pregnancy
Waaij, E.H. van der; Hazeleger, W. ; Soede, N.M. ; Laurenssen, B.F.A. ; Kemp, B. - \ 2010
Journal of Animal Science 88 (2010)8. - ISSN 0021-8812 - p. 2611 - 2619.
ovulation rate - litter size - swine - survival - number - sows - pig - fertilization - embryogenesis - responses
Selection for litter size may result in an increase in uterine crowding due to a faster increase in ovulation rate than in litter size. Increased ovulation rate does not result in a proportionally increased number of piglets born alive. In this study, the effect of ovulation rate on vitality characteristics of fetal-placental units at d 40 of pregnancy was investigated. For this, 43 Large White gilts were treated with hormones to induce superovulation. Average ovulation rate was 45.16 ± 13.22; average number of vital fetuses at d 40 of pregnancy was 17.09 ± 3.61 that weighed 11.26 ± 1.99 g; their placenta weighed 31.88 ± 14.79 g; and they occupied 11.69 ± 4.90 cm of the uterus. Loss in oocytes (i.e., that did not result in a vital fetus at d 40) increased with increasing ovulation rate and occurred before (early mortality; P = 0.0003) and after implantation (late mortality, i.e., traces visible at d 40; P <0.0001). With respect to the vital fetuses, increased ovulation rate resulted in decreased fetal (P = 0.0008) and placental weight (P = 0.0008) and decreased length of the area in the uterus that was occupied by the placenta (P = 0.0011). Strong correlations existed between placental and fetal weight [0.68; 95% confidence interval (CI) = 0.64 to 0.72], and placental weight and length (0.78; 95% CI = 0.74 to 0.82). Fetal-placental characteristics were weakly correlated to distance to the implantation sites of neighboring fetuses, a measure of crowdedness [-0.002 (95% CI = -0.042 to 0.038) with fetal weight to 0.16 (95% CI = 0.12 to 0.20) with placental length]. Increased ovulation rates, but more specifically increased late mortality rates, have negative effects on the remaining vital fetuses with respect to the fetal (P = 0.0085) and placental weight (P <0.0001) and length of the implantation site (P = 0.0016). The most extreme effect was on placental weight, in which a uterus with 18 cases of late mortality (P <0.0001). Furthermore, increased ovulation rates resulted in decreased within litter variation for fetal (P = 0.0018) and placental weight (P = 0.0084). At increased ovulation rates, the number of live fetuses remained similar, but placental development is impaired and the growth of the fetus is retarded compared with reduced ovulation rate, with effects likely lasting into adult life.
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