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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Dietary Protein Sources Differentially Affect the Growth of Akkermansia muciniphila and Maintenance of the Gut Mucus Barrier in Mice
Zhao, Fan ; Zhou, Guanghong ; Liu, Xinyue ; Song, Shangxin ; Xu, Xinglian ; Hooiveld, Guido ; Müller, Michael ; Liu, Li ; Kristiansen, Karsten ; Li, Chunbao - \ 2019
Molecular Nutrition & Food Research (2019). - ISSN 1613-4125
Akkermansia muciniphila - chicken protein - oxidative phosphorylation - soy protein

Scope: The gut microbiota plays an essential role in linking diet to host health. The specific role of different dietary proteins on the gut microbiota and health is less understood. Here, the impact of proteins derived from chicken and soy on the gut microbiota and host gut barrier in C57BL/6 mice is investigated. Methods and results: Specific-pathogen-free and germ-free mice are assigned to either a chicken- or a soy protein-based diet for 4 weeks. Compared with a chicken-protein-based diet, intake of a soy-protein-based diet reduces the abundance of A. muciniphila and the number of goblet cells, lowers the level of Muc2 mRNA, and decreases the thickness of the mucus layer in the colon of specific-pathogen-free mice. In germ-free mice, colonization with A. muciniphila combined with intake of a chicken-protein-based diet results in a higher expression of the Muc2 mRNA in colon, and surprisingly, an increased potential for oxidative phosphorylation in A. muciniphila compared with colonized mice fed a soy-protein-based diet. Conclusion: These findings suggest possible mutually beneficial interactions between the growth and function of A. muciniphila and host mucus barrier in response to intake of a chicken-protein-based diet contrasting the intake of a soy-protein-based diet.

The fertilization effect of global dimming on crop yields is not attributed to an improved light interception
Shao, Liping ; Li, Gang ; Zhao, Qiannan ; Li, Yabing ; Sun, Yutong ; Wang, Weinan ; Cai, Chuang ; Chen, Weiping ; Liu, Ronghua ; Luo, Weihong ; Yin, Xinyou ; Lee, Xuhui - \ 2019
Global Change Biology (2019). - ISSN 1354-1013
acclimation - diffuse radiation - fertilization effect - global dimming - radiation use efficiency - rice - wheat - yield

Global dimming, a decadal decrease in incident global radiation, is often accompanied with an increase in the diffuse radiation fraction, and, therefore, the impact of global dimming on crop production is hard to predict. A popular approach to quantify this impact is the statistical analysis of historical climate and crop data, or use of dynamic crop simulation modelling approach. Here, we show that statistical analysis of historical data did not provide plausible values for the effect of diffuse radiation versus direct radiation on rice or wheat yield. In contrast, our field experimental study of 3 years demonstrated a fertilization effect of increased diffuse radiation fraction, which partly offset yield losses caused by decreased global radiation, in both crops. The fertilization effect was not attributed to any improved canopy light interception but mainly to the increased radiation use efficiency (RUE). The increased RUE was explained not only by the saturating shape of photosynthetic light response curves but also by plant acclimation to dimming that gradually increased leaf nitrogen concentration. Crop harvest index slightly decreased under dimming, thereby discounting the fertilization effect on crop yields. These results challenge existing modelling paradigms, which assume that the fertilization effect on crop yields is mainly attributed to an improved light interception. Further studies on the physiological mechanism of plant acclimation are required to better quantify the global dimming impact on agroecosystem productivity under future climate change.

China’s pig relocation in balance
Bai, Zhaohai ; Jin, Shuqin ; Wu, Yan ; Ermgassen, Erasmus zu; Oenema, Oene ; Chadwick, David ; Lassaletta, Luis ; Velthof, Gerard ; Zhao, Jun ; Ma, Lin - \ 2019
Nature Sustainability 2 (2019)10. - ISSN 2398-9629 - 1 p.
Comparison of smoking-related DNA methylation between newborns from prenatal exposure and adults from personal smoking
Sikdar, Sinjini ; Joehanes, Roby ; Joubert, Bonnie R. ; Xu, Cheng Jian ; Vives-Usano, Marta ; Rezwan, Faisal I. ; Felix, Janine F. ; Ward, James M. ; Guan, Weihua ; Richmond, Rebecca C. ; Brody, Jennifer A. ; Küpers, Leanne K. ; Baïz, Nour ; Håberg, Siri E. ; Smith, Jennifer A. ; Reese, Sarah E. ; Aslibekyan, Stella ; Hoyo, Cathrine ; Dhingra, Radhika ; Markunas, Christina A. ; Xu, Tao ; Reynolds, Lindsay M. ; Just, Allan C. ; Mandaviya, Pooja R. ; Ghantous, Akram ; Bennett, Brian D. ; Wang, Tianyuan ; Consortium, The Bios ; Bakulski, Kelly M. ; Melen, Erik ; Zhao, Shanshan ; Jin, Jianping ; Herceg, Zdenko ; Meurs, Joyce Van; Taylor, Jack A. ; Baccarelli, Andrea A. ; Murphy, Susan K. ; Liu, Yongmei ; Munthe-Kaas, Monica Cheng ; Deary, Ian J. ; Nystad, Wenche ; Waldenberger, Melanie ; Annesi-Maesano, Isabella ; Conneely, Karen ; Jaddoe, Vincent W.V. ; Arnett, Donna ; Snieder, Harold ; Kardia, Sharon L.R. ; Relton, Caroline L. ; Ong, Ken K. ; Ewart, Susan ; Moreno-Macias, Hortensia ; Romieu, Isabelle ; Sotoodehnia, Nona ; Fornage, Myriam ; Motsinger-Reif, Alison ; Koppelman, Gerard H. ; Bustamante, Mariona ; Levy, Daniel ; London, Stephanie J. - \ 2019
Epigenomics 11 (2019)13. - ISSN 1750-1911 - p. 1487 - 1500.
cigarette smoking - epigenetics - infant - maternal exposure - methylation

Aim: Cigarette smoking influences DNA methylation genome wide, in newborns from pregnancy exposure and in adults from personal smoking. Whether a unique methylation signature exists for in utero exposure in newborns is unknown. Materials & methods: We separately meta-analyzed newborn blood DNA methylation (assessed using Illumina450k Beadchip), in relation to sustained maternal smoking during pregnancy (9 cohorts, 5648 newborns, 897 exposed) and adult blood methylation and personal smoking (16 cohorts, 15907 participants, 2433 current smokers). Results & conclusion: Comparing meta-analyses, we identified numerous signatures specific to newborns along with many shared between newborns and adults. Unique smoking-associated genes in newborns were enriched in xenobiotic metabolism pathways. Our findings may provide insights into specific health impacts of prenatal exposure on offspring.

Critical assessment of recent trends related to screening and confirmatory analytical methods for selected food contaminants and allergens
Tsagkaris, A.S. ; Nelis, J.L.D. ; Ross, G.M.S. ; Jafari, S. ; Guercetti, J. ; Kopper, K. ; Zhao, Y. ; Rafferty, K. ; Salvador, J.P. ; Migliorelli, D. ; Salentijn, G. ; Campbell, K. ; Marco, M.P. ; Elliot, C.T. ; Nielen, M.W.F. ; Pulkrabova, J. ; Hajslova, J. - \ 2019
TrAC : Trends in Analytical Chemistry 121 (2019). - ISSN 0165-9936
Confirmatory methods - EU legal framework - Food contaminants - Inventory - Screening methods - Smartphones

Food contaminants monitoring is conducted in an intensive manner yet, there are still food safety scandals related to various chemical compounds. This fact highlights the need to review the requirements posed by the current legal framework on analytical methods performance and evaluate its application in published studies. Herein, we present an inventory including more than 470 publications on screening and confirmatory methods, which were used to control hazardous compounds such as pesticides, antibiotics, mycotoxins, aquatic toxins and allergens. Analytical performance characteristics, trends and state of the art, both merits and shortcomings, are critically discussed and summarized in excel tabulations. This repository highlights the ever-increasing use of screening methods and the necessity to confirm their performance by applying confirmatory methods. In conclusion, more effort is needed on validation and benchmarking, especially of newly developed technology such as smartphone-based methods, to avoid false-negative results and ensure that methods fit for purpose.

Recently duplicated sesterpene (C25) gene clusters in Arabidopsis thaliana modulate root microbiota.
Chen, Qingwen ; Jiang, Ting ; Liu, Yong-Xiu ; Haili, Liu ; Zhao, T. ; Liu, Zhixi ; Gan, Xiangchao ; Hallab, Asis ; Wang, Xuemei ; He, Juan ; Ma, Yihua ; Zhang, Fengxia ; Jin, Tao ; Schranz, M.E. ; Wang, Yong ; Yang, Bai - \ 2019
Science in China Series C-Life Sciences 62 (2019)7. - ISSN 1006-9305 - p. 947 - 958.
Joint toxicity of binary complexes of cartap, spirotetramat, copper, and cadmium to Vibrio fischeri
Yin, Hong Yang ; Zhao, Yuan ; Zheng, Yi ; Bao, Cong ; Huang, Xin Xin ; Ding, Ying Jie ; Cai, Qiang - \ 2019
Journal of Agro-Environment Science 38 (2019)9. - ISSN 1672-2043 - p. 2080 - 2085.
Acute toxicity - Heavy metals - Joint toxicity evaluation - Pesticide - Vibrio fischeri

In view of the widespread use of cartap, spirotetramat, and common heavy metal pollutants, such as copper and cadmium in agri? cultural activities, the joint toxicity of their complexes on Vibrio fischeri was studied. The EC50(median effective concentration)was calcu? lated with the acute toxic effects of binary complex contamination on Vibrio fischeri employing different exposure times. The Mixtures Toxic? ity Index method was employed to evaluate the joint toxicity. The acute toxicity experiments showed that the EC50 of copper, cadmium, car? tap, and spirotetramat on Vibrio fischeri at 15 mins was 0.53, 0.74, 79.06 mg·L-1, and 116.67 mg·L-1, respectively. The joint toxicity of car? tap and heavy metals on Vibrio fischeri was mainly additive. When the spirotetramat accounted for a low proportion in the binary mixtures, the joint toxicity was partially additive. The presence of cartap and spirotetramat may slow down the rate of metal ions entering the cell. Therefore, the study of exposure time for joint toxicity on Vibrio fischeri should be extended to 45 mins.

Real Options and Environmental Policies: The Good, the Bad, and the Ugly
Wesseler, J.H.H. ; Zhao, Jinhua - \ 2019
Annual Review of Resource Economics 11 (2019). - ISSN 1941-1340 - p. 43 - 58.
real options - environmental policy - irreversibility - precautionary principle - sustainability - technological change
The literature on real options shows that irreversibilities, uncertainties aboutfuture benefits and costs, and the flexibility in decision making generate benefitsand costs of delaying immediate action. When applied to government policy making, real option models can lead to efficient policies that take full account of these trade-offs, but they can also cause strategic behavior that tries to delay policies through influencing important elements such as downside risks. This contribution reviews the latest developments in real option–based policy research by looking at what we know about the benefits from waiting (the good), the costs from waiting (the bad), and how strategic behavior can influence policies (the ugly). Much has been said in the literature about the good and the bad, but more work is needed to study the ugly aspects of real option–driven policies.
Further Improvement of Air Quality in China Needs Clear Ammonia Mitigation Target
Bai, Zhaohai ; Winiwarter, Wilfried ; Klimont, Zbigniew ; Velthof, Gerard ; Misselbrook, Tom ; Zhao, Zhanqing ; Jin, Xinpeng ; Oenema, Oene ; Hu, Chunsheng ; Ma, Lin - \ 2019
Environmental Science and Technology 53 (2019)18. - ISSN 0013-936X - p. 10542 - 10544.
Editorial: Organ Modification for Edible Parts of Horticultural Crops
He, Yuke ; Bonnema, Guusje ; Xiao, Han ; Zhao, Yunde - \ 2019
Frontiers in Plant Science 10 (2019). - ISSN 1664-462X
bulb - corm - curd - fleshy fruit - fleshy root - leafy head - morphological modification - tuber
Enlightening force chains: a review of photoelasticimetry in granular matter
Abed Zadeh, Aghil ; Barés, Jonathan ; Brzinski, Theodore A. ; Daniels, Karen E. ; Dijksman, Joshua ; Docquier, Nicolas ; Everitt, Henry O. ; Kollmer, Jonathan E. ; Lantsoght, Olivier ; Wang, Dong ; Workamp, Marcel ; Zhao, Yiqiu ; Zheng, Hu - \ 2019
Granular Matter 21 (2019). - ISSN 1434-5021
Experimental methods - Force chains - Image post-processing - Photoelasticimetry - Protocols

A photoelastic material will reveal its internal stresses when observed through polarizing filters. This eye-catching property has enlightened our understanding of granular materials for over half a century, whether in the service of art, education, or scientific research. In this review article in honor of Robert Behringer, we highlight both his pioneering use of the method in physics research, and its reach into the public sphere through museum exhibits and outreach programs. We aim to provide clear protocols for artists, exhibit-designers, educators, and scientists to use in their own endeavors. It is our hope that this will build awareness about the ubiquitous presence of granular matter in our lives, enlighten its puzzling behavior, and promote conversations about its importance in environmental and industrial contexts. To aid in this endeavor, this paper also serves as a front door to a detailed wiki containing open, community-curated guidance on putting these methods into practice (Abed-Zadeh et al. in Photoelastic methods wiki, 2019).

Colletotrichum species associated with anthracnose of Pyrus spp. in China
Fu, M. ; Crous, P.W. ; Bai, Q. ; Zhang, P.F. ; Xiang, J. ; Guo, Y.S. ; Zhao, F.F. ; Yang, M.M. ; Hong, N. ; Xu, W.X. ; Wang, G.P. - \ 2019
Persoonia 42 (2019). - ISSN 0031-5850 - p. 1 - 35.
Colletotrichum - Multi-gene phylogeny - Pathogenicity - Pyrus

Colletotrichum species are plant pathogens, saprobes, and endophytes on a range of economically important hosts. However, the species occurring on pear remain largely unresolved. To determine the morphology, phylogeny and biology of Colletotrichum species associated with Pyrus plants, a total of 295 samples were collected from cultivated pear species (including P. pyrifolia, P. bretschneideri, and P. communis) from seven major pear-cultivation provinces in China. The pear leaves and fruits affected by anthracnose were sampled and subjected to fungus isolation, resulting in a total of 488 Colletotrichum isolates. Phylogenetic analyses based on six loci (ACT, TUB2, CAL, CHS-1, GAPDH, and ITS) coupled with morphology of 90 representative isolates revealed that they belong to 10 known Colletotrichum species, including C. aenigma, C. citricola, C. conoides, C. fioriniae, C. fructicola, C. gloeosporioides, C. karstii, C. plurivorum, C. siamense, C. wuxiense, and two novel species, described here as C. jinshuiense and C. pyrifoliae. Of these, C. fructicola was the most dominant, occurring on P. pyrifolia and P. bretschneideri in all surveyed provinces except in Shandong, where C. siamense was dominant. In contrast, only C. siamense and C. fioriniae were isolated from P. communis, with the former being dominant. In order to prove Koch’s postulates, pathogenicity tests on pear leaves and fruits revealed a broad diversity in pathogenicity and aggressiveness among the species and isolates, of which C. citricola, C. jinshuiense, C. pyrifoliae, and C. conoides appeared to be organ-specific on either leaves or fruits. This study also represents the first reports of C. citricola, C. conoides, C. karstii, C. plurivorum, C. siamense, and C. wuxiense causing anthracnose on pear.

Multi-omics analysis reveals niche and fitness differences in typical denitrification microbial aggregations
Deng, Yale ; Ruan, Yunjie ; Ma, Bin ; Timmons, Michael B. ; Lu, Huifeng ; Xu, Xiangyang ; Zhao, Heping ; Yin, Xuwang - \ 2019
Environment International 132 (2019). - ISSN 0160-4120
Denitrification - Microbial aggregation - Multi-omics - Network - Niche difference

Suspended floc and fixed biofilm are two commonly applied strategies for heterotrophic denitrification in wastewater treatment. These two strategies use different carbon sources and reside within different ecological niches for microbial aggregation, which were hypothesized to show distinct microbial structures and metabolic fitness. We surveyed three floc reactors and three biofilm reactors for denitrification and determined if there were distinct microbial aggregations. Multiple molecular omics approaches were used to determine the microbial community composition, co-occurrence network and metabolic pathways. Proteobacteria was the dominating and most active phylum among all samples. Carbon source played an important role in shaping the microbial community composition while the distribution of functional protein was largely influenced by salinity. We found that the topological network features had different ecological patterns and that the microorganisms in the biofilm reactors had more nodes but less interactions than those in floc reactors. The large niche differences in the biofilm reactors explained the observed high microbial diversity, functional redundancy and resulting high system stability. We also observed a lower proportion of denitrifiers and higher resistance to oxygen and salinity perturbation in the biofilm reactors than the floc reactors. Our findings support our hypothesis that niche differences caused a distinct microbial structure and increased microbial ecology distribution, which has the potential to improve system efficiency and stability.

Predicting hydrological impacts of the Yangtze-to-Huaihe Water Diversion Project on habitat availability for wintering waterbirds at Caizi Lake
Li, Chunlin ; Li, Haifeng ; Zhang, Yong ; Zha, D. ; Zhao, Binbin ; Yang, Sen ; Zhang, Baowei ; Boer, Willem F. de - \ 2019
Journal of Environmental Management 249 (2019). - ISSN 0301-4797
Hydrological regime - Water project - Waterbird conservation - Wetland management - Yangtze

Quantifying the relationship between hydrological regime and habitat availability is the first step to predict potential impacts of water engineering projects on waterbirds, particularly in periodically flooded wetlands. The proposed Yangtze-to-Huaihe Water Diversion Project (YHWD) cuts through Caizi Lake, which is of international importance for wintering waterbirds. In order to explore the potential impacts of the project on habitat availability for the wintering waterbirds, we first built linear models to fit relationships between land cover patterns and water level dynamics in the lake, and then used generalized linear mixed models to test effects of habitat variables (water area, grassland area and mudflat area) on bird abundances of different functional groups. The avian habitat use differed among guilds, and was correlated with the land cover pattern, which was strongly dependent on seasonal water level fluctuations. Following water recession in autumn, the exposure of riparian habitats was more prominent in the eastern part of the lake, where the channel of the proposed YHWD project is located. This part of the lake is also where we located most of the important bird areas. Compared to the current situation, 54.3% of the grassland and 60.5% of the mudflats are predicted to be lost during winter due to the projected water level rise, resulting in reduced habitat availability for grass foragers, invertebrate eaters and tuber feeders. In order to mitigate potential impacts of the YHWD project, we suggest habitat compensations by construction of artificial habitats, and maintenance of water level regime at the whole lake by restoring similarity in water level fluctuations between Xizi Lake and Caizi Lake.

Author Correction: Climatic controls of decomposition drive the global biogeography of forest-tree symbioses
Steidinger, B.S. ; Crowther, T.W. ; Liang, J. ; Nuland, M.E. Van; Werner, G.D.A. ; Reich, P.B. ; Nabuurs, G.J. ; de-Miguel, S. ; Zhou, M. ; Picard, N. ; Herault, B. ; Zhao, X. ; Zhang, C. ; Routh, D. ; Peay, K.G. ; Abegg, Meinrad ; Adou Yao, C.Y. ; Alberti, Giorgio ; Almeyda Zambrano, Angelica ; Alvarez-Davila, Esteban ; Alvarez-Loayza, Patricia ; Alves, Luciana F. ; Ammer, Christian ; Antón-Fernández, Clara ; Araujo-Murakami, Alejandro ; Arroyo, Luzmila ; Avitabile, Valerio ; Aymard, Gerardo ; Baker, Timothy ; Bałazy, Radomir ; Banki, Olaf ; Barroso, Jorcely ; Bastian, Meredith ; Bastin, Jean Francois ; Birigazzi, Luca ; Birnbaum, Philippe ; Bitariho, Robert ; Boeckx, Pascal ; Bongers, Frans ; Bouriaud, Olivier ; Brancalion, Pedro H.H.S. ; Decuyper, Mathieu ; Hengeveld, Geerten ; Herold, Martin ; Lu, Huicui ; Parren, Marc ; Poorter, Lourens ; Schelhaas, Mart Jan ; Sheil, Douglas ; Zagt, Roderick - \ 2019
Nature 571 (2019)7765. - ISSN 0028-0836

In this Letter, the middle initial of author G. J. Nabuurs was omitted, and he should have been associated with an additional affiliation: ‘Forest Ecology and Forest Management Group, Wageningen University and Research, Wageningen, The Netherlands’ (now added as affiliation 182). In addition, the following two statements have been added to the Supplementary Acknowledgements. (1): ‘We would particularly like to thank The French NFI for the work of the many field teams and engineers, who have made extraordinary efforts to make forest inventory data publicly available.’ (1): ‘Sergio de Miguel benefited from a Serra- Húnter Fellowship provided by the Generalitat of Catalonia.’ Finally, the second sentence of the Methods section should have cited the French NFI, which provided a national forestry database used in our analysis, to read as follows: ‘The GFBi database consists of individual-based data that we compiled from all the regional and national GFBi forest-inventory datasets, including the French NFI (IGN—French National Forest Inventory, raw data, annual campaigns 2005 and following,, site accessed on 01 January 2015)’. All of these errors have been corrected online.

Contribution of methylation regulation of MpDREB2A promoter to drought resistance of Mauls prunifolia
Li, Xuewei ; Xie, Yinpeng ; Lu, Liyuan ; Yan, Mingjia ; Fang, Nan ; Xu, Jidi ; Wang, Liping ; Yan, Yan ; Zhao, Tao ; Nocker, Steve van; Ma, Fengwang ; Liang, Dong ; Guan, Qingmei - \ 2019
Plant and Soil 441 (2019)1-2. - ISSN 0032-079X - p. 15 - 32.
ChIP-seq - DNA methylation - DREB2A - Drought resistance - Gene expression - Malus

Background and aims: Malus prunifolia (Chinese name: Fu Ping Qiu Zi), a wild relative of cultivated apple (Malus x domestica Borkh), is extremely resistant to drought compared with domesticated cultivars, such as ‘Golden Delicious’. However, the molecular mechanisms underlying drought resistance of M. prunifolia have not been characterized. This study investigates a new regulatory mechanism to improve apple drought resistance. Methods: M. prunifolia and ‘Golden Delicious’ were each grafted on M. hupehensis for gene expression analysis. The methylation level of the DREB2A promoter was determined by bisulfite sequencing and ChIP-qPCR. Chromatin immunoprecipitation sequencing (ChIP-seq) was used to identify target genes of MpDREB2A in apple. Results: The exposure to drought stress stimulated the expression level of DREB2A gene more than 100-fold in M. prunifolia, but only 16-fold in ‘Golden Delicious’. This difference in gene expression could not be explained in terms of difference in leaf relative water content. Correspondingly, the methylation level of M. prunifolia DREB2A (MpDREB2A) promoter region was significantly reduced. Additionally, MpDREB2A conferred enhanced drought resistance when ectopically expressed in Arabidopsis. Over 2800 potential downstream target genes of MpDREB2A were identified by ChIP-seq and these downstream genes have diverse potential functions related to stress resistance. Conclusions: Methylation regulation in promoter of MpDREB2A may contribute to the drought resistance of M. prunifolia.

Data from: Horizontal and vertical diversity jointly shape food web stability against small and large perturbations
Zhao, Qinghua ; Brink, P.J. van den; Carpentier, Camille ; Wang, Yingying ; Rodríguez Sánchez, P. ; Xu, Chi ; Vollbrecht, Silke ; Gillissen, F. ; Vollebregt, M.E. ; Wang, Shaopeng ; Laender, Frederik De - \ 2019
The biodiversity of food webs is composed of horizontal (i.e. within trophic levels) and vertical diversity (i.e. the number of trophic levels). Understanding their joint effect on stability is a key challenge. Theory mostly considers their individual effects and focuses on small perturbations near equilibrium in hypothetical food webs. Here, we study the joint effects of horizontal and vertical diversity on the stability of hypothetical (modelled) and empirical food webs. In modelled food webs, horizontal and vertical diversity increased and decreased stability, respectively, with a stronger positive effect of producer diversity on stability at higher consumer diversity. Experiments with an empirical plankton food-web, where we manipulated horizontal and vertical diversity and measured stability from species interactions and from resilience against large perturbations, confirmed these predictions. Taken together, our findings highlight the need to conserve horizontal biodiversity at different trophic levels to ensure stability.
A new chicken 55K SNP genotyping array
Liu, Ranran ; Xing, Siyuan ; Wang, Jie ; Zheng, Maiqing ; Cui, Huanxian ; Crooijmans, Richard P.M.A. ; Li, Qinghe ; Zhao, Guiping ; Wen, Jie - \ 2019
BMC Genomics 20 (2019)1. - ISSN 1471-2164 - 1 p.
Chicken - Commercial line - Genotyping array - SNP

BACKGROUND: China has the richest local chicken breeding resources in the world and is the world's second largest producer of meat-type chickens. Development of a moderate-density SNP array for genetic analysis of chickens and breeding of meat-type chickens taking utility of those resources is urgently needed for conventional farms, breeding industry, and research areas. RESULTS: Eight representative local breeds or commercial broiler lines with 3 pools of 48 individuals within each breed/line were sequenced and supplied the major SNPs resource. There were 7.09 million - 9.41 million SNPs detected in each breed/line. After filtering using multiple criteria such as preferred incorporation of trait-related SNPs and uniformity of distribution across the genome, 52.18 K SNPs were selected in the final array. It consists of: (i) 19.22 K SNPs from the genomes of yellow-feathered, cyan-shank partridge and white-feathered chickens; (ii) 5.98 K SNPs related to economic traits from the Illumina 60 K SNP Bead Chip, which were found as significant associated SNPs with 15 traits in a Beijing-You crossed Cobb F2 resource population by genome-wide association study analysis; (iii) 7.63 K SNPs from 861 candidate genes of economic traits; (iv) the 0.94 K SNPs related to residual feed intake; and (v) 18.41 K from chicken SNPdb. The polymorphisms of 9 extra local breeds and 3 commercial lines were examined with this array, and 40 K - 47 K SNPs were polymorphic (with minor allele frequency > 0.05) in those breeds. The MDS result showed that those breeds can be clearly distinguished by this newly developed genotyping array. CONCLUSIONS: We successfully developed a 55K genotyping array by using SNPs segregated from typical local breeds and commercial lines. Compared to the existing Affy 600 K and Illumina 60 K arrays, there were 21,41 K new SNPs included on our Affy 55K array. The results of the 55K genotyping data can therefore be imputed to high-density SNPs genotyping data. The array offers a wide range of potential applications such as genomic selection breeding, GWAS of interested traits, and investigation of diversity of different chicken breeds.

Horizontal and vertical diversity jointly shape food web stability against small and large perturbations
Zhao, Qinghua ; Brink, Paul J. Van den; Carpentier, Camille ; Wang, Yingying X.G. ; Rodríguez-Sánchez, Pablo ; Xu, Chi ; Vollbrecht, Silke ; Gillissen, Frits ; Vollebregt, Marlies ; Wang, Shaopeng ; Laender, Frederik De - \ 2019
Ecology Letters 22 (2019)7. - ISSN 1461-023X - p. 1152 - 1162.
Equilibrium - horizontal diversity - large perturbations - small perturbations - stability - vertical diversity

The biodiversity of food webs is composed of horizontal (i.e. within trophic levels) and vertical diversity (i.e. the number of trophic levels). Understanding their joint effect on stability is a key challenge. Theory mostly considers their individual effects and focuses on small perturbations near equilibrium in hypothetical food webs. Here, we study the joint effects of horizontal and vertical diversity on the stability of hypothetical (modelled) and empirical food webs. In modelled food webs, horizontal and vertical diversity increased and decreased stability, respectively, with a stronger positive effect of producer diversity on stability at higher consumer diversity. Experiments with an empirical plankton food web, where we manipulated horizontal and vertical diversity and measured stability from species interactions and from resilience against large perturbations, confirmed these predictions. Taken together, our findings highlight the need to conserve horizontal biodiversity at different trophic levels to ensure stability.

Inter-provincial electricity transmissions’ co-benefit of national water savings in China
Liao, Xiawei ; Chai, Li ; Jiang, Yu ; Ji, Junping ; Zhao, Xu - \ 2019
Journal of Cleaner Production 229 (2019). - ISSN 0959-6526 - p. 350 - 357.
Co-benefit - Electricity transmission - Water conservation - Water-energy nexus

Interprovincial electricity transmissions have been utilised in China to overcome the country's imbalanced social-economic development and resource endowments. A bottom-up technology-based model is adopted to estimate water uses in electricity-exporting provinces to produce the transmitted electricity as well as opportunistic water savings in the receiving provinces. The results highlight that, in 2014, on a national scale, electricity transmissions generated co-benefit of saving 20.1 billion m³ of water nationally due to the electric power sector's water productivity differences in the exporting and importing provinces. Taking regional water stresses into account, 10.98 billion m³ of national scarce water saving is realized through electricity transmissions. Moreover, electricity transmissions by China's proposed 12 future transmission lines are expected to use additional 3.22 billion m³ of water in the electricity-exporting provinces. As more water-intensive technologies, e.g. open-loop cooling, are more commonly utilised in the electricity-receiving provinces, a total amount of 16.97 billion m³ of water use will be avoided nationally. Water-use efficiency for power production should be improved in all regions. Transmitted power imports should still be encouraged in water-scarce regions to alleviate their water stresses while power exports should be shifted away from water-stressed regions to water-abundant ones. Energy transformation by utilising gas-fired capacity and hydropower in water-abundant Southern China could be advanced.

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