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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    We will mail you new results for this query: keywords==Genetics
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Genetic manipulation of structural color in bacterial colonies
Johansen, Villads Egede ; Catón, Laura ; Hamidjaja, Raditijo ; Oosterink, Els ; Wilts, Bodo D. ; Rasmussen, Torben Sølbeck ; Sherlock, Michael Mario ; Ingham, Colin J. ; Vignolini, Silvia - \ 2018
Proceedings of the National Academy of Sciences of the United States of America 115 (2018)11. - ISSN 0027-8424 - p. 2652 - 2657.
Disorder - Flavobacteria - Genetics - Self-organization - Structural color
Naturally occurring photonic structures are responsible for the bright and vivid coloration in a large variety of living organisms. Despite efforts to understand their biological functions, development, and complex optical response, little is known of the underlying genes involved in the development of these nanostructures in any domain of life. Here, we used Flavobacterium colonies as a model system to demonstrate that genes responsible for gliding motility, cell shape, the stringent response, and tRNA modification contribute to the optical appearance of the colony. By structural and optical analysis, we obtained a detailed correlation of how genetic modifications alter structural color in bacterial colonies. Understanding of genotype and phenotype relations in this system opens the way to genetic engineering of on-demand living optical materials, for use as paints and living sensors.
A systematic survey to identify lethal recessive variation in highly managed pig populations
Derks, Martijn F.L. ; Megens, Hendrik Jan ; Bosse, Mirte ; Lopes, Marcos S. ; Harlizius, Barbara ; Groenen, Martien A.M. - \ 2017
BMC Genomics 18 (2017)1. - ISSN 1471-2164
Deleterious variation - Embryonic lethality - Genetics - Mummified piglets - Population genomics
Background: Lethal recessive variation can cause prenatal death of homozygous offspring. Although usually present at low-frequency in populations, the impact on individual fitness can be substantial. Until recently, the presence of recessive embryonic lethal variation could only be measured indirectly through reduced fertility. In this study, we estimate the presence of genetic loci associated with both early and late termination of development during gestation in pigs from the wealth of genome data routinely generated by a commercial breeding company. Results: We examined three commercial pig (Sus scrofa) populations for potentially deleterious genetic variation based on 80 K SNP-chip genotypes, and estimate the effects on reproductive traits. 24,000 pigs from three populations were analyzed for missing or depletion of homozygous haplotypes. We identified 145 haplotypes (ranging from 0.5-4 Mb in size) in the genome with complete absence or depletion of homozygous animals. Thirty-five haplotypes show a negative effect on at least one of the analysed reproductive traits (total number born, number of stillborn, and number of mummified piglets). One variant in particular appeared to result in relative late termination of development of fetuses, responsible for a significant fraction of observed stillborn piglets ('mummies'), as they die mid-gestation. Moreover, we identified the BMPER gene as a likely candidate underlying this phenomenon. Conclusions: Our study shows that although lethal recessive variation is present, the frequency of these alleles is invariably low in these highly managed populations. Nevertheless, due to cumulative effects of deleterious variants, large numbers of affected offspring are produced. Furthermore, our study demonstrates the use of a large-scale commercial genetic experiment to systematically screen for 'natural knockouts' that can increase understanding of gene function.
Isolation by oceanic distance and spatial genetic structure in an overharvested international fishery
Truelove, Nathan K. ; Box, Stephen J. ; Aiken, Karl A. ; Blythe-Mallett, Azra ; Boman, Erik M. ; Booker, Catherine J. ; Byfield, Tamsen T. ; Cox, Courtney E. ; Davis, Martha H. ; Delgado, Gabriel A. ; Glazer, Bob A. ; Griffiths, Sarah M. ; Kitson-Walters, Kimani ; Kough, Andy S. ; Pérez Enríquez, Ricardo ; Preziosi, Richard F. ; Roy, Marcia E. ; Segura-García, Iris ; Webber, Mona K. ; Stoner, Allan W. - \ 2017
Diversity and Distributions 23 (2017)11. - ISSN 1366-9516 - p. 1292 - 1300.
Connectivity - Conservation - Dispersal - Fisheries - Genetics - Spatial

Aim: A detailed understanding of spatial genetic structure (SGS) and the factors driving contemporary patterns of gene flow and genetic diversity are fundamental for developing conservation and management plans for marine fisheries. We performed a detailed study of SGS and genetic diversity throughout the overharvested queen conch (Lobatus gigas) fishery. Caribbean countries were presented as major populations to examine transboundary patterns of population differentiation. Location: Nineteen locations in the greater Caribbean from Anguilla, the Bahamas, Belize, Caribbean Netherlands, Honduras, Jamaica, Mexico, Turks and Caicos, and the USA. Methods: We genotyped 643 individuals with nine microsatellites. Population genetic and multivariate analyses characterized SGS. We tested the alternate hypotheses: (1) SGS is randomly distributed in space or (2) pairwise genetic structure among sites is correlated with oceanic distance (IBOD). Results: Our study found that L. gigas does not form a single panmictic population in the greater Caribbean. Significant levels of genetic differentiation were identified between Caribbean countries (FCT = 0.011; p = .0001), within Caribbean countries (FSC = 0.003; p = .001), and among sites irrespective of geographic location (FST = 0.013; p = .0001). Gene flow across the greater Caribbean was constrained by oceanic distance (p = .0009; Mantel r = .40), which acted to isolate local populations. Main conclusions: Gene flow over the spatial scale of the entire Caribbean basin is constrained by oceanic distance, which may impede the natural recovery of overfished L. gigas populations. Our results suggest a careful blend of local and international management will be required to ensure long-term sustainability for the species.

Improving feed efficiency in fish using selective breeding : A review
Verdal, Hugues de; Komen, Hans ; Quillet, Edwige ; Chatain, Béatrice ; Allal, François ; Benzie, John A.H. ; Vandeputte, Marc - \ 2017
Reviews in Aquaculture (2017). - ISSN 1753-5123
Feed conversion ratio - Feed efficiency - Feed intake - Fish - Genetics - Selection

Improving feed efficiency (FE) is key to reducing production costs in aquaculture and to achieving sustainability for the aquaculture industry. Feed costs account for 30-70% of total production costs in aquaculture; much work has been done on nutritional and husbandry approaches to improve FE but only a limited amount of research has been devoted to using genetics, despite its potential. This paper reviews past work to improve FE in fish using selective breeding and assess future directions. Direct selection on FE traits requires methods to measure individual feed consumption and estimate FE efficiently and accurately. This is particularly difficult to do in fish because of the environment in which they live. Many of the published studies on FE were found to be inaccurate because of methodological problems. The relatively low heritability estimates of FE traits in fish published to date are probably partly as a result of inaccurate measurements of feed intake. Improving ways to measure the individual feed intake with high accuracy will be critical to the successful application of genetics to improving FE. Indirect selection criteria that could be used to improve FE (including growth after starvation/refeeding, body composition, neuropeptides or hormone levels) are discussed. Promising approaches to measuring feed intake accurately that may enable these studies to be undertaken are identified. More work using these will be needed prior to assessing the practicality of the introduction of direct or indirect traits for FE in fish genetic improvement programmes.

Inheritance and QTL analysis of the determinants of flower color in tetraploid cut roses
Gitonga, Virginia W. ; Stolker, Robert ; Koning-Boucoiran, Carole F.S. ; Aelaei, Mitra ; Visser, Richard G.F. ; Maliepaard, Chris ; Krens, Frans A. - \ 2016
Molecular Breeding 36 (2016)10. - ISSN 1380-3743
Color determinants - Genetics - Inheritance - QTL analysis - Rosa × hybrida - Tetraploid rose

The success of cut rose cultivars is a direct result of their aesthetic value. The rose industry thrives on novelty, and the production of novel flower color has been extensively studied. The most popular color is red, and it is, therefore, important for breeders to produce a good red cultivar. The final visible color of the flower is a combination of a number of factors including the type of anthocyanin accumulating, modifications to the anthocyanidin molecule, co-pigmentation and vacuolar pH. Here, we analyze the quantitative variation of the biochemical constituents of flower color in a tetraploid rose population and combine this with marker information in the segregating rose population to map the chromosomal locations of putative QTLs for flower color traits. Within our tetraploid population, we found a number of QTLs that were mapped on ICM 1, 2, 6 and 7. We were able to show the effect of the different QTLs on the final visible color of the flower from salmon to dark red.

Biomass traits and candidate genes for bioenergy revealed through association genetics in coppiced European Populus nigra (L.)
Allwright, Mike Robert ; Payne, Adrienne ; Emiliani, Giovanni ; Milner, Suzanne ; Viger, Maud ; Rouse, Franchesca ; Keurentjes, Joost J.B. ; Bérard, Aurélie ; Wildhagen, Henning ; Faivre-Rampant, Patricia ; Polle, Andrea ; Morgante, Michele ; Taylor, Gail - \ 2016
Biotechnology for Biofuels 9 (2016)1. - ISSN 1754-6834
Genetics - Leaf area - Lignocellulosic - Salicaceae - Short rotation coppice (SRC) - Yield

Background: Second generation (2G) bioenergy from lignocellulosic feedstocks has the potential to develop as a sustainable source of renewable energy; however, significant hurdles still remain for large-scale commercialisation. Populus is considered as a promising 2G feedstock and understanding the genetic basis of biomass yield and feedstock quality are a research priority in this model tree species. Results: We report the first coppiced biomass study for 714 members of a wide population of European black poplar (Populus nigra L.), a native European tree, selected from 20 river populations ranging in latitude and longitude between 40.5 and 52.1°N and 1.0 and 16.4°E, respectively. When grown at a single site in southern UK, significant Site of Origin (SO) effects were seen for 14 of the 15 directly measured or derived traits including biomass yield, leaf area and stomatal index. There was significant correlation (p <0.001) between biomass yield traits over 3 years of harvest which identified leaf size and cell production as strong predictors of biomass yield. A 12 K Illumina genotyping array (constructed from 10,331 SNPs in 14 QTL regions and 4648 genes) highlighted significant population genetic structure with pairwise FST showing strong differentiation (p <0.001) between the Spanish and Italian subpopulations. Robust associations reaching genome-wide significance are reported for main stem height and cell number per leaf; two traits tightly linked to biomass yield. These genotyping and phenotypic data were also used to show the presence of significant isolation by distance (IBD) and isolation by adaption (IBA) within this population. Conclusions: The three associations identified reaching genome-wide significance at p <0.05 include a transcription factor; a putative stress response gene and a gene of unknown function. None of them have been previously linked to bioenergy yield; were shown to be differentially expressed in a panel of three selected genotypes from the collection and represent exciting, novel candidates for further study in a bioenergy tree native to Europe and Euro-Asia. A further 26 markers (22 genes) were found to reach putative significance and are also of interest for biomass yield, leaf area, epidermal cell expansion and stomatal patterning. This research on European P. nigra provides an important foundation for the development of commercial native trees for bioenergy and for advanced, molecular breeding in these species.

Epidemiology, presentation and population genetics of patent ductus arteriosus (PDA) in the Dutch Stabyhoun dog
Toom, Marjolein L. den; Meiling, Agnes E. ; Thomas, Rachel E. ; Leegwater, Peter A.J. ; Heuven, Henri C.M. - \ 2016
BMC Veterinary Research 12 (2016)1. - ISSN 1746-6148
Canine - Genetics - Heritability - Patent ductus arteriosus - PDA - Prevalence - Sex predisposition

Background: Patent ductus arteriosus (PDA) is one of the most common congenital heart defects in dogs and is considered to be a complex, polygenic threshold trait for which a female sex predisposition has been described. Histological studies in dogs suggest that smooth muscle hypoplasia and asymmetry of the ductus tissue is the major cause of PDA. The Stabyhoun population is small and a predisposition for PDA has been suggested. The aims of this study were to describe the incidence, presentation from a clinical and histopathological perspective, and the population genetics of PDA in the Dutch Stabyhoun population. Results: Forty-six cases were identified between 2000 and 2013. Between 2009 and 2012 the birth incidence of PDA in the Stabyhoun breed was 1.05 %. We estimated this to be 7-13 times higher than expected in the general dog population. Twelve of the 46 cases were part of a litter in which more than one sibling was affected. There was no sex predilection in our case cohort. Dogs diagnosed in adulthood showed severe cardiomegaly. The mean inbreeding coefficient of the reference population of Stabyhoun dogs was 31.4 % and the actual and effective numbers of founders were 14 and 6.5, respectively. The heritability of PDA was 0.51 (±0.09) for the reference population and 0.41 (±0.10) for the phenotyped population. Histopathology of sections of the PDA from two dogs showed findings similar to those described in other breeds although the smooth muscle of the ductus adjacent to the pulmonary artery appeared more hypoplastic than that in the ductus adjacent to the aorta. Conclusions: The Stabyhoun breed shows a strong predisposition for PDA. Apart from the absence of a higher incidence in females, no other significant features distinguish PDA in Stabyhouns from the condition in other dog breeds. Heritability and the mean inbreeding coefficient are both very high making the Dutch Stabyhoun breed particularly suited to the study of inherited risk factors for PDA.

Harnessing the genetics of the modern dairy cow to continue improvements in feed efficiency
VandeHaar, M.J. ; Armentano, L.E. ; Weigel, K. ; Spurlock, D.M. ; Tempelman, R.J. ; Veerkamp, R. - \ 2016
Journal of Dairy Science 99 (2016)6. - ISSN 0022-0302 - p. 4941 - 4954.
Dairy cattle - Feed efficiency - Genetics

Feed efficiency, as defined by the fraction of feed energy or dry matter captured in products, has more than doubled for the US dairy industry in the past 100 yr. This increased feed efficiency was the result of increased milk production per cow achieved through genetic selection, nutrition, and management with the desired goal being greater profitability. With increased milk production per cow, more feed is consumed per cow, but a greater portion of the feed is partitioned toward milk instead of maintenance and body growth. This dilution of maintenance has been the overwhelming driver of enhanced feed efficiency in the past, but its effect diminishes with each successive increment in production relative to body size and therefore will be less important in the future. Instead, we must also focus on new ways to enhance digestive and metabolic efficiency. One way to examine variation in efficiency among animals is residual feed intake (RFI), a measure of efficiency that is independent of the dilution of maintenance. Cows that convert feed gross energy to net energy more efficiently or have lower maintenance requirements than expected based on body weight use less feed than expected and thus have negative RFI. Cows with low RFI likely digest and metabolize nutrients more efficiently and should have overall greater efficiency and profitability if they are also healthy, fertile, and produce at a high multiple of maintenance. Genomic technologies will help to identify these animals for selection programs. Nutrition and management also will continue to play a major role in farm-level feed efficiency. Management practices such as grouping and total mixed ration feeding have improved rumen function and therefore efficiency, but they have also decreased our attention on individual cow needs. Nutritional grouping is key to helping each cow reach its genetic potential. Perhaps new computer-driven technologies, combined with genomics, will enable us to optimize management for each individual cow within a herd, or to optimize animal selection to match management environments. In the future, availability of feed resources may shift as competition for land increases. New approaches combining genetic, nutrition, and other management practices will help optimize feed efficiency, profitability, and environmental sustainability.

New developments in fiber hemp (Cannabis sativa L.) breeding
Salentijn, E.M.J. ; Zhang, Qingying ; Amaducci, Stefano ; Yang, Ming ; Trindade, L.M. - \ 2015
Industrial Crops and Products 68 (2015). - ISSN 0926-6690 - p. 32 - 41.
Breeding - Fiber quality - Genetics - Hemp

Fiber hemp (Cannabis sativa L.) is a sustainable and high yielding industrial crop that can help to meet the high global demand for fibers. Hemp can be grown for fiber, seeds, and/or for dual purpose in a wide range of geographic zones and climates. Currently the main hemp producing regions in the world are China, Europe, and Canada. The number of new cultivars developed for each of these regions has gradually increased, with each region producing its own typical hemp cultivars for different purposes. In this article, the state of the art of fiber hemp breeding programs in Europe, China, and Canada are reviewed. The breeding strategies and tools used in the breeding of hemp cultivars are discussed. We also provide an overview of genetic diversity in hemp for different traits. In addition, the current knowledge of the main breeding goals for fiber hemp, which are an improvement of fiber quality and fiber yield, breeding for specific cannabinoid profiles, control of flowering behavior, male flowering control, and breeding of cultivars for specific environments are evaluated. Lastly, we discuss the inestimable value of next generation technologies to breed new hemp cultivars that are suitable for a biobased economy.

Genetic improvement of percids
Blonk, R.J.W. ; Komen, J. - \ 2015
In: Biology and Culture of Percid Fishes / Kestemont, P., Dabrowski, K., Summerfelt, R.C., Springer Netherlands - ISBN 9789401772266 - p. 699 - 722.
Breeding programme - Genetics - Inbreeding - Percids - Selection

During the past years, breeding programs for aquaculture have shown fast development. Globally, economically highly relevant species have experienced implementation of large scale breeding programs and it is impossible to imagine life today without them as they significantly improve production and profitability of enterprises. However, there are still many aquatic species cultured that rely on wild broodstock and for which there is no breeding program. The reasons for not having breeding programs are diverse: The knowledge to execute a breeding program is often not available, and more importantly, breeding programs are considered expensive. Costs for separate family rearing systems, testing environments, extensive tagging etc. are often limiting. Farming of percids is a new sector where pioneering farmers have to develop rearing systems, reproduction methodology, fish feeds, etc., all at the same time. Especially in such cases, low-cost methods are required to get their business up and running. For this reason, many farms consider the foundation of a basic breeding program as their least concern, only to reduce costs. However, we argue that there are good reasons to start with selective breeding at the very start of an aquaculture enterprise. In the next chapters, the principles of selective breeding programs will be described. This includes a basic description of the concept of estimating the heritable components of the phenotypic appearance of fish. Next the most commonly used selection methods and their implication for percids will be discussed. The potential traits for selection that should be relevant in percid culture are reviewed. Some insights into the optimisation of breeding programs and an overview of basic breeding program management will be presented. We present an outline of how to maintain genetic diversity within cultured stocks, with a special focus on limiting rates of inbreeding while selecting. Finally, some insights on how to manage costs and benefits of breeding programs are discussed.

Current status of selective breeding in European aquaculture
Janssen, K.P.E. ; Berentsen, P.B.M. ; Komen, J. - \ 2015
breeding programs - Market share - Aquaculture - Genetics - Europe
For the EU funded FP7 research projects Aquatrace and Fishboost, surveys were conducted among breeding companies of the six main species cultured in Europe: Atlantic salmon, Rainbow trout, European seabass, gilthead seabream, common carp and turbot. The objectives were to describe the main characteristics of selective breeding in European aquaculture and to determine its market share in total production. The market share was estimated by comparing the egg or juvenile production originating from breeding companies to the European total egg or juvenile production (in 2012).
For Atlantic salmon all breeding companies performed family selection. Main traits in the breeding goal were growth, processing yield, product quality and disease resistance. Most salmon has been selected for about ten generations. The market share was 93-95%. For rainbow trout most breeding companies performed family selection; selected traits commonly included growth, morphology, processing yield, disease resistance and reproduction.
The number of selected generations in mass selection ranged up to 20 and in family selection up to 14. The market share was 65-68%. Most breeding companies of European seabass and gilthead seabream have integrated their breeding program with production, mainly selecting on growth and morphology. Some of the companies that performed family selection also selected on disease resistance, processing yield, product quality or feed efficiency. For European seabass the number of selected generations ranged from two to eight and for
gilthead seabream from one to five. The market shares were 43-56% for European seabass and 60-66% for gilthead seabream. In turbot two companies performed family selection and one performed mass selection. The number of selected generations was three to five. The market share was 100%. In common carp genetic improvement was largely based on crossbreeding of different lines. Important traits are scaling pattern, health status, sexual maturity and general appearance. It is concluded that, based on the volume of fish production, in total over 75% of the European aquaculture production originates from selective breeding, but there is much variation between species. Most breeding companies perform family selection and growth, morphology, disease resistance, processing yield and product quality are most commonly selected traits.
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