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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    The 'Water, food, energy and ecosystem Nexus’ and Migration : An explorative study of key drivers of migration flows and their impacts
    Rooij, Bertram de; Tabeau, Ewa ; Agricola, Herman ; Soma, Katrine ; Terwisscha van Scheltinga, Catharien ; Kuiper, Marijke ; Verma, Monika ; Stuiver, Marian - \ 2020
    Wageningen : Wageningen Environmental Research (Wageningen Environmental Research report 2981) - ISBN 9789463952293 - 53
    MagnetGrid : Model description and user guide
    Diogo, Vasco ; Hennen, Wil ; Verma, Monika ; Oudendag, Diti ; Kuiper, Marijke - \ 2020
    Wageningen : Wageningen Economic Research (Wageningen Economic Research report 2020-004) - 65
    MagnetGrid is een modulair economisch landgebruiksmodel dat ruimtelijk expliciete biofysische informatie combineert met macro-economische projecties. MagnetGrid visualiseert toekomstige agrarisch landgebruikspatronen gedreven door een combinatie van klimatologische en socioeconomische ontwikkelingen. Het model kwantificeert de impact van deze trends en de mogelijke uitruil tussen verschillende doelstellingen. De ruimtelijk expliciete analyses van MagnetGrid kunnen voor een breed publiek toegankelijk gemaakt worden door kaarten die veranderingen in landgebruik laten zien op wereld-, regio-, land- en lokaal niveau.
    Consumers discard a lot more food than widely believed : Estimates of global food waste using an energy gap approach and affluence elasticity of food waste
    Bos Verma, Monika van den; Vreede, Linda de; Achterbosch, Thom ; Rutten, Martine M. - \ 2020
    PLoS ONE 15 (2020)2. - ISSN 1932-6203

    This work provides an internationally comparable consumer food waste dataset based on food availability, energy gap and consumer affluence. Such data can be used for constructing meaningful and internationally comparable metrics on food waste, such as those for Sustainable Development Goal 12. The data suggests that consumer food waste follows a linear-log relationship with consumer affluence and starts to emerge when consumers reach a threshold of approximately $6.70/day/capita level of expenditure. These findings also imply that most empirical models overestimate consumption by not accounting for the possibility of food waste in their analysis. The results also show that the most widely cited global estimate of food waste is underestimated by a factor greater than 2 (214 Kcal/day/capita versus 527 Kcal/day/capita). Comparison with estimates of US consumer food waste based on national survey data shows this approach can reasonably reproduce the results without needing extensive data from national surveys.

    Putting people on the map – identifying the socio-economic contribution to spatially explicit food system assessments
    Kuiper, M.H. ; Verma, Monika - \ 2020
    Wageningen Economic Research (KB Working Paper )
    Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls
    Bodkhe, Rahul ; Shetty, Sudarshan A. ; Dhotre, Dhiraj P. ; Verma, Anil K. ; Bhatia, Khushbo ; Mishra, Asha ; Kaur, Gurvinder ; Pande, Pranav ; Bangarusamy, Dhinoth K. ; Santosh, Beena P. ; Perumal, Rajadurai C. ; Ahuja, Vineet ; Shouche, Yogesh S. ; Makharia, Govind K. - \ 2019
    Frontiers in Microbiology 10 (2019). - ISSN 1664-302X
    Recent studies on celiac disease (CeD) have reported alterations in the gut microbiome. Whether this alteration in the microbial community is the cause or effect of the disease is not well understood, especially in adult onset of disease. The first-degree relatives (FDRs) of CeD patients may provide an opportunity to study gut microbiome in pre-disease state as FDRs are genetically susceptible to CeD. By using 16S rRNA gene sequencing, we observed that ecosystem level diversity measures were not significantly different between the disease condition (CeD), pre-disease (FDR) and control subjects. However, differences were observed at the level of amplicon sequence variant (ASV), suggesting alterations in specific ASVs between pre-disease and diseased condition. Duodenal biopsies showed higher differences in ASVs compared to fecal samples indicating larger disruption of the microbiota at the disease site. The duodenal microbiota of FDR was characterized by significant abundance of ASVs belonging to Parvimonas, Granulicatella, Gemella, Bifidobacterium, Anaerostipes, and Actinomyces genera. The duodenal microbiota of CeD was characterized by higher abundance of ASVs from genera Megasphaera and Helicobacter compared to the FDR microbiota. The CeD and FDR fecal microbiota had reduced abundance of ASVs classified as Akkermansia and Dorea when compared to control group microbiota. In addition, predicted functional metagenome showed reduced ability of gluten degradation by CeD fecal microbiota in comparison to FDRs and controls. The findings of the present study demonstrate differences in ASVs and predicts reduced ability of CeD fecal microbiota to degrade gluten compared to the FDR fecal microbiota. Further research is required to investigate the strain level and active functional profiles of FDR and CeD microbiota to better understand the role of gut microbiome in pathophysiology of CeD.
    Food security impact of global equities : annex measurement methodology for yield
    Dijk, Michiel van; Morley, Tom ; Rau, Marie-Luise ; Verma, Monika - \ 2019
    Wageningen : Wageningen Economic Research (Report / Wageningen Economic Research 2019-043b) - 29
    Food security impact of global equities : executive summary
    Berkhout, Petra ; Dijk, Michiel van; Morley, Tom ; Rau, Marie-Luise ; Verma, Monika ; Snels, Joost ; Soethoudt, Han - \ 2019
    Wageningen : Wageningen Economic Research (Report / Wageningen Economic Research 2019-043) - ISBN 9789463439534 - 29
    This study describes methodologies that have been developed to assess the food security impact of agricultural technologies supplied by stock exchange companies on the basis of publicly available revenue data. The methods have been developed for fertiliser, improved seeds, cooling and packaging. Given the lack of information on key variables at present it is only possible to apply the method for fertiliser to all companies that sell the technology in their portfolio. For the other three technologies additional information is necessary that is not publicly available.
    Food security impact of global equities : annex measurement methodology for food loss avoided
    Snels, Joost ; Soethoudt, Han ; Verma, Monika - \ 2019
    Wageningen : Wageningen Economic Research (Report / Wageningen Economic Research 2019-043c) - 32
    A systematic analysis of social, economic and environmental sustainability metrics for the range of activities and world views encompassed in the EU food systems : Deliverable No. D6.3
    Achterbosch, T.J. ; Verma, Monika ; Leip, Adrian ; Zurek, Monika ; Oudendag, D.A. ; Geleijnse, J.M. ; Latka, Catharina ; Havlík, Petr ; Kuijsten, A. ; Kuiper, M.H. ; Farell, David ; Anderson, Ross ; Ruto, Elias - \ 2019
    SUSFANS - 119 p.
    Foresight of EU sustainable food and nutrition security: the interplay between major challenges and policy responses at different spatiotemporal scales : Deliverable No. 10.4
    Frank, Stefan ; Latka, Catharina ; Havlik, P. ; Kuiper, M.H. ; Dijk, M. van; Achterbosch, T.J. ; Cui, David ; Geleijnse, J.M. ; Hebinck, Aniek ; Heckelei, Thomas ; Kuijsten, A. ; Leip, Adrian ; Oudendag, D.A. ; Verma, Monika ; Witzke, Heinz-Peter ; Zurek, Monika - \ 2019
    SUSFANS - 75 p.
    Two large-effect QTLs, Ma and Ma3, determine genetic potential for acidity in apple fruit : breeding insights from a multi-family study
    Verma, S. ; Evans, K. ; Guan, Y. ; Luby, J.J. ; Rosyara, U.R. ; Howard, N.P. ; Bassil, N. ; Bink, M.C.A.M. ; Weg, W.E. van de; Peace, C.P. - \ 2019
    Tree Genetics and Genomes 15 (2019)2. - ISSN 1614-2942
    FlexQTL™ - Malic acid - Malus × domestica - Pedigree-Based Analysis - RosBREED

    Acidity is a critical component of the apple fruit consumption experience. In previous biparental family studies, two large-effect acidity QTLs were reported using freshly harvested fruit. Objectives of this study were to determine the number and location of QTLs for acidity variation in a large apple breeding program and ascertain the quantitative effects and breeding relevance of QTL allelic combinations at harvest and after commercially relevant periods of cold storage. Pedigree-connected germplasm of 16 full-sib families representing nine important breeding parents, genotyped for the 8K SNP array, was assessed for titratable acidity at harvest and after 10- and 20-week storage treatments, for three successive seasons. Using pedigree-based QTL mapping software, FlexQTL™, evidence was found for only two QTLs, on linkage groups 16 (the reported Ma locus) and LG 8 (here called Ma3) that jointly explained 66 ± 5% of the phenotypic variation. An additive allele dosage model for the two QTLs effectively explained most acidity variation, with an average of + 1.8 mg/L at harvest per high-acidity allele. The more high-acidity alleles, the faster the depletion with storage, with all combinations appearing to eventually converge to a common baseline. All parent cultivars and selections had one or two of the four possible high-acidity alleles. Each QTL had a rare second high-acidity allele with stronger or reduced effect. Diagnostic SNP markers were identified for QTL alleles derived from distinct sources. Combined QTL effects highlighted utility of the DNA-based information in new cultivar development for targeting desired fruit acidity levels before or after storage.

    A Systems Approach to Food Loss and Solutions : Understanding Practices, Causes, and Indicators
    Verma, Monika ; Plaisier, Christine ; Wagenberg, C.P.A. van; Achterbosch, T.J. - \ 2019
    Sustainability 11 (2019)3. - ISSN 2071-1050
    Reasons behind food loss can be very specific for each product and supply chain stage but it is also affected by factors independent of the product and stage. This work focuses on such generic factors and develops a framework to analyze food loss as a systemic outcome. The framework highlights the interconnected nature of problem across supply chain stages and therefore emphasizes the need to look at the whole system instead of specific stages, when proposing solutions. Practices and underlying causes contributing to food loss are identified for each stage of
    the supply chain using a literature search. Deductive logic is used to fill the gaps where literature was found to be scarce, and to derive socio-economic indicators that signal the presence of identified causes. Using this framework, we propose a non-exhaustive list of 30 socio-economic indicators, which can signal the presence of the 22 practices and 60 causes associated with food loss in supply
    chains. This list can serve as a starting list for practitioners and policymakers to build on when analyzing food losses in supply chains in their region. We evaluate the framework using a fieldstudy of a tomato supply chain in Nigeria, and conclude that it can be a useful tool to identify practices, causes, and indicators of food loss.
    Exploring the impact of alternative population projections on prices, growth and poverty developments
    Kuiper, Marijke ; Shutes, Lindsay ; Verma, Monika ; Tabeau, Andrzej ; Meijl, Hans van - \ 2018
    Rome : Food and Agriculture Organization of the United Nations - ISBN 9789251300961 - 51
    Erratum: Large meta-analysis of genome-wide association studies identifies five loci for lean body mass
    Zillikens, M.C. ; Demissie, Serkalem ; Hsu, Yi Hsiang ; Yerges-Armstrong, Laura M. ; Chou, Wen Chi ; Stolk, Lisette ; Livshits, Gregory ; Broer, Linda ; Johnson, Toby ; Koller, Daniel L. ; Kutalik, Zoltán ; Luan, J. ; Malkin, Ida ; Ried, Janina S. ; Smith, Albert V. ; Thorleifsson, Gudmar ; Vandenput, Liesbeth ; Hua Zhao, Jing ; Zhang, Weihua ; Aghdassi, Ali ; Åkesson, Kristina ; Amin, Najaf ; Baier, Leslie J. ; Barroso, Inês ; Bennett, David A. ; Bertram, Lars ; Biffar, Rainer ; Bochud, Murielle ; Boehnke, Michael ; Borecki, Ingrid B. ; Buchman, Aron S. ; Byberg, Liisa ; Campbell, Harry ; Campos Obanda, Natalia ; Cauley, Jane A. ; Cawthon, Peggy M. ; Cederberg, Henna ; Chen, Zhao ; Cho, Nam H. ; Jin Choi, Hyung ; Claussnitzer, Melina ; Collins, Francis ; Cummings, Steven R. ; Jager, Philip L. De; Demuth, Ilja ; Dhonukshe-Rutten, Rosalie A.M. ; Diatchenko, Luda ; Eiriksdottir, Gudny ; Enneman, Anke W. ; Erdos, Mike ; Eriksson, Johan G. ; Eriksson, Joel ; Estrada, Karol ; Evans, Daniel S. ; Feitosa, Mary F. ; Fu, Mao ; Garcia, Melissa ; Gieger, Christian ; Girke, Thomas ; Glazer, Nicole L. ; Grallert, Harald ; Grewal, Jagvir ; Han, Bok Ghee ; Hanson, Robert L. ; Hayward, Caroline ; Hofman, Albert ; Hoffman, Eric P. ; Homuth, Georg ; Hsueh, Wen Chi ; Hubal, Monica J. ; Hubbard, Alan ; Huffman, Kim M. ; Husted, Lise B. ; Illig, Thomas ; Ingelsson, Erik ; Ittermann, Till ; Jansson, John Olov ; Jordan, Joanne M. ; Jula, Antti ; Karlsson, Magnus ; Khaw, Kay Tee ; Kilpeläinen, Tuomas O. ; Klopp, Norman ; Kloth, Jacqueline S.L. ; Koistinen, Heikki A. ; Kraus, William E. ; Kritchevsky, Stephen ; Kuulasmaa, Teemu ; Kuusisto, Johanna ; Laakso, Markku ; Lahti, Jari ; Lang, Thomas ; Langdahl, Bente L. ; Launer, Lenore J. ; Lee, Jong Young ; Lerch, Markus M. ; Lewis, Joshua R. ; Lind, Lars ; Lindgren, Cecilia ; Liu, Yongmei ; Liu, Tian ; Liu, Youfang ; Ljunggren, Östen ; Lorentzon, Mattias ; Luben, Robert N. ; Maixner, William ; McGuigan, Fiona E. ; Medina-Gomez, Carolina ; Meitinger, Thomas ; Melhus, Håkan ; Mellström, Dan ; Melov, Simon ; Michaëlsson, Karl ; Mitchell, Braxton D. ; Morris, Andrew P. ; Mosekilde, Leif ; Newman, Anne ; Nielson, Carrie M. ; O'Connell, Jeffrey R. ; Oostra, Ben A. ; Orwoll, Eric S. ; Palotie, Aarno ; Parker, Stephen C.J. ; Peacock, Munro ; Perola, Markus ; Peters, Annette ; Polasek, Ozren ; Prince, Richard L. ; Räikkönen, Katri ; Ralston, Stuart H. ; Ripatti, Samuli ; Robbins, John A. ; Rotter, Jerome I. ; Rudan, Igor ; Salomaa, Veikko ; Satterfield, Suzanne ; Schadt, Eric E. ; Schipf, Sabine ; Scott, Laura ; Sehmi, Joban ; Shen, Jian ; Soo Shin, Chan ; Sigurdsson, Gunnar ; Smith, Shad ; Soranzo, Nicole ; Stančáková, Alena ; Steinhagen-Thiessen, Elisabeth ; Streeten, Elizabeth A. ; Styrkarsdottir, Unnur ; Swart, Karin M.A. ; Tan, Sian Tsung ; Tarnopolsky, Mark A. ; Thompson, Patricia ; Thomson, Cynthia A. ; Thorsteinsdottir, Unnur ; Tikkanen, Emmi ; Tranah, Gregory J. ; Tuomilehto, Jaakko ; Schoor, Natasja M. van; Verma, Arjun ; Vollenweider, Peter ; Völzke, Henry ; Wactawski-Wende, Jean ; Walker, Mark ; Weedon, Michael N. ; Welch, Ryan ; Wichmann, H.E. ; Widen, Elisabeth ; Williams, Frances M.K. ; Wilson, James F. ; Wright, Nicole C. ; Xie, Weijia ; Yu, Lei ; Zhou, Yanhua ; Chambers, John C. ; Döring, Angela ; Duijn, Cornelia M. van; Econs, Michael J. ; Gudnason, Vilmundur ; Kooner, Jaspal S. ; Psaty, Bruce M. ; Spector, Timothy D. ; Stefansson, Kari ; Rivadeneira, Fernando ; Uitterlinden, André G. ; Wareham, Nicholas J. ; Ossowski, Vicky ; Waterworth, Dawn ; Loos, Ruth J.F. ; Karasik, David ; Harris, Tamara B. ; Ohlsson, Claes ; Kiel, Douglas P. - \ 2017
    Nature Communications 8 (2017)1. - ISSN 2041-1723 - 1 p.

    A correction to this article has been published and is linked from the HTML version of this article.

    Consumer Food Waste: New estimates and approach Inferring consumption food waste from private expenditure
    Verma, Monika - \ 2017
    Consumer Food Waste: New estimates and approach Inferring consumption food waste from private expenditure
    Verma, Monika ; Vreede, Linda de; Rutten, M.M. ; Achterbosch, T.J. - \ 2017
    - 1 p.
    Given estimates of food waste often involve applying fixed factors or shares across different stages of food supply chain, missing the factors affecting food waste. We propose a first step in this direction by using an alternative way to impute consumer Food Waste and a first attempt at showing how it might be linked to consumer spending. In the process we derive implications for consumption elasticity and policy.
    Deliverable No. D9.4: Enhanced modelling of sustainable food and nutrition security: the agri-food commodity and nutrient flows and the food supply chains
    Carmona-Garcia, G. ; Leip, A. ; Weiss, F. ; Witzke, P. ; Verma, M. ; Philippidis, George ; Kuiper, M.H. - \ 2017
    SUSFANS - 86 p.
    Large meta-analysis of genome-wide association studies identifies five loci for lean body mass
    Zillikens, M.C. ; Demissie, Serkalem ; Hsu, Yi Hsiang ; Yerges-Armstrong, Laura M. ; Chou, Wen Chi ; Stolk, Lisette ; Livshits, Gregory ; Broer, Linda ; Johnson, Toby ; Koller, Daniel L. ; Kutalik, Zoltán ; Luan, J.A. ; Malkin, Ida ; Ried, Janina S. ; Smith, Albert V. ; Thorleifsson, Gudmar ; Vandenput, Liesbeth ; Hua Zhao, Jing ; Zhang, Weihua ; Aghdassi, Ali ; Åkesson, Kristina ; Amin, Najaf ; Baier, Leslie J. ; Barroso, Inês ; Bennett, David A. ; Bertram, Lars ; Biffar, Rainer ; Bochud, Murielle ; Boehnke, Michael ; Borecki, Ingrid B. ; Buchman, Aron S. ; Byberg, Liisa ; Campbell, Harry ; Campos Obanda, Natalia ; Cauley, Jane A. ; Cawthon, Peggy M. ; Cederberg, Henna ; Chen, Zhao ; Cho, Nam H. ; Jin Choi, Hyung ; Claussnitzer, Melina ; Collins, Francis ; Cummings, Steven R. ; Jager, Philip L. De; Demuth, Ilja ; Dhonukshe-Rutten, Rosalie A.M. ; DIatchenko, Luda ; Eiriksdottir, Gudny ; Enneman, Anke W. ; Erdos, Mike ; Eriksson, Johan G. ; Eriksson, Joel ; Estrada, Karol ; Evans, Daniel S. ; Feitosa, Mary F. ; Fu, Mao ; Garcia, Melissa ; Gieger, Christian ; Girke, Thomas ; Glazer, Nicole L. ; Grallert, Harald ; Grewal, Jagvir ; Han, Bok Ghee ; Hanson, Robert L. ; Hayward, Caroline ; Hofman, Albert ; Hoffman, Eric P. ; Homuth, Georg ; Hsueh, Wen Chi ; Hubal, Monica J. ; Hubbard, Alan ; Huffman, Kim M. ; Husted, Lise B. ; Illig, Thomas ; Ingelsson, Erik ; Ittermann, Till ; Jansson, John Olov ; Jordan, Joanne M. ; Jula, Antti ; Karlsson, Magnus ; Khaw, Kay Tee ; Kilpelaïnen, Tuomas O. ; Klopp, Norman ; Kloth, Jacqueline S.L. ; Koistinen, Heikki A. ; Kraus, William E. ; Kritchevsky, Stephen ; Kuulasmaa, Teemu ; Kuusisto, Johanna ; Laakso, Markku ; Lahti, Jari ; Lang, Thomas ; Langdahl, Bente L. ; Launer, Lenore J. ; Lee, Jong Young ; Lerch, Markus M. ; Lewis, Joshua R. ; Lind, Lars ; Lindgren, Cecilia M. ; Liu, Yongmei ; Liu, Tian ; Liu, Youfang ; Ljunggren, Östen ; Lorentzon, Mattias ; Luben, Robert N. ; Maixner, William ; McGuigan, Fiona E. ; Medina-Gomez, Carolina ; Meitinger, Thomas ; Melhus, Håkan ; Mellström, Dan ; Melov, Simon ; Michaëlsson, Karl ; Mitchell, Braxton D. ; Morris, Andrew P. ; Mosekilde, Leif ; Newman, Anne ; Nielson, Carrie M. ; O'Connell, Jeffrey R. ; Oostra, Ben A. ; Orwoll, Eric S. ; Palotie, Aarno ; Parker, Stephan ; Peacock, Munro ; Perola, Markus ; Peters, Annette ; Polasek, Ozren ; Prince, Richard L. ; Raïkkönen, Katri ; Ralston, Stuart H. ; Ripatti, Samuli ; Robbins, John A. ; Rotter, Jerome I. ; Rudan, Igor ; Salomaa, Veikko ; Satterfield, Suzanne ; Schadt, Eric E. ; Schipf, Sabine ; Scott, Laura ; Sehmi, Joban ; Shen, Jian ; Soo Shin, Chan ; Sigurdsson, Gunnar ; Smith, Shad ; Soranzo, Nicole ; Stančáková, Alena ; Steinhagen-Thiessen, Elisabeth ; Streeten, Elizabeth A. ; Styrkarsdottir, Unnur ; Swart, Karin M.A. ; Tan, Sian Tsung ; Tarnopolsky, Mark A. ; Thompson, Patricia ; Thomson, Cynthia A. ; Thorsteinsdottir, Unnur ; Tikkanen, Emmi ; Tranah, Gregory J. ; Tuomilehto, Jaakko ; Schoor, Natasja M. van; Verma, Arjun ; Vollenweider, Peter ; Völzke, Henry ; Wactawski-Wende, Jean ; Walker, Mark ; Weedon, Michael N. ; Welch, Ryan ; Wichman, H.E. ; Widen, Elisabeth ; Williams, Frances M.K. ; Wilson, James F. ; Wright, Nicole C. ; Xie, Weijia ; Yu, Lei ; Zhou, Yanhua ; Chambers, John C. ; Döring, Angela ; Duijn, Cornelia M. Van; Econs, Michael J. ; Gudnason, Vilmundur ; Kooner, Jaspal S. ; Psaty, Bruce M. ; Spector, Timothy D. ; Stefansson, Kari ; Rivadeneira, Fernando ; Uitterlinden, André G. ; Wareham, Nicholas J. ; Ossowski, Vicky ; Waterworth, Dawn M. ; Loos, Ruth J.F. ; Karasik, David ; Harris, Tamara B. ; Ohlsson, Claes ; Kiel, Douglas P. - \ 2017
    Nature Communications 8 (2017)1. - ISSN 2041-1723
    Lean body mass, consisting mostly of skeletal muscle, is important for healthy aging. We performed a genome-wide association study for whole body (20 cohorts of European ancestry with n = 38,292) and appendicular (arms and legs) lean body mass (n = 28,330) measured using dual energy X-ray absorptiometry or bioelectrical impedance analysis, adjusted for sex, age, height, and fat mass. Twenty-one single-nucleotide polymorphisms were significantly associated with lean body mass either genome wide (p < 5 × 10-8) or suggestively genome wide (p < 2.3 × 10-6). Replication in 63,475 (47,227 of European ancestry) individuals from 33 cohorts for whole body lean body mass and in 45,090 (42,360 of European ancestry) subjects from 25 cohorts for appendicular lean body mass was successful for five single-nucleotide polymorphisms in/near HSD17B11, VCAN, ADAMTSL3, IRS1, and FTO for total lean body mass and for three single-nucleotide polymorphisms in/near VCAN, ADAMTSL3, and IRS1 for appendicular lean body mass. Our findings provide new insight into the genetics of lean body mass.
    Pedigree-based analysis in a multiparental population of octoploid strawberry reveals QTL alleles conferring resistance to phytophthora cactorum
    Mangandi, Jozer ; Verma, Sujeet ; Osorio, Luis ; Peres, Natalia A. ; Weg, Eric van de; Whitaker, Vance M. - \ 2017
    G3 : Genes Genomes Genetics 7 (2017)6. - ISSN 2160-1836 - p. 1707 - 1719.
    disease resistance - FaRPc2 - FlexQTL - Fragaria - Haplotype quantitative trait locus - MPP - Multiparental population

    Understanding the genetic architecture of traits in breeding programs can be critical for making genetic progress. Important factors include the number of loci controlling a trait, allele frequencies at those loci, and allele effects in breeding germplasm. To this end, multiparental populations offer many advantages for quantitative trait locus (QTL) analyses compared to biparental populations. These include increased power for QTL detection, the ability to sample a larger number of segregating loci and alleles, and estimation of allele effects across diverse genetic backgrounds. Here, we investigate the genetic architecture of resistance to crown rot disease caused by Phytophthora cactorum in strawberry (Fragaria × ananassa), using connected full-sib families from a breeding population. Clonal replicates of > 1100 seedlings from 139 full-sib families arising from 61 parents were control-inoculated during two consecutive seasons. Subgenome-specific single nucleotide polymorphism (SNP) loci were mapped in allo-octoploid strawberry (2n = 8 × = 56), and FlexQTL software was utilized to perform a Bayesian, pedigree-based QTL analysis. A major locus on linkage group (LG) 7D, which we name FaRPc2, accounts for most of the genetic variation for resistance. Four predominant SNP haplotypes were detected in the FaRPc2 region, two of which are strongly associated with two different levels of resistance, suggesting the presence of multiple resistance alleles. The phenotypic effects of FaRPc2 alleles across trials and across numerous genetic backgrounds make this locus a highly desirable target for genetic improvement of resistance in cultivated strawberry.

    Development and evaluation of the Axiom® IStraw35 384HT array for the allo-octoploid cultivated strawberry Fragaria ×ananassa
    Verma, S. ; Bassil, N.V. ; Weg, E. van de; Harrison, R.J. ; Monfort, A. ; Hidalgo, J.M. ; Amaya, I. ; Denoyes, B. ; Mahoney, L.L. ; Davis, T.M. ; Fan, Z. ; Knapp, S. ; Whitaker, V.M. - \ 2017
    In: 8th International Strawberry Symposium. - International Society for Horticultural Science (Acta Horticulturae ) - ISBN 9789462611528 - p. 75 - 81.
    Breeding - Genotyping - IStraw90 - Single nucleotide polymorphism (SNP)

    The Axiom® IStraw90 SNP (single nucleotide polymorphism) array was developed to enable high-throughput genotyping in allo-octoploid cultivated strawberry (Fragaria ×ananassa). However, high cost ($ 80-105 sample-1) limits throughput for certain applications. On average the IStraw90 has yielded 50 to 60% usable data points, defined as PHR (Poly High Resolution) and NMH (No Minor Homozygote) marker classes. Thus, an array is needed with a higher percentage of usable data points at a lower cost. We initiated an effort to identify IStraw90 SNP markers that were genetically mapped in one or more strawberry populations from research programs around the world. Seven programs participated in this endeavor. A total of 41,183 SNP probes were submitted to Affymetrix for quality check, 38,506 of which were accommodated on the Axiom® IStraw35 384HT design. In order to assess the performance of the Axiom® IStraw35 384HT array, 384 DNA samples from the University of Florida strawberry breeding program were assayed at a cost of $ 50 per sample, all inclusive. The performance of the array met expectations. More than 87% of markers belonged to the PHR and NMH categories. This array is expected to provide high-quality genome scanning at a more affordable price for strawberry researchers worldwide.

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