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    Ex Situ Conservation Priorities for the Wild Relatives of Potato (Solanum L. Section Petota)
    Castaneda-Alvarez, N.P. ; Haan, S. de; Juarez, H. ; Khoury, C.K. ; Achicanoy, H.A. ; Sosa, C.C. ; Bernau, V. ; Salas, A. ; Heider, B. ; Simon, R. ; Maxted, N. ; Spooner, D.M. - \ 2015
    PLoS ONE 10 (2015)4. - ISSN 1932-6203 - 19 p.
    globodera-pallida stone - late blight resistance - tuber-bearing solanum - somatic hybrids - cultivated potato - phytophthora-infestans - ralstonia-solanacearum - species distributions - ortholog sequences - genetic-resources
    Crop wild relatives have a long history of use in potato breeding, particularly for pest and disease resistance, and are expected to be increasingly used in the search for tolerance to biotic and abiotic stresses. Their current and future use in crop improvement depends on their availability in ex situ germplasm collections. As these plants are impacted in the wild by habitat destruction and climate change, actions to ensure their conservation ex situ become ever more urgent. We analyzed the state of ex situ conservation of 73 of the closest wild relatives of potato (Solanum section Petota) with the aim of establishing priorities for further collecting to fill important gaps in germplasm collections. A total of 32 species (43.8%), were assigned high priority for further collecting due to severe gaps in their ex situ collections. Such gaps are most pronounced in the geographic center of diversity of the wild relatives in Peru. A total of 20 and 18 species were assessed as medium and low priority for further collecting, respectively, with only three species determined to be sufficiently represented currently. Priorities for further collecting include: (i) species completely lacking representation in germplasm collections; (ii) other high priority taxa, with geographic emphasis on the center of species diversity; (iii) medium priority species. Such collecting efforts combined with further emphasis on improving ex situ conservation technologies and methods, performing genotypic and phenotypic characterization of wild relative diversity, monitoring wild populations in situ, and making conserved wild relatives and their associated data accessible to the global research community, represent key steps in ensuring the long-term availability of the wild genetic resources of this important crop.
    Distributions, ex situ conservation priorities, and genetic resource potential of crop wild relatives of sweetpotato [Ipomoea batatas (L.) Lam., I. series Batatas]
    Khoury, C.K. ; Heider, B. ; Castaneda-Alvarez, N.P. ; Achicanoy, H.A. ; Sosa, C.C. ; Miller, R.E. ; Scotland, R.W. ; Wood, J.R.I. ; Rossel, G. ; Eserman, L.A. ; Jarret, R.L. ; Yencho, G.C. ; Bernau, V. ; Juarez, H. ; Sotelo, S. ; Haan, S. de; Struik, P.C. - \ 2015
    Frontiers in Plant Science 6 (2015). - ISSN 1664-462X - 14 p.
    species distribution models - phylogenetic-relationships - beta-carotene - convolvulaceae - sequences - diversity - evolution - bias - challenges - tolerance
    Crop wild relatives of sweetpotato [Ipomoea batatas (L.) Lam., I. series Batatas] have the potential to contribute to breeding objectives for this important root crop. Uncertainty in regard to species boundaries and their phylogenetic relationships, the limited availability of germplasm with which to perform crosses, and the difficulty of introgression of genes from wild species has constrained their utilization. Here, we compile geographic occurrence data on relevant sweetpotato wild relatives and produce potential distribution models for the species. We then assess the comprehensiveness of ex situ germplasm collections, contextualize these results with research and breeding priorities, and use ecogeographic information to identify species with the potential to contribute desirable agronomic traits. The fourteen species that are considered the closest wild relatives of sweetpotato generally occur from the central United States to Argentina, with richness concentrated in Mesoamerica and in the extreme Southeastern United States. Currently designated species differ among themselves and in comparison to the crop in their adaptations to temperature, precipitation, and edaphic characteristics and most species also show considerable intraspecific variation. With 79% of species identified as high priority for further collecting, we find that these crop genetic resources are highly under-represented in ex situ conservation systems and thus their availability to breeders and researchers is inadequate. We prioritize taxa and specific geographic locations for further collecting in order to improve the completeness of germplasm collections. In concert with enhanced conservation of sweetpotato wild relatives, further taxonomic research, characterization and evaluation of germplasm, and improving the techniques to overcome barriers to introgression with wild species are needed in order to mobilize these genetic resources for crop breeding.
    Cabauw Experimental Site for Atmospheric Research (CESAR) - The Netherlands: An initial GRUAN atmospheric profiling station
    Boers, R. ; Bosveld, F. ; Knap, W. ; Klein Baltink, H. ; Donovan, D. ; Haan, S. de; Russchenberg, H. ; Apituley, A. ; Brink ten, H. ; Henzing, B. ; Leeuw de, G. ; Uijlenhoet, R. ; Arbesser-Rastburg, B. ; Röckman, T. - \ 2009
    Real-Time Water Vapor Maps from a GPS Surface Network: Construction, Validation, and Applications
    Haan, S. de; Holleman, I. ; Holtslag, A.A.M. - \ 2009
    Journal of Applied Meteorology and Climatology 48 (2009)7. - ISSN 1558-8424 - p. 1302 - 1316.
    global positioning system - precipitable water - model - verification - netherlands - meteorology - radiosonde - radiometer - errors - delay
    In this paper the construction of real-time integrated water vapor (IWV) maps from a surface network of global positioning system (GPS) receivers is presented. The IWV maps are constructed using a twodimensional variational technique with a persistence background that is 15 min old. The background error covariances are determined using a novel two-step method, which is based on the Hollingsworth¿Lonnberg method. The quality of these maps is assessed by comparison with radiosonde observations and IWV maps from a numerical weather prediction (NWP) model. The analyzed GPS IWV maps have no bias against radiosonde observations and a small bias against NWP analysis and forecasts up to 9 h. The standard deviation with radiosonde observations is around 2 kg m-2, and the standard deviation with NWP increases with increasing forecast length (from 2 kg m-2 for the NWP analysis to 4 kg m-2 for a forecast length of 48 h). To illustrate the additional value of these real-time products for nowcasting, three thunderstorm cases are discussed. The constructed GPS IWV maps are combined with data from the weather radar, a lightning detection network, and surface wind observations. All cases show that the location of developing thunderstorms can be identified 2 h prior to initiation in the convergence of moist air.
    Potato diversity at height: multiple dimensions of farmer-driven in-situ conservation in the Andes
    Haan, S. de - \ 2009
    Wageningen University. Promotor(en): Jos van der Maesen, co-promotor(en): Conny Almekinders; M. Bonierbale; G. Thiele. - - 245
    Solanum - potatoes - in situ conservation - plant genetic resources - species - cultivars - taxonomy - diversity - andes - Solanum - aardappelen - in-situ conservering - genetische bronnen van plantensoorten - soorten - cultivars - taxonomie - diversiteit - andes
    In-situ conservation
    Two types of in-situ conservation of crop genetic resources can be distinguished: farmer-driven and
    externally driven. The first is subject of this thesis and refers to the persistence of potato genetic resources
    in areas where everyday practices of farmers maintain diversity on-farm. The second concerns the more
    recent phenomenon of Research & Development (R&D) interventions which aim to support in-situ
    conservation by farmers. In this study, farmer-driven in-situ conservation of the potato in the central Andes
    of Peru is investigated at different system levels from alleles, cultivars, and botanical species up to the level
    of the landscape, as well as the interconnected seed and food systems. Dimensions of time and space are
    inferred upon by taking both annual and longer-term spatial patterns into account. Further, diversity is
    linked to selected farmer-based and external drivers.
    Objective and study area
    The overall objective of the study is to enhance our understanding of farmer-driven in-situ conservation
    and the context in which it takes place. The main field research was conducted between 2003 and 2006 in
    eight farmer communities following a north-south transect through the department of Huancavelica.
    Communities were selected on the basis of distribution and distance along the north-south transect,
    tradition of potato cultivation, ethnicity, and relative distance from major markets or cities. Depending on
    the specific dimension of farmer-driven in-situ conservation investigated, a range of different methods
    and tools were used. Chapter 1 provides a brief description of the study area and an overview of the research
    methods used.
    Species, cultivar and allelic diversity
    In chapter 2 the species, morphological and molecular diversity of Andean potatoes in Huancavelica is
    treated at different scales of conservation: farmer family, community, geographically distanced, regional,
    in-situ and ex-situ subpopulations. The infraspecific diversity of in-situ collections was characterized using
    morphological descriptor lists and 18 polymorphic microsatellite markers (SSR). Botanical species were
    determined through ploidy counts in combination with morphological keys. Datasets were used for
    descriptive statistics, (dis)similarity analysis, dendrogram construction, cophenetic analysis, matrix
    correlations calculations (Mantel tests), and Analysis of Molecular Variance (AMOVA).
    Results show that farmers in Huancavelica maintain high levels of species, morphological and molecular
    diversity. All cultivated potato species with the exception of Solanum phureja and Solanum ajanhuiri proved
    to be present. Tetraploid species were most abundant followed by diploids, triploids and pentaploids. A
    total of 557 morphologically unique cultivars were identified based on the morphological characterization
    of 2,481 accessions belonging to 38 in-situ collections. Genetic fingerprinting of 989 accessions belonging
    to 8 in-situ collections resulted in the identification of 406 genetically unique cultivars. AMOVA shows that
    the principal source of molecular variation is found within rather than between geographically distanced
    and farmer family subpopulations. No evidence of genetic erosion was found as the contemporary regional
    in-situ population and a geographically restricted subset of CIP´s ex-situ core collection share 98.8% of
    allelic diversity. Yet, in-situ collections contain numerous unique genotypes.
    Indigenous biosystematics
    The indigenous biosystematics of potatoes (folk taxonomy, folk descriptors and nomenclature) is
    investigated in chapter 3. The chapter includes an extensive literature review on the subject. Folk taxonomy
    was investigated with the use of grouping exercises with farmers, participant observation, and comparison
    of farmer-recognized groups with formal classification based on morphological descriptors and 18
    polymorphic microsatellite markers (SSR). Analysis of the latter was based on (dis)similarity analysis,
    dendrogram construction and consequent levels of coherent clustering by folk taxonomic entity (folk
    specific and varietal taxon). Ethnobotanical free and indicated listing exercises with farmers were used for
    research concerning folk descriptors. Descriptive statistics were used for analysis and interpretation.
    Nomenclature was investigated by applying nomenclature surveys, participant observation and basic
    ethnolinguistic analysis of regional names.
    Folk taxonomy of the potato consists of no less than five ranks. The folk generic rank is composed of
    three taxa: Araq Papa (semi-wild / consumed), Papa Tarpuy (cultivated / consumed), and Atoq Papa (wild /
    not consumed). Folk specific taxa (= cultivar groups) and varietal taxa (= cultivars) within the generic taxon
    of Papa Tarpuy are abundant. Use categories and agroecological criteria are of little importance in the folk
    taxonomical system of the potato. Folk varietal taxa cluster well when using formal morphological
    descriptors; folk specific taxa less so. A moderate concordance, albeit with considerable exceptions, exists
    between folk specific or varietal taxa and their genetic make-up as characterized with molecular markers
    (18 SSR microsatellites). The coherence of clustering in a dissimilarity tree varies for each folk specific or
    varietal taxon considered. Farmers use 22 plant and 15 tuber folk descriptors with recognized character
    states in the Quechua language. Farmers are well able to recognize specific cultivars based on aboveground
    plant parts only (without exposing tubers). Nomenclature is regionally consistent for common cultivars,
    while inconsistent for scarce cultivars. Primary cultivar names (nouns) generally refer to a folk specific taxon
    through predominant metaphorical reference to tuber shape. Secondary cultivar names (adjectives)
    predominantly provide direct reference to tuber color.
    Annual spatial patterns
    Annual spatial management of the potato consists of cropping and labor calendars, field scattering practices,
    and genotype by environmental management. These three dimensions of agrobiodiversity management
    are explored in chapter 4. A structured survey was conducted to investigate the potato cropping and labor
    calendars. Participatory cartography resulted in the detailed mapping of 601 scattered potato fields,
    including their cultivar content, belonging to a total of 122 households. A genotype by environment (GxE)
    experiment employing 4 environments and 31 cultivars was conducted following an altitudinal transect.
    Data obtained was analyzed and interpreted using descriptive statistics, correlation analysis, Geographical
    Information Systems (GIS), Additive main Effects and Multiplicative Interaction (AMMI) analysis, and analysis
    of variance (ANOVA).
    The annual distribution of tasks and labor is primarily an adaptation to the single-season rain-fed
    character and climate extremes of high-altitude agriculture. Three different footplough-based tillage
    systems allow farmers to efficiently manage scarce labor availability for soil preparation. Native-floury, nativebitter
    and improved potato cultivars show considerable overlap concerning their altitudinal distribution
    patterns. The notion that these cultivar categories occupy separate production spaces (so-called “altitudinal
    belts”) is rejected as results show that differences between the altitudinal medians for areal distribution by
    altitude of the different cultivar categories are modest (chapter 4). Field scattering is based on a combined
    logic which results in a patchy distribution of potato genetic diversity across the agricultural landscape.
    Depending on the community, farmers annually crop an average of 3.2 to 9.1 potato fields measuring
    between 660 to 1,576 m² and containing up to a hundred cultivars per field. However, neither field scattering
    nor the management of high levels of diversity by farmers is a direct consequence of niche adaptation as
    most cultivars are versatile (chapter 4). Rather, it is suggested that farmers conduct annual spatial
    management by deploying combined tolerance and resistance traits imbedded in particular cultivar
    combinations in order to confront the predominant biotic and abiotic stresses present in different
    agroecologies. Andean farmers manage GxE adaptation for overall yield stability rather than fine-grained
    environmental adaptation of native cultivars.
    Dimensions of land use
    Three specific dimensions of potato land use were researched in order to gain insights into possible
    contemporary changes affecting the in-situ conservation of potato genetic resources: land use tendencies,
    rotation designs and their intensity, and sectoral fallowing systems (chapter 5). The main research method
    involved participatory cartography using printed poster-size high-resolution Quickbird satellite images
    combined with in-depth consultation through interviews and focus group meetings with members of the
    communities. A total of 4,343 fields and their 1995-2005 crop contents were mapped. The evolution over a
    30-year time-span (1975-2005) of traditional sectoral fallow systems (“diversity hotspots”) was documented
    for each community. Data was analyzed using descriptive statistics and Geographical Information Systems
    (GIS). Processes of change and adaptive innovation were documented by building case studies.
    Land use tendencies between 1995 and 2005 shows that the total cropping area dedicated to improved
    cultivars has grown fast while the area dedicated to native-floury and native-bitter cultivars has remained
    more or less stable. Reduced fallow periods for existing fields and the gradual incorporating of high-altitude
    virgin pasture lands sustain areal growth. Areal growth is particularly fast at extreme altitudes between
    3,900 and 4,350 m. However, fallow periods at these altitudes are still relatively long compared to fields at
    lower altitudes. Results show that fallowing rates increase by altitude for all cultivar categories, but tend to
    be lowest for improved cultivars followed by native-floury and native-bitter cultivars. There is no evidence
    of a straightforward replacement of one cultivar category by another resulting in the replacement and loss
    of infraspecific diversity. Inquiry into the dynamics of sectoral fallow systems over a 30 year period evidences
    the gradual disintegration and abandonment of these systems rich in cultivar diversity. They are replaced
    by more individualist management regimes based on household decision making. Nowadays, the spatial
    patterning of potato genetic diversity within the agricultural landscape is increasingly characterized by
    patchy distribution patterns rather than its concentration within a single communal sector. Where sectoral
    rotation designs survive local innovations have been adopted.
    Farmer seed systems
    Farmer seed systems can be conceived as an overlay of crop genetic diversity determining its temporal
    and spatial patterning. Chapter 6 investigates the relation between selected farmer seed system components
    (storage, health and procurement) and infraspecific diversity of potato in Huancavelica. A sampling exercise
    was carried out in farmer seed stores in order to gain insight into the internal organization of seed stores
    and how this relates to the management of infraspecific diversity. Virus infection rates were determined by
    taking seed tuber samples of diverse cultivars from farmer’s storage facilities. ELISA tests were conduced
    for APMoV, PLRV, PMTV, PVY and PVX. Seed procurement was investigated through a series of structured
    surveys focusing on household seed exchange, the role of regular markets and biodiversity seed fairs, and
    seed provision after severe regional frost. Data was analyzed and interpreted using descriptive statistics.
    Potato seed stores contain different seed lots, reflecting the rationales underlying management of
    cultivar diversity at the field level and the overall structure of infraspecific diversity. Seed health of farmer
    conserved cultivar stocks in Huancavelica is affected by Diabrotica leaf beetle and contact transmitted
    viruses (APMoV, PVX) while aphid and powdery scab transmitted viruses (PMTV, PLRV, PVY) are of limited
    importance. During normal years without extreme events seed exchange of native-floury cultivars is
    practiced by few households and characterized by a limited number of transactions involving small
    quantities of seed of few cultivars covering relatively short distances. Native-bitter and uncommon nativefloury
    cultivars are rarely exchanged and generally reproduced year after year by the same households
    that maintain them. High-altitude diversity-rich communities tend to be net seed exporters. However, the
    capacity of the farmer seed system to annually widely supply and distribute infraspecific diversity is limited.
    Regular markets have a decentralized capacity to supply and widely distribute seed of a limited number of
    well-known cultivars. Frequencies of seed exchange at biodiversity seed fairs are low and involve small
    quantities of a few uncommon cultivars. The resilience of the farmer seed system to cope with severe regional
    seed stress is insufficient for households to be able to restore volumes and cultivar portfolios within a
    short period of time.
    The potato-based food system
    The role of biodiverse potatoes within the human diet in Huancavelica is investigated in chapter 7. Analysis
    to determine the dry matter, gross energy, crude protein, iron (Fe) and zinc (Zn) content of 12 native-floury
    cultivars (fresh / boiled tuber samples) and 9 native-bitter cultivars (boiled unprocessed / boiled processed
    tuber samples) was conduced. Additionally, the nutritional composition of the native-floury cultivars was
    determined after 3 and 5 months of storage under farmer conditions. A food intake study was conducted
    during two contrasting periods of food availability (abundance versus scarcity) in order to quantify and
    characterize the contribution of the potato, different cultivar categories and other food sources to the diet
    of children between 6 and 36 months of age and their mothers. The specific method consisted of direct
    measurement of food intake by weight during a 24 hour period for each household (77 households). Further,
    the overall nutritional status of 340 children aged between 4 and 16 years was determined. Selected cultural
    connotations of the highland diet were investigated through participant and ethnographic observation,
    surveys, and workshops.
    Results show that several native-floury cultivars contain higher contents of specific nutrients (protein,
    iron) than those commonly reported as representative for native potato cultivars. This suggests that
    infraspecific diversity can make a valuable contribution to enhanced nutrition. Storage does not affect the
    nutritional quality of native-floury cultivars very significantly while traditional freeze-drying of native-bitter
    cultivars considerably reduces protein and zinc content. The research shows that malnutrition in
    Huancavelica is primarily a consequence of micronutrient deficiency and secondarily of insufficient total
    energy coverage. The highland diet is heavily dependent on staple foods, particularly potato and barley,
    and generally short in vegetable, fruit, meat and milk intake. The potato contributes significantly to the
    nutritional balance and the recommended requirements for energy, protein, iron and zinc of women and
    children during periods of both food abundance and scarcity. Improved and native-floury cultivars
    complement each other as each category provides the bulk of potatoes consumed at different moments in
    time. The consumption of diverse potato cultivars is entangled with cultural constructions of meals and
    local perceptions of preference traits and quality. The potato itself, as a food item, is no socioeconomic class
    marker. However, certain dishes or products and the overall cultivar diversity grown and used by a household
    shape perceptions of relative wealth.
    Conclusions and implications
    Chapter 8 highlights the main conclusions of the study and provides answers to the original research
    questions while taking the different system levels explored throughout the thesis into account. Selected
    priority areas of future research are identified and, where appropriate, links to other parts of the Andes are
    drawn. Furthermore, the implications for externally driven R&D oriented in-situ conservation efforts seeking
    to support dynamic and ongoing farmer-driven conservation are discussed. It is argued that the science
    and practice of R&D oriented in-situ conservation lag behind the policy commitments to its implementation
    and that institutional learning from diverse projects already implemented throughout the Andes and the
    diffusion of key lessons is essential for the success of future interventions.
    Meteorological applications of a surface network of Global Positioning System receivers
    Haan, S. de - \ 2008
    Wageningen University. Promotor(en): Bert Holtslag, co-promotor(en): H. van der Marel; I. Holleman. - S.l. : S.n. - ISBN 9789085048817 - 143
    meteorologie - meteorologische waarnemingen - meteorologische instrumenten - globale plaatsbepalingssystemen - netwerken - meteorology - meteorological observations - meteorological instruments - global positioning systems - networks
    This thesis presents meteorological applications of water vapour observations from a surface network of Global Positioning System (GPS) receivers. GPS signals are delayed by the atmo¬sphere due to atmospheric refraction and bending. Mapped to the zenith, this delay is called Zenith Total Delay (ZTD). The ZTD can be separated in a hydrostatic and a wet delay. The first can be approximated by the surface pressure, while the second is related to Integrated Wa¬ter Vapour (IWV); this relation depends on the surface temperature. Currently, radiosondes are the only operational source of upper air humidity observations, however these observations are sparse in space and time. GPS IWV can fill this gap, albeit that the observable is an integral quantity. A study of the correlation of radiosonde observations and IWV shows that the change over time of IWV is closely related to the change in specific humidity at 2 km. The quality of the GPS IWV, assessed by comparison with numerical weather prediction (NWP) model and radiosonde observations, shows accuracies of 14 mm in ZTD and 2 kg m~2 in IWV.
    In the processing of GPS signals it is assumed that the atmosphere through which the signals propogate is symmetric and close to climatology. A consequence of this assumption is that when a strong water vapour gradient is present at a GPS site, systematic errors of around -3 mm in ZTD are observed (which corresponds to approximately -0.5 kg m~2 in IWV).
    Geostationary satellites can observe upper tropospheric water vapour in cloud free areas.
    Timeseries analysis of the change in GPS IWV and change in upper tropospheric water vapour
    gives a rough estimate of the change in vertical water vapour distribution. A spectral analysis
    of timeseries of the residual signal of GPS zenith delay estimates shows that there is a relation
    between the power of the residual signal and Convective Available Potential Energy (CAPE)
    from radiosonde. A correlation of 0.6 is observed which is remarkable because the power of
    the residual is based on a timeseries of one hour of GPS residuals while CAPE is derived from
    atmospheric profile information.
    Real-time GPS IWV maps are constructed using a two-dimensional variational technique. These maps are validated against NWP analyses and forecast fields. The statistics show that the IWV maps are of good quality. Two thunderstorm cases show the applicability of these maps for nowcasting.
    A comparison study shows that slant delay estimates from GPS contain information with a three-dimensional character. This three-dimensional character is exploited further by assim¬ilating slant delay observations using a three-dimensional variational (3DVAR) scheme. The used GPS network had a horizontal resolution of approximately 100 km, which impaired the resolution of the analysed water vapour field. Nevertheless, when compared to independent ra¬diosonde observations, the bias of 3DVAR GPS was smaller than the NWP six hour forecasts.
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