Cultivating participatory policy processes for genetic resources policy: lessons from the Genetic Resources Policy Initiative (GRPI) project

The purpose of the paper is to draw lessons and document experiences from the Genetic Resources Policy Initiative (GRPI) project, a project which has been underway in six countries and two sub-regions during the last 5 years. Its focus has been to experiment an approach to participatory policy processes, coined by the project, called the multi-stakeholder, multi-disciplinary and multi-sector or in short the 3M. This approach, which was demand-driven due to the nature of the policy problems being examined, aims to create a platform to address competing interests inherent in genetic resources issues from multiple perspectives. It is meant to enable different stakeholders to balance issues they diverge and/or converge upon in genetic resources management, thereby harmonizing trade-offs, objectives and strategies. Experiences from the project in applying the 3M in Egypt, Nepal, Vietnam Peru and Zambia highlight several lessons in participatory policy processes. The experiences show that the success or otherwise of participatory policy making processes is dependent on various factors that have to do with stakeholder capacities, process orientation, shared understanding versus vested interests and institutional functions. They highlight that the most effective approach to stakeholder engagement in policy processes is to construct them around an actively engaged ‘process leader’ that possesses, or has the potential to champion the process by mobilising the required cognitive knowledge and institutional engagement. They further suggest that since genetic resources policy issues are cross-cutting, they will demand a more holistic approach with a clear identification of impact pathways through which policy changes can be expected to influence the outcome variables. Since policy making processes are perpetual, the question of sustaining project ideas and recommendations beyond the life of a project has to be part of the planning exercise in any participatory genetic resources policy research and formulation.

Discursive Shifts in Dutch River Management: ‘Deep’ Institutional Change or Adaptation Strategy?

This paper argues that a discursive shift is taking place in Dutch water policy, from ‘a battle against water’ to ‘living with water’ or ‘accommodating water’. Yet we ask ourselves whether this shift is just an adaptation strategy of the existing elite group of water managers, who pay lip-service to new management approaches in order to maintain their vested interests, as some authors claim, or whether it implies ‘deep’ institutional change, e.g. in terms of the emergence of new water institutions, power relations and procedures. While investigating this question, we make use of the ‘policy arrangement approach’, which pays attention to institutional and discursive aspects of policy making alike. Our conclusion is that we are currently observing institutional changes beyond ‘policy talk’, particularly in terms of new legislation and procedures. However, it is too early to speak of ‘deep’ institutional change in Dutch water management, because the former water institutions are still maintaining their power positions, despite the availability of additional resources for policy and research as well as the emergence of several new modes of governance.     

Assaying polymorphism at DNA level for genetic diversity diagnostics of the safflower (Carthamus tinctorius L.) world germplasm resources

Carthamus tinctorius (2n = 2x = 24), commonly known as safflower, is widely cultivated in agricultural production systems of Asia, Europe, Australia, and the Americas as a source of high quality vegetable and industrial oil. Twenty-two RAPD primers, 18 SSR primers, and 10 AFLP primer combinations were used to assess: (1) the genetic diversity of 85 accessions (originating from 24 countries) representing global germplasm variability of safflower and (2) the interrelationships among safflower ‘centers of similarity’ or ‘regional gene pools’ proposed earlier. The RAPD and SSR primers and AFLP primer combinations revealed 57.6, 68.0, and 71.2% polymorphism, respectively, among 111, 72, and 330 genetic loci amplified from the accessions. The sum of effective number of alleles (66.44), resolving power (59.16), and marker index (51.3) explicitly revealed the relative superiority of AFLP as a marker system in uncovering variation in safflower. Overall, AFLP markers could recognize ‘centers of similarity’ or ‘regional gene pools’. Analysis of molecular variance and Shannon’s information index provided corroborating evidences for the present and previous studies that concluded fragmentation of safflower gene pool into many gene pools. Divergent directional selection is likely to have played an important role in shaping the diversity. From the practical applications standpoint, the diversity of Iran–Afghanistan gene pool is very high, equivalent to the total diversity of the species. The Far East gene pool is the least diverse. The present comprehensive input, first of its own kind in safflower, will assist marker based improvement programmes in the crop.     

Genetic variability and structure of natural and domesticated populations of Caribbean pine (Pinus caribaea Morelet)

 Isozyme analysis of seed samples derived from natural and managed populations of the tropical pine Pinus caribaea vars ‘bahamensis’ and ‘caribaea’ was used to assess population genetic structure in its native range and to detect changes occurring during early domestication of the species. Baseline data from natural populations of the two varieties showed that populations sampled as seed are characterized by high gene diversity (mean H_e=0.26) and a low level of inbreeding ( mean F_is=0.15). A UPGMA tree of genetic relatedness among populations indicates that the two varieties represent distinct evolutionary units. Within each variety there is significant differentiation among populations, and this is greater for the more fragmented populations of var ‘bahamensis’ (F_st=0.08) than for var ‘caribaea’ (F_st=0.02). Seed from a seed orchard population of var ‘caribaea’ established within its natural range showed no change in genetic diversity but did show a reduced inbreeding coefficient (F_is=0.09) compared with its progenitor populations, suggesting a decrease in selfing and/or biparental inbreeding. A bulked seed sample from an exotic plantation of var ‘bahamensis’ in Australia displayed a large increase in the inbreeding coefficient (F_is=0.324) compared with that found in natural populations, possibly due to elevated self-fertilization. Finally, a bulked seed sample from an exotic plantation population of var ‘caribaea’ from China showed enhanced genetic diversity, an increase in the inbreeding coefficient and more linkage disequilibrium than its presumed progenitor populations. It was also genetically divergent from them. RFLP analysis of chloroplast DNA variation in the Chinese sample suggested that seeds of the related taxa P. elliottii and P. taeda, or seeds derived from hybridization with these taxa growing in the seed production area, had been included in the seed crop during harvesting. We conclude that monitoring of appropriate genetic markers may be an effective means of identifying potentially deleterious genetic changes occurring during forest tree domestication. Received: 10 August 1998 / Accepted: 8 September 1998     

Construction of a dense genetic linkage map for apple rootstocks using SSRs developed from Malus ESTs and Pyrus genomic sequences

Marker-assisted selection (MAS) offers quick and reliable prediction of the phenotypes of seedlings in large populations and thus opens new approaches for selection to breeders of apple (Malus x domestica Borkh.). The development of framework maps enables the discovery of genetic markers linked to desired traits. Although genetic maps have been reported for apple scion cultivars, none has previously been constructed for apple rootstocks. We report the construction of framework genetic maps in a cross between ‘M.9’ (‘Malling 9’) and ‘R.5’ (‘Robusta 5’) apple rootstocks. The maps comprise 224 simple sequence repeat (SSR) markers, 18 sequence-characterised amplified regions, 14 single nucleotide polymorphisms and 42 random amplified polymorphic DNAs. A new set of 47 polymorphic SSRs was developed from apple EST sequences and used for construction of this rootstock map. All 17 linkage groups have been identified and aligned to existing apple genetic maps. The maps span 1,175.7 cM (‘M.9’) and 1,086.7 cM (‘R.5’). To improve the efficiency of mapping markers to this framework map, we developed a bin mapping set. Applications of these new genetic maps include the elucidation of the genetic basis of the dwarfing effect of the apple rootstock ‘M.9’ and the analysis of disease and insect resistance traits such as fire blight (Erwinia amylovora), apple scab (Venturia inaequalis) and woolly apple aphid (Eriosoma lanigerum). Markers for traits mapped in this population will be of direct use to apple breeders for MAS and for identification of causative genes by map-based cloning.     

Classification of rice germplasm: III. High-resolution fingerprinting of cytoplasmic genetic male-sterile (CMS) lines with AFLP

 The cytoplasmic genetic male-sterile (CMS) lines developed at the International Rice Research Institute are valuable in producing tropical rice hybrids. Efficient use of CMS lines in hybrid rice production will depend on their level of genetic diversity. Aside from morphological characterization, molecular analysis based on DNA markers can provide information on the genetic diversity of the germplasm. The Amplified Fragment Length Polymorphism (AFLP) technique was used to fingerprint 71 CMS lines and four rice cultivars, ‘IR64’, ‘Azucena’, ‘IR74’, and ‘FR13A’. Eleven primer pair combinations specific to the enzymes PstI and MseI were used to generate 530 AFLP markers, 176 of which were polymorphic. Each CMS line revealed a distinct fingerprint. The AFLP marker-based dendrogram depicted genetic variation among the CMS lines. The CMS lines developed in japonica background grouped with ‘Azucena’, a japonica cultivar. None of the CMS lines clustered with ‘FR13A’, a flood-tolerant traditional indica variety. ‘IR64’ was found to be distinct from the other indica CMS lines and clustered with lines developed in its background. The grouping of CMS lines into a few groups is useful for breeders in selecting genetically diverse CMS lines for hybrid rice production and in avoiding test crossing every CMS line empirically. This study demonstrated that AFLP is a powerful and reliable tool in determining the genetic relationships and in producing distinct fingerprints of rice cultivars. Received: 20 December 1996 / Accepted: 9 October 1997     

Songbird genetic diversity is lower in anthropogenically versus naturally fragmented landscapes

Natural habitats, and the populations they sustain, are becoming increasingly fragmented by human activities. Parallels between ‘true’ islands and ‘habitat’ islands suggest that standing levels of individual genetic diversity in naturally fragmented populations may predict the genetic fate of their anthropogenically fragmented counterparts, but this hypothesis remains largely untested. We compared neutral-locus genetic diversity of individual song sparrows (Melospiza melodia) breeding in a naturally fragmented landscape (small coastal islands) to that of song sparrows in similar-sized ‘urban islands’ separated by roads and housing developments rather than by water. Individuals on coastal islands were more heterozygous and less inbred than those in urban islands. Estimates of population genetic structuring (assessed by pairwise genetic differentiation and Bayesian clustering methods) and contemporary dispersal (based on assignment tests) revealed little structure within either landscape, suggesting that lack of connectivity at the geographic scale we investigated cannot explain the reduced heterozygosity of urban birds. However, within-site genetic similarity was higher in the urban than the coastal landscape. Assuming that historic genetic diversity was similar in these two environments, our findings suggest that anthropogenically fragmented populations may lose genetic diversity faster than their naturally fragmented counterparts.     

Casares’ map function: no need for a ‘corrected’ Haldane’s map function

A genetic map function M(d) = RF provides a mapping from the additive genetic distance d to the non-additive recombination fraction RF between a given pair of loci, where the recombination fraction is the proportion of gametes that are recombinant between the two loci. Genetic map functions are needed because in most experiments all we can directly observe are the recombination events. However, since a recombination event is only observed if there are an odd number of crossovers between the two loci, recombination fractions are not additive. One of the most widely used map functions is Haldane’s map function, which is derived under the assumptions of no chiasma and no chromatid interference, and has been in widespread use since 1919. However, Casares recently proposed a ‘corrected’ Haldane’s map function – we show here that this ‘corrected’ map function is not correct due to faulty assumptions and mistakes in its derivation.     

Microsatellite diversity in tetraploid <Emphasis Type="Italic">Gossypium</Emphasis> germplasm: assembling a highly informative genotyping set of cotton SSRs

A series of 320 mapped simple sequence repeats (SSRs) have been used to screen the allelic diversity of tetraploid Gossypium species. Fourty-seven genotypes were analyzed representing (i) the wide spectrum of diversity of the cultivated pool and of the primitive landraces of species G. hirsutum (‘marie-galante’, ‘punctatum’, ‘richmondi’, ‘morrilli’, ‘palmeri’, and ‘latifolium’, and ‘yucatanense’), and (ii) species G. barbadense, G. darwinii and G. tomentosum. The polymorphism of 201 SSR loci revealed 1128 allelic variants ranging from 3 to 17 per locus. Neighbor-joining (NJ) method based on genetic dissimilarities produced groupings consistent with the assignments of accessions both at species and at race level. Our data confirmed the proximity of the Galapagos endemic species G. darwinii to species G. barbadense. Within species G. hirsutum, and as compared to the other 6 races, race yucatanense appeared as the most distant from cultivated genotypes. Race yucatanense also exhibited the highest number of unique alleles. The important informative heterogeneity of the 201 SSR loci was exploited to select the most polymorphic ones that were assembled into three series of genome-wide (i.e. each homoeologous AD chromosome pair being equally represented) and mutliplexable (× 3) SSRs. Using one of these ‘genotyping set’, consisting of 39 SSRs (one 3-plex for each of the 13 AD chromosomes pairs) or 45 loci, we were able to assess the relationships between accessions and the topology in the genetic diversity sampled. Such genotyping set of highly informative SSR markers assembled in PCR-multiplex, while increasing genotyping throughput, will be applicable for molecular genetic diversity studies of large germplasm collections. Electronic Supplementary Material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

A parentage study of closely related Ukrainian wine grape varieties using microsatellite markers

Four bred grapevine varieties released for commercial cultivation in Ukraine, namely ‘Antey Magarachskii’, ‘Rubinovyi Magaracha’, ‘Granatovyi Magaracha’ and ‘Rubin Golodrigi’, and their putative parental forms were genotyped using six microsatellite loci. Genotypes were compared with breeding records to verify genetic relationships among varieties. Results of the analysis confirmed four of six parent-offspring relationships. Results of the analysis allow to assume that genotype ‘Seyve Villard 20347’ is the direct parent of ‘Antey Magarachskii’ instead of its grandparent. The first-studied accession believed to be that of ‘Granatovyi Magaracha’ was identified as impurity. In order to verify the parentage of ‘Granatovyi Magaracha’, rest accessions of that variety and its putative parent ‘Antey Magarachskii’ were additionally genotyped at 13 nuclear loci and at three chloroplast loci. The parent-offspring relationship was confirmed, as all ‘Granatovyi Magaracha’ accessions had a common allele with the parent variety ‘Antey Magarachskii’ at each locus and the same chlorotype A. Different ‘Granatovyi Magaracha’ accessions could have been obtained via vegetative propagation of two seedlings which arose from one crossing.     

Genetic diversity amongst landraces of a dioecious vegetatively propagated plant,betelvine (<Emphasis Type="Italic">Piper betle</Emphasis> L.)

Betelvine (Piper betle L., family Piperaceae) is an important, traditional and widely cultivated crop of India. The cultivators and consumers recognize more than 100 cultivars (landraces) based on regional and organoleptic considerations, while in terms of phytochemical constituents only five groups have been identified for all the landraces. Since betelvine is an obligate vegetatively propagated species, genomic changes, if any, may have become ‘fixed’ in the landraces. We carried out random amplified polymorphic DNA (RAPD) analysis in several landraces considered in four groups, namely, ‘Kapoori’, ‘Bangla’, ‘Sanchi’ and ‘Others’ in order to ascertain their genetic diversity. On the basis of the data from eleven RAPD primers, we distinguished genetic variation within and among the four groups of landraces. The results indicate the’Kapoori’ group is the most diverse. The neighbour joining (NJ) tree after a bootstrap (500 replicate) test of robustness clearly shows the four groups to be well separated. Interestingly, all known male or female betelvine landraces have separated in the NJ tree indicating an apparent gender-based distinction among the betelvines.     

Using a limited mapping strategy to identify major QTLs for resistance to grapevine powdery mildew (<Emphasis Type="Italic">Erysiphe necator</Emphasis>) and their use in marker-assisted breeding

A limited genetic mapping strategy based on simple sequence repeat (SSR) marker data was used with five grape populations segregating for powdery mildew (Erysiphe necator) resistance in an effort to develop genetic markers from multiple sources and enable the pyramiding of resistance loci. Three populations derived their resistance from Muscadinia rotundifolia ‘Magnolia’. The first population (06708) had 97 progeny and was screened with 137 SSR markers from seven chromosomes (4, 7, 9, 12, 13, 15, and 18) that have been reported to be associated with powdery or downy mildew resistance. A genetic map was constructed using the pseudo-testcross strategy and QTL analysis was carried out. Only markers from chromosome 13 and 18 were mapped in the second (04327) and third (06712) populations, which had 47 and 80 progeny, respectively. Significant QTLs for powdery mildew resistance with overlapping genomic regions were identified for different tissue types (leaf, stem, rachis, and berry) on chromosome 18, which distinguishes the resistance in ‘Magnolia’ from that present in other accessions of M. rotundifolia and controlled by the Run1 gene on chromosome 12. The ‘Magnolia’ resistance locus was termed as Run2.1. Powdery mildew resistance was also mapped in a fourth population (08391), which had 255 progeny and resistance from M. rotundifolia ‘Trayshed’. A locus accounting for 50% of the phenotypic variation mapped to chromosome 18 and was named Run2.2. This locus overlapped the region found in the ‘Magnolia’-based populations, but the allele sizes of the flanking markers were different. ‘Trayshed’ and ‘Magnolia’ shared at least one allele for 68% of the tested markers, but alleles of the other 32% of the markers were not shared indicating that the two M. rotundifolia selections were very different. The last population, 08306 with 42 progeny, derived its resistance from a selection Vitis romanetii C166-043. Genetic mapping discovered a major powdery mildew resistance locus termed Ren4 on chromosome 18, which explained 70% of the phenotypic variation in the same region of chromosome 18 found in the two M. rotundifolia resistant accessions. The mapping results indicate that powdery mildew resistance genes from different backgrounds reside on chromosome 18, and that genetic markers can be used as a powerful tool to pyramid these loci and other powdery mildew resistance loci into a single line.     

Biocultural Diversity: Moving Beyond the Realm of ‘Indigenous’ and ‘Local’ People

During the past decade the relationship between biodiversity and human diversity has received increased attention, resulting in the identification of what the Declaration of Belém calls an ‘inextricable link’ between biological and cultural diversity. Although the term biocultural diversity, introduced to denote this link, is being used increasingly, there has been little critical reflection on what it precisely refers to. I argue that it is used with particular reference to ‘indigenous traditional’ people, but that there is scope for extending its application within biocultural discourse. I therefore review the concept of culture and discuss what constitutes cultural values of the natural environment. I conclude that the concept of culture must be understood as involving a dynamic process of transcultural exchange and constant re-articulations of tradition resulting in the persistence of certain cultural practices. This approach ultimately reveals that the concept of biocultural diversity is also applicable to non-indigenous traditional communities.     

AFLP analysis of nephthytis (Syngonium podophyllum Schott) selected from somaclonal variants

This study analyzed genetic differences of 19 cultivars selected from somaclonal variants of Syngonium podophyllum Schott along with their parents as well as seven additional Syngonium species and six other aroids using amplified fragment length polymorphism (AFLP) markers generated by 12 primer sets. Among the 19 somaclonal cultivars, ‘Pink Allusion’ was selected from ‘White Butterfly’. Tissue culture of ‘Pink Allusion’ through organogenesis resulted in the development of 13 additional cultivars. Self-pollination of ‘Pink Allusion’ obtained a cultivar, ‘Regina Red Allusion’, and tissue culture propagation of ‘Regina Red Allusion’ led to the release of five other cultivars. The 12 primer sets generated a total of 1,583 scorable fragments from all accessions, of which 1,284 were polymorphic (81.9%). The percentages of polymorphic fragments within ‘White Butterfly’ and ‘Regina Red Allusion’ groups, however, were only 1.2% and 0.4%, respectively. Jaccard's similarity coefficients among somaclonal cultivars derived from ‘White Butterfly’ and ‘Regina Red Allusion’, on average, were 0.98 and 0.99, respectively. Seven out of the 15 cultivars from the ‘White Butterfly’ group and three out of six from the ‘Regina Red Allusion’ group were clearly distinguished by AFLP analysis as unique fragments were associated with respective cultivars. The unsuccessful attempt to distinguish the remaining eight cultivars from the ‘White Butterfly’ group and three from the ‘Regina Red Allusion’ group was not attributed to experimental errors or the number of primer sets used; rather it is hypothesized to be caused by DNA methylation and/or some rare mutations. This study also calls for increased genetic diversity of cultivated Syngonium as they are largely derived from somaclonal variants.     

Genetic diversity of globe artichoke landraces from Sicilian small-holdings: implications for evolution and domestication of the species

Globe artichoke (Cynara cardunculus var. scolymus) is native to the Mediterranean Basin, where it grows in close proximity with its ancestor wild cardoon (C. cardunculus var. sylvestris); its commercial production is mainly based on vegetatively propagated clones which guarantee high yields of marketable product (i.e. immature inflorescence or capitula). A collection of 24 landraces of globe artichoke was made from small-holdings in Sicily, which is assumed to be one of the possible centres of its domestication. These landraces have been cultivated for centuries by local farmers, mainly due to their culinary uniqueness. The collection was characterised for a combination of morphological traits and AFLP, gSSR and cpSSr markers. Molecular analyses included genotypes of wild cardoon collected from different sites in Sicily as well as accessions of the most widely grown Sicilian varietal types: the spiny ‘Spinoso di Palermo’ and the non-spiny ‘Violetto di Sicilia’. The landraces follow a gradient of ‘ennoblement’ towards either the domesticated spiny or the non-spiny types. ‘Cimiciusa di Mazzarino’ was an outlier, in that it resembled the cultivated forms with respect to its AFLP fingerprint, but was more closely related to the wild cardoon on the basis of SSR profile. This particular landrace presents an example of an intermediary form in the domestication process, although it could also have derived from introgression from sympatric wild cardoon, followed by farmer selection. The abundant genetic variation present demonstrates the key role of farmers’ practice in the maintenance of genetic diversity, which should be preserved because of its potential value for plant breeders.     

Are all genes regulatory genes?

Although much has been learned about hereditary mechanisms since Gregor Mendel’s famous experiments, gene concepts have always remained vague, notwithstanding their central role in biology. During over hundred years of genetic research, gene concepts have often and dynamically changed to accommodate novel experimental findings, without ever providing a generally accepted definition of the ‘gene.’ Yet, the distinction between ‘regulatory genes’ and ‘structural genes’ has remained a common theme in modern gene concepts since the definition of the operon-model. This distinction is now challenged by recent findings which suggest that, at least in eukaryotes, structural genes may in many situations have a regulatory function that is independent of the function of the gene product (protein or non-coding RNA molecule). This brief paper discusses these new findings and some possible implications for the notion of the ‘regulatory gene.’     

Subtle ‘boom and bust’ response of <Emphasis Type="Italic">Macquaria ambigua</Emphasis> to flooding in an Australian dryland river

The ecology of dryland rivers is driven by their highly variable hydrology, particularly flooding regimes, whereby intermittent floods typically generate ‘booms’ of primary and secondary productivity, including massive fish production. We tested these concepts in the Moonie River, Australia, using the percichthyid, Macquaria ambigua, a dryland river species known to display pronounced ‘boom and bust’ abundance patterns in response to floodplain inundation followed by extended periods of low to no channel flow. We expected that body condition (as measured by whole body lipid content) and biomass of M. ambigua would be related to prey biomass, and that these factors would all ‘spike’ following widespread flooding. Instead we found more subtle responses. There were ‘booms’ in biomass of Macrobrachium and zooplankton, two important food items, whereas M. ambigua maintained relatively low but sustained lipid and biomass levels following flooding. It appears that instead of a ‘boom’ in fish biomass, abundant invertebrate food resources and sustained lipid levels contributed to high survivorship of this species during the ‘bust’ period over cool dry months.     

Condition-dependence, genotype-by-environment interactions and the lek paradox

The lek paradox states that maintaining genetic variation necessary for ‘indirect benefit’ models of female choice is difficult, and two interrelated solutions have been proposed. ‘Genic capture’ assumes condition-dependence of sexual traits, while genotype-by-environment interactions (GEIs) offer an additional way to maintain diversity. However, condition-dependence, particularly with GEIs, implies that environmental variation can blur the relationship between male displays and offspring fitness. These issues have been treated separately in the past. Here we combine them in a population genetic model, and show that predictions change not only in magnitude but also in direction when the timing of dispersal between environments relative to the life cycle is changed. GEIs can dramatically improve the evolution of costly female preferences, but also hamper it if much dispersal occurs between the life history stage where condition is determined and mating. This situation also arises if selection or mutation rates are too high. In general, our results highlight that when evaluating any mechanism promoted as a potential resolution of the lek paradox, it is not sufficient to focus on its effects on genetic variation. It also has to be assessed to what extent the proposed mechanism blurs the association between male attractiveness and offspring fitness; the net balance of these two effects can be positive or negative, and often strongly context-dependent.