Towards a definition of a crop wild relative

Crop wild relatives are an important socio-economic resource that is currently being eroded or even extinguished through careless human activities. If the Conference of the Parties (COP) to the CBD 2010 Biodiversity Target of achieving a significant reduction in the current rate of loss is to be achieved, we must first define what crop wild relatives are and how their conservation might be prioritised. A definition of a crop wild relative is proposed and illustrated in the light of previous Gene Pool concept theory. Where crossing and genetic diversity information is unavailable, the Taxon Group concept is introduced to assist recognition of the degree of crop wild relative relatedness by using the existing taxonomic hierarchy.     

Assignment of 3 genetic linkage groups to 3 chromosomes of narrow-leafed lupin

The legume genus, Lupinus, has many notable properties that make it interesting from a scientific perspective, including its basal position in the evolution of Papilionoid legumes. As the most economically important legume species, L. angustifolius L. (narrow-leafed lupin) has been subjected to much genetic analysis including linkage mapping and genomic library development. Cytogenetic analysis has been hindered by the large number of small morphologically uniform chromosomes (2n = 40). Here, we present a significant advance: the development of chromosome-specific cytogenetic markers and assignment of the first genetic linkage groups (LGs) to chromosomal maps of L. angustifolius using the bacterial artificial chromosome (BAC)-fluorescence in situ hybridization approach. Twelve clones produced single-locus signals that "landed" on 7 different chromosomes. Based on BAC-end sequences of those clones, genetic markers were generated. Eight clones localized on 3 chromosomes, allowed these chromosomes to be assigned to 3 LGs. An additional single-locus clone may be useful to combine an unassigned group (Cluster-2) with main LGs. This work provides a strong foundation for future identification of all chromosomes with specific markers and for complete integration of narrow-leafed lupin LGs. This resource will greatly facilitate the chromosome assignment and ordering of sequence contigs in sequencing the L. angustifolius genome.     

The western Mediterranean region provided the founder population of domesticated narrow-leafed lupin

Key message

This study revealed that the western Mediterranean provided the founder population for domesticated narrow-leafed lupin and that genetic diversity decreased significantly during narrow-leafed lupin domestication.

Abstract

The evolutionary history of plants during domestication profoundly shaped the genome structure and genetic diversity of today’s crops. Advances in next-generation sequencing technologies allow unprecedented opportunities to understand genome evolution in minor crops, which constitute the majority of plant domestications. A diverse set of 231 wild and domesticated narrow-leafed lupin (Lupinus angustifolius L.) accessions were subjected to genotyping-by-sequencing using diversity arrays technology. Phylogenetic, genome-wide divergence and linkage disequilibrium analyses were applied to identify the founder population of domesticated narrow-leafed lupin and the genome-wide effect of domestication on its genome. We found wild western Mediterranean population as the founder of domesticated narrow-leafed lupin. Domestication was associated with an almost threefold reduction in genome diversity in domesticated accessions compared to their wild relatives. Selective sweep analysis identified no significant footprints of selection around domestication loci. A genome-wide association study identified single nucleotide polymorphism markers associated with pod dehiscence. This new understanding of the genomic consequences of narrow-leafed lupin domestication along with molecular marker tools developed here will assist plant breeders more effectively access wild genetic diversity for crop improvement.

     

CWRML: representing crop wild relative conservation and use data in XML

Background  

Crop wild relatives are wild species that are closely related to crops. They are valuable as potential gene donors for crop improvement and may help to ensure food security for the future. However, they are becoming increasingly threatened in the wild and are inadequately conserved, both in situ and ex situ. Information about the conservation status and utilisation potential of crop wild relatives is diverse and dispersed, and no single agreed standard exists for representing such information; yet, this information is vital to ensure these species are effectively conserved and utilised. The European Community-funded project, European Crop Wild Relative Diversity Assessment and Conservation Forum, determined the minimum information requirements for the conservation and utilisation of crop wild relatives and created the Crop Wild Relative Information System, incorporating an eXtensible Markup Language (XML) schema to aid data sharing and exchange.     

Defining the landscape of adaptive genetic diversity

Whether they are used to describe fitness, genome architecture or the spatial distribution of environmental variables, the concept of a landscape has figured prominently in our collective reasoning. The tradition of landscapes in evolutionary biology is one of fitness mapped onto axes defined by phenotypes or molecular sequence states. The characteristics of these landscapes depend on natural selection, which is structured across both genomic and environmental landscapes, and thus, the bridge among differing uses of the landscape concept (i.e. metaphorically or literally) is that of an adaptive phenotype and its distribution across geographical landscapes in relation to selective pressures. One of the ultimate goals of evolutionary biology should thus be to construct fitness landscapes in geographical space. Natural plant populations are ideal systems with which to explore the feasibility of attaining this goal, because much is known about the quantitative genetic architecture of complex traits for many different plant species. What is less known are the molecular components of this architecture. In this issue of Molecular Ecology, Parchman et al. (2012) pioneer one of the first truly genome-wide association studies in a tree that moves us closer to this form of mechanistic understanding for an adaptive phenotype in natural populations of lodgepole pine (Pinus contorta Dougl. ex Loud.).     

Modelling root plasticity and response of narrow-leafed lupin to heterogeneous phosphorus supply

Background & Aims

Searching for root traits underpinning efficient nutrient acquisition has received increased attention in modern breeding programs aimed at improved crop productivity. Root models provide an opportunity to investigate root-soil interactions through representing the relationships between rooting traits and the non-uniform supply of soil resources. This study used simulation modelling to predict and identify phenotypic plasticity, root growth responses and phosphorus (P) use efficiency of contrasting Lupinus angustifolius genotypes to localised soil P in a glasshouse.

Methods

Two L. angustifolius genotypes with contrasting root systems were grown in cylindrical columns containing uniform soil with three P treatments (nil and 20 mg P kg^?1 either top-dressed or banded) in the glasshouse. Computer simulations were carried out with root architecture model ROOTMAP which was parameterized with root architectural data from an earlier published hydroponic phenotyping study.

Results

The experimental and simulated results showed that plants supplied with banded P had the largest root system and the greatest P-uptake efficiency. The P addition significantly stimulated root branching in the topsoil, whereas plants with nil P had relatively deeper roots. Genotype-dependent root growth plasticity in response to P supply was shown, with the greatest response to banded P.

Conclusions

Both experimental and simulation outcomes demonstrated that 1) root hairs and root proliferation increased plant P acquisition and were more beneficial in the localised P fertilisation scenario, 2) placing P deeper in the soil might be a more effective fertilisation method with greater P uptake than top dressing, and 3) the combination of P foraging strategies (including root architecture, root hairs and root growth plasticity) is important for efficient P acquisition from a localised source of fertiliser P.     

Risk of ectoparasitism and genetic diversity in a wild lesser kestrel population

Parasites and infectious diseases are major determinants of population dynamics and adaptive processes, imposing fitness costs to their hosts and promoting genetic variation in natural populations. In the present study, we evaluate the role of individual genetic diversity on risk of parasitism by feather lice Degeeriella rufa in a wild lesser kestrel population (Falco naumanni). Genetic diversity at 11 microsatellite loci was associated with risk of parasitism by feather lice, with more heterozygous individuals being less likely to be parasitized, and this effect was statistically independent of other nongenetic parameters (colony size, sex, location, and year) which were also associated with lice prevalence. This relationship was nonlinear, with low and consistent prevalences among individuals showing high levels of genetic diversity that increased markedly at low levels of individual heterozygosity. This result appeared to reflect a genome-wide effect, with no single locus contributing disproportionably to the observed effect. Thus, overall genetic variation, rather than linkage of markers to genes experiencing single-locus heterosis, seems to be the underlying mechanism determining the association between risk of parasitism and individual genetic diversity in the study host-parasite system. However, feather lice burden was not affected by individual heterozygosity; what suggest that differences in susceptibility, rather than variation in defences once the parasite has been established, may shape the observed pattern. Overall, our results highlight the role of individual genetic diversity on risk of parasitism in wild populations, what has both important evolutionary implications and major consequences for conservation research on the light of emerging infectious diseases that may endanger genetically depauperated populations.     

Construction of a genetic linkage map using MFLP and identification of molecular markers linked to domestication genes in narrow-leafed lupin (Lupinus angustifolius L.)

A mapping population of F(8)derived recombinant inbred lines (RILs) was established from a cross between a domesticated breeding line 83A:476 and a wild type P27255 in narrow-leaf lupin (Lupinus angustifolius L.). The parents together with the 89 RILs were subjected to DNA fingerprinting using microsatellite-anchored fragment length polymorphism (MFLP) to rapidly generate DNA markers to construct a linkage map. Five hundred and twenty two unique markers of which 21% were co-dominant, were generated and mapped. Phenotypic data for the domestication traits: mollis (soft seeds), leucospermus (white flower and seed colour); Lentus (reduced pod-shattering), iucundis (low alkaloid), Ku (early flowering) and moustache pattern on seed coats; were included. Three to 7 molecular markers were identified within 5 cM of each of these domestication genes. The anthracnose resistance gene Lanr1 was also mapped. Linkage groups were constructed using MapManager version QTXb20, resulting in 21 linkage groups consisting of 7 or more markers. The total map length was 1543 cM, with an average distance of 3.4 cM between adjacent markers. This is the first published map for a lupin species. The map can be exploited for marker assisted selection for genetic improvement in lupin breeding programs.     

Comparative assessment of genetic diversity in wild and primitive cultivated barley in a center of diversity

Wild barley (Hordeum spontaneum K.) and indigenous primitive varieties of cultivated barley (Hordeum vulgare L.), collected from 43 locations in four eastern Mediterranean countries, Jordan, Syria, Turkey and Greece, were electrophoretically assayed for genetic diversity at 16 isozyme loci. Contrary to a common impression, cultivated barley populations were found to maintain a level of diversity similar to that in its wild progenitor species. Apportionment of overall diversity in the region showed that in cultivated barley within-populations diversity was of higher magnitude than the between-populations component. Neighboring populations of wild and cultivated barleys showed high degree of genetic identity. Groups of 3 or 4 isozyme loci were analyzed to detect associations among loci. Multilocus associations of varying order were detected for all three groups chosen for the analysis. Some of the association terms differed between the two species in the region. Although there was no clear evidence for decrease in diversity attributable to the domestication of barley in the region, there was an indication of different multilocus organizations in the two closely related species.     

A global approach to crop wild relative conservation: securing the gene pool for food and agriculture

In light of the growing concern over the potentially devastating impacts on biodiversity and food security of climate change and the massively growing world population, taking action to conserve crop wild relatives (CWR), is no longer an option — it is a priority. Crop wild relatives are species closely related to crops, including their progenitors, many of which have the potential to contribute beneficial traits to crops, such as pest or disease resistance, yield improvement or stability. They are a critical component of plant genetic resources for food and agriculture (PGRFA), have already made major contributions to crop production and are vital for future food security; their systematic conservation in ways that ensure their continuing availability for use is therefore imperative. This is a complex, interdisciplinary, global issue that has been addressed by various national and international initiatives. Drawing on the lessons learnt from these initiatives we can now propose a global approach to CWR conservation, the key elements of which are: (1) estimating global CWR numbers, (2) assessment of the global importance of CWR diversity, (3) current conservation status, (4) threats to CWR diversity, (5) systematic approaches to CWR conservation, (6) CWR informatics, and (7) enhancing the use of CWR diversity.     

Colonization history and genetic diversity: adaptive potential in early stage invasions

The introduction of Anolis cristatellus from the multiple species anole community of Puerto Rico in the Greater Antilles to the island of Dominica in the Lesser Antilles, with its solitary endemic anole, provides an example of a very recent, timed, single colonization. We investigate the geographic origin and adaptive potential of the Dominican population using a range of methods including mtDNA phylogeography, nuclear microsatellite variation and multiple paternity studies, as well as heritability estimates, common garden experiments and comparative geographic studies of quantitative scalation traits. Phylogeographic analysis of NADH2 and microsatellite studies suggests that the Dominican population arose from a set of individuals from the central west area of Puerto Rico within their endemic range. The multiple‐individual inoculation, together with sperm storage and evidence of multiple paternity indicate genetic variability and suggest the potential for adaptation by natural selection. Estimates of heritability, common garden experiments and broad sense Q_ST/F_ST ratios, linked to replicated comparisons along elevational transects go some way to suggesting that the invasive populations may be adapting by natural selection, in parallel with the endemic anole, in the brief period since their introduction.     

iPBS-Retrotransposons-based genetic diversity and relationship among wild annual Cicer species

Lack of requisite genetic variation in cultivated species has necessitated systematic collection, documentation and evaluation of wild Cicer species for use in chickpea variety improvement programs. Cicer arietinum has very narrow genetic variation, and the use of a wild relative in chickpea breeding could provide a good opportunity for increasing the available genetic variation of cultivated chickpea. Genetic diversity and the relationship of 71 accessions, from the core area of chickpea origin and domestication (Southeastern Turkey), belonging to five wild annual species and one cultivated species (Cicer arietinum) were analysed using iPBS-retrotransposon and ISSR markers. A total of 136 scorable bands were detected using 10 ISSR primers among 71 accessions belonging to 6 species, out of which 135 were polymorphic (99.3 %), with an average of 13.5 polymorphic fragments per primer, whereas iPBS detected 130 bands with 100 % polymorphism with an average of 13.0 bands per primer. C. echinospermum and C. pinnatifidum were the most diverse among species, whereas C. arietinum exhibited lower polymorphism. The average polymorphism information contents (PIC) value for both marker systems was 0.91. The clustering of the accessions and species within groups was almost similar, when iPBS and ISSR NeighborNet (NNet) planar graphs were compared. Further detailed studies are indispensable in order to collect Cicer germplasm, especially C. reticulatum, from southeastern Turkey particularly, from Karacada? Mountain for preservation, management of this species, and to study their genetic diversity at molecular level. This study also demonstrates the utility and role of iPBS-retrotransposons, a dominant and ubiquitous part of eukaryotic genomes, for diversity studies in wild chickpea and in cultivated chickpea.     

Simple sequence repeat marker diversity in cassava landraces: genetic diversity and differentiation in an asexually propagated crop

Cassava (Manihot esculenta) is an allogamous, vegetatively propagated, Neotropical crop that is also widely grown in tropical Africa and Southeast Asia. To elucidate genetic diversity and differentiation in the crop's primary and secondary centers of diversity, and the forces shaping them, SSR marker variation was assessed at 67 loci in 283 accessions of cassava landraces from Africa (Tanzania and Nigeria) and the Neotropics (Brazil, Colombia, Peru, Venezuela, Guatemala, Mexico and Argentina). Average gene diversity (i.e., genetic diversity) was high in all countries, with an average heterozygosity of 0.5358 ± 0.1184. Although the highest was found in Brazilian and Colombian accessions, genetic diversity in Neotropical and African materials is comparable. Despite the low level of differentiation [F_st(theta) = 0.091 ± 0.005] found among country samples, sufficient genetic distance (1-proportion of shared alleles) existed between individual genotypes to separate African from Neotropical accessions and to reveal a more pronounced substructure in the African landraces. Forces shaping differences in allele frequency at SSR loci and possibly counterbalancing successive founder effects involve probably spontaneous recombination, as assessed by parent-offspring relationships, and farmer-selection for adaptation.Communicated by H.C. Becker     

Allozyme diversity in wild Phaseolus vulgaris: further evidence for two major centers of genetic diversity

Summary Allozyme analysis was performed on 83 wild Phaseolus vulgaris accessions, representing a wide geographical distribution from Mesoamerica to Argentina, to determine levels of genetic diversity and geographic patterns of variability at nine polymorphic isozyme loci. The collection can be divided into two major groups, one consisting of accessions from Mexico, Central America, Colombia and Peru, and the other consisting of accessions from Peru and Argentina. One accession from northern Peru is distinct from the two major groups, and may delineate a transition zone between the two divergent groups. The level of genetic diversity within wild P. vulgaris (Ht=0.132) is comparable with those found in other Phaseolus species. There was no significant within-accession gene diversity (Hs=0.006); however, there is a moderate level of genetic diversity (Dst=0.126) between accessions. Our results are consistent with previous studies on the genetic diversity of wild P. vulgaris using phaseolin, the major seed storage protein of beans.     

Novel adenoviruses in wild primates: a high level of genetic diversity and evidence of zoonotic transmissions

Adenoviruses (AdVs) broadly infect vertebrate hosts, including a variety of nonhuman primates (NHPs). In the present study, we identified AdVs in NHPs living in their natural habitats, and through the combination of phylogenetic analyses and information on the habitats and epidemiological settings, we detected possible horizontal transmission events between NHPs and humans. Wild NHPs were analyzed with a pan-primate AdV-specific PCR using a degenerate nested primer set that targets the highly conserved adenovirus DNA polymerase gene. A plethora of novel AdV sequences were identified, representing at least 45 distinct AdVs. From the AdV-positive individuals, 29 nearly complete hexon genes were amplified and, based on phylogenetic analysis, tentatively allocated to all known human AdV species (Human adenovirus A to Human adenovirus G [HAdV-A to -G]) as well as to the only simian AdV species (Simian adenovirus A [SAdV-A]). Interestingly, five of the AdVs detected in great apes grouped into the HAdV-A, HAdV-D, HAdV-F, or SAdV-A clade. Furthermore, we report the first detection of AdVs in New World monkeys, clustering at the base of the primate AdV evolutionary tree. Most notably, six chimpanzee AdVs of species HAdV-A to HAdV-F revealed a remarkably close relationship to human AdVs, possibly indicating recent interspecies transmission events.     

Evidence of parasite-mediated disruptive selection on genetic diversity in a wild fish population

Identifying the processes maintaining genetic variability in wild populations is a major concern in conservation and evolutionary biology. Parasite-mediated selection may strongly affect genetic variability in wild populations. The inbreeding depression theory predicts that directional selection imposed by parasites should act against the most inbred hosts, thus favouring genetic diversity in wild populations. We have tested this prediction by evaluating the strength and shape of the relationship between the load of a harmful fin-feeder ectoparasite ( Tracheliastes polycolpus ) and the genome-wide genetic diversity (i.e. heterozygosity measured at a set of 15 microsatellites) of its fish host, the rostrum dace ( Leuciscus leuciscus ). Contrary to expectation, we found a nonlinear relationship between host genetic diversity and ectoparasite load, with hosts that were either homozygous or heterozygous harbouring significantly fewer parasites than hosts with an intermediate level of heterozygosity. This relationship suggests that parasites could increase the variance of global heterozygosity in this host population through disruptive selection on genetic diversity. Moreover, when genetic diversity was measured at each locus separately, we found two very strong positive associations between host genetic diversity and the ectoparasite load. This latter result has three main implications: (i) genome-wide effect cannot alone explain the nonlinear relationship between global heterozygosity and ectoparasite load, (ii) negative non-additive allelic interactions (i.e. underdominance) may be a mechanism for resisting ectoparasite infection, and (iii) ectoparasites may favour homozygosity at some loci in this host population.     

The genetic diversity of annual wild soybeans grown in China

Annual wild soybeans (Glycine soja), the ancestors of cultivated soybeans (G. max), are important sources of major genes for resistance to pests, diseases and environmental stresses. The study of their genetic diversity is invaluable for efficient utilization, conservation and management of germplasm collections. In this paper, the number of accessions, the variation of traits, the genetic diversity indexes (Shannon index) and the coefficient of variation were employed to study the geographical distribution of accessions, genetic diversity of characters and genetic diversity centers of annual wild soybean by statistical analysis of the database from the National Germplasm Evaluation Program of China. Most annual wild soybeans are distributed in Northeast China, and the number of accessions decreases from the Northeast to other directions in China. The genetic diversity indexes (Shannon index) were 0.49, 0.74, 0.02, 0.55, 1.45, 2.41, 1.27 and 1.89 for flower color, sootiness of seed coat, cotyledon color, pubescence color, hilum color, leaf shape, stem type and seed color, respectively. Coefficients of variation were 7.1%, 28.7%, 76.43% and 18.2% for protein content, oil content, 100-seed weight and days to maturity, respectively. Three genetic diversity centers, the Northeast, the Yellow River Valley and the Southeast Coasts of China, are proposed based on the geographical distribution of the number of accessions, genetic diversity and the multivariate variation coefficient. Based on these results and Vavilov’s theory of crop origination, two opposing possible models for the formation of the three centers are proposed, either these centers are independent of each other and the annual wild soybeans in these centers originated separately, or the Northeast center was the primary center for annual wild soybeans in China, while the Yellow River Valley center was derived from this primary center and served as the origin for the Southeast Coast center. Received: 25 June 2000 / Accepted: 18 October 2000     

Capturing cold-stress-related sequence diversity from a wild relative of common bean (Phaseolus angustissimus)

One restriction to the cultivation of common bean, Phaseolus vulgaris L., is its limited tolerance to low temperatures. In the present study, subtraction suppression hybridization was employed to enrich for stress responsive genes in both a chilling-susceptible common bean and a relatively more chilling-tolerant wild bean species, Phaseolus angustissimus. For each species, approximately 11 000 expressed sequence tags were generated. Comparative sequence analysis of the EST collection with the available annotated genome sequences of the model Fabaceae species Medicago truncatula and Glycine max identified protein homologues for approximately 65% and 80% of the Phaseolus sequences, respectively. This difference reflects the closer phylogenetic relationship between the genera Phaseolus and Glycine compared with Medicago. Annotation of the Phaseolus sequences was facilitated through this comparative analysis and indicated that several heat shock proteins, cytochrome P450s, and DNA binding factors were uniquely found among the sequences from the wild species P. angustissimus. The Phaseolus sequences have been made available on a GBrowse implementation using M. truncatula as the reference genome, providing rapid access to the sequence data and associated comparative genome data.     

Geographical approaches to crop conservation: The partitioning of genetic diversity in andean potatoes

The geographical concepts of spatial scale and the human-geographic region offer significant contributions to the conservation of crop genetic resources. They are used in the present study to examine the partitioning of genetic diversity along two axes: geographical location and landrace population. Locations in the study consist of three micro-regions within the highland Paucartambo region of southern Peru. Six widely distributed landraces of the potato species Solatium stenotomum Juz. et Buk. and S. tuberosum subsp. andigena (Juz. et Buk.) Hawkes are evaluated. Electrophoretic analysis of isozyme loci demonstrates that the majority of allelic variation is contained within the geographical and landrace populations. Geographically, greater than 99% of total variation is found within single micro-regions. Taxonomically, approximately 75% of variation occurs within individual landraces. The weak geographical partitioning of allelic variation is due in part to formerly high rates of seed-tuber exchange. The weak-moderate taxonomic partitioning of variation is attributed to common parentage and shared introgression. Unique genotypes are microgeographically concentrated. Findings recommend that conservation strategies focus on intensive sampling or preservation in micro-regional areas due to the concentration of unique genotypes. Evaluation of the spatial patterning of diversity and recognition of the taxonomic specificity of results (not necessarily applicable even to related potato landraces) rely on biogeographical and human-geographic concepts.