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.     

Climate drives global soil carbon sequestration and crop yield changes under conservation agriculture

Conservation agriculture has been shown to have multiple benefits for soils, crop yield and the environment, and consequently, no‐till, the central practice of conservation agriculture, has rapidly expanded. However, studies show that the potential for carbon (C) sequestration in no‐till farming sometimes is not realized, let alone the ability to maintain or improve crop yield. Here we present a global analysis of no‐till‐induced changes of soil C and crop yield based on 260 and 1,970 paired studies; respectively. We show that, relative to local conventional tillage, arid regions can benefit the most from conservation agriculture by achieving a win‐win outcome of enhanced C sequestration and increased crop yield. However, more humid regions are more likely to increase SOC only, while some colder regions have yield losses and soil C loss as likely as soil C gains. In addition to site‐specific characteristics and management, a careful assessment of the regional climate is needed to determine the potential benefits of adopting conservation agriculture.     

Metabolite variation in the lettuce gene pool: towards healthier crop varieties and food

Introduction

Lettuce (Lactuca sativa L.) is generally not specifically acknowledged for its taste and nutritional value, while its cultivation suffers from limited resistance against several pests and diseases. Such key traits are known to be largely dependent on the ability of varieties to produce specific phytochemicals.

Objectives

We aimed to identify promising genetic resources for the improvement of phytochemical composition of lettuce varieties.

Methods

Phytochemical variation was investigated using 150 Lactuca genebank accessions, comprising a core set of the lettuce gene pool, and resulting data were related to available phenotypic information.

Results

A hierarchical cluster analysis of the variation in relative abundance of 2026 phytochemicals, revealed by untargeted metabolic profiling, strongly resembled the known lettuce gene pool structure, indicating that the observed variation was to a large extent genetically determined. Many phytochemicals appeared species-specific, of which several are generally related to traits that are associated with plant health or nutritional value. For a large number of phytochemicals the relative abundance was either positively or negatively correlated with available phenotypic data on resistances against pests and diseases, indicating their potential role in plant resistance. Particularly the more primitive lettuces and the closely related wild relatives showed high levels of (poly)phenols and vitamin C, thus representing potential genetic resources for improving nutritional traits in modern crop types.

Conclusion

Our large-scale analysis of phytochemical variation is unprecedented in lettuce and demonstrated the ample availability of suitable genetic resources for the development of improved lettuce varieties with higher nutritional quality and more sustainable production.

     

A global foresight on food crop needs for livestock

Increasingly more studies are raising concerns about the increasing consumption of meat and the increasing amount of crops (cereals and oilseeds in particular) used to feed animals and that could be used to feed people. The evolution of this amount is very sensitive to human diets and to the productivity of feed. This article provides a 2050 foresight on the necessary increase in crop production for food and feed in three contrasting scenarios: diets with no animal products; current diets in each main region of the world; and the average diet of developed countries extended to the whole world. We develop empirical aggregate production models for seven world regions, using 43 years and 150 countries. These models realistically account for the contribution of feed from food plants (i.e. plants that would be edible for humans) and of grassland to animal products. We find that the amount of edible crops necessary to feed livestock in 2050 is between 8% and 117% of today's need. The latter figure is lower than that in comparable foresight studies because our models take into account empirical features occurring at an aggregate level, such as the increasing share of animal production from regions using less crop product per unit of animal product. In particular, the expected increase in animal production is estimated to occur mostly in Sub-Saharan Africa and Asia, where the amount of feed from food crops required per unit of animal product proves to be lower than that in other areas. This 117% increase indicates that crop production would have to double if the whole world adopted the present diet of developed countries.     

Balancing selection and wild gene pool contribute to resistance in global rice germplasm against planthopper

Interactions and co-evolution between plants and herbivorous insects are critically important in agriculture. Brown planthopper (BPH) is the most severe insect of rice, and the biotypes adapt to feed on different rice genotypes. Here, we present genomics analyses on 1,520 global rice germplasms for resistance to three BPH biotypes. Genome-wide association studies identified 3,502 single nucleotide polymorphisms (SNPs) and 59 loci associated with BPH resistance in rice. We cloned a previously unidentified gene Bph37 that confers resistance to BPH. The associated loci showed high nucleotide diversity. Genome-wide scans for trans-species polymorphisms revealed ancient balancing selection at the loci. The secondarily evolved insect biotypes II and III exhibited significantly higher virulence and overcame more rice varieties than the primary biotype I. In response, more SNPs and loci evolved in rice for resistance to biotypes II and III. Notably, three exceptional large regions with high SNP density and resistance-associated loci on chromosomes 4 and 6 appear distinct between the resistant and susceptible rice varieties. Surprisingly, these regions in resistant rice might have been retained from wild species Oryza nivara. Our findings expand the understanding of long-term interactions between rice and BPH and provide resistance genes and germplasm resources for breeding durable BPH-resistant rice varieties.     

A climatic stability approach to prioritizing global conservation investments

Climate change is impacting species and ecosystems globally. Many existing templates to identify the most important areas to conserve terrestrial biodiversity at the global scale neglect the future impacts of climate change. Unstable climatic conditions are predicted to undermine conservation investments in the future. This paper presents an approach to developing a resource allocation algorithm for conservation investment that incorporates the ecological stability of ecoregions under climate change. We discover that allocating funds in this way changes the optimal schedule of global investments both spatially and temporally. This allocation reduces the biodiversity loss of terrestrial endemic species from protected areas due to climate change by 22% for the period of 2002-2052, when compared to allocations that do not consider climate change. To maximize the resilience of global biodiversity to climate change we recommend that funding be increased in ecoregions located in the tropics and/or mid-elevation habitats, where climatic conditions are predicted to remain relatively stable. Accounting for the ecological stability of ecoregions provides a realistic approach to incorporating climate change into global conservation planning, with potential to save more species from extinction in the long term.     

A cytomolecular approach to assess the potential of gene transfer from a crop (Triticum turgidum L.) to a wild relative (Aegilops geniculata Roth.)

When a crop hybridizes with a wild relative, the potential for stable transmission to the wild of any crop gene is directly related to the frequency of crop–wild homoeologous pairing for the chromosomal region where it is located within the crop genome. Pairing pattern at metaphase I (MI) has been examined in durum wheat × Aegilops geniculata interspecific hybrids (2n=4x=ABU^gM^g) by means of a genomic in-situ hybridization procedure that resulted in simultaneous discrimination of A, B and wild genomes. The level of MI pairing in the hybrids varied greatly depending on the crop genotype. However, their pattern of homoeologous association was very similar, with a frequency of wheat–wild association close to 60% in all genotype combinations. A–wild represented 80–85% of wheat–wild associations which supports that, on average, A genome sequences are much more likely to be transferred to this wild relative following interspecific hybridization and backcrossing. Combination of genomic DNA probes and the ribosomal pTa71 probe has allowed to determine the MI pairing behaviour of the major NOR-bearing chromosomes in these hybrids (1B, 6B, 1U^g and 5U^g), in addition to wheat chromosome 4A which could be identified with the sole use of genomic probes. The MI pairing pattern of the wild chromosome arms individually examined has confirmed a higher chance of gene escape from the wheat A genome. However, a wide variation regarding the amount of wheat–wild MI pairing among the specific wheat chromosome regions under analysis suggests that the study should be extended to other homoeologous groups.     

In situ conservation of crop wild relatives: status and trends

Recognized as a priority three decades ago, in situ conservation of crop wild relatives has developed theoretical and methodological focus and achieved significant on-the-ground progress in the last 10 years, most notably under the impetus of the plant genetic resources community. Literature and Internet searches and interviews with experts were undertaken as a basis for reviewing the current status and trends of this effort worldwide. Country-by-country summaries on in situ crop wild relatives conservation activities are presented, and recommendations are made for future action. Principal recommendations include flagging of appropriate taxa as crop wild relatives in botanical and conservation databases, undertaking gap analyses to locate crop wild relatives hotspots, and enhancing cooperation between the plant genetic resources and plant conservation communities.     

A spatially explicit representation of conservation agriculture for application in global change studies

Conservation agriculture (CA) is widely promoted as a sustainable agricultural management strategy with the potential to alleviate some of the adverse effects of modern, industrial agriculture such as large‐scale soil erosion, nutrient leaching and overexploitation of water resources. Moreover, agricultural land managed under CA is proposed to contribute to climate change mitigation and adaptation through reduced emission of greenhouse gases, increased solar radiation reflection, and the sustainable use of soil and water resources. Due to the lack of official reporting schemes, the amount of agricultural land managed under CA systems is uncertain and spatially explicit information about the distribution of CA required for various modeling studies is missing. Here, we present an approach to downscale present‐day national‐level estimates of CA to a 5 arcminute regular grid, based on multicriteria analysis. We provide a best estimate of CA distribution and an uncertainty range in the form of a low and high estimate of CA distribution, reflecting the inconsistency in CA definitions. We also design two scenarios of the potential future development of CA combining present‐day data and an assessment of the potential for implementation using biophysical and socioeconomic factors. By our estimates, 122–215 Mha or 9%–15% of global arable land is currently managed under CA systems. The lower end of the range represents CA as an integrated system of permanent no‐tillage, crop residue management and crop rotations, while the high estimate includes a wider range of areas primarily devoted to temporary no‐tillage or reduced tillage operations. Our scenario analysis suggests a future potential of CA in the range of 533–1130 Mha (38%–81% of global arable land). Our estimates can be used in various ecosystem modeling applications and are expected to help identifying more realistic climate mitigation and adaptation potentials of agricultural practices.     

Exploring the genetic and adaptive diversity of a pan-Mediterranean crop wild relative: narrow-leafed lupin

Key message

This first pan-Mediterranean analysis of genetic diversity in wild narrow-leafed lupin revealed strong East–West genetic differentiation of populations, an historic eastward migration, and signatures of genetic adaptation to climatic variables.

Abstract

Most grain crops suffer from a narrow genetic base, which limits their potential for adapting to new challenges such as increased stresses associated with climate change. Plant breeders are returning to the wild ancestors of crops and their close relatives to broaden the genetic base of their crops. Understanding the genetic adaptation of these wild relatives will help plant breeders most effectively use available wild diversity. Here, we took narrow-leafed lupin (Lupinus angustifolius L.) as a model to understand adaptation in a wild crop ancestor. A set of 142 wild accessions of narrow-leafed lupin from across the Mediterranean basin were subjected to genotyping-by-sequencing using Diversity Arrays Technology. Phylogenetic, linkage disequilibrium and demographic analyses were employed to explore the history of narrow-leafed lupin within the Mediterranean region. We found strong genetic differentiation between accessions from the western and eastern Mediterranean, evidence of an historic West to East migration, and that eastern Mediterranean narrow-leafed lupin experienced a severe and recent genetic bottleneck. We showed that these two populations differ for flowering time as a result of local adaptation, with the West flowering late while the East flowers early. A genome-wide association study identified single nucleotide polymorphism markers associated with climatic adaptation. Resolving the origin of wild narrow-leafed lupin and how its migration has induced adaptation to specific regions of the Mediterranean serves as a useful resource not only for developing narrow-leafed lupin cultivars with greater resilience to a changing climate, but also as a model which can be applied to other legumes.

     

Dynamic management of crop diversity: From an experimental approach to on-farm conservation

In agricultural systems, biodiversity includes diversity within species and among species and provides many benefits for production, resilience and conservation. This article addresses the effects of a strategy of in situ conservation called dynamic management (DM) on population evolution, adaptation and diversity. Two French DM initiatives are considered, the first one corresponding to an experimental context, the second to an on-farm management. Results from a study over 26 years of experimental DM of bread wheat (Triticum aestivum L.) are first presented, including the evolution of agronomic traits and genetic diversity at neutral and fitness related loci. While this experiment greatly increased scientific knowledge of the effects of natural selection on cultivated populations, it also showed that population conservation cannot rely only on a network of experimental stations. In collaboration with a farmers' network in France, researchers have begun studying the effects of on-farm DM (conservation and selection) on diversity and adaptation. Results from these studies show that on-farm DM is a key element for the long-term conservation and use of agricultural biodiversity. This method of in situ conservation deserves more attention in industrialised countries.     

Important Plant Areas: revised selection criteria for a global approach to plant conservation

Despite the severe threats to plant habitats and high levels of extinction risk for plant species in many parts of the world, plant conservation priorities are often poorly represented in national and global frameworks because of a lack of data in an accessible and consistent format to inform conservation decision making. The Important Plant Areas (IPAs) criteria system offers a pragmatic yet scientifically rigorous means of delivering these datasets, enabling informed national- or regional-scale conservation prioritisation, and contributing significantly towards global prioritisation systems including the International Union for Conservation of Nature Key Biodiversity Areas (KBAs) Standard. In this paper, we review the IPA rationale and progress on IPA identification to date, including the perceived limitations of the process and how these may be overcome. We then present a revised set of criteria for use globally, developed through the combined experiences of IPA identification over the past decade and a half and through a recent global consultation process. An overview of how the revised IPA criteria can work alongside the newly published KBA Standard is also provided. IPA criteria are based around a sound, scientific, global framework which acknowledges the practical problems of gathering plant and habitat data in many regions of the world, and recognises the role of peer reviewed expert opinion in the selection process. National and sub-national engagement in IPA identification is essential, providing a primary route towards long term conservation of key sites for plant diversity. The IPA criteria can be applied to the conservation of all organism groups within the plant and fungal kingdoms.     

Gap analyses of priority wild relatives of food crop in current ex situ and in situ conservation in Indonesia

Conservation programmes are always limited by available resources. Careful planning is therefore required to increase the efficiency of conservation and gap analysis can be used for this purpose. This method was used to assess the representativeness of current ex situ and in situ conservation actions of 234 priority crop wild relatives (CWR) in Indonesia. This analysis also included species distribution modelling, the creation of an ecogeographical land characterization map, and a complementarity analysis to identify priorities area for in situ conservation and for further collecting of ex situ conservation programmes. The results show that both current ex situ and in situ conservation actions are insufficient. Sixty-six percent of priority CWRs have no recorded ex situ collections. Eighty CWRs with ex situ collections are still under-represented in the national genebanks and 65 CWRs have no presence records within the existing protected area network although 60 are predicted to exist in several protected areas according to their potential distribution models. The complementarity analysis shows that a minimum of 61 complementary grid areas (complementary based on grid cells) are required to conserve all priority taxa and 40 complementary protected areas (complementary based on existing protected areas) are required to conserve those with known populations within the existing in situ protected area network. The top ten of complementary protected areas are proposed as the initial areas for the development of CWR genetic reserves network in Indonesia. It is recommended to enhanced coordination between ex situ and in situ conservation stakeholders for sustaining the long term conservation of CWR in Indonesia. Implementation of the research recommendations will provide for the first time an effective conservation planning of Indonesia’s CWR diversity and will significantly enhance the country’s food and nutritional security.

     

Freshwater wild biota exposure to microplastics: A global perspective

1. Current understanding on the exposure of freshwater organisms to microplastics (plastics sized between 1 µm and 5 mm) has arisen mostly from laboratory experiments—often conducted under artificial circumstances and with unrealistic concentrations. In order to improve scientific links through real ecosystem exposure, we review field data on the exposure of free‐living organisms to microplastics.
2. We highlight that the main outputs provided by field research are an assessment of the occurrence and, at times, the quantification of microplastics in different animal taxa. Topics of investigation also include the causes of contamination and the development of biological monitoring tools. With regard to taxa, fish, mollusks, and arthropods are at the center of the research, but birds and amphibians are also investigated. The ingestion or occurrence of microplastics in organs and tissues, such as livers and muscles, are the main data obtained. Microorganisms are studied differently than other taxa, highlighting interesting aspects on the freshwater plastisphere, for example, related to the structure and functionality of communities. Many taxa, that is, mammals, reptiles, and plants, are still under‐examined with regard to exposure to microplastics; this is surprising as they are generally endangered.
3. As biota contamination is acknowledged, we contribute to an interdisciplinary scientific discussion aimed at a better assessment of knowledge gaps on methodology, impact assessment, and monitoring.

     

A security game approach for strategic conservation against poaching considering food web complexities

Mitigating the poaching pressure on food webs under multiple constraints (including financial and ecological ones) remains an open problem within conservation. Within this field, mathematically modeling the effects of poaching threats on managerial decision-making is a novel approach. To fill this scientific gap, the present paper uses a security game approach to model the interactions between an environmental manager (defender) and a group of profit-seeking pursuit poachers (attackers) who target species which are nodes of the food web. Based upon the non-cooperative Stackelberg game, the objective of the defender (as leader) is to keep the food web at or near equilibrium through optimally manipulating the populations of an optimal subset of species. In contrast, each attacker strives to maximize monetary profit by hunting an optimal population size of the selected species. The model is validated by a numerical example examining the food web of the endangered Persian leopard (Panthera pardus saxicolor), which lives in Golestan National Park (GNP), Iran. The model provides an overarching biotic intervention strategy to keep the (1 predator-4 prey) food web near equilibrium, while only 2 prey species (the urial (Ovis vignei) and the red deer (Cervus elaphus)) are directly threatened by poachers. The examination revealed that both species population data and poaching data should be taken into account to set effective multi-species conservation prioritization levels. In a sensitivity analysis approach, it was found that, despite the fact that red deer is endangered and preferred by poachers, the deterrent penalty measure should be 1.5 times greater for poaching urial than red deer. The output analysis illustrated that, in order to bring the urial deterrent penalty measure closer to the red deer one, enforcement measures should be about 2.5 times stricter for poaching urial than red deer. The results specifically yield insight into how to optimally conserve a food web equilibrium under poaching pressure and within several constraints.     

Molecular diversity and landscape genomics of the crop wild relative Triticum urartu across the Fertile Crescent

Modern plant breeding can benefit from the allelic variation that exists in natural populations of crop wild relatives that evolved under natural selection in varying pedoclimatic conditions. In this study, next‐generation sequencing was used to generate 1.3 million genome‐wide single nucleotide polymorphisms (SNPs) on ex situ collections of Triticum urartu L., the wild donor of the A^u subgenome of modern wheat. A set of 75 511 high‐quality SNPs were retained to describe 298 T. urartu accessions collected throughout the Fertile Crescent. Triticum urartu showed a complex pattern of genetic diversity, with two main genetic groups distributed sequentially from west to east. The incorporation of geographical information on sampling points showed that genetic diversity was correlated to the geographical distance (R² = 0.19) separating samples from Jordan and Lebanon, from Syria and southern Turkey, and from eastern Turkey, Iran and Iraq. The wild emmer genome was used to derive the physical positions of SNPs on the seven chromosomes of the A^u subgenome, allowing us to describe a relatively slow decay of linkage disequilibrium in the collection. Outlier loci were described on the basis of the geographic distribution of the T. urartu accessions, identifying a hotspot of directional selection on chromosome 4A. Bioclimatic variation was derived from grid data and related to allelic variation using a genome‐wide association approach, identifying several marker–environment associations (MEAs). Fifty‐seven MEAs were associated with altitude and temperature measures while 358 were associated with rainfall measures. The most significant MEAs and outlier loci were used to identify genomic loci with adaptive potential (some already reported in wheat), including dormancy and frost resistance loci. We advocate the application of genomics and landscape genomics on ex situ collections of crop wild relatives to efficiently identify promising alleles and genetic materials for incorporation into modern crop breeding.