Valuing genebanks

Abiotic Stress Tolerance Boosted by Genetic Diversity in Plants

Plant breeding [...].

Genebanks at Risk: Hazard Assessment and Risk Management of National and International Genebanks

Genebanks are crucial for safeguarding global crop diversity but are themselves exposed to several risks. However, a scientific basis for identifying, assessing, and managing risks is still lacking. Addressing these research gaps, this study provides risk analysis for three key risk groups: natural hazards, political risks, and financial risks, carried out on a sample of 80 important national and international genebanks, comprising at least 4.78 million accessions or roughly 65% of the reported total of ex situ conserved accessions worldwide. The assessment tool of Munich Re "Natural Hazards Edition" allowed a location-specific comparison of the natural hazard exposure. Results showed that genebanks in the Asia-Pacific region are most exposed to natural hazards, while institutions in African and some Asian countries are rather vulnerable to political risks. Financing is a major problem for national genebanks in developing countries, whereas the Global Crop Diversity Trust achieved considerable financial security for international genebanks. Large differences in the risk exposure of genebanks exist, making a location- and institution-specific risk assessment indispensable. Moreover, there is significant room for improvement with respect to quality and risk management at genebanks. Transferring risks of genebanks to third parties is underdeveloped and should be used more widely.

Molecular Genetics Enhances Plant Breeding

Human-driven plant selection, a practice as ancient as agriculture itself, has laid the foundations of plant breeding and contemporary farming [...].

Genetic resources and breeding of maize for Striga resistance: a review

The potential yield of maize (Zea mays L.) and other major crops is curtailed by several biotic, abiotic, and socio-economic constraints. Parasitic weeds, Striga spp., are major constraints to cereal and legume crop production in sub-Saharan Africa (SSA). Yield losses reaching 100% are reported in maize under severe Striga infestation. Breeding for Striga resistance has been shown to be the most economical, feasible, and sustainable approach for resource-poor farmers and for being environmentally friendly. Knowledge of the genetic and genomic resources and components of Striga resistance is vital to guide genetic analysis and precision breeding of maize varieties with desirable product profiles under Striga infestation. This review aims to present the genetic and genomic resources, research progress, and opportunities in the genetic analysis of Striga resistance and yield components in maize for breeding. The paper outlines the vital genetic resources of maize for Striga resistance, including landraces, wild relatives, mutants, and synthetic varieties, followed by breeding technologies and genomic resources. Integrating conventional breeding, mutation breeding, and genomic-assisted breeding [i.e., marker-assisted selection, quantitative trait loci (QTL) analysis, next-generation sequencing, and genome editing] will enhance genetic gains in Striga resistance breeding programs. This review may guide new variety designs for Striga-resistance and desirable product profiles in maize.

Perspective article: Food security in tropical Africa through climate-smart plant health management

Each year, Africa loses half of its harvest to pests (insects, pathogens, nematodes, weeds). To offset these losses and improve food security, pest management needs to be revamped urgently. Based on a synthesis of all 58 pest management projects conducted by IITA in its 55-year history, we advocate here for the implementation of the five following key climate-smart interventions, which have been shown to increase yields and decreasing CO₂ outputs compared to the current practices that are largely based on the use of synthetic pesticides: 1. Sanitation at the country's borders and at the field level is the most cost-efficient way to prevent pest damage and losses from exotic pests entering new territories. 2. Good soil management strengthens the crop plant and enhances the effectiveness of all other interventions. 3. Biological control is the quickest and in the long run most cost-effective way to control invading insect pests and weeds. 4. Resistant varieties are often the only way to control already established diseases and are a mainstay control method in combination with other practices. 5. Various bio-pesticides based on viruses, bacteria and fungi against insects have been commercialized or can be produced on-farm; they are to replace synthetic pesticides, which continue to have large negative impacts on the environment and human health. To apply these five practices, new decision-support and climate services tools should be used to empower low-literacy farmers to take timely decisions about pest control and to act as business partners. Meanwhile, all actors in the pest control community should account for their environmental costs, which up to now are born solely by the community, while profits from pesticide sales are pocketed privately. To successfully disseminate these practices across the continent, enhanced and harmonized policy support is required.

Genome-Environment Associations, an Innovative Tool for Studying Heritable Evolutionary Adaptation in Orphan Crops and Wild Relatives

Leveraging innovative tools to speed up prebreeding and discovery of genotypic sources of adaptation from landraces, crop wild relatives, and orphan crops is a key prerequisite to accelerate genetic gain of abiotic stress tolerance in annual crops such as legumes and cereals, many of which are still orphan species despite advances in major row crops. Here, we review a novel, interdisciplinary approach to combine ecological climate data with evolutionary genomics under the paradigm of a new field of study: genome-environment associations (GEAs). We first exemplify how GEA utilizes in situ georeferencing from genotypically characterized, gene bank accessions to pinpoint genomic signatures of natural selection. We later discuss the necessity to update the current GEA models to predict both regional- and local- or micro-habitat-based adaptation with mechanistic ecophysiological climate indices and cutting-edge GWAS-type genetic association models. Furthermore, to account for polygenic evolutionary adaptation, we encourage the community to start gathering genomic estimated adaptive values (GEAVs) for genomic prediction (GP) and multi-dimensional machine learning (ML) models. The latter two should ideally be weighted by de novo GWAS-based GEA estimates and optimized for a scalable marker subset. We end the review by envisioning avenues to make adaptation inferences more robust through the merging of high-resolution data sources, such as environmental remote sensing and summary statistics of the genomic site frequency spectrum, with the epigenetic molecular functionality responsible for plastic inheritance in the wild. Ultimately, we believe that coupling evolutionary adaptive predictions with innovations in ecological genomics such as GEA will help capture hidden genetic adaptations to abiotic stresses based on crop germplasm resources to assist responses to climate change. "I shall endeavor to find out how nature's forces act upon one another, and in what manner the geographic environment exerts its influence on animals and plants. In short, I must find out about the harmony in nature" Alexander von Humboldt-Letter to Karl Freiesleben, June 1799.

Adapting Agriculture to Climate Change: A Synopsis of Coordinated National Crop Wild Relative Seed Collecting Programs across Five Continents

The Adapting Agriculture to Climate Change Project set out to improve the diversity, quantity, and accessibility of germplasm collections of crop wild relatives (CWR). Between 2013 and 2018, partners in 25 countries, heirs to the globetrotting legacy of Nikolai Vavilov, undertook seed collecting expeditions targeting CWR of 28 crops of global significance for agriculture. Here, we describe the implementation of the 25 national collecting programs and present the key results. A total of 4587 unique seed samples from at least 355 CWR taxa were collected, conserved ex situ, safety duplicated in national and international genebanks, and made available through the Multilateral System (MLS) of the International Treaty on Plant Genetic Resources for Food and Agriculture (Plant Treaty). Collections of CWR were made for all 28 targeted crops. Potato and eggplant were the most collected genepools, although the greatest number of primary genepool collections were made for rice. Overall, alfalfa, Bambara groundnut, grass pea and wheat were the genepools for which targets were best achieved. Several of the newly collected samples have already been used in pre-breeding programs to adapt crops to future challenges.

Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR

Threats to global biodiversity are increasingly recognised by scientists and the public as a critical challenge. Molecular sequencing technologies offer means to catalogue, explore, and monitor the richness and biogeography of life on Earth. However, exploiting their full potential requires tools that connect biodiversity infrastructures and resources. As a research infrastructure developing services and technical solutions that help integrate and coordinate life science resources across Europe, ELIXIR is a key player. To identify opportunities, highlight priorities, and aid strategic thinking, here we survey approaches by which molecular technologies help inform understanding of biodiversity. We detail example use cases to highlight how DNA sequencing is: resolving taxonomic issues; Increasing knowledge of marine biodiversity; helping understand how agriculture and biodiversity are critically linked; and playing an essential role in ecological studies. Together with examples of national biodiversity programmes, the use cases show where progress is being made but also highlight common challenges and opportunities for future enhancement of underlying technologies and services that connect molecular and wider biodiversity domains. Based on emerging themes, we propose key recommendations to guide future funding for biodiversity research: biodiversity and bioinformatic infrastructures need to collaborate closely and strategically; taxonomic efforts need to be aligned and harmonised across domains; metadata needs to be standardised and common data management approaches widely adopted; current approaches need to be scaled up dramatically to address the anticipated explosion of molecular data; bioinformatics support for biodiversity research needs to be enabled and sustained; training for end users of biodiversity research infrastructures needs to be prioritised; and community initiatives need to be proactive and focused on enabling solutions. For sequencing data to deliver their full potential they must be connected to knowledge: together, molecular sequence data collection initiatives and biodiversity research infrastructures can advance global efforts to prevent further decline of Earth's biodiversity.

Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR

Threats to global biodiversity are increasingly recognised by scientists and the public as a critical challenge. Molecular sequencing technologies offer means to catalogue, explore, and monitor the richness and biogeography of life on Earth. However, exploiting their full potential requires tools that connect biodiversity infrastructures and resources. As a research infrastructure developing services and technical solutions that help integrate and coordinate life science resources across Europe, ELIXIR is a key player. To identify opportunities, highlight priorities, and aid strategic thinking, here we survey approaches by which molecular technologies help inform understanding of biodiversity. We detail example use cases to highlight how DNA sequencing is: resolving taxonomic issues; Increasing knowledge of marine biodiversity; helping understand how agriculture and biodiversity are critically linked; and playing an essential role in ecological studies. Together with examples of national biodiversity programmes, the use cases show where progress is being made but also highlight common challenges and opportunities for future enhancement of underlying technologies and services that connect molecular and wider biodiversity domains. Based on emerging themes, we propose key recommendations to guide future funding for biodiversity research: biodiversity and bioinformatic infrastructures need to collaborate closely and strategically; taxonomic efforts need to be aligned and harmonised across domains; metadata needs to be standardised and common data management approaches widely adopted; current approaches need to be scaled up dramatically to address the anticipated explosion of molecular data; bioinformatics support for biodiversity research needs to be enabled and sustained; training for end users of biodiversity research infrastructures needs to be prioritised; and community initiatives need to be proactive and focused on enabling solutions. For sequencing data to deliver their full potential they must be connected to knowledge: together, molecular sequence data collection initiatives and biodiversity research infrastructures can advance global efforts to prevent further decline of Earth's biodiversity.

Germplasm Conservation: Instrumental in Agricultural Biodiversity—A Review

Germplasm is a valuable natural resource that provides knowledge about the genetic composition of a species and is crucial for conserving plant diversity. Germplasm protection strategies not only involve rescuing plant species threatened with extinction, but also help preserve all essential plants, on which rests the survival of all organisms. The successful use of genetic resources necessitates their diligent collection, storage, analysis, documentation, and exchange. Slow growth cultures, cryopreservation, pollen and DNA banks, botanical gardens, genetic reserves, and farmers’ fields are a few germplasm conservation techniques being employed. However, the adoption of in-vitro techniques with any chance of genetic instability could lead to the destruction of the entire substance, but the improved understanding of basic regeneration biology would, in turn, undoubtedly increase the capacity to regenerate new plants, thus expanding selection possibilities. Germplasm conservation seeks to conserve endangered and vulnerable plant species worldwide for future proliferation and development; it is also the bedrock of agricultural production.

Germplasm Acquisition and Distribution by CGIAR Genebanks

The international collections of plant genetic resources for food and agriculture (PGRFA) hosted by 11 CGIAR Centers are important components of the United Nations Food and Agriculture Organization's global system of conservation and use of PGRFA. They also play an important supportive role in realizing Target 2.5 of the Sustainable Development Goals. This paper analyzes CGIAR genebanks' trends in acquiring and distributing PGRFA over the last 35 years, with a particular focus on the last decade. The paper highlights a number of factors influencing the Centers' acquisition of new PGRFA to include in the international collections, including increased capacity to analyze gaps in those collections and precisely target new collecting missions, availability of financial resources, and the state of international and national access and benefit-sharing laws and phytosanitary regulations. Factors contributing to Centers' distributions of PGRFA included the extent of accession-level information, users' capacity to identify the materials they want, and policies. The genebanks' rates of both acquisition and distribution increased over the last decade. The paper ends on a cautionary note concerning the potential of unresolved tensions regarding access and benefit sharing and digital genomic sequence information to undermine international cooperation to conserve and use PGRFA.