Reap the crop wild relatives for breeding future crops Bohra, Abhishek; Kilian, Benjamin; Sivasankar, Shoba ...
Trends in biotechnology (Regular ed.),
April 2022, 2022-04-00, 20220401, Volume:
40, Issue:
4
Journal Article
Peer reviewed
Open access
Crop wild relatives (CWRs) have provided breeders with several 'game-changing' traits or genes that have boosted crop resilience and global agricultural production. Advances in breeding and genomics ...have accelerated the identification of valuable CWRs for use in crop improvement. The enhanced genetic diversity of breeding pools carrying optimum combinations of favorable alleles for targeted crop-growing regions is crucial to sustain genetic gain. In parallel, growing sequence information on wild genomes in combination with precise gene-editing tools provide a fast-track route to transform CWRs into ideal future crops. Data-informed germplasm collection and management strategies together with adequate policy support will be equally important to improve access to CWRs and their sustainable use to meet food and nutrition security targets.
Exotic genetic libraries in different crops are valuable genetic resources for genetic dissection of complex quantitative traits.An informed choice of crop wild relatives (CWRs) for genetic studies and breeding can be made by taking account of the environmental variables of the collection sites.New breeding tools such as genomic selection and optimum contribution selection help to achieve the optimal combinations of beneficial alleles in exotic × elite crosses.Precise gene-editing tools open new avenues to broaden the array of current food crops by domesticating wild species de novo.Regulating the known crossover suppressors through mutagenesis and ploidy-level change has great potential to disrupt linkage drag.Systematic analysis of genebank collections would guide future germplasm collection strategies by prioritizing both target species and global sites.
Genebanks underpin global food security, conserving and distributing agrobiodiversity for use in research and breeding. The CGIAR collections include >700,000 seed accessions, held in trust as global ...public goods. However, the role of genebanks in contributing to global food security can only be realized if collections are effectively managed. Examination of the historical viability monitoring data from seven CGIAR genebanks confirmed that high seed viability was maintained for many decades for the various crops and forage species. However, departures from optimum management procedures were revealed, and there were insufficient data gathered to derive reliable estimates of longevity needed to better forecast regeneration requirements, estimate the size of seed lots that should be stored, and optimize accession monitoring intervals.
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•833,364 viability records from seven CGIAR genebanks were downloaded from the respective databases between 2013 and 2019.•At the time of testing, the seed lots had been in medium-(MTS) or long-term storage (LTS) for up to 37.5 years.•The study highlighted the importance of a robust information management system and of effective and consistent documentation processes.•It also highlighted the competing needs when trying to manage genebank collections according to international standards.•There is a need for a culture and capacity that encourages critical review and refinement of genebank operations.
Grass pea (Lathyrus sativus) is a valuable grain legume known for its high protein content and rich essential amino acid profile. Its exceptional characteristics such as drought tolerance, high ...adaptability to extreme conditions, disease resistance, and low cultivation inputs, make it particularly suitable for cultivation by resource-poor farmers. However, the potential use of grass pea is limited due to the presence of anti-nutritional factors, including protease inhibitors, especially trypsin inhibitor. This study aimed to develop a rapid and reliable method for measuring TI activity in seeds of grass pea and to investigate the influence of genotype and environment on trypsin inhibitor (TI) activity in seeds of grass pea. A set of 25 grass pea accessions from seven European countries was cultivated in Slovenia at the Agricultural Institute of Slovenia, and a set of 12 grass pea accessions from the Serbian gene bank was grown in Serbia at the Institute of Field and Vegetable Crops. The TI activity varied considerably among the grass pea accessions studied, with values ranging from 26.7 to 90.3 TUI/mg. To further evaluate the effects of environmental conditions on TI activity, eight grass pea accessions originating from Serbia were grown in both Slovenia and Serbia. The TI activity of the accessions grown in Slovenia ranged from 26.7 to 81.0 TUI/mg, while the activity of the accessions grown in Serbia ranged from 40.3 to 57.0 TUI/mg. The correlation of TI activity between grass pea accessions grown in Slovenia and those grown in Serbia was 0.39, with genotype diversity being the largest contributor (55.9%). This study provides a valuable insight into the variability of TI activity in grass pea and shows the possible influence of environmental conditions on this trait. However, since the data are only from a one-year field trial, further studies are needed to fully evaluate the influence of different environmental factors on TI activity.
This perspective describes the opportunities and challenges of data-driven approaches for crop diversity management (genebanks and breeding) in the context of agricultural research for sustainable ...development in the Global South. Data-driven approaches build on larger volumes of data and flexible analyses that link different datasets across domains and disciplines. This can lead to more information-rich management of crop diversity, which can address the complex interactions between crop diversity, production environments, and socioeconomic heterogeneity and help to deliver more suitable portfolios of crop diversity to users with highly diverse demands. We describe recent efforts that illustrate the potential of data-driven approaches for crop diversity management. A continued investment in this area should fill remaining gaps and seize opportunities, including i) supporting genebanks to play a more active role in linking with farmers using data-driven approaches; ii) designing low-cost, appropriate technologies for phenotyping; iii) generating more and better gender and socioeconomic data; iv) designing information products to facilitate decision-making; and v) building more capacity in data science. Broad, well-coordinated policies and investments are needed to avoid fragmentation of such capacities and achieve coherence between domains and disciplines so that crop diversity management systems can become more effective in delivering benefits to farmers, consumers, and other users of crop diversity.
This review examines the issues of ex situ conservation of Rubus L. genetic resources in the world’s genebanks and various institutions in different countries. The most urgent among the studied ...problems are the issues of preserving interspecific and intraspecific diversity and its sustainable utilization in breeding programs. The main attention is paid to pomologically important subgenera – raspberries Idaeobatus Focke (= Batidaea (Dumort.) Greene) and blackberries Rubus (= Eubatus Focke).Detailed information is provided on the composition and size of field, in vitro and cryogenic collections as well as seed collections. Specific features of conserving the genus’s genetic resources in collections of different types are analyzed. Information on collections of the genus preserved in the Russian Federation, unavailable in international databases, is summarized. Particular attention is paid to the collection of raspberries and blackberries held by the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), including the history of its formation and the current state.VIR’s clonal genebank currently preserves 359 accessions of Rubus L., belonging mainly to the subgenera of raspberries (Idaeobatus) and blackberries (Rubus): 209 of these accessions are maintained in the field collection, and 150 in the in vitro collection. Raspberry cultivars developed through breeding dominate in the VIR collection – 170 accessions, among which 126 have been released by domestic breeders. Wild species are mainly represented by those collected in the Russian North – 49 clones of red raspberry (Rubus idaeus L.) and 6 of cloudberries (R. chamaemorus L.) – and in the Caucasus (35 accessions of 26 species). The data on the species diversity of the genus in Russian natural flora are presented and the strategy of replenishment, study and conservation of Rubus L. genetic resources at VIR’s genebank is discussed.
This paper examines the vital role of genebanks in the conservation and use of plant genetic resources, highlighting the South Pacific’s version of the Irish Potato Famine and the organizational ...interdependence necessary to respond to disastrous losses in a cultivated food crop. We conducted an ethnobotanical fieldwork in Fiji, Vanuatu, and the Cook Islands, interviewing over 50 taro experts and farmers to gather the ‘Tale of Taro Leaf Blight’. Taro is the staple ‘prestige’ food crop of Samoa but in 1993, taro leaf blight (TLB),
Phytophthora colocasiae
, caused an almost 100% loss of the crop, threatening both food security and traditional cultural practices. Several international organizations were formed to conduct botanical expeditions to re-gather crop wild relatives of taro,
Colocasia esculenta
, from their various centres of origin. This parental material was used in a 10-year breeding cycle process to produce viable TLB-resistant varieties and replant the fallow fields of Samoa. The duty to safeguard these global accessions led to the formalization of CePaCT, which houses this core collection. The collection, conservation, multiplication, and distribution of taro has had a significant impact beyond the regional needs of the Pacific. Taro germplasm samples were distributed to countries worldwide affected by the blight, aiding in staving off potential famines and economic crises. This ancient aroid is one of the most consumed vegetables in the Pacific. It is an indispensable nutritional and caloric resource for subsistence farming nations, and carries deep ethnobotanical and cultural significance.
Crop genebank collections are important resources for preserving genetic diversity to face the worldwide demand for food and coping with crop diseases and climate change. However, genebanks tend to ...accumulate materials without systematic collection growth. Thus, tools for optimizing collections are expected to help improvement of genebanks quality. Furthermore, the genotyping efforts of genebanks would benefit from tools that can help to sample the accessions. A set of parameters to aid the optimization of genebanks are defined, in which Relative Balance is central. In this study, the foundation of our mathematical approach was Kullback-Leibler divergence, providing formulas with consistent properties. Two examples were used as proof of concept. The first one was the comparison between actual and putative optimal numbers of accessions in the Triticum set of the CIMMYT (Centro Internacional de Mejoramiento de Maiz y Trigo) Wheat Germplasm Bank, with 135,236 entries classified into ten groups. The second one was based on a set containing Triticum plus eight related genera, with 159,741 accessions classified into 217 end-groups, with the goal of illustrating the use of the analytical tools to optimize the ongoing genotyping process. The first example shows a scenario with a well-balanced allocation of accessions. The second example illustrates the optimized choice of end-groups to add 10,000 accessions to the genotyping process. The proof of concept showed the consistency and usefulness of the proposed methods for the improvement of composition in collections and their characterization.
Warming and drought are reducing global crop production with a potential to substantially worsen global malnutrition. As with the green revolution in the last century, plant genetics may offer ...concrete opportunities to increase yield and crop adaptability. However, the rate at which the threat is happening requires powering new strategies in order to meet the global food demand. In this review, we highlight major recent ‘big data’ developments from both empirical and theoretical genomics that may speed up the identification, conservation, and breeding of exotic and elite crop varieties with the potential to feed humans. We first emphasize the major bottlenecks to capture and utilize novel sources of variation in abiotic stress (i.e., heat and drought) tolerance. We argue that adaptation of crop wild relatives to dry environments could be informative on how plant phenotypes may react to a drier climate because natural selection has already tested more options than humans ever will. Because isolated pockets of cryptic diversity may still persist in remote semi-arid regions, we encourage new habitat-based population-guided collections for genebanks. We continue discussing how to systematically study abiotic stress tolerance in these crop collections of wild and landraces using geo-referencing and extensive environmental data. By uncovering the genes that underlie the tolerance adaptive trait, natural variation has the potential to be introgressed into elite cultivars. However, unlocking adaptive genetic variation hidden in related wild species and early landraces remains a major challenge for complex traits that, as abiotic stress tolerance, are polygenic (i.e., regulated by many low-effect genes). Therefore, we finish prospecting modern analytical approaches that will serve to overcome this issue. Concretely, genomic prediction, machine learning, and multi-trait gene editing, all offer innovative alternatives to speed up more accurate pre- and breeding efforts toward the increase in crop adaptability and yield, while matching future global food demands in the face of increased heat and drought. In order for these ‘big data’ approaches to succeed, we advocate for a trans-disciplinary approach with open-source data and long-term funding. The recent developments and perspectives discussed throughout this review ultimately aim to contribute to increased crop adaptability and yield in the face of heat waves and drought events.
Among the most important users of plant genetic resources, conserved predominantly in public genebanks around the world, are public and private plant breeders. Through their breeding efforts, they ...contribute significantly to global, regional, and local food and nutrition security. Plant breeders need genetic diversity to be able to develop competitive new varieties that are adapted to the changing environmental conditions and suit the needs of consumers. To ensure continued and timely access to the genetic resources that contain the required characteristics and traits, plant breeders established working collections with breeding materials and germplasm for the crops they were breeding. However, with the changing and increasingly more restrictive access conditions, triggered by new global legal instruments like the Convention on Biological Diversity/Nagoya Protocol and the International Treaty, plant breeders started to establish their own genebanks at the turn of the 21st century. This paper analyses the conditions that contributed to this situation as well as the historical ways that plant breeders used to acquire the germplasm they needed. Public genebanks played and continue to play a conducive role in providing genetic resources to users, including private-sector plant breeders. However, also the practices of the germplasm curators to collect and distribute germplasm were affected by the new legal framework that had been developed in global fora. It is against this background that the complementarity and collaboration between public and private sector genebanks have been assessed. Whenever possible, vegetable genetic resources and vegetable private breeding companies have been used to analyze and illustrate such collaboration. The authors look at reported successful examples of collaborative efforts and consider opportunities and approaches under which such collaboration can be established and strengthened to ensure the continued availability of the building blocks for food and nutrition security.
Adult-plant resistance (APR) is a type of genetic resistance in cereals that is effective during the later growth stages and can protect plants from a range of disease-causing pathogens. Our ...understanding of the functions of APR-associated genes stems from the well-studied wheat-rust pathosystem. Genes conferring APR can offer pathogen-specific resistance or multi-pathogen resistance, whereby resistance is activated following a molecular recognition event. The breeding community prefers APR to other types of resistance because it offers broad-spectrum protection that has proven to be more durable. In practice, however, deployment of new cultivars incorporating APR is challenging because there is a lack of well-characterised APRs in elite germplasm and multiple loci must be combined to achieve high levels of resistance. Genebanks provide an excellent source of genetic diversity that can be used to diversify resistance factors, but introgression of novel alleles into elite germplasm is a lengthy and challenging process. To overcome this bottleneck, new tools in breeding for resistance must be integrated to fast-track the discovery, introgression and pyramiding of APR genes. This review highlights recent advances in understanding the functions of APR genes in the well-studied wheat-rust pathosystem, the opportunities to adopt APR genes in other crops and the technology that can speed up the utilisation of new sources of APR in genebank accessions.
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