Designing Novel Strategies for Improving Old Legumes: An Overview from Common Vetch

Common vetch (Vicia sativa L.) is a grain legume used in animal feeding, rich in protein content, fatty acid, and mineral composition that makes for a very adequate component to enrich feedstuff. In addition, relevant pharmacological properties have been reported in humans. The common vetch, similar to other legumes, can fix atmospheric nitrogen, a crucial feature for sustainable agricultural systems. These properties enhance the use of vetch as a cover crop and its sowing in intercropping systems. Moreover, several studies have recently pointed out the potential of vetch in the phytoremediation of contaminated soils. These characteristics make vetch a relevant crop, which different potential improvements target. Varieties with different yields, flowering times, shattering resistance, nutritional composition, rhizobacteria associations, drought tolerance, nitrogen fixation capacity, and other agronomic-relevant traits have been identified when different vetch accessions are compared. Recently, the analysis of genomic and transcriptomic data has allowed the development of different molecular markers to be used for assisted breeding purposes, promoting crop improvement. Here, we review the potential of using the variability of V. sativa genetic resources and new biotechnological and molecular tools for selecting varieties with improved traits to be used in sustainable agriculture systems.

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.

Towards the Development, Maintenance and Standardized Phenotypic Characterization of Single-Seed-Descent Genetic Resources for Chickpea

Here we present the approach used to develop the INCREASE "Intelligent Chickpea" Collections, from analysis of the information on the life history and population structure of chickpea germplasm, the availability of genomic and genetic resources, the identification of key phenotypic traits and methodologies to characterize chickpea. We present two phenotypic protocols within H2O20 Project INCREASE to characterize, develop, and maintain chickpea single-seed-descent (SSD) line collections. Such protocols and related genetic resource data from the project will be available for the legume community to apply the standardized approaches to develop Chickpea Intelligent Collections further or for multiplication/seed-increase purposes. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Characterization of chickpea seeds for seed-trait descriptors Basic Protocol 2: Characterization of chickpea lines for plant-trait descriptors specific for primary seed increase.

The INCREASE project: Intelligent Collections of food-legume genetic resources for European agrofood systems

Food legumes are crucial for all agriculture-related societal challenges, including climate change mitigation, agrobiodiversity conservation, sustainable agriculture, food security and human health. The transition to plant-based diets, largely based on food legumes, could present major opportunities for adaptation and mitigation, generating significant co-benefits for human health. The characterization, maintenance and exploitation of food-legume genetic resources, to date largely unexploited, form the core development of both sustainable agriculture and a healthy food system. INCREASE will implement, on chickpea (Cicer arietinum), common bean (Phaseolus vulgaris), lentil (Lens culinaris) and lupin (Lupinus albus and L. mutabilis), a new approach to conserve, manage and characterize genetic resources. Intelligent Collections, consisting of nested core collections composed of single-seed descent-purified accessions (i.e., inbred lines), will be developed, exploiting germplasm available both from genebanks and on-farm and subjected to different levels of genotypic and phenotypic characterization. Phenotyping and gene discovery activities will meet, via a participatory approach, the needs of various actors, including breeders, scientists, farmers and agri-food and non-food industries, exploiting also the power of massive metabolomics and transcriptomics and of artificial intelligence and smart tools. Moreover, INCREASE will test, with a citizen science experiment, an innovative system of conservation and use of genetic resources based on a decentralized approach for data management and dynamic conservation. By promoting the use of food legumes, improving their quality, adaptation and yield and boosting the competitiveness of the agriculture and food sector, the INCREASE strategy will have a major impact on economy and society and represents a case study of integrative and participatory approaches towards conservation and exploitation of crop genetic resources.

Common Vetch, Valuable Germplasm for Resilient Agriculture: Genetic Characterization and Spanish Core Collection Development

Common vetch (Vicia sativa L.) is a legume used for animal feed because of its high protein content and great capacity for nitrogen fixation, making this crop relevant in sustainable agriculture. The Spanish vetch collection, conserved at the Spanish Plant Genetic Resources Center (CRF), is one of the largest collections of this species worldwide, including landraces, wild relatives mainly collected in Spain, and commercial cultivars, but also accessions of international origin. The analysis of the genetic diversity of this material, whose genome has not been sequenced yet, and the assembly of a representative collection could play a pivotal role in conserving and exploiting these genetic resources in breeding programs mainly in those focused on consequences and demands of climate change. In this work, a set of 14 simple sequence repeat (SSR) reference alleles for genetic diversity analysis of the CRF vetch collection has been developed, used for genotyping more than 545 common vetch accessions from all over the world and validated. All the tested markers were polymorphic for the analyzed accessions. Overall, at least 86 different loci were identified with 2-11 alleles per locus with an average of 6.1 alleles per locus. Also, the analyses of the generated SSR database support that most of these SSR markers are transferable across closely related species of Vicia genus. Analysis of molecular variance revealed that wild relatives have a higher genetic diversity than landraces. However, cultivars have similar diversity than landraces, indicating that genetic variability has been barely lost due to the breeding of this legume. Low differences of genetic variations between Spanish and non-Spanish accessions have been observed, suggesting a high degree of diversity within Spanish genotypes, which provide 95% of the total genetic variation, so we have focused our efforts on characterizing genotypes of Spanish origin that were further studied using storage protein profiles. Based on SSR, seed protein profiles, and agromorphological and passport data, a vetch core collection (VCC) containing 47 V. sativa accessions of Spanish origin has been established. In this collection, the characterization has been expanded using ISSR markers, and it has been reevaluated with new agromorphological data, including drought tolerance characters. This VCC presents a minimum loss of genetic diversity concerning the total collection and constitutes an invaluable material that can be used in future breeding programs for direct use in a resilient agricultural system.

Molecular bases for drought tolerance in common vetch: designing new molecular breeding tools

BACKGROUND

Common vetch (Vicia sativa L.) is a forage grain legume of high protein content and high nitrogen fixation, relevant in sustainable agriculture systems. Drought is the main limiting factor of this crop yield. Genetic resources collections are essential to provide genetic variability for breeding. The analysis of drought associated parameters has allowed us to identify drought tolerant and sensitive ecotypes in a vetch core collection.

RESULTS

To understand the mechanisms involved in drought response we analysed transcriptomic differences between tolerant and sensitive accessions. Polymorphic variants (SNPs and SSRs) in these differential expressed genes (DEGs) have also been analysed for the design of drought-associated markers. A total of 1332 transcripts were commonly deregulated in both genotypes under drought. To know the drought adaptive response, we also analysed DEGs between accessions. A total of 2646 transcripts are DEG between sensitive and tolerant ecotypes, in watered and drought conditions, including important genes involved in redox homeostasis, cell wall modifications and stress-response. The integration of this functional and genetic information will contribute to understand the molecular mechanisms of drought response and the adaptive mechanisms of drought tolerance in common vetch. The identification of polymorphic variants in these DEGs has also been screened for the design of drought-associated markers that could be used in future breeding program strategies.

CONCLUSIONS

Our studies shed light for the first time in common vetch about the genes and pathways associated with drought tolerance. In addition, we identify over 100 potential drought associated polymorphism, as SNPs or SSRs, which are differently present in drought and tolerant genotypes. The use of these molecular markers for trait prediction would enable the development of genomic tools for future engineering strategies by screening of germplasm crop collections for traits related with crop drought resilience, adaptability or yield in vetch.

Plant Genebanks: Present Situation and Proposals for Their Improvement. the Case of the Spanish Network

Genebanks were created by the middle of the twentieth century to preserve cultivated biodiversity when landraces began to be substituted by modern varieties. This move was generally accepted as a necessary step to safeguard the future. After about 75 years of collecting and maintaining genetic resources, the increasing ability of biotechnology to create new variability brings the roles of genebanks in the present and near future into question. As a continuation of several workshops that started in 2014, staff of some representative genebanks have met to discuss how the Spanish Plant Genetic Resources Network can be improved, identifying the following major shortcomings: lack of efficient coordination in the distribution of species among genebanks; too many genebanks; existence of detected and undetected duplicates; insufficient rate of regeneration; insufficient phenotyping, genotyping, and epiphenotyping; unsatisfactory rate of use by end users; and, insufficient funding. As a considerable increase in public funding is unlikely, we propose some strategies to increase the efficiency of the system. The most urgent tasks are to strengthen the rationalization of the network by establishing a clear hierarchy and functions, to improve the information in the base collection by deep characterization including not only phenotypes but also uses and utilities, to progressively replace the active collections with focused core collections constructed to meet users' needs, to optimize regeneration protocols, to limit new collecting expeditions of Spanish crop wild relatives to those growing in threatened habitats, and to develop user-friendly platforms to access germplasm documentation, including a unified system of descriptors and classification categories. Current advances in biotechnology, and especially those in gene editing will have without doubt an impact on the role of genebanks. However, the high number of genes and gene combinations created by evolution they hold cannot be produced by these techniques at present. So, these reservoirs of variability will continue to be indispensable for the near-medium future while the function of all the genes is unveiled. In turn, biotechnologies and gene editing will allow us to take advantage of the information held in genebanks in a more efficient and fast way, contributing to a better rationalization and functioning.