Insights into a genomics‐based pre‐breeding program in wheat

There is growing recognition that sustainable intensification of agricultural production systems and their successful adaptation to changes in climate will depend upon the improved access to, and use of, genetic diversity. This paper analyzes how the collection, use and distribution of plant genetic resources by the Consortium of International Research Centers of the CGIAR are influenced by international and national policies, treaties and agreements. Some concerns exist among CGIAR scientists about continued access to, and distribution of, plant genetic resources. Study findings point to an increasing influence of international and national policies and legal frameworks on the conservation and use of plant genetic resources for food and agriculture (PGRFA) by the CGIAR centers and the dissemination of CGIAR-improved germplasm first to partners in agricultural research organizations and then to final users of new plant varieties developed through research partnerships. This situation may, in the longer term, have a serious impact on the utilization of plant genetic diversity to cope with current and predicted challenges to agricultural production and, in particular, climate change.

Insect and mite damage accounts for a significant level (30−70%) of total crop production losses. Conservation and use of plant genetic resources are required to endow crops with pest resistance, as well as to enhance crop yields and nutritional qualities. Advancements in molecular genetic technologies have the potential to facilitate the introgression of insect resistance genes from conserved and unadapted germplasm into cultivated crops. Long−term food security and the sustainability of agricultural productivity worldwide can be enhanced with the conservation and use of global plant genetic resources.

Bread wheat (Triticum aestivum) is one of the most important crop species. It has been further developed since its initial domestication, with significant acceleration of wheat breeding within the last 100 years. In this study, a set of 355 wheat accessions were selected to document the history of bread wheat breeding in Central Europe. Although six periods of breeding were assumed, a notable turning point was identified between periods 3 and 4 around the year 1970 based on phenotype and genotype data, dividing the more than 100 years of bread wheat breeding into only two periods. While the first period corresponded to the use of landraces and genetically diverse varieties for breeding, the second period was typically characterized by reliance on relatively few varieties, leading to modern varieties with very good yields and high resistance to lodging and powdery mildew. A drawback of these breeding programmes was a substantial reduction in genetic diversity. The analysis of population structure showed that genetic diversity is influenced more by pedigree than by the period of breeding. In total, five genetic populations were identified, corresponding (especially within the last 50 years) to the leading genotypes used in breeding programmes: Bankuti 1205, Mironovskaja 808 and Moisson. A high level of correlation was found between the genotype and phenotype data (R = 0.91; p < 0.01). The results of this study indicated the need to broaden the genetic diversity of bread wheat by including landraces and possibly wild relatives of crops in new breeding or prebreeding programmes.

Technical advances and development in the market for genomic tools have facilitated access to whole-genome data across species. Building-up on the acquired knowledge of the genome sequences, large-scale genotyping has been optimized for broad use, so genotype information can be routinely used to predict genetic merit. Genomic selection (GS) refers to the use of aggregates of estimated marker effects as predictors which allow improved individual differentiation at young age. Realizable benefits of GS are influenced by several factors and vary in quantity and quality between species. General characteristics and challenges of GS in implementation and routine application are described, followed by an overview over the current status of its use, prospects and challenges in important animal species. Genetic gain for a particular trait can be enhanced by shortening of the generation interval, increased selection accuracy and increased selection intensity, with species- and breed-specific relevance of the determinants. Reliable predictions based on genetic marker effects require assembly of a reference for linking of phenotype and genotype data to allow estimation and regular re-estimation. Experiences from dairy breeding have shown that international collaboration can set the course for fast and successful implementation of innovative selection tools, so genomics may significantly impact the structures of future breeding and breeding programmes. Traits of great and increasing importance, which were difficult to improve in the conventional systems, could be emphasized, if continuous availability of high-quality phenotype data can be assured. Equally elaborate strategies for genotyping and phenotyping will allow tailored approaches to balance efficient animal production, sustainability, animal health and welfare in future.

Peru is a place with abundant biological resources that should be employed for the benefit of society in general. However, to date, the use of Peruvian plant genetic resources was not fully exploited for the development of improved crops. This work was mostly conducted by the international private sector. The Climate Change Laboratory at Instituto Nacional de Innovación Agraria, and other laboratories at Universidad Nacional José Faustino Sánchez Carrión and Universidad Nacional Agraria La Molina together with other research programs of other institutions seek to promote the massive and sustainable use of plant genetic resources maintained in germplasm banks. It is planned to make use of modern molecular and morphological techniques. Moreover, infrastructure and human resources are being improved. As a result, we will be able to maintain the growth of the agricultural activity in Peru in terms of space and time.

Plant genetic resources are a link between agriculture, environment and trade, so their conservation requires cooperation from different sectors. The existing diversity in genetic resources is the foundation in breeding for new challenges or new markets in the future. The number of crop genetic resources in Serbia is obscure because there is no national inventory. It is thought that there are about 15,000 seed accessions and 3500 accessions of fruit trees and grape in collections of different national institutes and stakeholders. In the National Plant Gene Bank, there are more than 4000 accessions of nearly 250 plant species. Crops kept in ex situ collections are used in breeding programs and interspecific crosses, for selection and introduction of desired traits through pre-breeding programs. Serbia as a state participates in all national and international efforts for preservation, management and use of plant genetic resources. Additionally, Serbia has also established a set of national regulations related to plant genetic resources and their use in breeding. Since Serbia is one of Europe’s most important crop producers, especially in maize (11% of EU-27 production), soya (35%), sunflowers (6%) and sugar beet (2.5%), this paper discusses certain issues and achievements in the use of plant genetic resources in cereal and oil crops improvement in Serbia, as well as national and international regulations affecting their exploitation.

TrG2P: A transfer-learning-based tool integrating multi-trait data for accurate prediction of crop yield

The chapter describes three international agreements that have been or are being negotiated by countries through the FAO Commission on Genetic Resources for Food and Agriculture, focusing primarily on the International Treaty on Plant Genetic Resources for Food and Agriculture, which entered into force in June, 2004. The economic, technical, and legal issues which arose over the long negotiating process of this multilateral agreement for the conservation and sustainable use of plant genetic resources are described, as well as their implications for the design of the Treaty. The chapter describes the Treaty’s multilateral system of access to, and the sharing of benefits resulting from the use of plant genetic resources, including provisions on how it relates to intellectual property rights. It also discusses the role of Farmers’ Rights through which governments can protect relevant local knowledge, and recognizes farmers’ rights to equitable benefit-sharing and to participate in relevant national decisions providing access and benefits to farmers from plant genetic resources. The chapter includes a discussion of the International Code of Conduct for Plant Germplasm Collecting and Transfer, and the negotiations on a Code of Conduct on Biotechnology as it relates to genetic resources for food and agriculture.

The use of plant genetic diversity is essential for ensuring an adequate and stable supply of diverse food crops as well as for enhancing their nutritional quality. The role of effective conservation, management, and use of plant genetic resources in ensuring the availability of a diverse range of nutritious food crops is recognized throughout the work of the International Plant Genetic Resources Institute (IPGRI). Several research activities in the Institute's programme highlight how the diversity between and within food crop species is inextricably linked to the diversity of human cultural needs, preferences, and knowledge systems with respect to the management and use of plant genetic resources. The nutritional quality of food crops is among the major considerations that are important in both the improvement and conservation of genetic resources. Specific examples from IPGRI's work are used to illustrate these linkages.

Farmers’ Rights are basically about enabling farmers to conserve, develop and utilise plant genetic resources and traditional knowledge and recognising and rewarding them for their contribution to the global genetic pool. The Convention on Biological Diversity recognised the sovereign rights of countries for use of these resources. It affirmed that the owners have rights of their innovations, associated traditional knowledge and traditional practices whether or not it can be protected by intellectual property rights. It is an obligation for the governments to protect the ownership of the resources and associated knowledge through legal policy or law. Subsequently, the International Treaty on Plant Genetic Resources for Food and Agriculture ensured the conservation and sustainable use of plant genetic resources and the equitable sharing of benefits from their use. Farmers’ Rights are a foundation stone of this Treaty, as their realisation is a precondition for the conservation and sustainable use of the world’s vital plant genetic resources and traditional knowledge. The Treaty recognises the enormous contribution that the farmers of all regions have made, and will continue to make, for the conservation and development of these resources throughout the world. It further stipulates that governments to protect and promote Farmers’ Rights and choose the measures to do so according to their needs and priorities.

Variation in plant populations is very important for plant breeders. The basic aims of plant breeding are ‘high yield, high quality and quantity, extension of adaptation ability to climate and soil conditions and tolerance or resistance to pests and diseases’. Plant breeders use the genetic variations between plants to attain these objectives. Successful adaptation to environmental conditions and success in plant breeding are bounded by the range of the genetic base, as measured by genetic diversity. Genetic variation is needed to address many problems in plant breeding and it obtained from the biodiversity within the plant genetic resources (such as Breeding lines, Landraces, Primitive Forms, Wilds and Wild relatives, Weed races, etc.).

Plant genetic resources for food and agriculture are necessary in food production and biodiversity conservation. These are the most important natural resources, in addition to air, water and soil. Unfortunately, during the evolution large number of plant genetic resources has been lost. The biggest negative impact on loss of plant genetic resources had been made by humans through the modernization of agriculture and the creation of varieties of high genetic uniformity. FAO and its operation through international mechanisms, such as the adoption of the Convention on Biological Diversity, the first legal act which regulates all levels of biodiversity: ecosystems, species and genetic resources, biotechnology, including the Cartagena Protocol on Biosafety (regulates the transfer of genetic material across the border), contributed to the conservation of plant genetic resources for food and agriculture. In addition to the Convention on Biological Diversity, FAO has been defined by the International Treaty on Plant Genetic Resources for Food and Agriculture in more specific and detailed way, the preservation of genetic resources. The objectives of the International Treaty on Plant Genetic Resources for Food and Agriculture are the conservation and sustainable use of all plant genetic resources for food and agriculture and the fair and equitable sharing of the benefits arising out of their use. There are four basic pillars which form the substance of the Contract, Sustainable use of plant genetic resources, Farmers' Rights, the Multilateral System and the Global Information System. Two organizations, the International Biodiversity and the International Union for the Protection of New Varieties of Plants trying to solve the issues of protection of the population and old varieties as intellectual property.

The 1992 United Nations Conference on Environment and Development (UNCED) and the Convention on Biological Diversity (CBD) have propelled issues relating to the conservation and sustainable use of plant genetic resources to the fore. This paper attempts an objective appraisal from India's viewpoint of these relevant but contentious issues. After taking stock of crop genetic wealth, the shortcomings in the present structure of legal framework for conservation of the nation's genetic resources are examined. Property rights in plant genetic resources are the key to their conservation and wise use. Although India is a treasure-house of plant biodiversity, demographic factors, lack of a property rights regime and general ignorance have resulted in the plundering of these invaluable natural resources. This paper's argument is that if intellectual property rights (IPR) are imaginatively adapted to actual needs, they can go a long way towards the conservation of crop genetic resources. The dilemmas that developing countries face in the post-World Trade Organization (WTO) scenario are presented on the one hand as the all-important goal of food security (which calls for agricultural intensification), and habitat conservation on the other. Finally, a framework is suggested for the conservation and sustainable use of plant genetic resources.

In 1975, the International Board for Plant Genetic Resources created the first internationally linked system of genebanks, known as the Registry of Base Collections (RBC), to conserve plant germplasm and make it available globally for agricultural research and development. Over time, international efforts shifted away from enhancing and building the RBC toward other means to promote the conservation and sustainable use of plant genetic resources. Perhaps the most important development in this regard was the negotiation of the International Treaty on Plant Genetic Resources for Food and Agriculture (Plant Treaty or ITPGRFA) and the development of its multilateral system for access and benefit sharing (multilateral system). Our study aimed to ascertain whether the RBC materials are still being conserved/curated in the original recipient organizations. We also sought to assess whether those materials have been included in, and are available through, the ITPGRFA’s multilateral system. This outcome would be significant since, in many ways, the multilateral system reflects the spirit, commitment, and objectives of the RBC, with important additional components (e.g. obligations to share monetary benefits derived from the uses of plant genetic resources for food and agriculture). We identify four levels of probability that RBC materials are included in, and available through, the multilateral system. Ultimately, we find that there is a high level of probability that approximately 80% of the RBC materials are currently available through the multilateral system. We further identify a number of possible interventions that could be made to ensure that all RBC materials are conserved and made available through the multilateral system (or on similar terms and conditions of facilitated access and benefit sharing).

The efficient conservation and judicious use of plant genetic resources and related traditional knowledge is vital for food, health, and nutritional security. Plant genetic diversity available in gene banks, in the wild, and in farmer’s fields is crucial resource for food, health, and nutritional security, augmenting livelihoods and environmental services. These resources could support acclimatization of primary food crops to climate change impacts. In pursuit of improved cereal, pulse, horticultural, medicinal, aromatic, and other cash crop varieties suitable for particular agroecosystem, availability of a diversity of alleles/genes in terms of yield, quality, resistance against disease and pest, and tolerance for drought, heat, salt, and water in the wild relatives, indigenous, local land races, and farmer cultivars is the prime prerequisite, which limits the options for sustainable resilient agriculture management. To prevent their genetic erosion, a well-devised strong linkage between in situ resource conservation, collection and ex situ conservation in gene banks and their utilization for genetic improvement through research and breeding is required for their subsequent availability to farmer, pharmaceutical and seed community. Conserving plant genetic resources in situ as well as ex situ ensures efficient explorations in order to implement the International Treaty and Global Plan of Action on Plant Genetic Resources for Food and Agriculture. These collections are valuable genetic resource of resistance to diseases and pests, tolerance to climatic stresses, and improved targeted “trait” through crop improvement and assurance against genetic erosion. It is important to support in situ/on-farm conservation of agroecosystems because ex situ conservation cannot replicate the evolutionary processes and cultural practices but can act as crucial reservoir to safeguard them from calamities.