Innovations In Plant Breeding Research Articles

Enhancement of Production and Food Security Through Sustainable Shallot Cultivation

Abstract Increasing food production and security has become the main focus in facing global challenges. In this context, cultivating shallots (Allium cepa var. aggregatum) with a sustainable approach is critical to meeting sustainable food needs. Shallot is one of the horticultural crops that contribute significantly to farmers’ food needs, income, economy, and food supply in Indonesia. However, conventional shallot cultivation practices often face problems such as soil degradation, ecosystem damage, and dependence on synthetic chemicals. Therefore, sustainable shallot cultivation is vital to increase productivity, yield quality, and environmental sustainability. This article provides information and examines a sustainable systems approach in shallot cultivation involving organic farming practices, efficient water management, integrated weed control, and biological protection against diseases and pests. The use of varieties that are resistant to diseases and pests, as well as adaptive to climate change, are also important factors in sustainable shallot cultivation. In this case, technology and innovation in plant breeding can provide solutions to produce more resilient and productive shallot varieties. Sustainable shallot cultivation offers economic benefits for farmers and maintains environmental sustainability and food availability for the community. Therefore, collaboration between the government, farmers, research institutions, and the private sector is key in encouraging the adoption of sustainable practices in shallot cultivation.

Efficiency of Biological Typing Methods in Maize Hybrid Genetic Purity Estimation.

A high level of genetic purity in crop varieties must be achieved and maintained for agronomic performance, encouraging investment and innovation in plant breeding and ensuring that the improvements in productivity and quality imparted by breeders are delivered to the consumer. Since the success of hybrid seed production is dependent upon the genetic purity of the parental lines, in this study, the experimental F1exp maize hybrid and its parental inbreeds were used as a model system to examine the discriminative power of morphological, biochemical and SSR markers for seed purity assay. The highest number of off-type plants was estimated by morphological markers. According to the comparison of prolamins and albumins banding patterns of parental and derived F1exp seeds, genetic impurities could not be detected. Molecular analysis detected two types of genetic profile irregularity. Beside its use for verifying varieties of maize, report on umc1545 primer pair ability to detect non-specific bands (i.e., off-types), in both the maternal component and F1exp, which is the first report on this issue yet, strongly supports the recommendation of this SSR marker use for more accurate and time-efficient maize hybrids and parental lines genetic pyrity testing.

Responsible Innovation in Plant Breeding: The Case of Hybrid Potato Breeding.

As an emerging innovation, hybrid potato breeding raises high expectations about faster variety development and clean true potato seed as a new source of planting material. Hybrid breeding could, therefore, substantially contribute to global food security and other major sustainable development goals. However, its success will not only depend on the performance of hybrid potato in the field, but also on a range of complex and dynamic system conditions. This article is based on a multidisciplinary project in which we have studied the innovation dynamics of hybrid potato breeding and explored how these dynamics may shape the future of hybrid potato. Inspired by the approach of responsible innovation, we closely involved key players in the Dutch and international potato sector and other relevant actors in thinking about these potato futures. An important and recurrent theme in our work is the tension between the predominant commercial innovation dynamics in plant breeding and promises to respond to the global challenges of food security, agrobiodiversity and climate change. In this article, we, therefore, discuss responsible innovation strategies in (hybrid) potato breeding, which may help to bridge this tension and finally reflect on the implications for the field of plant breeding in general.

Understanding chromosome elimination in hybrid embryo cells for innovations in plant breeding

Understanding chromosome elimination in hybrid embryo cells for innovations in plant breeding

Contributions of Genome Editing Technologies Towards Improved Nutrition, Environmental Sustainability and Poverty Reduction.

The Sustainable Development Goals (SDGs) were launched in 2015, with the top three goals being poverty eradication, improved food security and increased human health. All 17 SDGs have a target achievement date of 2030. These are ambitious and inspirational goals that require substantial innovation and technology adoption for successful achievement. Innovations in plant breeding have substantially contributed to transforming the efficiency of food production since the mid 20th century, with innovations emerging in the current millennium demonstrating enhanced potential to improve crop yields, the nutritional values of food crops and environmental impacts. These outcomes underpin several SDGs, but in particular the first three. As climate change is expected to become increasingly variable, with greater impacts on agriculture, the ability to ensure increased food production is going to be increasingly important, as higher yields directly contribute to reducing poverty. This article reviews recent reports of potential contributions from genome editing technologies in terms of increased yield, enhanced nutrition and greater sustainability, highlighting their importance for achieving the leading three SDGs.

Towards a Fair Scope of Protection for Plant Breeders’ Rights in an Era of New Breeding Techniques: Proposals for a Modernization of the Essentially Derived Variety Concept

Plant breeders’ rights (PBRs) are an important IP right, and as plant breeding has a crucial role to play in sustainability, it is vital that innovations in plant breeding receive the appropriate innovation incentives. The full breeders’ exemption ensures that there is always free access to the plant variety protected by a PBR for developing new varieties. The price to pay for this exemption is that PBR holders cannot prevent third parties from taking advantage of their efforts and investments in developing a new variety. This invites free-riding, at the detriment of the PBR holder. The concept of “essentially derived varieties” (EDV), introduced in 1991, provided a “fix” for this problem. It allows PBR holders to extend, at least to some extent, the scope of protection of their PBR to those varieties which use all or most essential characteristics of the initial protection variety. Decades have passed, but no adequate interpretation of the complex EDV concept has been found. The advent of new breeding techniques (NBTs) has made the discussion about a fair scope of protection of PBRs all the more relevant. This necessitates a modernization of the EDV concept, if the PBR system is to remain relevant and continue to be an innovation-incentivizing mechanism. I argue that a broader scope for the EDV concept is essential and fair. Determining what essential derivation is will remain a difficult task also in the future. This is why I have additionally proposed a collaborative reward model, which will facilitate the functioning of the EDV system and is capable of providing more legal certainty in this area.

Role of information in consumers' preferences for eco-sustainable genetic improvements in plant breeding.

Consumers’ preferences for products derived from genetic improvements and innovations in plant breeding are often conditioned by technophobia and negative public imaginaries. The current study addresses this issue by analyzing consumers’ monetary preferences for a win-win innovation (generating gains for both private actors and the community) in the viticulture sector, namely fungus resistant grapes (FRG). The use of these grapes reduces the quantity of chemical inputs applied to vineyards, simultaneously improving firms’ economic performance. This study aimed to assess whether consumers prefer wines originating from FRG varieties to conventional wines. In particular, through an experimental online survey involving 627 Italian regular wine drinkers, the study compares individuals’ willingness to pay (WTP) for conventional wines with the WTP for two FRG wines produced with two different techniques: horticultural hybridization and genome editing. The study also assesses the potential effect of polarized media coverage on preferences by testing, in a between-subjects experimental design, two diverging (positive/negative) information scenarios, and the core drivers of these preferences. The findings suggest that respondents express a premium price for horticultural FRG wines compared to conventional wines (+9.14%) and a strong discount for genome edited FRG wines (–21.13%). The results also reveal that negative information reduces consumers’ WTP for horticultural FRG wines, while positive information increases their WTP for genome edited FRG wines. Last, the study highlights that individuals concerned with food sustainability issues and knowledgeable about wine are more likely to accept both FRG typologies. Overall, the study confirms the crucial role of appropriate information for market acceptance of innovations based on plant genetics to foster the adoption of sustainable pest-reducing practices in wine production.

The Use of Intellectual Property Systems in Plant Breeding for Ensuring Deployment of Good Agricultural Practices

Breeding innovations are relevant for sustainable agricultural development and food security, as new, resilient production systems require crop varieties optimally suited for these systems. In the societal debate around genetic engineering and other plant breeding innovations, ownership of patents on the technology used in the hands of large companies is often seen as a reason that small breeding companies are denied opportunities for further improving varieties or that farmers are restricted in using such varieties. However, intellectual property (IP) systems may also be used as tools to ensure the use of good agricultural practices when cultivating the resulting varieties. This paper explores documented cases in which IP systems (plant variety rights, patents and brand names) are used to promote that innovative varieties are grown according to good agricultural practices (GAP). These include effective disease resistance management regimes in innovative crop varieties of potato in order to prevent or delay pathogens from overcoming disease resistance genes, management regimes for transgenic insect-resistant Bt or herbicide-tolerant crops to prevent the development of resistant pests or weeds, respectively. The results are discussed with respect to the influence of breeders on GAP measures through various forms of IP and the contribution and role of other stakeholders, authorities and society at large in stimulating and ensuring the use of GAP.

Evolution and Application of Genome Editing Techniques for Achieving Food and Nutritional Security.

A world with zero hunger is possible only through a sustainable increase in food production and distribution and the elimination of poverty. Scientific, logistical, and humanitarian approaches must be employed simultaneously to ensure food security, starting with farmers and breeders and extending to policy makers and governments. The current agricultural production system is facing the challenge of sustainably increasing grain quality and yield and enhancing resistance to biotic and abiotic stress under the intensifying pressure of climate change. Under present circumstances, conventional breeding techniques are not sufficient. Innovation in plant breeding is critical in managing agricultural challenges and achieving sustainable crop production. Novel plant breeding techniques, involving a series of developments from genome editing techniques to speed breeding and the integration of omics technology, offer relevant, versatile, cost-effective, and less time-consuming ways of achieving precision in plant breeding. Opportunities to edit agriculturally significant genes now exist as a result of new genome editing techniques. These range from random (physical and chemical mutagens) to non-random meganucleases (MegaN), zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein system 9 (CRISPR/Cas9), the CRISPR system from Prevotella and Francisella1 (Cpf1), base editing (BE), and prime editing (PE). Genome editing techniques that promote crop improvement through hybrid seed production, induced apomixis, and resistance to biotic and abiotic stress are prioritized when selecting for genetic gain in a restricted timeframe. The novel CRISPR-associated protein system 9 variants, namely BE and PE, can generate transgene-free plants with more frequency and are therefore being used for knocking out of genes of interest. We provide a comprehensive review of the evolution of genome editing technologies, especially the application of the third-generation genome editing technologies to achieve various plant breeding objectives within the regulatory regimes adopted by various countries. Future development and the optimization of forward and reverse genetics to achieve food security are evaluated.

CRISPR innovations in plant breeding

CRISPR innovations in plant breeding

Potential, Challenges, and Threats for the Application of New Breeding Techniques by the Private Plant Breeding Sector in the EU

Reconciling sustainability with agricultural productivity in the face of climate change relies strongly on the development of resilient, high-yielding crops of superior nutritional value that can be grown more resource efficiently. Therefore, innovation in plant breeding has gained unprecedented importance. Plant breeding depends upon genetic variability within crops and their relatives as a basis for developing new plant varieties with improved characteristics. Plant breeders are continuously integrating the latest methods in plant biology and genetics into their breeding toolbox to more efficiently use existing diversity but also to induce new genetic variation. Over the past years, ever more precise and efficient plant breeding methods have been developed. This plant breeding innovation leap is based on an in-depth understanding of plant genomes and refinement of breeding methods, enabling more efficient, more precise and faster progress in achieving the desired breeding goals. Consequently, these plant breeding innovations are rapidly being developed and utilized internationally and across the seed sector, public and private research, plant species and markets. The results of a survey among 62 private plant breeding companies conducted by Euroseeds and presented in this publication confirm the enormous interest of companies in using new breeding techniques (NBTs) for a wide range of crop species and traits and the negative impact of the current regulatory situation in the EU on companies’ decisions for investments in NBT-related R&D activities for the EU market and beyond.

Puzzling out plant reproduction by haploid induction for innovations in plant breeding.

Mixing maternal and paternal genomes in embryos is not only responsible for the evolutionary success of sexual reproduction, but is also a cornerstone of plant breeding. However, once an interesting gene combination is obtained, further genetic mixing is problematic. To rapidly fix genetic information, doubled haploid plants can be produced: haploid embryos having solely the genetic information from one parent are allowed to develop, and chromosome doubling generates fully homozygous plants. A powerful path to the production of doubled haploids is based on haploid inducer lines. A simple cross between a haploid inducer line and the line with gene combinations to be fixed will trigger haploid embryo development. However, the exact mechanism behind in planta haploid induction remains an enduring mystery. The recent discoveries of molecular actors triggering haploid induction in the maize crop and the model Arabidopsis thaliana pinpoint an essential role of processes related to gamete development, gamete interactions and genome stability. These findings enabled translation of haploid induction capacity to other crops as well as the use of haploid inducer lines to deliver genome editing machinery into various crop varieties. These recent advances not only hold promise for the next generations of plant breeding strategies, but they also provide a deeper insight into the fundamental bases of sexual reproduction in plants.

The impact of a pulsed electromagnetic field on the seed protein content of soybean

Many studies show that in the last 20 years, the increase in production per hectare has been achieved mainly due to the creation of new varieties and the development of plant breeding. Innovations in plant breeding are the main way to find new traits, values and tolerances, which are the only ones that can respond to the increased demand for yield and more efficient production. In addition to high and stable yields, it is very important that the soybean seed has a satisfactory technological quality. Therefore, the aim of this study was to examine how the application of pulsed electromagnetic fields (PEMFs) affected the protein yield of soybean seed depending on the year, exposure time and frequency. The field trials were conducted in the experimental field of the Institute of Field and Vegetable Crops in Novi Sad, Serbia in 2010-2013. For this research, the seeds of a medium-sized variety Valjevka exposed to a pulsed electromagnetic field (PEMF) using a pulse generator and a strip applicator were used. A low frequency pulsed electromagnetic field (16, 24, 30, 72 Hz) was used at the exposure times of 0, 30, 60, and 90 minutes. The results of the research show that the application of this method can increase the yield of protein in soybean seed for more than 20%, which is a significant increase, especially in organic production, where the use of seed treatment agents is very restricted. However, this measure can also have an inhibitory effect if an adverse combination of exposure time and frequency strength is selected.

CRISPR/Cas-based genome editing to improve abiotic stress tolerance in plants

Climate change is affecting agriculture in a number of ways, such as changing water distribution, daily temperatures and salinity patterns. In this regard, plant breeding innovations and genetic engineering approaches to improve abiotic stress tolerance are necessary to avoid a decline in crop yields caused by climate change during the 21st century. In the last few years, genome editing using the CRISPR/Cas system has attracted attention as a powerful tool that can generate hereditary mutations. So far, only a few studies using the CRISPR/Cas system have been reported to improve abiotic stress tolerance, but they have clearly suggested its effective role for future applications in molecular breeding to improve abiotic stress tolerance. Accordingly, the CRISPR/Cas system application is introduced in this mini-review as a way to improve abiotic stress tolerance. Although editing efficiency and target discovery for plant CRISPR/Cas systems require further improvement, CRISPR/Cas systems will be the key approach to maintaining global food security during climate change.

Will the EU stay out of step with science and the rest of the world on plant breeding innovation?

Innovations in plant breeding like genome editing methods raised questions about the adequacy of established regulatory policies for plant breeding and biotechnology in view of these new breeding methods and the resulting products. Most countries follow the principle approach that only those plants will be regulated under biotech regulations that include a novel combination of genetic material following the Cartagena protocol. In contrast to this, the European Court of Justice interpreted the current EU biotech regulations in a way that these also apply to plants resulting from new mutagenesis breeding, even if these plants are indistinguishable from conventionally bred plants. This ruling created strong reactions and concerns stating that recent technical developments have made the EU GMO Directive no longer fit for purpose. The article describes ongoing policy developments on EU level that might result in an update of current regulations.

Modernising breeding for orphan crops: tools, methodologies, and beyond.

In spite of the limited investment in orphan crops, access to new technologies such as bioinformatics and low-cost genotyping opens new doors to modernise their breeding effectively. Innovation in plant breeding is imperative to meet the world's growing demand for staple food and feed crops, and orphan crops can play a significant role in increasing productivity and quality, especially in developing countries. The short breeding history of most orphan crops implies that genetic gain should be achievable through easy-to-implement approaches such as forward breeding for simple traits or introgression of elite alleles at key target trait loci. However, limited financial support and access to sufficient, relevant and reliable phenotypic data continue to pose major challenges in terms of resources and capabilities. Digitalisation of orphan-crop breeding programmes can help not only to improve data quality and management, but also to mitigate data scarcity by allowing data to be accumulated and analysed over time and across teams. Bioinformatics tools and access to technologies such as molecular markers, some of them provided as services via specific platforms, allow breeders to implement modern strategies to improve breeding efficiency. In orphan crops, more marker-trait associations relevant to breeding germplasm are generally needed, but implementing digitalization, marker-based quality control or simple trait screening and introgression will help modernising breeding. Finally, the development of local capacities-of both people and infrastructure-remains a necessity to ensure the sustainable adoption of modern breeding approaches.

Evolving Regulatory Landscape for Genome-Edited Plants.

New plant breeding innovations, including CRISPR-mediated genome editing, are enhancing the development of new plant varieties, many of which are on the cusp of entering market places internationally. The lack of clear and consistent regulatory policies globally for genome-edited plants, and their products, may limit the adoption and commercialization of these products; In contrast to the positive trends of regulatory agencies in Argentina, Brazil, Colombia, Chile, and the United States, which are at the forefront of a wave of countries that are implementing policies facilitating the development of genome-edited plants, the European Union has adopted a more restrictive approach that considers any new mutagenesis technique developed after 2001 as subject to regulation as genetically modified plants.

Plant breeding innovation: A global regulatory perspective

Background and objectivesWhile there has been continued improvement and increasing accessibility of enabling biotechnological tools, their ultimate deployment and range of applications in support of plant breeding will largely depend on how the resulting products are regulated and the extent of premarket assessment required. The features of GMO regulatory systems throughout the world are reviewed, with a focus on recent developments aimed at clarifying their application to biotechnological tools used for targeted mutagenesis and transfer of genetic material between crossable species.FindingsTo date, regulatory clarity for biotechnological innovations in plant breeding is limited to a small number of countries; the few countries with product‐based regulatory systems are generally able to continue using exiting regulatory provisions, and others have provided timely solutions that can result in the exclusion of some types of plant products from the scope of GMO regulations. However, the majority of countries are yet to take decisions on the topic. Their challenge is to achieve proportionate risk regulation for products developed using recent biotechnological tools that can result in a range of products, from transgenic plants to plants that are indistinguishable from conventionally bred plants.ConclusionsThe challenges for providing clarity on the regulation of plant breeding innovations are strongly linked to the features of the existing GMO regulations. Countries that regulate product risks are better equipped to adapt to technological change; conversely, countries that use process‐based regulatory triggers face the challenge of continuously adjusting to technological development and will lag behind unless they can timely develop criteria for regulatory exclusions. As a consequence of these different approaches, adopters of plant breeding innovations are faced with an uncertain and complex global regulatory situation that is unlikely to be resolved in the near future.Significance and noveltyThis review of the global regulatory status of plant breeding innovations demonstrates that to date, few countries have provided regulatory clarity. However, regulatory clarity, including consistent and predictable legislation with clear scope, triggers, and technical criteria, is required to facilitate technology adoption. The current uncertain and complex global regulatory situation is stifling innovation and the realization of the full potential of these technologies.

Breeding crops for the future

Breeding crops for the future

An innovative procedure of genome-wide association analysis fits studies on germplasm population and plant breeding.

The innovative RTM-GWAS procedure provides a relatively thorough detection of QTL and their multiple alleles for germplasm population characterization, gene network identification, and genomic selection strategy innovation in plant breeding. The previous genome-wide association studies (GWAS) have been concentrated on finding a handful of major quantitative trait loci (QTL), but plant breeders are interested in revealing the whole-genome QTL-allele constitution in breeding materials/germplasm (in which tremendous historical allelic variation has been accumulated) for genome-wide improvement. To match this requirement, two innovations were suggested for GWAS: first grouping tightly linked sequential SNPs into linkage disequilibrium blocks (SNPLDBs) to form markers with multi-allelic haplotypes, and second utilizing two-stage association analysis for QTL identification, where the markers were preselected by single-locus model followed by multi-locus multi-allele model stepwise regression. Our proposed GWAS procedure is characterized as a novel restricted two-stage multi-locus multi-allele GWAS (RTM-GWAS, https://github.com/njau-sri/rtm-gwas ). The Chinese soybean germplasm population (CSGP) composed of 1024 accessions with 36,952 SNPLDBs (generated from 145,558 SNPs, with reduced linkage disequilibrium decay distance) was used to demonstrate the power and efficiency of RTM-GWAS. Using the CSGP marker information, simulation studies demonstrated that RTM-GWAS achieved the highest QTL detection power and efficiency compared with the previous procedures, especially under large sample size and high trait heritability conditions. A relatively thorough detection of QTL with their multiple alleles was achieved by RTM-GWAS compared with the linear mixed model method on 100-seed weight in CSGP. A QTL-allele matrix (402 alleles of 139 QTL×1024 accessions) was established as a compact form of the population genetic constitution. The 100-seed weight QTL-allele matrix was used for genetic characterization, candidate gene prediction, and genomic selection for optimal crosses in the germplasm population.