Genome engineering and plant breeding: impact on trait discovery and development

Strategies for breeding crops for future environments

The green revolution successfully increased agricultural output in the early 1960s by relying primarily on three pillars: plant breeding, irrigation, and chemical fertilization. Today, the need to reduce the use of chemical fertilizers, water scarcity, and future environmental changes, together with a growing population, requires innovative strategies to adapt to a new context and prevent food shortages. Therefore, scientists from around the world are directing their efforts to breed crops for future environments to sustainably produce more nutritious food. Herein, we propose scientific avenues to be reinforced in selecting varieties, including crop wild relatives, either for monoculture or mixed cropping systems, taking advantage of plant-microbial interactions, while considering the diversity of organisms associated with crops and unlocking combinatorial nutritional stresses.

Biotechnological Advances to Improve Abiotic Stress Tolerance in Crops

The major challenges that agriculture is facing in the twenty-first century are increasing droughts, water scarcity, flooding, poorer soils, and extreme temperatures due to climate change. However, most crops are not tolerant to extreme climatic environments. The aim in the near future, in a world with hunger and an increasing population, is to breed and/or engineer crops to tolerate abiotic stress with a higher yield. Some crop varieties display a certain degree of tolerance, which has been exploited by plant breeders to develop varieties that thrive under stress conditions. Moreover, a long list of genes involved in abiotic stress tolerance have been identified and characterized by molecular techniques and overexpressed individually in plant transformation experiments. Nevertheless, stress tolerance phenotypes are polygenetic traits, which current genomic tools are dissecting to exploit their use by accelerating genetic introgression using molecular markers or site-directed mutagenesis such as CRISPR-Cas9. In this review, we describe plant mechanisms to sense and tolerate adverse climate conditions and examine and discuss classic and new molecular tools to select and improve abiotic stress tolerance in major crops.

Aligning Policy Design With Science to Achieve Food Security: The Contribution of Genome Editing to Sustainable Agriculture

The need to meet the food demands of the world's growing population is the main challenge to global agricultural policy and economy. Issues in food security require innovative solutions. Modern biotechnology has a significant potential to contribute to food security, wealth, and sustainable development. Genetic engineering offers tools to improve nutrition, increase yield, and enhance crop resilience. New techniques of genome editing provide ample means to overcome limitations inherent in conventional plant breeding, but their industrial applicability depends on regulatory environment, decision making, and public perception. An alignment of goals between science and policy can help realise the potential of modern biotechnology to contribute to food security, wealth, and sustainable development.

Targeted plant improvement through genome editing: from laboratory to field

This review illustrates how far we have come since the emergence of GE technologies and how they could be applied to obtain superior and sustainable crop production. The main challenges of today's agriculture are maintaining and raising productivity, reducing its negative impact on the environment, and adapting to climate change. Efficient plant breeding can generate elite varieties that will rapidly replace obsolete ones and address ongoing challenges in an efficient and sustainable manner. Site-specific genome editing in plants is a rapidly evolving field with tangible results. The technology is equipped with a powerful toolbox of molecular scissors to cut DNA at a pre-determined site with different efficiencies for designing an approach that best suits the objectives of each plant breeding strategy. Genome editing (GE) not only revolutionizes plant biology, but provides the means to solve challenges related to plant architecture, food security, nutrient content, adaptation to the environment, resistance to diseases and production of plant-based materials. This review illustrates how far we have come since the emergence of these technologies and how these technologies could be applied to obtain superior, safe and sustainable crop production. Synergies of genome editing with other technological platforms that are gaining significance in plants lead to an exciting new, post-genomic era for plant research and production. In previous months, we have seen what global changes might arise from one new virus, reminding us of what drastic effects such events could have on food production. This demonstrates how important science, technology, and tools are to meet the current time and the future. Plant GE can make a real difference to future sustainable food production to the benefit of both mankind and our environment.

Advanced domestication: harnessing the precision of gene editing in crop breeding

Human population growth has increased the demand for food crops, animal feed, biofuel and biomaterials, all the while climate change is impacting environmental growth conditions. There is an urgent need to develop crop varieties which tolerate adverse growth conditions while requiring fewer inputs. Plant breeding is critical to global food security and, while it has benefited from modern technologies, it remains constrained by a lack of valuable genetic diversity, linkage drag, and an effective way to combine multiple favourable alleles for complex traits. CRISPR/Cas technology has transformed genome editing across biological systems and promises to transform agriculture with its high precision, ease of design, multiplexing ability and low cost. We discuss the integration of CRISPR/Cas-based gene editing into crop breeding to advance domestication and refine inbred crop varieties for various applications and growth environments. We highlight the use of CRISPR/Cas-based gene editing to fix desirable allelic variants, generate novel alleles, break deleterious genetic linkages, support pre-breeding and for introgression of favourable loci into elite lines.

Plant Co-expression Annotation Resource: a web server for identifying targets for genetically modified crop breeding pipelines

The development of genetically modified crops (GM) includes the discovery of candidate genes through bioinformatics analysis using genomics data, gene expression, and others. Proteins of unknown function (PUFs) are interesting targets for GM crops breeding pipelines for the novelty associated with such targets and also to avoid copyright protection. One method of inferring the putative function of PUFs is by relating them to factors of interest such as abiotic stresses using orthology and co-expression networks, in a guilt-by-association manner. In this regard, we have downloaded, analyzed, and processed genomics data of 53 angiosperms, totaling 1,862,010 genes and 2,332,974 RNA. Diamond and InterproScan were used to discover 72,266 PUFs for all organisms. RNA-seq datasets related to abiotic stresses were downloaded from NCBI/GEO. The RNA-seq data was used as input to the LSTrAP software to construct co-expression networks. LSTrAP also created clusters of transcripts with correlated expression, whose members are more probably related to the molecular mechanisms associated with abiotic stresses in the plants. Orthologous groups were created (OrhtoMCL) using all 2,332,974 proteins in order to associate PUFs to abiotic stress-related clusters of co-expression and therefore infer their function in a guilt-by-association manner. A freely available web resource named "Plant Co-expression Annotation Resource" ( https://www.machado.cnptia.embrapa.br/plantannot ), Plantannot, was created to provide indexed queries to search for PUF putatively associated with abiotic stresses. The web interface also allows browsing, querying, and retrieving of public genomics data from 53 plants. We hope Plantannot to be useful for researchers trying to obtain novel GM crops resistant to climate change hazards.

Chile as a key enabler country for global plant breeding, agricultural innovation, and biotechnology

Chile has become one of the main global players in seed production for counter-season markets and research purposes. Chile has a key role contributing to the reduction in seed production shortages in the Northern Hemisphere by speeding up the development of new hybrids, cultivars, and genetically modified (GM) organisms. The seeds that Chile produces for export include a considerable amount of GM seeds. Between 2009 and 2018, 1,081 different seed-planting events were undertaken for seed multiplication and/or research purposes. Every single event that had commodity cultivation status in 2018 in at least one country underwent field activities in Chile at least once over the last 10 y. Chile just adopted a regulatory approach for new plant breeding techniques. This type of regulatory approach should contribute to maintaining the status of Chile as a hot spot for future innovation in plant breeding-based biotechnology.

Genome assembly provides insights into the genome evolution and flowering regulation of orchardgrass

Orchardgrass (Dactylis glomerata L.) is an important forage grass for cultivating livestock worldwide. Here, we report an ~1.84-Gb chromosome-scale diploid genome assembly of orchardgrass, with a contig N50 of 0.93 Mb, a scaffold N50 of 6.08 Mb and a super-scaffold N50 of 252.52 Mb, which is the first chromosome-scale assembled genome of a cool-season forage grass. The genome includes 40 088 protein-coding genes, and 69% of the assembled sequences are transposable elements, with long terminal repeats (LTRs) being the most abundant. The LTRretrotransposons may have been activated and expanded in the grass genome in response to environmental changes during the Pleistocene between 0 and 1 million years ago. Phylogenetic analysis reveals that orchardgrass diverged after rice but before three Triticeae species, and evolutionarily conserved chromosomes were detected by analysing ancient chromosome rearrangements in these grass species. We also resequenced the whole genome of 76 orchardgrass accessions and found that germplasm from Northern Europe and East Asia clustered together, likely due to the exchange of plants along the 'Silk Road' or other ancient trade routes connecting the East and West. Last, a combined transcriptome, quantitative genetic and bulk segregant analysis provided insights into the genetic network regulating flowering time in orchardgrass and revealed four main candidate genes controlling this trait. This chromosome-scale genome and the online database of orchardgrass developed here will facilitate the discovery of genes controlling agronomically important traits, stimulate genetic improvement of and functional genetic research on orchardgrass and provide comparative genetic resources for other forage grasses.

Construction, characteristics and high throughput molecular screening methodologies in some special breeding populations: a horticultural perspective

Advanced marker technologies are widely used for evaluation of genetic diversity in cultivated crops, wild ancestors, landraces or any special plant genotypes. Developing agricultural cultivars requires the following steps: (i) determining desired characteristics to be improved, (ii) screening genetic resources to help find a superior cultivar, (iii) intercrossing selected individuals, (iv) generating genetically hybrid populations and screening them for agro-morphological or molecular traits, (v) evaluating the superior cultivar candidates, (vi) testing field performance at different locations, and (vii) certifying. In the cultivar development process valuable genes can be identified by creating special biparental or multiparental populations and analysing their association using suitable markers in given populations. These special populations and advanced marker technologies give us a deeper knowledge about the inherited agronomic characteristics. Unaffected by the changing environmental conditions, these provide a higher understanding of genome dynamics in plants. The last decade witnessed new applications for advanced molecular techniques in the area of breeding,with low costs per sample. These, especially, include next-generation sequencing technologies like reduced representation genome sequencing (genotyping by sequencing, restriction site-associated DNA). These enabled researchers to develop new markers, such as simple sequence repeat and single- nucleotide polymorphism, for expanding the qualitative and quantitative information onpopulation dynamics. Thus, the knowledge acquired from novel technologies is a valuable asset for the breeding process and to better understand the population dynamics, their properties, and analysis methods.

Insights into deployment of DNA markers in plant variety protection and registration

The efficiency of phenotype-based assessments of plant variety protection and registration could be improved by the integration of DNA-based testing. We review the current and proposed models in the era of next-generation breeding. The current plant variety protection system relies on morphological description of plant varieties. Distinctness, uniformity, and stability (DUS) assessments determine whether a new variety is distinguishable from common knowledge varieties and exhibits sufficient phenotypic uniformity and stability during two independent growing cycles. However, DUS assessment can be costly, time-consuming and often restricted to a relatively small number of traits that can be influenced by environmental conditions. This calls for the adoption of a DNA-based system which is endorsed by the International Union for the Protection of New Varieties of Plants (UPOV). This could enable examiners to deploy trait-specific DNA markers in DUS testing as well as using such genetic markers to manage reference collections. Within UPOV's system, breeders can freely use protected varieties in breeding programs. However, breeders of protected varieties may seek sharing in ownership of essentially derived varieties once it is proven that they, with the exception of a few distinctive DUS trait(s), conform to parental varieties in essential characteristics. As well as their complementary role in DUS testing, DNA markers have been known as a good replacement of morphological traits in defining boundaries between independently and essentially derived varieties. With the advent of new breeding technologies that allow minor modification in varieties with outcomes of specific merit or utility, detecting distinctness between varieties may become increasingly challenging. This, together with the ever-increasing number of varieties with which to compare new candidate varieties, supports the potential utility of using DNA-based approaches in variety description.

Estimating the cost of regulating genome edited crops: expert judgment and overconfidence

Experts are often called on to inform decision makers with subjective estimates of uncertain events. Their judgment serves as the basis for policy-related decision-making. This paper analyzes survey results used to collect experts' opinions of the likely cost to bring genome edited crops to market. We also examine the effect of expertise (scientific experts versus social scientists in plant biotechnology) and possible knowledge mis-calibration, both in terms of overconfidence (i.e., when subjective knowledge is inflated) and under-confidence (i.e., when subjective knowledge is deflated), on the estimation of cost involved in the development and commercial release of genome edited crops. We found that the expected costs of genome edited crops are case specific and depend on whether crops will likely be regulated as genetically modified or accepted as conventional varieties and not subject to any regulatory oversight by federal regulators. While cost evaluation of genome edited crops did not vary among scientific and social experts, it did vary among domains of knowledge. Hence, expert's performance can be described as task-specific in the context of this study.

Plant breeding at the speed of light: the power of CRISPR/Cas to generate directed genetic diversity at multiple sites

Classical plant breeding was extremely successful in generating high yielding crop varieties. Yet, in modern crops, the long domestication process has impoverished the genetic diversity available for breeding. This is limiting further improvements of elite germplasm by classical approaches. The CRISPR/Cas system now enables promising new opportunities to create genetic diversity for breeding in an unprecedented way. Due to its multiplexing ability, multiple targets can be modified simultaneously in an efficient way, enabling immediate pyramiding of multiple beneficial traits into an elite background within one generation. By targeting regulatory elements, a selectable range of transcriptional alleles can be generated, enabling precise fine-tuning of desirable traits. In addition, by targeting homologues of so-called domestication genes within one generation, it is now possible to catapult neglected, semi-domesticated and wild plants quickly into the focus of mainstream agriculture. This further enables the use of the enormous genetic diversity present in wild species or uncultured varieties of crops as a source of allele-mining, widely expanding the crop germplasm pool.

CRISPR/Cas9-mediated efficient editing in phytoene desaturase (PDS) demonstrates precise manipulation in banana cv. Rasthali genome

The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) has been reported for precise genome modification in many plants. In the current study, we demonstrate a successful mutation in phytoene desaturase (RAS-PDS) of banana cv. Rasthali using the CRISPR/Cas9 system. Two PDS genes were isolated from Rasthali (RAS-PDS1 and RAS-PDS2), and their protein sequence analysis confirmed that both PDS comprises conserved motifs for enzyme activity. Phylogenetic analysis of RAS-PDS1 and RAS-PDS2 revealed a close evolutionary relationship with other monocot species. The tissue-specific expression profile of RAS-PDS1 and RAS-PDS2 in Rasthali suggested differential regulation of the genes. A single 19-bp guide RNA (gRNA) was designed to target the conserved region of these two RAS-PDS and transformed with Cas9 in embryogenic cell suspension (ECS) cultures of cv. Rasthali. Complete albino and variegated phenotype were observed among regenerated plantlets. DNA sequencing of 13 plants confirmed the indels with 59% mutation frequency in RAS-PDS, suggesting activation of the non-homologous end-joining (NHEJ) pathway. The majority of mutations were either insertion (1-5) or deletion (1-4) of nucleotides near to protospacer adjacent motif (PAM). These mutations have created stop codons in RAS-PDS sequences which suggest premature termination of RAS-PDS protein synthesis. The decreased chlorophyll and total carotenoid contents were detected in mutant lines that revealed the functional disruption of both RAS-PDS genes. Our results demonstrate that genome editing through CRISPR/Cas9 can be applied as an efficient tool for banana genome modification.

Opportunities for genome editing in vegetable crops

Vegetables include high-value crops with health-promoting effects and reduced environmental impact. The availability of genomic and biotechnological tools in certain species, coupled with the recent development of new breeding techniques based on precise editing of DNA, provides unique opportunities to finally take advantage of the past decades of detailed genetic analyses, thus making improvement of traits related to quality and stress tolerance achievable in a reasonable time frame. Recent reports of such approaches in vegetables illustrate the feasibility of obtaining multiple homozygous mutations in a single generation, heritable by the progeny, using stable or transient transformation approaches, which may not rely on the integration of unwanted foreign DNA. Application of these approaches to currently non-sequenced/tissue culture recalcitrant crops will contribute to meet the challenges posed by the increase in population and climate change.

Toward Genomics-Based Breeding in C3 Cool-Season Perennial Grasses

Most important food and feed crops in the world belong to the C3 grass family. The future of food security is highly reliant on achieving genetic gains of those grasses. Conventional breeding methods have already reached a plateau for improving major crops. Genomics tools and resources have opened an avenue to explore genome-wide variability and make use of the variation for enhancing genetic gains in breeding programs. Major C3 annual cereal breeding programs are well equipped with genomic tools; however, genomic research of C3 cool-season perennial grasses is lagging behind. In this review, we discuss the currently available genomics tools and approaches useful for C3 cool-season perennial grass breeding. Along with a general review, we emphasize the discussion focusing on forage grasses that were considered orphan and have little or no genetic information available. Transcriptome sequencing and genotype-by-sequencing technology for genome-wide marker detection using next-generation sequencing (NGS) are very promising as genomics tools. Most C3 cool-season perennial grass members have no prior genetic information; thus NGS technology will enhance collinear study with other C3 model grasses like Brachypodium and rice. Transcriptomics data can be used for identification of functional genes and molecular markers, i.e., polymorphism markers and simple sequence repeats (SSRs). Genome-wide association study with NGS-based markers will facilitate marker identification for marker-assisted selection. With limited genetic information, genomic selection holds great promise to breeders for attaining maximum genetic gain of the cool-season C3 perennial grasses. Application of all these tools can ensure better genetic gains, reduce length of selection cycles, and facilitate cultivar development to meet the future demand for food and fodder.

Liquid-phase sequence capture and targeted re-sequencing revealed novel polymorphisms in tomato genes belonging to the MEP carotenoid pathway

Tomato (Solanum lycopersicum L.) plants are characterized by having a variety of fruit colours that reflect the composition and accumulation of diverse carotenoids in the berries. Carotenoids are extensively studied for their health-promoting effects and this explains the great attention these pigments received by breeders and researchers worldwide. In this work we applied Agilent’s SureSelect liquid-phase sequence capture and Illumina targeted re-sequencing of 34 tomato genes belonging to the methylerythritol phosphate (MEP) carotenoid pathway on a panel of 48 genotypes which differ for carotenoid content calculated as the sum of β-carotene, cis- and trans-lycopene. We targeted 230 kb of genomic regions including all exons and regulatory regions and observed ~40% of on-target capture. We found ample genetic variation among all the genotypes under study and generated an extensive catalog of SNPs/InDels located in both genic and regulatory regions. SNPs/InDels were also classified based on genomic location and putative biological effect. With our work we contributed to the identification of allelic variations possibly underpinning a key agronomic trait in tomato. Results from this study can be exploited for the promotion of novel studies on tomato bio-fortification as well as of breeding programs related to carotenoid accumulation in fruits.

Selective gene dosage by CRISPR-Cas9 genome editing in hexaploid Camelina sativa

In many plant species, gene dosage is an important cause of phenotype variation. Engineering gene dosage, particularly in polyploid genomes, would provide an efficient tool for plant breeding. The hexaploid oilseed crop Camelina sativa, which has three closely related expressed subgenomes, is an ideal species for investigation of the possibility of creating a large collection of combinatorial mutants. Selective, targeted mutagenesis of the three delta-12-desaturase (FAD2) genes was achieved by CRISPR-Cas9 gene editing, leading to reduced levels of polyunsaturated fatty acids and increased accumulation of oleic acid in the oil. Analysis of mutations over four generations demonstrated the presence of a large variety of heritable mutations in the three isologous CsFAD2 genes. The different combinations of single, double and triple mutants in the T3 generation were isolated, and the complete loss-of-function mutants revealed the importance of delta-12-desaturation for Camelina development. Combinatorial association of different alleles for the three FAD2 loci provided a large diversity of Camelina lines with various lipid profiles, ranging from 10% to 62% oleic acid accumulation in the oil. The different allelic combinations allowed an unbiased analysis of gene dosage and function in this hexaploid species, but also provided a unique source of genetic variability for plant breeding.

Genetic Transformation and Genomic Resources for Next-Generation Precise Genome Engineering in Vegetable Crops

In the frame of modern agriculture facing the predicted increase of population and general environmental changes, the securement of high quality food remains a major challenge to deal with. Vegetable crops include a large number of species, characterized by multiple geographical origins, large genetic variability and diverse reproductive features. Due to their nutritional value, they have an important place in human diet. In recent years, many crop genomes have been sequenced permitting the identification of genes and superior alleles associated with desirable traits. Furthermore, innovative biotechnological approaches allow to take a step forward towards the development of new improved cultivars harboring precise genome modifications. Sequence-based knowledge coupled with advanced biotechnologies is supporting the widespread application of new plant breeding techniques to enhance the success in modification and transfer of useful alleles into target varieties. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 system, zinc-finger nucleases, and transcription activator-like effector nucleases represent the main methods available for plant genome engineering through targeted modifications. Such technologies, however, require efficient transformation protocols as well as extensive genomic resources and accurate knowledge before they can be efficiently exploited in practical breeding programs. In this review, we revise the state of the art in relation to availability of such scientific and technological resources in various groups of vegetables, describe genome editing results obtained so far and discuss the implications for future applications.

Toward an Evolved Concept of Landrace

The term "landrace" has generally been defined as a cultivated, genetically heterogeneous variety that has evolved in a certain ecogeographical area and is therefore adapted to the edaphic and climatic conditions and to its traditional management and uses. Despite being considered by many to be inalterable, landraces have been and are in a constant state of evolution as a result of natural and artificial selection. Many landraces have disappeared from cultivation but are preserved in gene banks. Using modern selection and breeding technology tools to shape these preserved landraces together with the ones that are still cultivated is a further step in their evolution in order to preserve their agricultural significance. Adapting historical landraces to present agricultural conditions using cutting-edge breeding technology represents a challenging opportunity to use them in a modern sustainable agriculture, as an immediate return on the investment is highly unlikely. Consequently, we propose a more inclusive definition of landraces, namely that they consist of cultivated varieties that have evolved and may continue evolving, using conventional or modern breeding techniques, in traditional or new agricultural environments within a defined ecogeographical area and under the influence of the local human culture. This includes adaptation of landraces to new management systems and the unconscious or conscious selection made by farmers or breeders using available technology. In this respect, a mixed selection system might be established in which farmers and other social agents develop evolved landraces from the variability generated by public entities.