Plant Mutagenesis

Induced mutations play an important role in increasing the genetic diversity of desirable traits in various edible and agricultural plants. It is useful for the development of novel kinds with enhanced agronomic traits, such as the greater capacity for coping with biotic and abiotic stress and improving the nutritional quality of food crops. There are numerous plant-induced mutagenesis techniques available including physical mutagens, such as UV, X-rays, and gamma rays, as well as chemical mutagens, like sodium azide, methyl methanesulfonate (MMS), or ethyl methanesulfonate (EMS). Agrobacterium and transposon-based chromosomal integration are further biological mutagens. Induced mutations contribute significantly to the development of sustainable agricultural systems for food security and economic growth. Rice, barley, chrysanthemum, wheat, soybean, and maize are the six top plants with a high number of mutant varieties. The creation of new varieties as a result of induced mutation has increased genetic diversity. This study highlights the recent advances in a field-induced mutation that enhance the potential of plant germplasm.

Induced mutation has contributed to a great extent in crop improvement. Mutant lines with agronomic important traits are created by induced mutagenesis through physical, chemical and biological means. Although radiation mutation was predominantly used initially, due its harsh effects on plants chemical mutagens were used to induce mutation at later stage of mutation breeding. Recent advancements in genomics have developed various techniques for creation of mutants as well as their detection. Development of genome editing tools like TALENS, ZFN, and CRISPR has enabled targeted mutagenesis to create desirable traits in agronomically important crops. Presently, in the era of next generation sequencing (NGS) the detection of mutation is fast and cost effective. For characterization of the mutant lines in the omics era several molecular markers like RFLP, RAPD, SSR, SNP, etc. and transcriptome as well as smallRNA profiling are performed. This chapter deals with the various strategies applied to generate mutants in agriculture through classical and molecular means.

Nowadays, world food security is more and more threatened by the extreme events caused by climate change associated with the increasing population. Particularly, drought is reported to be the most harmful for agricultural production, including oilseed crops. However, some key traits for adaptation to this stress may be lost as a result of the restriction of wild germplasm and natural genetic diversity due to overexploitation and climate change. Hence, mutagenesis breeding has been widely adopted to ensure a sustainable genetic gain in crop adaptation and tolerance to drought as well as other abiotic stresses. In oilseed crops, many efforts have been expended during the last 50 years in mutation breeding, mainly to improve oil and seed quality for feed, food, and industrial applications. Like other crops, major advances in rapeseed and sesame have been achieved in the alteration of seed oil fatty acid composition and modification of some bioactive compounds. However, fewer reports have been published on the improvement of drought tolerance. In this chapter, we will present and discuss the main achievements in drought tolerance and seed and oil quality in rapeseed and sesame through induced mutagenesis breeding. The emphasis will be on the application of random mutagenesis, which is widely accepted, via the use of physical or chemical mutagen agents. New genome editing techniques, such as TALEN, ZFN, and CRISPR-Cas9 targeted mutagenesis, are increasingly applied to edit some genes associated with seed quality and to target specific drought-associated genes.

Intellectual property rights can cover biological inventions including plants, plant varieties, and plant parts. Defining stable boundaries for plant inventions as legal objects has proven difficult, and these challenges have been exacerbated by the focus on trait breeding in the creation of mutant and gene edited plants. We explore how intellectual property is used to claim ownership of plant inventions, and how this intersects with developments in genetic science. In particular, we analyse how genetic assessment has shaped the UPOV concept of essential determination, the determinative role genetics have played in essential derivation disputes, and proposals to rework essential derivation for the trait breeding era.

The primary objective of sustainable agriculture is to rise food production in order to ensure global food security. However, various environmental factors impose limitations on crop yields, which threaten food sustainability across the world. The appearance of next-generation sequencing techniques and the generation of extensive genomic sequencing input for diverse crop plant species, alongside the progress of transcriptome, proteome, and metabolome data, have opened up opportunities to create new varieties of crop through genetic engineering. Advances in genome editing techniques revolutionized plant breeding through targeted alteration of different genes among diverse crop plant species. The bacterial derived Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated protein 9 nuclease (Cas9), are among the most effective genome editing techniques that have been advanced in recent years. In addition to their universal application in all organisms tested thus far, CRISPR/Cas9 has also been praised for its simplicity, high efficiency, precision, versatility, and reproducibility. CRISPR/Cas9 has been used to achieve an extensive modifications, from subtle nucleotide changes as insertions/deletions within host genes, gene replacements and gene knock-ins by homologous recombination. Many agriculturally important and desirable traits result from random point mutations or indels at specific loci in either coding region of genes or respective promoters. Therefore, simulating these mutations in the genome of agricultural plants using gene editing methods can be a great progress in plant breeding. In this regard, the CRISPR/Cas platform has been used to target several genes implicated in phytopathogenic resistance, as well as abiotic stress and product quality. This chapter discusses the application of the CRISPR system in sustainable agriculture, along with challenges and future prospects.

Factors such as abiotic and biotic stress, pests, diseases, and climate change can affect the morpho-physiological and biochemical status of the plant and alter its growth and development. Therefore, there is a need for mutation breeding studies using chemical mutagens to increase genetic variation and to obtain new varieties with improved existing characteristics (high yield, resistance to diseases and pests, etc.) that can adapt to adverse conditions. For this reason, studies to determine the mutagen dose and application duration that will be exerted on plant species and varieties should be increased. In addition to in vivo mutation breeding, mutagen can be applied to plant parts (somatic parts such as leaves, shoots, and flowers) incubated in vitro, and by using the tissue culture technique, it is possible to be successful in developing varieties in a short time. In addition, molecular studies on the extent and, type and level of genetic variation in mutants obtained by mutation, and the identification and detection of mutant genes should be emphasized.

Advances in tissue culture methods have made the micropropagation of plants a viable option to regenerate plantlets in large quantities, which usually runs for commercial-level propagation. A diverse range of methods is readily usable for application on plants. Clonal propagations as well as the protection of superior genotypes that have been selected for efficiency necessitate genetic stability and uniformity among plantlets. The tissue culture of plants sometimes entails the emergence of genetic dissimilarities between explants, i.e. somaclonal variants which result from mutated genes or modifications in epigenetics. The restoration of in vitro genetic variability can lead to subtle somatic cell variability. Thus, it is crucial to ensure genetic homogeneity among in vitro-raised plantlets at a preliminary phase. The genetic stability of in vitro-made progenies can be studied through morpho-physiological, physiochemical, cytogenetic, and DNA-based molecular techniques. Phylogenetic analysis variance may be a significant matter in any micropropagation plan, whereby propagating true-to-type plant materials is prioritized. Somaclonal variation, on the other hand, generates genotypic lines via new, distinct tools that facilitate the emergence of variation in plants. This is especially important in the case of difficult-to-breed species or plants with limited genetic diversity. The effects of somaclonal variation can be manifested within relatively short timeframes and without requiring sophisticated technology.

Fruit crops are an important entity of the agriculture sector that plays a significant role in global nutritional health and food security. It has been estimated that by 2050, there will be 70% more food demand to meet the requirements of the fast-growing world population. Therefore, there is a need to improve the existing fruit crop cultivars by enhancing their diversity, productivity, nutritional attributes, and adaptability within ever-climate-changing scenarios. Conventional breeding methods for fruit crop improvement have been in practice for a long time, however, these techniques are laborious as they have a long phase of juvenility, heterozygosity issues, and are time-consuming. Mutation breeding's role in fruit crop improvement has been documented because of its ability in creating variability and shortening the time for new cultivar development. The mutation breeding for crop improvement through physical and chemical mutagens has been successfully exploited in fruit crops like pear, peach, banana, papaya, grapes, almond, plum, sour and sweet cherry, apple, lemon, blueberry, and rough lemon. In fruit crops, mutagenesis has shown evidence in improving the fruit traits like color development, fruit size enhancement, taste, aroma, and has induced dwarfism and self-incompatibility. The artificial plant mutation techniques such as physical and chemical mutations are very fascinating and the application of these techniques in fruit crops is resulting in new sustainable commercial cultivars.

Biotechnological tools and approaches have emerged as viable alternatives to traditional breeding programs, particularly in genetic improvement of crops. Among these approaches, in vitro mutagenesis stands out as a pioneering technique in creating variation among existing breeding material as well as screening of superior mutants. This technique has wide applications in bolstering both crop yield and quality and increasing resistance to different abiotic and biotic stresses. The present chapter briefly describes the different physical and chemical mutagens that are predominantly employed in in-vitro random mutagenesis. Additionally, the we focused into the realm of genome editing tools, which have proven invaluable in tailoring precise and targeted mutations. An emphasis is placed on outlining the manifold applications of in vitro mutagenesis, including its role in instilling stress tolerance and effecting improvements in crop yield and quality.

Induced mutation mimics the natural process of spontaneous mutation, which is the main working force behind the evolution of living beings. Among various mutagens, the gamma ray emitted from the ‘⁶⁰CO’ source is the most potent mutagen exploited for crop improvement, with the development of more than 50% of mutant varieties. The beauty of mutation breeding lies in its ability to improve one or a few traits while keeping the genetic makeup of the original variety intact. Most of the economic traits of important crops, right from yield, quality, and biotic and abiotic stresses to some novel variability which does not exist in the germplasm were successfully targeted for genetic improvement through gamma-ray-induced mutation. A large number of mutants were reported to have been induced through gamma rays in various crops and were either used directly as new varieties or as donor parents in hybridization program to develop improved varieties and hybrids. Among 3402 mutant varieties released worldwide for commercial cultivation in various crops including horticultural crops, gamma ray has contributed 1716 mutant varieties (50.44%). In the era of molecular biology, induced mutation is gaining more importance as mutants are the ideal genetic material for identification, isolation of genes, and study of the structure and functions of mutated genes. The recent advances in molecular biology, like next-generation sequencing (NGS), changed the scenario of mutant screening with MutMap (mapping-by-sequencing) and MutChromSeq (assorting the desired genes in the shortest time), thereby making the induced mutation relevant even in the genomic era. The present book chapter discusses the use of gamma rays in crop improvement through the creation of invaluable genetic variability to combat the challenges posed by climate change and population explosion and its contribution to food and nutritional security by developing mutant varieties throughout the world.

Rural landraces are heterogeneous cultivars possessing valuable, unique characteristics, and are widely adapted to specific eco-geographical areas. Due to the absence of artificial selection, formal breeding applications, and minimum bottle neck event, rural landraces have classically preserved, and retained most of the beneficial genes. Since long ago rural landraces have been explored for the genes of interest for various breeding programs for improvement of yield, quality, as well as stress tolerance traits. Rural landraces are generally not cultivated for commercial purpose due to the lower economic returns, and fail to compete with other commercial, and modern cultivars. However, improvement of specific defects can fit the rural landraces for commercial purpose. Mutation approaches have been exploited intensively for improving yield contributing characters, quality, and resistance for biotic and abiotic stresses in crops. Hence, mutation could be a potential strategy for improving the specific traits of rural landraces. In addition to utilize the physical and chemical mutagens, advanced genome editing tools have been utilized for editing specific genes and/or base pair mutation. This chapter discusses the potential applications of mutation to improve the rural landraces for agronomic, quality, and resistance to biotic and abiotic stresses. In addition to highlight the successful stories, the chapter also covers the current progress of mutation research as well as their potential challenges, and limitations in landraces improvement.

Modern agricultural operations employ crop improvement methods that have paradoxically diminished the genetic diversity of crop plants. Traditional crop development processes aimed at managing biotic and abiotic stresses often employ common genes, alleles, or parent lines, rendering them more susceptible to rapid failure. Contrarily, landraces of customary agricultural plants have consistently demonstrated resilience against unfavourable climatic conditions despite being limited to marginal areas. These landraces possess a substantial genetic potential that can be harnessed in pre-breeding or other plant breeding activities. Efforts are ongoing to preserve this genetic potential through on-farm, in-situ, or ex-situ conservation. Gene introgression into new varieties from landraces has shown promise. This is achieved through genomic selection based on the phenotypic and/or genotypic screening of desired traits. Modern molecular plant breeding tools such as QTL mapping and marker-assisted selection, alongside biotechnological tools for gene pyramiding, can be employed to prepare parental lines for crosses or to directly introduce them into a desired cultivar. Mutation breeding, an emerging tool in plant breeding, has shown considerable promise. It is now used with high throughput screening and/or genomic selection to identify beneficial heritable changes at the genome level with precision and speed. Given that rural landraces are reservoirs of extensive genetic variability, tools like mutation breeding can facilitate more significant deviations among the parentage of newly developed crops. Genetic homogeneity among crops poses an inherent risk when exposed to pertinent biotic or abiotic factors, potentially leading to total crop failure. Thus, the ultimate aim of new-age plant breeding programs is strategically exploiting and utilizing landraces. This is achieved by extending plant breeding activities, and leveraging new generation technology to expedite the process with greater precision, thereby enhancing the development of rural landraces through mutation breeding.

Mutagenesis and genome editing has emerged as a substitute to traditional plant breeding and transgenics for crop improvement and hence ensure sustainable food production. Plant breeding depends on combination of novel allelic variations which can be produced only by targeted or random mutagenesis. Mutagenesis has played a key role in the elucidation of plant growth and development mechanisms, adaptation, metabolic pathways, and signal transduction. During last few decades, different nucleases are capable of generating targeted mutations and have became important tools to improve gene editing and site-specific integration in various crop species. The rapid and exciting progress in genome editing for crop development has revolutionized plant breeding. This chapter provides insights on the methodology and applications of mutation induction and genome editing in crop improvement.

Rice is an important staple food for half of the world’s population. Development of high yielding varieties and large-scale cultivation of these varieties resulted in genetic erosion. Climate change is also posing a serious threat to crop cultivation. Unpredictable monsoon, sudden pest and disease outbreak, frequent droughts, floods, etc., increase the pressure to develop resistant genotypes. Traditional landraces are well adapted to local environment, possess resistant genes and some landraces have consumer preference due to aroma, medicinal properties, grain dimensions, etc. But they are late maturing, tall, lodging susceptible and photoperiod sensitive. Mutation breeding is a powerful method for developing new variation. Combining mutation breeding with rice landraces can help in tackling the problem of genetic erosion by genetic improvement of rice landraces. Gamma ray is the most commonly used mutagen in rice. Finding optimum dose (LD₅₀) of mutagen for a given material is essential for a successful breeding program. Trueness of mutants to parent can be confirmed by SSR marked based studies or whole genome sequencing. Mutation studies in rice landraces can also help in understanding gene function of genes responsible for special characters like aroma in rice using forward or reverse genetics. Targeted mutation using CRISPR/Cas technology can be used for understanding gene function.

Landraces serve as reservoirs of genetic diversity, contributing to the enrichment of biodiversity and the preservation and stabilization of ecosystems in a sustainable manner, thereby promoting their functional integrity. These landraces serve as invaluable genetic assets, embodying a rich blend of genes and traits shaped by the interactions between farmers, crops, and their environment. Over centuries, they have laid the genetic foundation of agriculture, offering traits associated with local adaptation, stress resilience, consistent yields, and nutritional value. Despite their comparatively lower productivity than modern cultivars, landraces have gained significance as reservoirs of genetic diversity, particularly for traits related to stress tolerance and resistance. They possess a diverse genetic heritage, making them valuable resources for future crop development, potentially enhancing crop performance, albeit with interactions with environmental factors. Landraces have also shown resistance to pathogens, holding untapped potential for further utilization. Moreover, they offer the prospect of improving the nutritional quality of cereal crops by enhancing traits like antioxidants, phenolics, carotenoids, and mineral content. This chapter emphasizes the importance of participatory plant breeding and variety selection in improving landraces, particularly in stressed situations where sustainability is a top goal. It also underscores the pivotal role of landraces in scientific plant breeding and their contribution to maintaining genetic diversity essential for creating new crop varieties. Additionally, mentions the current trend of landrace abandonment in favor of modern, high-yielding varieties in certain areas and emphasizes the multifaceted impact of enhancing landraces on rural development, encompassing food security, nutrition, income generation, and climate resilience.