Speed Breeding Research Articles

Omics-Driven Strategies for Developing Saline-Smart Lentils: A Comprehensive Review

A number of consequences of climate change, notably salinity, put global food security at risk by impacting the development and production of lentils. Salinity-induced stress alters lentil genetics, resulting in severe developmental issues and eventual phenotypic damage. Lentils have evolved sophisticated signaling networks to combat salinity stress. Lentil genomics and transcriptomics have discovered key genes and pathways that play an important role in mitigating salinity stress. The development of saline-smart cultivars can be further revolutionized by implementing proteomics, metabolomics, miRNAomics, epigenomics, phenomics, ionomics, machine learning, and speed breeding approaches. All these cutting-edge approaches represent a viable path toward creating saline-tolerant lentil cultivars that can withstand climate change and meet the growing demand for high-quality food worldwide. The review emphasizes the gaps that must be filled for future food security in a changing climate while also highlighting the significant discoveries and insights made possible by omics and other state-of-the-art biotechnological techniques.

Accelerating genetic gain through strategic speed breeding in spring wheat

AbstractSpring wheat (Triticum aestivum L.) is a popular bread wheat with high milling and baking requirements. Vernalization is not required for spring wheat, which allows for fast growth under manipulated conditions. This experiment's objective was rapid development of inbred lines of hard red spring wheat throughout the off‐season and preserve enough genetic variability to perform selection. A total of 1575 F2 heads from three distinct populations were randomly harvested in the field‐season 2021. To break seed dormancy, seeds were held for 2 days at 0°C. Three breeding cycles were performed through single seed descent under manipulated growth condition during the off‐season 2021–2022. We were able to harvest plant materials as quickly as 54 days after planting in comparison to 110 days average field season. We lost a total of 36.4% during the three off‐season fast advancement generations and 711 genotypes reached the F5:6 generation with enough seed to perform a partially replicated small plot yield trial at two locations during the 2022 field‐season. Response traits collected included grain yield, grain protein, plant height, days to heading, and bacterial leaf streak (Xanthomonas transluens) disease severity. Heritability of collected traits varied between 0.61 and 0.92. Although we had considerable loss during the speed breeding, we were able to identify superior genotypes compared to the parents.

Editorial: Speed breeding systems for food

Editorial: Speed breeding systems for food

Plant Factory Speed Breeding Significantly Shortens Rice Generation Time and Enhances Metabolic Diversity

Rice (Oryza sativa L.) plays a pivotal role in global food security, yet its breeding is constrained by its long generation time and seasonality. To enhance rice breeding efficiency and meet future food demands, we have developed a vertical hydroponic breeding system integrated with light-emitting diodes (LEDs) lighting in a closed plant factory (PF), which significantly accelerates rice growth and generation advancement. The results show that indica rice can be harvested as early as after 63 days of cultivation, a 50% reduction compared with field cultivation, enabling the annual harvesting of 5–6 generations within the PF. A hyperspectral imaging system (HSI) and attenuated total reflectance infrared (ATR-IR) spectroscopy were further employed to characterize the chemical composition of the PF- and field-cultivated rice. Metabolomics analysis with ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) and gas chromatography-mass spectrometry (GC-MS) revealed that, compared with the field-cultivated rice, the PF-cultivated rice exhibited an up-regulation of total phenolic acids along with 68 non-volatile and 19 volatile metabolites, such as isovitexin, succinic acid, and methylillicinone F. Overall, this study reveals the unique metabolic profile of PF-cultivated rice and highlights the potential of PFs to accelerate the breeding of crops such as rice, offering an innovative agricultural strategy to support food security in the face of global population growth and climate change.

Revolutionizing plant breeding: a historical perspective from cross-pollination to gene editing

The history of plant breeding can be broadly divided into four eras: the Pre-Mendelian era (before 1900), the Mendelian era (1900-1920), the post-Mendelian era (1921-1950), and the Modern era (after 1950). Significant milestones include the release of the first hybrid maize varieties in 1961, the first sorghum hybrid (CSH-1) in 1964, the first bajra hybrid (HB-1) in 1965, and the first pigeon pea hybrid (ICPH-8) in 1991. Achieving a world with zero hunger requires a sustainable increase in food production and distribution and elimination of poverty. This goal demands scientific, logistical, and humanitarian approaches to ensure food security from farmers and breeders to policymakers and governments. Conventional breeding techniques alone are insufficient to meet the challenges posed by climate change, biotic and abiotic stress, and the growing global population projected to reach 10 billion by 2050. Novel plant breeding techniques, such as genome editing, speed breeding, and omics technology integration, offer precise, cost-effective, and less time-consuming solutions. These techniques enable the editing of agriculturally significant genes, promoting hybrid seed production, induced apomixis, and resistance to biotic and abiotic stress. Genome editing technologies have evolved, with CRISPR/Cas9 and its variants, base editing (BE), and prime editing (PE) playing pivotal roles in generating transgene-free plants. These advancements have significant implications for crop improvement, meeting food and nutrition security, and catering to regional preferences. Syngenta's initiative to open rights to CRISPR-based technologies through the Shoots by Syngenta platform exemplifies the collaborative efforts needed to drive agricultural innovation and sustainability. The review discusses the current regulatory regimes governing genome-edited crops, prospects of new tools such as DNA-free editing systems and nanotechnology, and their applicability in crop improvement. A multidisciplinary approach involving political, social, economic, and scientific stakeholders is essential for the successful adoption of genome editing technologies, which will ultimately make agriculture a lucrative profession and attract youth to the field.

Cassava breeding: Classical to recent breeding approaches for food, industry and climate resilience

Cassava ranks as the fourth-most significant starchy root crop in underdeveloped countries in terms of future food and acting as a key source of income for small and marginal farmers. To meet the growing demands for food security and economic development, it is imperative to develop improved cassava varieties that offer higher yields, enhanced nutritional content, safer for consumption, greater resistance to diseases and climate change. The development of these improved varieties necessitates advancements in breeding techniques, leveraging both traditional methods and modern biotechnological tools. However, a major challenge in cassava breeding is heterozygous nature and the crop’s sparse flowering, which limits the potential for sexual reproduction, thereby constraining breeding efforts for predominantly clonal selection. The continuous clonal propagation impedes genetic diversity and the introduction of novel traits, narrowing the overall progress of breeding programs. Integrating genomic tools and accelerating the adoption of biotechnological advancements can overcome these limitations and expedite the development of superior cassava varieties. This review highlights the need of cassava breeding for addressing these challenges with conventional as well as with new breeding techniques with the aim to provide a comprehensive understanding of the current scenario and future directions of cassava breeding research. Key words: Climate change, CRISPR/Cas 9, New breeding techniques, PPD, speed breeding, Waxy cassava

Molecular Marker Applications in the Selection of Elite Genotypes for Plant Stress Tolerance and Genetic Fidelity

Molecular markers play a crucial role in accelerating crop production for sustainable agriculture by identifying resistant traits and enhancing genetic diversity. In this review, we examine the impact of the molecular markers on advancing our understanding of stress tolerance mechanisms in plants, addressing the pressing imperative to bolster global food production to meet the escalating demands of the growing population. Additionally, the application of molecular markers to evaluate the genetic accuracy of plants due to genetic changes caused by somaclonal variation during <em>in vitro</em> propagation is mentioned. Specifically, we highlight emerging technologies like MAS, MARS, MABC, GWAS, GS, DH production, speed breeding, and genome editing, which offer promising opportunities to enhance stress tolerance and genetic integrity in crop cultivars, aiding in addressing global food security challenges. The literature search focused on studies published in the last ten years. We utilized a combination of specific and broad keywords such as genetic stability, <em>in vitro</em> propagation, molecular markers, abiotic-biotic stress, and plant biotechnology. In conclusion, this review analyzes the use of molecular markers in assessing the stress tolerance and genetic fidelity of <em>in vitro</em> grown plants.

Biotechnological studies towards improvement of finger millet using multi-omics approaches.

A plethora of studies have uncovered numerous important genes with agricultural significance in staple crops. However, when it comes to orphan crops like minor millet, genomic research lags significantly behind that of major crops. This situation has promoted a focus on exploring research opportunities in minor millets, particularly in finger millet, using cutting-edge methods. Finger millet, a coarse cereal known for its exceptional nutritional content and ability to withstand environmental stresses represents a promising climate-smart and nutritional crop in the battle against escalating environmental challenges. The existing traditional improvement programs for finger millet are insufficient to address global hunger effectively. The lack of utilization of high-throughput platforms, genome editing, haplotype breeding, and advanced breeding approaches hinders the systematic multi-omics studies on finger millet, which are essential for pinpointing crucial genes related to agronomically important and various stress responses. The growing environmental uncertainties have widened the gap between the anticipated and real progress in crop improvement. To overcome these challenges a combination of cutting-edge multi-omics techniques such as high-throughput sequencing, speed breeding, mutational breeding, haplotype-based breeding, genomic selection, high-throughput phenotyping, pangenomics, genome editing, and more along with integration of deep learning and artificial intelligence technologies are essential to accelerate research efforts in finger millet. The scarcity of multi-omics approaches in finger millet leaves breeders with limited modern tools for crop enhancement. Therefore, leveraging datasets from previous studies could prove effective in implementing the necessary multi-omics interventions to enrich the genetic resource in finger millet.

Strategies for enhancing productivity, resilience, nutritional quality, and consumption of pearl millet [Pennisetum glaucum (L.) R. Br.] for food and nutritional security in India

AbstractPearl millet [Pennisetum glaucum (L.) R. Br.] is an important component of agri‐food system in areas experiencing drought and high temperature and for increasing the resilience to climatic stresses and addressing malnutrition. The purpose of this review is to examine strategies for improving productivity, stress resilience, and nutritional quality of pearl millet and to understand its consumption pattern. Genetic diversification of hybrid parental lines remains strategically important to breed diverse, disease‐resistant and drought‐tolerant hybrids. Resistance to diseases, tolerance to drought, and high temperature and greater contents of iron and zinc are targeted in improving hybrid parental lines. Lodging resistance, compact panicles, panicle exertion, and improved seed set are universal traits, whereas duration, tillering ability, seed color, and seed size have a strong regional preference. The strategy of developing high‐yielding and disease‐resistant hybrids with adaptation to challenged agro‐ecologies has led to increase in yield from 303 to 1219 kg/ha between 1960 and 2020. Yield and stress resilience are to be increased further using conventional breeding and new tools like genomic selection, speed breeding, genome editing, and precision phenotyping. Mainstreaming grain nutritional traits, viz., iron and zinc contents in genetic improvement are essential to develop high‐yielding and nutrient‐rich pearl millet. There is need to enhance the consumption of pearl millet by strengthening existing value‐chain, providing consumer a choice of diverse range of food products, creating awareness about its health benefits and promotion through government schemes.

Plant breeding simulations with AlphaSimR

AbstractPlant breeding plays a crucial role in the development of high‐performing crop varieties that meet the demands of society. Emerging breeding techniques offer the potential to improve the precision and efficiency of plant breeding programs; however, their optimal implementation requires refinement of existing breeding programs or the design of new ones. Stochastic simulations are a cost‐effective solution for testing and optimizing new breeding strategies. The aim of this paper is to provide an introduction to stochastic simulation with software AlphaSimR for plant breeding students, researchers, and experienced breeders. We present an overview of how to use the software and provide an introductory AlphaSimR vignette as well as complete AlphaSimR scripts of breeding programs for self‐pollinated, clonal, and hybrid crops, including relevant breeding techniques, such as backcrossing, speed breeding, genomic selection, index selection, and others. Our objective is to provide a foundation for understanding and utilizing simulation software, enabling readers to adapt the provided scripts for their own use or even develop completely new plant breeding programs. By incorporating simulation software into plant breeding education and practice, the next generation of plant breeders will have a valuable tool in their quest to provide sustainable and nutritious food sources for a growing population.

Modified speed breeding approach reduced breeding cycle to less than half in vegetable soybean [Glycine max (L.) Merr.

The online version contains supplementary material available at 10.1007/s12298-024-01503-z.

SpeedyPaddy: a revolutionized cost-effective protocol for large scale offseason advancement of rice germplasm

BackgroundImproving the rate of genetic gain of cereal crop will rely on the accelerated crop breeding pipelines to allow rapid delivery of improved crop varieties. The laborious, time-consuming traditional breeding cycle, and the seasonal variations are the key factor restricting the breeder to develop new varieties. To address these issues, a revolutionized cost-effective speed breeding protocol for large-scale rice germplasm advancement is presented in the present study. The protocol emphasises on optimizing potting material, balancing the double-edged sword of limited nutritional dose, mode and stage of application, plant density, temperature, humidity, light spectrum, intensity, photoperiod, and hormonal regulation to accelerate rice growth and development.ResultsThe plant density of 700 plants/m2, cost-effective halogen tubes (B:G:R:FR-7.0:27.6:65.4:89.2) with an intensity of ∼ 750–800 µmol/m2/s and photoperiod of 13 h light and 11 h dark during seedling and vegetative stage and 8 h light and 16 h dark during reproductive stage had a significant effect (P < 0.05) on reducing the mean plant height, tillering, and inducing early flowering. Our results confirmed that one generation can be achieved within 68–75 days using the cost-effective SpeedyPaddy protocol resulting in 4–5 generations per year across different duration of rice varieties. The other applications include hybridization, trait-based phenotyping, and mapping of QTL/genes. The estimated cost to run one breeding cycle with plant capacity of 15,680 plants in SpeedyPaddy was $2941 including one-time miscellaneous cost which is much lower than the advanced controlled environment speed breeding facilities.ConclusionThe protocol offers a promising cost-effective solution with average saving of 2.0 to 2.6 months per breeding cycle with an integration of genomics-assisted selection, trait-based phenotyping, mapping of QTL/genes, marker development may accelerate the varietal development and release. This outstanding cost-effective break-through marks a significant leap in rice breeding addressing climate change and food security.

Influence of red–blue light ratio on the phenology and morphology of different lentil (Lens culinaris Medik) and chickpea (Cicer arietinum) genotypes under a simple and resource‐efficient in‐house speed breeding method based on the application of extended photoperiod

Influence of red–blue light ratio on the phenology and morphology of different lentil (<scp><i>Lens culinaris</i></scp> Medik) and chickpea (<scp><i>Cicer arietinum</i></scp>) genotypes under a simple and resource‐efficient in‐house speed breeding method based on the application of extended photoperiod

Revolutionizing Crop Production: The Imperative of Speed Breeding Technology in Modern Crop Improvement

Revolutionizing Crop Production: The Imperative of Speed Breeding Technology in Modern Crop Improvement

Controlled Environment Ecosystem: A Cutting-Edge Technology in Speed Breeding.

The controlled environment ecosystem is a meticulously designed plant growing chamber utilized for cultivating biofortified crops and microgreens, addressing hidden hunger and malnutrition prevalent in the growing population. The integration of speed breeding within such controlled environments effectively eradicates morphological disruptions encountered in traditional breeding methods such as inbreeding depression, male sterility, self-incompatibility, embryo abortion, and other unsuccessful attempts. In contrast to the unpredictable climate conditions that often prolong breeding cycles to 10-15 years in traditional breeding and 4-5 years in transgenic breeding within open ecosystems, speed breeding techniques expedite the achievement of breeding objectives and F1-F6 generations within 2-3 years under controlled growing conditions. In comparison, traditional breeding may take 5-10 years for plant population line creation, 3-5 years for field trials, and 1-2 years for variety release. The effectiveness of speed breeding in trait improvement and population line development varies across different crops, requiring approximately 4 generations in rice and groundnut, 5 generations in soybean, pea, and oat, 6 generations in sorghum, Amaranthus sp., and subterranean clover, 6-7 generations in bread wheat, durum wheat, and chickpea, 7 generations in broad bean, 8 generations in lentil, and 10 generations in Arabidopsis thaliana annually within controlled environment ecosystems. Artificial intelligence leverages neural networks and algorithm models to screen phenotypic traits and assess their role in diverse crop species. Moreover, in controlled environment systems, mechanistic models combined with machine learning effectively regulate stable nutrient use efficiency, water use efficiency, photosynthetic assimilation product, metabolic use efficiency, climatic factors, greenhouse gas emissions, carbon sequestration, and carbon footprints. However, any negligence, even minor, in maintaining optimal photoperiodism, temperature, humidity, and controlling pests or diseases can lead to the deterioration of crop trials and speed breeding techniques within the controlled environment system. Further comparative studies are imperative to comprehend and justify the efficacy of climate management techniques in controlled environment ecosystems compared to natural environments, with or without soil.

Accelerated breeding strategies for biochemical marker-assisted backcross breeding and mapping population development in bread wheat (Triticum aestivum L.)

In order to rapidly adapt to the evolving climate and sustainably nourish the growing global population, plant breeders are actively investigating more efficient strategies to enhance crop yields. In this study, we present the development of a bread wheat mapping population and backcross breeding program, serving as a valuable genetic resource for mapping the effects of different alleles on trait performance. We employed innovative methodologies to rapidly introgress traits into the bread wheat cultivar. Specifically, we utilized two parents, including Tosunbey x Tahirova2000, in a recombinant inbred line population, in addition, a backcross strategy was applied with line 148 (obtained by crossing Tosunbey x Tahirova2000 with high gluten quality) as the recipient parent of the Nevzatbey cv., known for its awnless feature. The two most important applications of the rapid breeding method are extending the light period and breaking dormancy in early harvested seeds. Both applications were successfully implemented in our study. Our vegetation periods ranging from approximately 50–60 days. Additionally, an early genotype in our developed population was harvested in 40 days. Considering that the genotype underwent a 15-day vernalization period, the generation cycle, including vernalization, drying, and refrigeration, was completed in a total of 64 days. Notably, we employed not only biochemical markers for selection but also incorporated the rapid generation advance technology known as ‘speed breeding’, allowing us to develop BC5F1 within a span of two years. We posit that this approach proves instrumental in swiftly transferring genes for multiple target traits into adapted wheat cultivars or in pyramiding desirable traits within elite breeding material.

Advancement in modern breeding and genomic approaches to accelerate rice improvement: speed breeding focus

Advancement in modern breeding and genomic approaches to accelerate rice improvement: speed breeding focus

Alien introgression to wheat for food security: functional and nutritional quality for novel products under climate change.

Crop yield and quality has increased globally during recent decades due to plant breeding, resulting in improved food security. However, climate change and shifts in human dietary habits and preferences display novel pressure on crop production to deliver enough quantity and quality to secure food for future generations. This review paper describes the current state-of-the-art and presents innovative approaches related to alien introgressions into wheat, focusing on aspects related to quality, functional characteristics, nutritional attributes, and development of novel food products. The benefits and opportunities that the novel and traditional plant breeding methods contribute to using alien germplasm in plant breeding are also discussed. In principle, gene introgressions from rye have been the most widely utilized alien gene source for wheat. Furthermore, the incorporation of novel resistance genes toward diseases and pests have been the most transferred type of genes into the wheat genome. The incorporation of novel resistance genes toward diseases and pests into the wheat genome is important in breeding for increased food security. Alien introgressions to wheat from e.g. rye and Aegilops spp. have also contributed to improved nutritional and functional quality. Recent studies have shown that introgressions to wheat of genes from chromosome 3 in rye have an impact on both yield, nutritional and functional quality, and quality stability during drought treatment, another character of high importance for food security under climate change scenarios. Additionally, the introgression of alien genes into wheat has the potential to improve the nutritional profiles of future food products, by contributing higher minerals levels or lower levels of anti-nutritional compounds into e.g., plant-based products substituting animal-based food alternatives. To conclude, the present review paper highlights great opportunities and shows a few examples of how food security and functional-nutritional quality in traditional and novel wheat products can be improved by the use of genes from alien sources, such as rye and other relatives to wheat. Novel and upcoming plant breeding methods such as genome-wide association studies, gene editing, genomic selection and speed breeding, have the potential to complement traditional technologies to keep pace with climate change and consumer eating habits.

Speed Breeding: A Transformative Approach to Accelerate Crop Improvement

Speed breeding has emerged as a transformative approach to expedite crop improvement by optimizing environmental conditions to achieve rapid generation turnover. This technique manipulates factors such as photoperiod, temperature, light intensity, and nutrition to hasten plant growth and reproduction cycles. Through the production of 4-6 generations per year, compared to 1-2 generations in traditional breeding, speed breeding unlocks the potential for rapid development of crop varieties with enhanced yield potential, biotic and abiotic stress resilience, improved nutritional quality, and climate adaptation. The key principles involve tailoring photoperiods, controlling temperatures, employing specialized lighting, creating controlled environments, and formulating targeted nutrition. Speed breeding has diverse applications across cereals, legumes, vegetables, and other crops, enabling accelerated introgression of desirable traits, efficient hybrid breeding, and integration with contemporary genomics technologies. The primary advantages of speed breeding include rapid genetic gain, year-round breeding, precision phenotyping and selection, flexibility across diverse species, and seamless integration with molecular tools. However, challenges such as infrastructure costs, protocol optimization needs, genetic diversity implications, phenotyping data management, and accessibility constraints, particularly in developing countries, require attention. Future prospects encompass the integration of advanced genomics techniques, next-generation phenotyping, sustainable approaches, global consortiums for collaboration, capacity building initiatives, and responsible governance frameworks. Realizing the immense potential of speed breeding through collaborative efforts, cutting-edge innovations, and participatory approaches can contribute significantly to global food and nutritional security in the face of climate change.

Tools and Techniques to Accelerate Crop Breeding.

As climate changes and a growing global population continue to escalate the need for greater production capabilities of food crops, technological advances in agricultural and crop research will remain a necessity. While great advances in crop improvement over the past century have contributed to massive increases in yield, classic breeding schemes lack the rate of genetic gain needed to meet future demands. In the past decade, new breeding techniques and tools have been developed to aid in crop improvement. One such advancement is the use of speed breeding. Speed breeding is known as the application of methods that significantly reduce the time between crop generations, thereby streamlining breeding and research efforts. These rapid-generation advancement tactics help to accelerate the pace of crop improvement efforts to sustain food security and meet the food, feed, and fiber demands of the world's growing population. Speed breeding may be achieved through a variety of techniques, including environmental optimization, genomic selection, CRISPR-Cas9 technology, and epigenomic tools. This review aims to discuss these prominent advances in crop breeding technologies and techniques that have the potential to greatly improve plant breeders' ability to rapidly produce vital cultivars.