Speed breeding for multiple quantitative traits in durum wheat

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.

Designing future peanut: the power of genomics-assisted breeding

KEY MESSAGE

Integrating GAB methods with high-throughput phenotyping, genome editing, and speed breeding hold great potential in designing future smart peanut cultivars to meet market and food supply demands. Cultivated peanut (Arachis hypogaea L.), a legume crop greatly valued for its nourishing food, cooking oil, and fodder, is extensively grown worldwide. Despite decades of classical breeding efforts, the actual on-farm yield of peanut remains below its potential productivity due to the complicated interplay of genotype, environment, and management factors, as well as their intricate interactions. Integrating modern genomics tools into crop breeding is necessary to fast-track breeding efficiency and rapid progress. When combined with speed breeding methods, this integration can substantially accelerate the breeding process, leading to faster access of improved varieties to farmers. Availability of high-quality reference genomes for wild diploid progenitors and cultivated peanuts has accelerated the process of gene/quantitative locus discovery, developing markers and genotyping assays as well as a few molecular breeding products with improved resistance and oil quality. The use of new breeding tools, e.g., genomic selection, haplotype-based breeding, speed breeding, high-throughput phenotyping, and genome editing, is probable to boost genetic gains in peanut. Moreover, renewed attention to efficient selection and exploitation of targeted genetic resources is also needed to design high-quality and high-yielding peanut cultivars with main adaptation attributes. In this context, the combination of genomics-assisted breeding (GAB), genome editing, and speed breeding hold great potential in designing future improved peanut cultivars to meet market and food supply demands.

A comprehensive review on Gossypium hirsutum resistance against cotton leaf curl virus

Cotton (Gossypium hirsutum L.) is a significant fiber crop. Being a major contributor to the textile industry requires continuous care and attention. Cotton is subjected to various biotic and abiotic constraints. Among these, biotic factors including cotton leaf curl virus (CLCuV) are dominant. CLCuV is a notorious disease of cotton and is acquired, carried, and transmitted by the whitefly (Bemisia tabaci). A cotton plant affected with CLCuV may show a wide range of symptoms such as yellowing of leaves, thickening of veins, upward or downward curling, formation of enations, and stunted growth. Though there are many efforts to protect the crop from CLCuV, long-term results are not yet obtained as CLCuV strains are capable of mutating and overcoming plant resistance. However, systemic-induced resistance using a gene-based approach remained effective until new virulent strains of CLCuV (like Cotton Leaf Curl Burewala Virus and others) came into existence. Disease control by biological means and the development of CLCuV-resistant cotton varieties are in progress. In this review, we first discussed in detail the evolution of cotton and CLCuV strains, the transmission mechanism of CLCuV, the genetic architecture of CLCuV vectors, and the use of pathogen and nonpathogen-based approaches to control CLCuD. Next, we delineate the uses of cutting-edge technologies like genome editing (with a special focus on CRISPR-Cas), next-generation technologies, and their application in cotton genomics and speed breeding to develop CLCuD resistant cotton germplasm in a short time. Finally, we delve into the current obstacles related to cotton genome editing and explore forthcoming pathways for enhancing precision in genome editing through the utilization of advanced genome editing technologies. These endeavors aim to enhance cotton's resilience against CLCuD.

Genetic biofortification: advancing crop nutrition to tackle hidden hunger

Malnutrition, often termed "hidden hunger," represents a pervasive global issue carrying significant implications for health, development, and socioeconomic conditions. Addressing the challenge of inadequate essential nutrients, despite sufficient caloric intake, is crucial. Biofortification emerges as a promising solution by enhance the presence of vital nutrients like iron, zinc, iodine, and vitamin A in edible parts of different crop plants. Crop biofortification can be attained through either agronomic methods or genetic breeding techniques. Agronomic strategies for biofortification encompass the application of mineral fertilizers through foliar or soil methods, as well as leveraging microbe-mediated mechanisms to enhance nutrient uptake. On the other hand, genetic biofortification involves the strategic crossing of plants to achieve a desired combination of genes, promoting balanced nutrient uptake and bioavailability. Additionally, genetic biofortification encompasses innovative methods such as speed breeding, transgenic approaches, genome editing techniques, and integrated omics approaches. These diverse strategies collectively contribute to enhancing the nutritional profile of crops. This review highlights the above-said genetic biofortification strategies and it also covers the aspect of reduction in antinutritional components in food through genetic biofortification.

Robotized indoor phenotyping allows genomic prediction of adaptive traits in the field

Breeding for resilience to climate change requires considering adaptive traits such as plant architecture, stomatal conductance and growth, beyond the current selection for yield. Robotized indoor phenotyping allows measuring such traits at high throughput for speed breeding, but is often considered as non-relevant for field conditions. Here, we show that maize adaptive traits can be inferred in different fields, based on genotypic values obtained indoor and on environmental conditions in each considered field. The modelling of environmental effects allows translation from indoor to fields, but also from one field to another field. Furthermore, genotypic values of considered traits match between indoor and field conditions. Genomic prediction results in adequate ranking of genotypes for the tested traits, although with lesser precision for elite varieties presenting reduced phenotypic variability. Hence, it distinguishes genotypes with high or low values for adaptive traits, conferring either spender or conservative strategies for water use under future climates.

Crop/Plant Modeling Supports Plant Breeding: I. Optimization of Environmental Factors in Accelerating Crop Growth and Development for Speed Breeding

The environmental conditions in customered speed breeding practice are, to some extent, empirical and, thus, can be further optimized. Crop and plant models have been developed as powerful tools in predicting growth and development under various environments for extensive crop species. To improve speed breeding, crop models can be used to predict the phenotypes resulted from genotype by environment by management at the population level, while plant models can be used to examine 3-dimensional plant architectural development by microenvironments at the organ level. By justifying the simulations via numerous virtual trials using models in testing genotype × environment × management, an optimized combination of environmental factors in achieving desired plant phenotypes can be quickly determined. Artificial intelligence in assisting for optimization is also discussed. We admit that the appropriate modifications on modeling algorithms or adding new modules may be necessary in optimizing speed breeding for specific uses. Overall, this review demonstrates that crop and plant models are promising tools in providing the optimized combinations of environment factors in advancing crop growth and development for speed breeding.

Genetic approaches to exploit landraces for improvement of Triticum turgidum ssp. durum in the age of climate change

Addressing the challenges of climate change and durum wheat production is becoming an important driver for food and nutrition security in the Mediterranean area, where are located the major producing countries (Italy, Spain, France, Greece, Morocco, Algeria, Tunisia, Turkey, and Syria). One of the emergent strategies, to cope with durum wheat adaptation, is the exploration and exploitation of the existing genetic variability in landrace populations. In this context, this review aims to highlight the important role of durum wheat landraces as a useful genetic resource to improve the sustainability of Mediterranean agroecosystems, with a focus on adaptation to environmental stresses. We described the most recent molecular techniques and statistical approaches suitable for the identification of beneficial genes/alleles related to the most important traits in landraces and the development of molecular markers for marker-assisted selection. Finally, we outline the state of the art about landraces genetic diversity and signature of selection, already identified from these accessions, for adaptability to the environment.

Improving Coconut Using Modern Breeding Technologies: Challenges and Opportunities

Coconut (Cocos nucifera L.) is a perennial palm with a wide range of distribution across tropical islands and coastlines. Multitude use of coconut by nature is important in the socio-economic fabric framework among rural smallholders in producing countries. It is a major source of income for 30 million farmers, while 60 million households rely on the coconut industry directly as farm workers and indirectly through the distribution, marketing, and processing of coconut and coconut-based products. Stagnant production, inadequate planting materials, the effects of climate change, as well as pests and diseases are among the key issues that need to be urgently addressed in the global coconut industry. Biotechnology has revolutionized conventional breeding approaches in creating genetic variation for trait improvement in a shorter period of time. In this review, we highlighted the challenges of current breeding strategies and the potential of biotechnological approaches, such as genomic-assisted breeding, next-generation sequencing (NGS)-based genotyping and genome editing tools in improving the coconut. Also, combining these technologies with high-throughput phenotyping approaches and speed breeding could speed up the rate of genetic gain in coconut breeding to solve problems that have been plaguing the industry for decades.

The extended day length promotes earlier flowering of bermudagrass

Day length is a very critical environmental factor affecting plant growth and development. The extension of light application time has been shown to promote flowering in the long-day plant and to shorten breeding time in some crops. However, previous research on the regulation of bermudagrass flowering by light application time is scarce. Therefore, this study investigated the effect of day length on the growth and flowering of bermudagrass by prolonging the light application time in a controlled greenhouse. Three different light application times were set up in the experiment: 22/2 h (22 hours light/2 hours dark), 18/6 h (18 hours light/6 hours dark), 14/10 h (14 hours light/10 hours dark). Results showed that extending the light application time not only promoted the growth of bermudagrass (plant height, fresh weight, dry weight) but also its nutrient uptake (nitrogen (N) and phosphorous (P) content). In addition, daily light integrals were different when flowering under different light application times. Most importantly, under the 22/2 h condition, flowering time was successfully reduced to 44 days for common bermudagrass (Cynodon dactylon [L.] pers) genotype A12359 and 36 days for African bermudagrass (Cynodon transvaalensis Burtt-Davy) genotype ABD11. This study demonstrated a successful method of bermudagrass flowering earlier than usual time by manipulating light application time which may provide useful insights for bermudagrass breeding.

Domestication of newly evolved hexaploid wheat—A journey of wild grass to cultivated wheat

Domestication of wheat started with the dawn of human civilization. Since then, improvement in various traits including resistance to diseases, insect pests, saline and drought stresses, grain yield, and quality were improved through selections by early farmers and then planned hybridization after the discovery of Mendel’s laws. In the 1950s, genetic variability was created using mutagens followed by the selection of superior mutants. Over the last 3 decades, research was focused on developing superior hybrids, initiating marker-assisted selection and targeted breeding, and developing genetically modified wheat to improve the grain yield, tolerance to drought, salinity, terminal heat and herbicide, and nutritive quality. Acceptability of genetically modified wheat by the end-user remained a major hurdle in releasing into the environment. Since the beginning of the 21st century, changing environmental conditions proved detrimental to achieving sustainability in wheat production particularly in developing countries. It is suggested that high-tech phenotyping assays and genomic procedures together with speed breeding procedures will be instrumental in achieving food security beyond 2050.

Strategies for accelerating genetic gains in crop plants: special focus on speed breeding

Feeding 10 billion people sustainably by 2050 in the era of slow genetic progress has spurred urgent calls to bring more crops per unit time. Over the last century, crop physiologists and breeders have been trying to alter plant biology to investigate and intervene in developmental processes under controlled chambers. Accelerating the breeding cycle via "speed breeding" was the outcome of these experiments. Speed breeding accelerates the genetic gain via phenome and genome-assisted trait introgression, re-domestication, and plant variety registration. Furthermore, early varietal release through speed breeding offers incremental benefits over conventional methods. However, a lack of resources and species-specific protocols encumber the technological implementation, which can be alleviated by reallocating funds to establish speed breeding units. This review discusses the limitations of conventional breeding methods and various alternative strategies to accelerate the breeding process. It also discusses the intervention at various developmental stages to reduce the generation time and global impacts of speed breeding protocols developed so far. Low-cost, field-based speed breeding protocol developed by Punjab Agricultural University, Ludhiana, Punjab, India to harvest at least three generations of wheat in a year without demanding the expensive greenhouses or growth chambers is also discussed.

Cowpea speed breeding using regulated growth chamber conditions and seeds of oven-dried immature pods potentially accommodates eight generations per year

BACKGROUND

Cowpea is a dryland crop with potential to improve food security in sub-Saharan Africa, where it is mostly produced and consumed. Contemporary plant improvement technologies, including genome editing, marker-assisted selection, and optimized transformation protocols, are being deployed to improve cowpea characteristics. Integrating speed breeding with these technologies would accelerate genetic gain in cowpea breeding. There are established speed breeding protocols for other important legumes, such as soybean, peanut, and chickpea, but none has been previously reported for cowpea.

RESULTS

With the aid of regulated growth conditions in two different chamber types, as well as the cultivation of new plant generations from seeds of oven-dried immature pods, we developed and validated, for the first time, an efficient speed breeding protocol that accommodates approximately seven to eight breeding generations per year for 3 cowpea genotypes. The 3 cowpea genotypes were evaluated under controlled growth conditions in light-emitting diode and metal halide lamp chambers to determine the effect of CO₂ supplementation on flowering and maturation durations, optimum conditions for plant growth, cross pollination, and pod development. Elevated CO₂ concentration had no influence on either flowering time or pod development. Adequate temperature, relative humidity and light intensity improved plant development and the rate of successful hand pollination, and  cultivating seeds of 11-day-old immature pods oven-dried at 39 °C for 2 days resulted in at least a 62% reduction in the time between pollination and sowing of the next plant generation. The plants cultivated from seeds of the oven-dried immature pods showed no defect at any stage of development.

CONCLUSIONS

Using the speed breeding protocol developed in this study, cowpea breeding cycles can be increased from the traditional one cycle per year in the field to as many as 8 generations per year in regulated growth chamber conditions. This protocol has no special technical requirements; hence, it can be implemented in any standard growth chamber. This would fast-track development, testing, validation, and utilization of improved cowpea cultivars.

Harnessing adult-plant resistance genes to deploy durable disease resistance in crops

Adult-plant resistance (APR) is a type of genetic resistance in cereals that is effective during the later growth stages and can protect plants from a range of disease-causing pathogens. Our understanding of the functions of APR-associated genes stems from the well-studied wheat-rust pathosystem. Genes conferring APR can offer pathogen-specific resistance or multi-pathogen resistance, whereby resistance is activated following a molecular recognition event. The breeding community prefers APR to other types of resistance because it offers broad-spectrum protection that has proven to be more durable. In practice, however, deployment of new cultivars incorporating APR is challenging because there is a lack of well-characterised APRs in elite germplasm and multiple loci must be combined to achieve high levels of resistance. Genebanks provide an excellent source of genetic diversity that can be used to diversify resistance factors, but introgression of novel alleles into elite germplasm is a lengthy and challenging process. To overcome this bottleneck, new tools in breeding for resistance must be integrated to fast-track the discovery, introgression and pyramiding of APR genes. This review highlights recent advances in understanding the functions of APR genes in the well-studied wheat-rust pathosystem, the opportunities to adopt APR genes in other crops and the technology that can speed up the utilisation of new sources of APR in genebank accessions.

Chile Pepper (Capsicum) Breeding and Improvement in the "Multi-Omics" Era

Chile pepper (Capsicum spp.) is a major culinary, medicinal, and economic crop in most areas of the world. For more than hundreds of years, chile peppers have "defined" the state of New Mexico, USA. The official state question, "Red or Green?" refers to the preference for either red or the green stage of chile pepper, respectively, reflects the value of these important commodities. The presence of major diseases, low yields, decreased acreages, and costs associated with manual labor limit production in all growing regions of the world. The New Mexico State University (NMSU) Chile Pepper Breeding Program continues to serve as a key player in the development of improved chile pepper varieties for growers and in discoveries that assist plant breeders worldwide. Among the traits of interest for genetic improvement include yield, disease resistance, flavor, and mechanical harvestability. While progress has been made, the use of conventional breeding approaches has yet to fully address producer and consumer demand for these traits in available cultivars. Recent developments in "multi-omics," that is, the simultaneous application of multiple omics approaches to study biological systems, have allowed the genetic dissection of important phenotypes. Given the current needs and production constraints, and the availability of multi-omics tools, it would be relevant to examine the application of these approaches in chile pepper breeding and improvement. In this review, we summarize the major developments in chile pepper breeding and present novel tools that can be implemented to facilitate genetic improvement. In the future, chile pepper improvement is anticipated to be more data and multi-omics driven as more advanced genetics, breeding, and phenotyping tools are developed.

Novel Plant Breeding Techniques Shake Hands with Cereals to Increase Production

Cereals are the main source of human food on our planet. The ever-increasing food demand, continuously changing environment, and diseases of cereal crops have made adequate production a challenging task for feeding the ever-increasing population. Plant breeders are striving their hardest to increase production by manipulating conventional breeding methods based on the biology of plants, either self-pollinating or cross-pollinating. However, traditional approaches take a decade, space, and inputs in order to make crosses and release improved varieties. Recent advancements in genome editing tools (GETs) have increased the possibility of precise and rapid genome editing. New GETs such as CRISPR/Cas9, CRISPR/Cpf1, prime editing, base editing, dCas9 epigenetic modification, and several other transgene-free genome editing approaches are available to fill the lacuna of selection cycles and limited genetic diversity. Over the last few years, these technologies have led to revolutionary developments and researchers have quickly attained remarkable achievements. However, GETs are associated with various bottlenecks that prevent the scaling development of new varieties that can be dealt with by integrating the GETs with the improved conventional breeding methods such as speed breeding, which would take plant breeding to the next level. In this review, we have summarized all these traditional, molecular, and integrated approaches to speed up the breeding procedure of cereals.

Orphan Crops: A Best Fit for Dietary Enrichment and Diversification in Highly Deteriorated Marginal Environments

Orphan crops are indigenous and invariably grown by small and marginal farmers under subsistence farming systems. These crops, which are common and widely accepted by local farmers, are highly rich in nutritional profile, good for medicinal purposes, and well adapted to suboptimal growing conditions. However, these crops have suffered neglect and abandonment from the scientific community because of very low or no investments in research and genetic improvement. A plausible reason for this is that these crops are not traded internationally at a rate comparable to that of the major food crops such as wheat, rice, and maize. Furthermore, marginal environments have poor soils and are characterized by extreme weather conditions such as heat, erratic rainfall, water deficit, and soil and water salinity, among others. With more frequent extreme climatic events and continued land degradation, orphan crops are beginning to receive renewed attention as alternative crops for dietary diversification in marginal environments and, by extension, across the globe. Increased awareness of good health is also a major contributor to the revived attention accorded to orphan crops. Thus, the introduction, evaluation, and adaptation of outstanding varieties of orphan crops for dietary diversification will contribute not only to sustained food production but also to improved nutrition in marginal environments. In this review article, the concept of orphan crops vis-à-vis marginality and food and nutritional security is defined for a few orphan crops. We also examined recent advances in research involving orphan crops and the potential of these crops for dietary diversification within the context of harsh marginal environments. Recent advances in genomics coupled with molecular breeding will play a pivotal role in improving the genetic potential of orphan crops and help in developing sustainable food systems. We concluded by presenting a potential roadmap to future research engagement and a policy framework with recommendations aimed at facilitating and enhancing the adoption and sustainable production of orphan crops under agriculturally marginal conditions.

Breeding More Crops in Less Time: A Perspective on Speed Breeding

Simple Summary

Feeding our growing population is one of the primary concerns of plant breeders. Plant breeding needs to deliver a steady stream of modern cultivars in a time- and resource-efficient manner. This review discusses the speed breeding (SB) techniques which allow breeders to advance the crop generation in a shorter period of time. In addition, we highlight the current SB applications in major crops and explore ways to integrate SB with new breeding techniques for efficient and faster production of stable lines for basic and applied research.

Abstract

Breeding crops in a conventional way demands considerable time, space, inputs for selection, and the subsequent crossing of desirable plants. The duration of the seed-to-seed cycle is one of the crucial bottlenecks in the progress of plant research and breeding. In this context, speed breeding (SB), relying mainly on photoperiod extension, temperature control, and early seed harvest, has the potential to accelerate the rate of plant improvement. Well demonstrated in the case of long-day plants, the SB protocols are being extended to short-day plants to reduce the generation interval time. Flexibility in SB protocols allows them to align and integrate with diverse research purposes including population development, genomic selection, phenotyping, and genomic editing. In this review, we discuss the different SB methodologies and their application to hasten future plant improvement. Though SB has been extensively used in plant phenotyping and the pyramiding of multiple traits for the development of new crop varieties, certain challenges and limitations hamper its widespread application across diverse crops. However, the existing constraints can be resolved by further optimization of the SB protocols for critical food crops and their efficient integration in plant breeding pipelines.

Evaluation of Durum Wheat Genotypes for Resistance against Root Rot Disease Caused by Moroccan Fusarium culmorum Isolates

Fusarium culmorum is one of the most important causal agents of root rot of wheat. In this study, 10 F. culmorum isolates were collected from farms located in five agro-ecological regions of Morocco. These were used to challenge 20 durum wheat genotypes via artificial inoculation of plant roots under controlled conditions. The isolate virulence was determined by three traits (roots browning index, stem browning index, and severity of root rot). An alpha-lattice design with three replicates was used, and the resulting ANOVA revealed a significant (P < 0.01) effect of isolate (I), genotype (G), and G × I interaction. A total of four response types were observed (R, MR, MS, and S) revealing that different genes in both the pathogen and the host were activated in 53% of interactions. Most genotypes were susceptible to eight or more isolates, while the Moroccan cultivar Marouan was reported resistant to three isolates and moderately resistant to three others. Similarly, the Australian breeding line SSD1479-117 was reported resistant to two isolates and moderately resistant to four others. The ICARDA elites Icaverve, Berghisyr, Berghisyr2, Amina, and Icaverve2 were identified as moderately resistant. Principal component analysis based on the genotypes responses defined two major clusters and two sub-clusters for the 10 F. culmorum isolates. Isolate Fc9 collected in Khemis Zemamra was the most virulent while isolate Fc3 collected in Haj-Kaddour was the least virulent. This work provides initial results for the discovery of differential reactions between the durum lines and isolates and the identification of novel sources of resistance.

A toolkit to rapidly modify root systems through single plant selection

BACKGROUND

The incorporation of root traits into elite germplasm is typically a slow process. Thus, innovative approaches are required to accelerate research and pre-breeding programs targeting root traits to improve yield stability in different environments and soil types. Marker-assisted selection (MAS) can help to speed up the process by selecting key genes or quantitative trait loci (QTL) associated with root traits. However, this approach is limited due to the complex genetic control of root traits and the limited number of well-characterised large effect QTL. Coupling MAS with phenotyping could increase the reliability of selection. Here we present a useful framework to rapidly modify root traits in elite germplasm. In this wheat exemplar, a single plant selection (SPS) approach combined three main elements: phenotypic selection (in this case for seminal root angle); MAS using KASP markers (targeting a root biomass QTL); and speed breeding to accelerate each cycle.

RESULTS

To develop a SPS approach that integrates non-destructive screening for seminal root angle and root biomass, two initial experiments were conducted. Firstly, we demonstrated that transplanting wheat seedlings from clear pots (for seminal root angle assessment) into sand pots (for root biomass assessment) did not impact the ability to differentiate genotypes with high and low root biomass. Secondly, we demonstrated that visual scores for root biomass were correlated with root dry weight (r = 0.72), indicating that single plants could be evaluated for root biomass in a non-destructive manner. To highlight the potential of the approach, we applied SPS in a backcrossing program which integrated MAS and speed breeding for the purpose of rapidly modifying the root system of elite bread wheat line Borlaug100. Bi-directional selection for root angle in segregating generations successfully shifted the mean root angle by 30° in the subsequent generation (P ≤ 0.05). Within 18 months, BC₂F₄:F₅ introgression lines were developed that displayed a full range of root configurations, while retaining similar above-ground traits to the recurrent parent. Notably, the seminal root angle displayed by introgression lines varied more than 30° compared to the recurrent parent, resulting in lines with both narrow and wide root angles, and high and low root biomass phenotypes.

CONCLUSION

The SPS approach enables researchers and plant breeders to rapidly manipulate root traits of future crop varieties, which could help improve productivity in the face of increasing environmental fluctuations. The newly developed elite wheat lines with modified root traits provide valuable materials to study the value of different root systems to support yield in different environments and soil types.

Biofortification of Cereals and Pulses Using New Breeding Techniques: Current and Future Perspectives

Cereals and pulses are consumed as a staple food in low-income countries for the fulfillment of daily dietary requirements and as a source of micronutrients. However, they are failing to offer balanced nutrition due to deficiencies of some essential compounds, macronutrients, and micronutrients, i.e., cereals are deficient in iron, zinc, some essential amino acids, and quality proteins. Meanwhile, the pulses are rich in anti-nutrient compounds that restrict the bioavailability of micronutrients. As a result, the population is suffering from malnutrition and resultantly different diseases, i.e., anemia, beriberi, pellagra, night blindness, rickets, and scurvy are common in the society. These facts highlight the need for the biofortification of cereals and pulses for the provision of balanced diets to masses and reduction of malnutrition. Biofortification of crops may be achieved through conventional approaches or new breeding techniques (NBTs). Conventional approaches for biofortification cover mineral fertilization through foliar or soil application, microbe-mediated enhanced uptake of nutrients, and conventional crossing of plants to obtain the desired combination of genes for balanced nutrient uptake and bioavailability. Whereas, NBTs rely on gene silencing, gene editing, overexpression, and gene transfer from other species for the acquisition of balanced nutritional profiles in mutant plants. Thus, we have highlighted the significance of conventional and NBTs for the biofortification of cereals and pulses. Current and future perspectives and opportunities are also discussed. Further, the regulatory aspects of newly developed biofortified transgenic and/or non-transgenic crop varieties via NBTs are also presented.

Speed-Breeding System in Soybean: Integrating Off-Site Generation Advancement, Fresh Seeding, and Marker-Assisted Selection

Speed breeding by artificial control of photothermal conditions facilitates generation advancement but was limited in scale and cost. In this study, we demonstrated a cost-saving off-site summer nursery pattern, taking full advantage of shorter daylength and higher temperature with lower latitude compared to the origin of the soybean cultivars used in the study. This substantially reduced the generation cycles under totally natural conditions. Using this approach, two generations of soybean cultivars from Northeastern Spring Planting Region (NE) and Yellow-Huai-Hai Valleys Summer Planting Region (YHH) were successfully obtained in Beijing and Hainan, respectively, compared to one generation in origin. Fresh-seeding method was also used to further shorten the generation duration by 7-10 days, thereby allowing at least four generations per year. Using DNA markers to define haplotypes of maturity genes E1-E4, we proposed a model to predict the optimum adaptation region of the advanced generation lines. Taken together, we present a speed-breeding methodology combining off-site nursery, fresh-seeding method, and marker-assisted selection, aimed at accelerating soybean improvement.

Genetics and breeding for climate change in Orphan crops

Climate change is rapidly changing how we live, what we eat and produce, the crops we breed and the target traits. Previously underutilized orphan crops that are climate resilient are receiving much attention from the crops research community, as they are often the only crops left in the field after periods of extreme weather conditions. There are several orphan crops with incredible resilience to biotic and abiotic stresses. Some are nutritious, while others provide good sources of biofuel, medicine and other industrial raw materials. Despite these benefits, orphan crops are still lacking in important genetic and genomic resources that could be used to fast track their improvement and make their production profitable. Progress has been made in generating draft genomes of at least 28 orphan crops over the last decade, thanks to the reducing cost of sequencing. The implementation of a structured breeding program that takes advantage of additional modern crop improvement tools such as genomic selection, speed breeding, genome editing, high throughput phenotyping and breeding digitization would make rapid improvement of these orphan crops possible, but would require coordinated research investment. Other production challenges such as lack of adequate germplasm conservation, poor/non-existent seed systems and agricultural extension services, as well as poor marketing channels will also need to be improved if orphan crops were to be profitable. We review the importance of breeding orphan crops under the increasing effects of climate change, highlight existing gaps that need to be addressed and share some lessons to be learned from major crops.

Need for speed: manipulating plant growth to accelerate breeding cycles

To develop more productive and resilient crops that are capable of feeding 10 billion people by 2050, we must accelerate the rate of genetic improvement in plant breeding programs. Speed breeding manipulates the growing environment by regulating light and temperature for the purpose of rapid generation advance. Protocols are now available for a range of short-day and long-day species and the approach is highly compatible with other cutting-edge breeding tools such as genomic selection. Here, we highlight how speed breeding hijacks biological processes for applied plant breeding outcomes and provide a case study examining wheat growth and development under speed breeding conditions. The establishment of speed breeding facilities worldwide is expected to provide benefits for capacity building, discovery research, pre-breeding, and plant breeding to accelerate the development of productive and robust crops.

Small "Nested" Introgressions from Wild Thinopyrum Species, Conferring Effective Resistance to Fusarium Diseases, Positively Impact Durum Wheat Yield Potential

Today wheat cultivation is facing rapidly changing climate scenarios and yield instability, aggravated by the spreading of severe diseases such as Fusarium head blight (FHB) and Fusarium crown rot (FCR). To obtain productive genotypes resilient to stress pressure, smart breeding approaches must be envisaged, including the exploitation of wild relatives. Here we report on the assessment of the breeding potential of six durum wheat-Thinopyrum spp. recombinant lines (RLs) obtained through chromosome engineering. They are characterized by having 23% or 28% of their 7AL chromosome arm replaced by a "nested" alien segment, composed of homoeologous group 7 chromosome fractions from Th. ponticum and Th. elongatum (=7el1L + 7EL) or from different Th. ponticum accessions (=7el1L + 7el2L). In addition to the 7el1L genes Lr19 + Yp (leaf rust resistance, and yellow pigment content, respectively), these recombinant lines (RLs) possess a highly effective QTL for resistance to FHB and FCR within their 7el2L or 7EL portion. The RLs, their null segregants and well-adapted and productive durum wheat cultivars were evaluated for 16 yield-related traits over two seasons under rainfed and irrigated conditions. The absence of yield penalties and excellent genetic stability of RLs was revealed in the presence of all the alien segment combinations. Both 7el2L and 7EL stacked introgressions had positive impacts on source and sink yield traits, as well as on the overall performance of RLs in conditions of reduced water availability. The four "nested" RLs tested in 2020 were among the top five yielders, overall representing good candidates to be employed in breeding programs to enhance crop security and safety.

From Genetic Maps to QTL Cloning: An Overview for Durum Wheat

Durum wheat is one of the most important cultivated cereal crops, providing nutrients to humans and domestic animals. Durum breeding programs prioritize the improvement of its main agronomic traits; however, the majority of these traits involve complex characteristics with a quantitative inheritance (quantitative trait loci, QTL). This can be solved with the use of genetic maps, new molecular markers, phenotyping data of segregating populations, and increased accessibility to sequences from next-generation sequencing (NGS) technologies. This allows for high-density genetic maps to be developed for localizing candidate loci within a few Kb in a complex genome, such as durum wheat. Here, we review the identified QTL, fine mapping, and cloning of QTL or candidate genes involved in the main traits regarding the quality and biotic and abiotic stresses of durum wheat. The current knowledge on the used molecular markers, sequence data, and how they changed the development of genetic maps and the characterization of QTL is summarized. A deeper understanding of the trait architecture useful in accelerating durum wheat breeding programs is envisioned.

Role of Genetics, Genomics, and Breeding Approaches to Combat Stripe Rust of Wheat

Puccinia striiformis (Pst) is a devastating biotrophic fungal pathogen that causes wheat stripe rust. It usually loves cool and moist places and can cause 100% crop yield losses in a single field when ideal conditions for disease incidence prevails. Billions of dollars are lost due to fungicide application to reduce stripe rust damage worldwide. Pst is a macrocyclic, heteroecious fungus that requires primary (wheat or grasses) as well as secondary host (Berberis or Mahonia spp.) for completion of life cycle. In this review, we have summarized the knowledge about pathogen life cycle, genes responsible for stripe rust resistance, and susceptibility in wheat. In the end, we discussed the importance of conventional and modern breeding tools for the development of Pst-resistant wheat varieties. According to our findings, genetic engineering and genome editing are less explored tools for the development of Pst-resistant wheat varieties; hence, we highlighted the putative use of advanced genome-modifying tools, i.e., base editing and prime editing, for the development of Pst-resistant wheat.

Identification of novel QTLs for late leaf spot resistance and validation of a major rust QTL in peanut (Arachis hypogaea L.)

Co-occurrence of two devastating foliar-fungal diseases of peanut, viz., late leaf spot (LLS), and rust may cause heavy yield loss besides adversely affecting the quality of kernel and fodder. This study reports the mapping of seven novel stress-related candidate EST-SSRs in a region having major QTLs for LLS and rust diseases using an F₂ mapping population (GJG17 × GPBD4) consisting of 328 individuals. The parental polymorphism using 1311 SSRs revealed 84 SSRs (6.4%) as polymorphic and of these 70 SSRs could be mapped on 14 linkage groups (LG). QTL analysis has identified a common QTL (LLS_QTL1/Rust_QTL) for LLS and rust diseases in the map interval of 1.41 cM on A03 chromosome, explaining 47.45% and 70.52% phenotypic variations, respectively. Another major QTL for LLS (LLS_QTL1), explaining a 29.06% phenotypic variation was also found on LG_A03. A major rust QTL has been validated which was found harboring R-gene and resistance-related genes having a role in inducing hypersensitive response (HR). Further, 23 linked SSRs including seven novel EST-SSRs were also validated in 177 diverse Indian groundnut genotypes. Twelve genotypes resistant to both LLS and rust were found carrying the common (rust and LLS) QTL region, LLS QTL region, and surrounding regions. These identified and validated candidate EST-SSR markers would be of great use for the peanut breeding groups working for the improvement of foliar-fungal disease resistance.

Adaptive Traits to Improve Durum Wheat Yield in Drought and Crown Rot Environments

Durum wheat (Triticum turgidum L. ssp. durum) production can experience significant yield losses due to crown rot (CR) disease. Losses are usually exacerbated when disease infection coincides with terminal drought. Durum wheat is very susceptible to CR, and resistant germplasm is not currently available in elite breeding pools. We hypothesize that deploying physiological traits for drought adaptation, such as optimal root system architecture to reduce water stress, might minimize losses due to CR infection. This study evaluated a subset of lines from a nested association mapping population for stay-green traits, CR incidence and yield in field experiments as well as root traits under controlled conditions. Weekly measurements of normalized difference vegetative index (NDVI) in the field were used to model canopy senescence and to determine stay-green traits for each genotype. Genome-wide association studies using DArTseq molecular markers identified quantitative trait loci (QTLs) on chromosome 6B (qCR-6B) associated with CR tolerance and stay-green. We explored the value of qCR-6B and a major QTL for root angle QTL qSRA-6A using yield datasets from six rainfed environments, including two environments with high CR disease pressure. In the absence of CR, the favorable allele for qSRA-6A provided an average yield advantage of 0.57 t·ha⁻¹, whereas in the presence of CR, the combination of favorable alleles for both qSRA-6A and qCR-6B resulted in a yield advantage of 0.90 t·ha⁻¹. Results of this study highlight the value of combining above- and belowground physiological traits to enhance yield potential. We anticipate that these insights will assist breeders to design improved durum varieties that mitigate production losses due to water deficit and CR.

A Systematic Review of Durum Wheat: Enhancing Production Systems by Exploring Genotype, Environment, and Management (G × E × M) Synergies

According to the UN-FAO, agricultural production must increase by 50% by 2050 to meet global demand for food. This goal can be accomplished, in part, by the development of improved cultivars coupled with modern best management practices. Overall, wheat production on farms will have to increase significantly to meet future demand, and in the face of a changing climate that poses risk to even current rates of production. Durum wheat [Triticum turgidum L. ssp. durum (Desf.)] is used largely for pasta, couscous and bulgur production. Durum producers face a range of factors spanning abiotic (frost damage, drought, and sprouting) and biotic (weed, disease, and insect pests) stresses that impact yields and quality specifications desired by export market end-users. Serious biotic threats include Fusarium head blight (FHB) and weed pest pressures, which have increased as a result of herbicide resistance. While genetic progress for yield and quality is on pace with common wheat (Triticum aestivum L.), development of resistant durum cultivars to FHB is still lagging. Thus, successful biotic and abiotic threat mitigation are ideal case studies in Genotype (G) × Environment (E) × Management (M) interactions where superior cultivars (G) are grown in at-risk regions (E) and require unique approaches to management (M) for sustainable durum production. Transformational approaches to research are needed in order for agronomists, breeders and durum producers to overcome production constraints. Designing robust agronomic systems for durum demands scientific creativity and foresight based on a deep understanding of constitutive components and their innumerable interactions with each other and the environment. This encompasses development of durum production systems that suit specific agro-ecozones and close the yield gap between genetic potential and on-farm achieved yield. Advances in individual technologies (e.g., genetic improvements, new pesticides, seeding technologies) are of little benefit until they are melded into resilient G × E × M systems that will flourish in the field under unpredictable conditions of prairie farmlands. We explore how recent genetic progress and selected management innovations can lead to a resilient and transformative durum production system.

Accelerating Breeding for Heat Tolerance in Tomato (Solanum lycopersicum L.): An Integrated Approach

Heat stress is a major limiting factor for crop productivity. Tomato is highly sensitive to heat stress, which can result in a total yield loss. To adapt to current and future heat stress, there is a dire need to develop heat tolerant cultivars. Here, we review recent attempts to improve screening for heat tolerance and to exploit genetic and genomic resources in tomatoes. We provide key factors related to phenotyping environments and traits (morphological, physiological, and metabolic) to be considered to identify and breed thermo-tolerant genotypes. There is significant variability in tomato germplasm that can be harnessed to breed for thermo-tolerance. Based on our review, we propose that the use of advanced backcross populations and chromosome segments substitution lines is the best means to exploit variability for heat tolerance in non-cultivated tomato species. We applied a meta quantitative trait loci (MQTL) analysis on data from four mapping experiments to co-localize QTL associated with heat tolerance traits (e.g., pollen viability, number of pollen, number of flowers, style protrusion, style length). The analysis revealed 13 MQTL of which 11 were composed of a cluster of QTL. Overall, there was a reduction of about 1.5-fold in the confidence interval (CI) of the MQTL (31.82 cM) compared to the average CI of individual QTL (47.4 cM). This confidence interval is still large and additional mapping resolution approaches such as association mapping and multi-parent linkage mapping are needed. Further investigations are required to decipher the genetic architecture of heat tolerance surrogate traits in tomatoes. Genomic selection and new breeding techniques including genome editing and speed breeding hold promise to fast-track development of improved heat tolerance and other farmer- and consumer-preferred traits in tomatoes.

Using Yield Response Curves to Measure Variation in the Tolerance and Resistance of Wheat Cultivars to Fusarium Crown Rot

The disease crown rot, caused predominantly by the fungal pathogen Fusarium pseudograminearum, is a major disease of winter cereals in many regions of the world, including Australia. A methodology is proposed, using response curves, to robustly estimate the relationship between grain yield and increasing crown rot pathogen burdens. Using data from a field experiment conducted in northern New South Wales, Australia in 2016, response curves were derived for five commercial wheat cultivars exposed to six increasing rates of crown rot inoculum, where the rates served to establish a range of crown rot pathogen burdens. In this way, the response curve methodology is fundamentally different from alternate approaches that rely on genetic or environmental variation to establish a range in pathogen burdens over which yield loss relationships are estimated. By manipulating only the rates of crown rot inoculum and, thus, pathogen burden directly, the number of additional confounding factors and interactions are minimized, enabling the robust estimation of the rate of change in yield due to increasing crown rot pathogen burdens for each cultivar. The methodology revealed variation in the rate of change in yield between cultivars, along with the extent of crown rot symptoms expressed by the cultivars. Variation in the rate of change in yield between cultivars provides definitive evidence of differences in the tolerance of commercial Australian wheat cultivars to crown rot caused by F. pseudograminearum, while variation in the extent of crown rot symptoms signifies differences in the resistance of the cultivars to this disease. The response curve methodology also revealed variation in how the different mechanisms of tolerance and resistance act to limit yield losses due to crown rot for different cultivars.

Speed breeding in growth chambers and glasshouses for crop breeding and model plant research

'Speed breeding' (SB) shortens the breeding cycle and accelerates crop research through rapid generation advancement. SB can be carried out in numerous ways, one of which involves extending the duration of plants' daily exposure to light, combined with early seed harvest, to cycle quickly from seed to seed, thereby reducing the generation times for some long-day (LD) or day-neutral crops. In this protocol, we present glasshouse and growth chamber-based SB approaches with supporting data from experimentation with several crops. We describe the conditions that promote the rapid growth of bread wheat, durum wheat, barley, oat, various Brassica species, chickpea, pea, grass pea, quinoa and Brachypodium distachyon. Points of flexibility within the protocols are highlighted, including how plant density can be increased to efficiently scale up plant numbers for single-seed descent (SSD). In addition, instructions are provided on how to perform SB on a small scale in a benchtop growth cabinet, enabling optimization of parameters at a low cost.

A Major Root Architecture QTL Responding to Water Limitation in Durum Wheat

The optimal root system architecture (RSA) of a crop is context dependent and critical for efficient resource capture in the soil. Narrow root growth angle promoting deeper root growth is often associated with improved access to water and nutrients in deep soils during terminal drought. RSA, therefore is a drought-adaptive trait that could minimize yield losses in regions with limited rainfall. Here, GWAS for seminal root angle (SRA) identified seven marker-trait associations clustered on chromosome 6A, representing a major quantitative trait locus (qSRA-6A) which also displayed high levels of pairwise LD (r 2 = 0.67). Subsequent haplotype analysis revealed significant differences between major groups. Candidate gene analysis revealed loci related to gravitropism, polar growth and hormonal signaling. No differences were observed for root biomass between lines carrying hap1 and hap2 for qSRA-6A, highlighting the opportunity to perform marker-assisted selection for the qSRA-6A locus and directly select for wide or narrow RSA, without influencing root biomass. Our study revealed that the genetic predisposition for deep rooting was best expressed under water-limitation, yet the root system displayed plasticity producing root growth in response to water availability in upper soil layers. We discuss the potential to deploy root architectural traits in cultivars to enhance yield stability in environments that experience limited rainfall.

Speed breeding in growth chambers and glasshouses for crop breeding and model plant research

'Speed breeding' (SB) shortens the breeding cycle and accelerates crop research through rapid generation advancement. SB can be carried out in numerous ways, one of which involves extending the duration of plants' daily exposure to light, combined with early seed harvest, to cycle quickly from seed to seed, thereby reducing the generation times for some long-day (LD) or day-neutral crops. In this protocol, we present glasshouse and growth chamber-based SB approaches with supporting data from experimentation with several crops. We describe the conditions that promote the rapid growth of bread wheat, durum wheat, barley, oat, various Brassica species, chickpea, pea, grass pea, quinoa and Brachypodium distachyon. Points of flexibility within the protocols are highlighted, including how plant density can be increased to efficiently scale up plant numbers for single-seed descent (SSD). In addition, instructions are provided on how to perform SB on a small scale in a benchtop growth cabinet, enabling optimization of parameters at a low cost.

ADAM-Plant: A Software for Stochastic Simulations of Plant Breeding From Molecular to Phenotypic Level and From Simple Selection to Complex Speed Breeding Programs

Making decisions on plant breeding programs require plant breeders to be able to test different breeding strategies by taking into account all the crucial factors affecting crop genetic improvement. Due to the complexity of the decisions, computer simulation serves as an important tool for researchers and plant breeders. This paper describes ADAM-plant, which is a computer software that models breeding schemes for self-pollinated and cross-pollinated crop plants using stochastic simulation. The program simulates a population of plants and traces the genetic changes in the population under different breeding scenarios. It takes into account different population structures, genomic models, selection (strategies and units) and crossing strategies. It also covers important features e.g., allowing users to perform genomic selection (GS) and speed breeding, simulate genotype-by-environment interactions using multiple trait approach, simulate parallel breeding cycles and consider plot sizes. In addition, the software can be used to simulate datasets produced from very complex breeding program in order to test new statistical methodology to analyze such data. As an example, three wheat-breeding strategies were simulated in the current study: (1) phenotypic selection, (2) GS, and (3) speed breeding with genomic information. The results indicate that the genetic gain can be doubled by GS compared to phenotypic selection and genetic gain can be further increased considerably by speed breeding. In conclusion, ADAM-plant is an important tool for comparing strategies for plant breeding and for estimating the effects of allocation of different resources to the breeding program. In the current study, it was used to compare different methodologies for utilizing genomic information in cereal breeding programs for selection of best-fit breeding strategy as per available resources.