Strategies, Advances, and Challenges in Breeding Perennial Grain Crops

Improving complex agronomic and domestication traits in the perennial grain crop intermediate wheatgrass with genetic mapping and genomic prediction

The perennial grass Thinopyrum intermedium (intermediate wheatgrass [IWG]) is being domesticated as a food crop. With a deep root system and high biomass, IWG can help reduce soil and water erosion and limit nutrient runoff. As a novel grain crop undergoing domestication, IWG lags in yield, seed size, and other agronomic traits compared to annual grains. Better characterization of trait variation and identification of genetic markers associated with loci controlling the traits could help in further improving this crop. The University of Minnesota's Cycle 5 IWG breeding population of 595 spaced plants was evaluated at two locations in 2021 and 2022 for agronomic traits plant height, grain yield, and spike weight, and domestication traits shatter resistance, free grain threshing, and seed size. Pairwise trait correlations were weak to moderate with the highest correlation observed between seed size and height (0.41). Broad-sense trait heritabilities were high (0.68-0.77) except for spike weight (0.49) and yield (0.44). Association mapping using 24,284 genome-wide single nucleotide polymorphism markers identified 30 main quantitative trait loci (QTLs) across all environments and 32 QTL-by-environment interactions (QTE) at each environment. The genomic prediction model significantly improved predictions when parents were used in the training set and significant QTLs and QTEs used as covariates. Seed size was the best predicted trait with model predictive ability (r) of 0.72; yield was predicted moderately well (r = 0.45). We expect this discovery of significant genomic loci and mostly high trait predictions from genomic prediction models to help improve future IWG breeding populations.

xAgrotriticum spp.: Quality properties of a potential perennial cereal candidate for sustainable agriculture

Perennial crop species have gained greater importance with regard to agricultural sustainability because of the ecological concerns related to annual crops. This study aimed to determine some of the primary quality traits of xAgrotriticum grains, a potential perennial wheat genotype, in comparison to the annual bread wheat variety Fineway. The antioxidant activity of xAgrotriticum was 2.79-, 1.38-, and 2.35-fold higher than that of bread wheat according to the 2,2-diphenyl-1picrylhydrazyl (DPPH), ferric reducing antioxidant power (FRAP), and cupric ion reducing antioxidant capacity (CURPAC) methods, respectively. The free, bound, and total phenolic contents in xAgrotriticum were 1.34-, 1.59-, and 1.54-fold higher than those in bread wheat. The protein content (19.58 %) of xAgrotriticum was 1.48-fold higher than that of bread wheat. Essential amino acids constituted 28.65 % of the total amino acids in xAgrotriticum and 30.38 % in Fineway. Interestingly, methionine and tryptophan were present in xAgrotriticum although both were below the detection limits in wheat. However, compared with wheat, the arginine content of xAgrotriticum was 18-fold higher with glycine and tyrosine both 8-fold more abundant. xAgrotriticum has significantly richer iron, zinc, and copper contents; 1.31-, 1.74-, and 2.02-fold, respectively, than wheat. xAgrotriticum may offer potential for direct use as a foodstuff or raw material due to its nutritional elements, in addition to its potential as a genitor in hybridisation programs to improve the nutritional values of annual wheat and its prenniality which is considered one of the primary necessities for more sustainable agriculture.

Review: Nitrogen acquisition, assimilation, and seasonal cycling in perennial grasses

Perennial grasses seasonal nitrogen (N) cycle extends the residence and reuse time of N within the plant system, thereby enhancing N use efficiency. Currently, the mechanism of N metabolism has been extensively examined in model plants and annual grasses, and although perennial grasses exhibit similarities, they also possess distinct characteristics. Apart from assimilating and utilizing N throughout the growing season, perennial grasses also translocate N from aerial parts to perennial tissues, such as rhizomes, after autumn senescence. Subsequently, they remobilize the N from these perennial tissues to support new growth in the subsequent year, thereby ensuring their persistence. Previous studies indicate that the seasonal storage and remobilization of N in perennial grasses are not significantly associated with winter survival despite some amino acids and proteins associated with low temperature tolerance accumulating, but primarily with regrowth during the subsequent spring green-up stage. Further investigation can be conducted in perennial grasses to explore the correlation between stored N and dormant bud outgrowth in perennial tissues, such as rhizomes, during the spring green-up stage, building upon previous research on the relationship between N and axillary bud outgrowth in annual grasses. This exploration on seasonal N cycling in perennial grasses can offer valuable theoretical insights for new perennial grasses varieties with high N use efficiency through the application of gene editing and other advanced technologies.

Perenniality: From model plants to applications in agriculture

To compensate for their sessile nature, plants have evolved sophisticated mechanisms enabling them to adapt to ever-changing environments. One such prominent feature is the evolution of diverse life history strategies, particularly such that annuals reproduce once followed by seasonal death, while perennials live longer by cycling growth seasonally. This intrinsic phenology is primarily genetic and can be altered by environmental factors. Although evolutionary transitions between annual and perennial life history strategies are common, perennials account for most species in nature because they survive well under year-round stresses. This proportion, however, is reversed in agriculture. Hence, perennial crops promise to likewise protect and enhance the resilience of agricultural ecosystems in response to climate change. Despite significant endeavors that have been made to generate perennial crops, progress is slow because of barriers in studying perennials, and many developed species await further improvement. Recent findings in model species have illustrated that simply rewiring existing genetic networks can lead to lifestyle variation. This implies that engineering plant life history strategy can be achieved by manipulating only a few key genes. In this review, we summarize our current understanding of genetic basis of perenniality and discuss major questions and challenges that remain to be addressed.

The improvement of agronomic performances in the cold weather conditions for perennial wheatgrass by crossing Thinopyrum intermedium with wheat-Th. intermedium partial amphiploids

Thinopyrum intermedium (2n=6x=42, StStJrJrJvsJvs) is resistant or tolerant to biotic and abiotic stresses, making it suitable for developing perennial crops and forage. Through five cycles of selection, we developed 24 perennial wheatgrass lines, designated 19HSC-Q and 20HSC-Z, by crossing wheat-Th. intermedium partial amphiploids with Th. intermedium. The cold resistance, morphological performance, chromosome composition, and yield components of these perennial lines were investigated from 2019 to 2022. Six lines of 19HSC-Q had higher 1,000-kernel weight, grains per spike, and tiller number than Th. intermedium, as well as surviving -30°C in winter. Lines 19HSC-Q14, 19HSC-Q18, and 19HSC-Q20 had the best performances for grain number per spike and 1,000-kernel weight. The 20HSC-Z lines, 20HSC-Z1, 20HSC-Z2, and 20HSC-Z3, were able to survive in the cold winter in Harbin and had been grown for two years. Sequential multicolor GISH analysis revealed that the Jvs subgenome of Th. intermedium were divided into two karyotypes, three pairs of type-I Jvs chromosomes and four pairs of type-II Jvs chromosomes. Both Th. intermedium and the 24 advanced perennial wheatgrass lines had similar chromosome compositions, but the translocations among subgenome chromosomes were detected in some lines with prominent agronomic traits, such as 19HSC-Q11, 19HSC-Q14, 19HSC-Q18, 19HSC-Q20, and the three 20HSC-Z lines. The chromosome aberrations were distinguished into two types: the large fragment translocation with St-Jr, Jvs-St, Jr-IIJvs, and Jvs-Jr and the small fragment introgression of Jr-St, St-IJvs, and Jvs-Jr. These chromosomal variations can be used to further analyze the relationship between the subgenomes and phenotypes of Th. intermedium. The results of this study provide valuable materials for the next selection cycle of cold-resistant perennial wheatgrass.

The legacies of the "Father of Hybrid Rice" and the seven representative achievements of Chinese rice research: A pioneering perspective towards sustainable development

The "Father of Hybrid Rice", Yuan Longping, created high-yield hybrid rice that can feed tens of millions of people annually. The research achievements of Yuan and his team on low cadmium-accumulating rice and sea rice, in addition to hybrid rice, as well as those of a large number of Chinese scientists engaged in rice research in other six areas, including the rice genome, purple endosperm rice, de novo domestication of tetraploid rice, perennial rice, rice blast disease, and key genes for high nitrogen use efficiency, play an important role in promoting the realization of the United Nations Sustainable Development Goals 2 and 12. The purpose of this review is not to elaborate on the details of each research, but to innovatively summarize the significance and inspiration of these achievements to ensure global food security and achieve sustainable agriculture. In the future, cultivating new rice varieties through modern biotechnology, such as genome editing, will not only reduce hunger, but potentially reduce human-land conflicts, improve the environment, and mitigate climate change.

Improving crop yield potential: Underlying biological processes and future prospects

The growing world population and global increases in the standard of living both result in an increasing demand for food, feed and other plant-derived products. In the coming years, plant-based research will be among the major drivers ensuring food security and the expansion of the bio-based economy. Crop productivity is determined by several factors, including the available physical and agricultural resources, crop management, and the resource use efficiency, quality and intrinsic yield potential of the chosen crop. This review focuses on intrinsic yield potential, since understanding its determinants and their biological basis will allow to maximize the plant's potential in food and energy production. Yield potential is determined by a variety of complex traits that integrate strictly regulated processes and their underlying gene regulatory networks. Due to this inherent complexity, numerous potential targets have been identified that could be exploited to increase crop yield. These encompass diverse metabolic and physical processes at the cellular, organ and canopy level. We present an overview of some of the distinct biological processes considered to be crucial for yield determination that could further be exploited to improve future crop productivity.

Integrating speed breeding with artificial intelligence for developing climate-smart crops

INTRODUCTION

In climate change, breeding crop plants with improved productivity, sustainability, and adaptability has become a daunting challenge to ensure global food security for the ever-growing global population. Correspondingly, climate-smart crops are also the need to regulate biomass production, which is imperative for the maintenance of ecosystem services worldwide. Since conventional breeding technologies for crop improvement are limited, time-consuming, and involve laborious selection processes to foster new and improved crop varieties. An urgent need is to accelerate the plant breeding cycle using artificial intelligence (AI) to depict plant responses to environmental perturbations in real-time.

MATERIALS AND METHODS

The review is a collection of authorized information from various sources such as journals, books, book chapters, technical bulletins, conference papers, and verified online contents.

CONCLUSIONS

Speed breeding has emerged as an essential strategy for accelerating the breeding cycles of crop plants by growing them under artificial light and temperature conditions. Furthermore, speed breeding can also integrate marker-assisted selection and cutting-edged gene-editing tools for early selection and manipulation of essential crops with superior agronomic traits. Scientists have recently applied next-generation AI to delve deeper into the complex biological and molecular mechanisms that govern plant functions under environmental cues. In addition, AIs can integrate, assimilate, and analyze complex OMICS data sets, an essential prerequisite for successful speed breeding protocol implementation to breed crop plants with superior yield and adaptability.

Perennials as Future Grain Crops: Opportunities and Challenges

Perennial grain crops could make a valuable addition to sustainable agriculture, potentially even as an alternative to their annual counterparts. The ability of perennials to grow year after year significantly reduces the number of agricultural inputs required, in terms of both planting and weed control, while reduced tillage improves soil health and on-farm biodiversity. Presently, perennial grain crops are not grown at large scale, mainly due to their early stages of domestication and current low yields. Narrowing the yield gap between perennial and annual grain crops will depend on characterizing differences in their life cycles, resource allocation, and reproductive strategies and understanding the trade-offs between annualism, perennialism, and yield. The genetic and biochemical pathways controlling plant growth, physiology, and senescence should be analyzed in perennial crop plants. This information could then be used to facilitate tailored genetic improvement of selected perennial grain crops to improve agronomic traits and enhance yield, while maintaining the benefits associated with perennialism.

QTL Map of Early- and Late-Stage Perennial Regrowth in Zea diploperennis

Numerous climate change threats will necessitate a shift toward more sustainable agricultural practices during the 21st century. Conversion of annual crops to perennials that are capable of regrowing over multiple yearly growth cycles could help to facilitate this transition. Perennials can capture greater amounts of carbon and access more water and soil nutrients compared to annuals. In principle it should be possible to identify genes that confer perenniality from wild relatives and transfer them into existing breeding lines to create novel perennial crops. Two major loci controlling perennial regrowth in the maize relative Zea diploperennis were previously mapped to chromosome 2 (reg1) and chromosome 7 (reg2). Here we extend this work by mapping perennial regrowth in segregating populations involving Z. diploperennis and the maize inbreds P39 and Hp301 using QTL-seq and traditional QTL mapping approaches. The results confirmed the existence of a major perennial regrowth QTL on chromosome 2 (reg1). Although we did not observe the reg2 QTL in these populations, we discovered a third QTL on chromosome 8 which we named regrowth3 (reg3). The reg3 locus exerts its strongest effect late in the regrowth cycle. Neither reg1 nor reg3 overlapped with tiller number QTL scored in the same population, suggesting specific roles in the perennial phenotype. Our data, along with prior work, indicate that perennial regrowth in maize is conferred by relatively few major QTL.

Understanding Omics Driven Plant Improvement and de novo Crop Domestication: Some Examples

In the current era, one of biggest challenges is to shorten the breeding cycle for rapid generation of a new crop variety having high yield capacity, disease resistance, high nutrient content, etc. Advances in the "-omics" technology have revolutionized the discovery of genes and bio-molecules with remarkable precision, resulting in significant development of plant-focused metabolic databases and resources. Metabolomics has been widely used in several model plants and crop species to examine metabolic drift and changes in metabolic composition during various developmental stages and in response to stimuli. Over the last few decades, these efforts have resulted in a significantly improved understanding of the metabolic pathways of plants through identification of several unknown intermediates. This has assisted in developing several new metabolically engineered important crops with desirable agronomic traits, and has facilitated the de novo domestication of new crops for sustainable agriculture and food security. In this review, we discuss how "omics" technologies, particularly metabolomics, has enhanced our understanding of important traits and allowed speedy domestication of novel crop plants.

Narrowing uncertainties in the effects of elevated CO2 on crops

Plant responses to rising atmospheric carbon dioxide (CO₂) concentrations, together with projected variations in temperature and precipitation will determine future agricultural production. Estimates of the impacts of climate change on agriculture provide essential information to design effective adaptation strategies, and develop sustainable food systems. Here, we review the current experimental evidence and crop models on the effects of elevated CO₂ concentrations. Recent concerted efforts have narrowed the uncertainties in CO₂-induced crop responses so that climate change impact simulations omitting CO₂ can now be eliminated. To address remaining knowledge gaps and uncertainties in estimating the effects of elevated CO₂ and climate change on crops, future research should expand experiments on more crop species under a wider range of growing conditions, improve the representation of responses to climate extremes in crop models, and simulate additional crop physiological processes related to nutritional quality.

Behavioural frameworks to understand public perceptions of and risk response to carbon dioxide removal

The adoption of carbon dioxide removal (CDR) technologies at a scale sufficient to draw down carbon emissions will require both individual and collective decisions that happen over time in different locations to enable a massive scale-up. Members of the public and other decision-makers have not yet formed strong attitudes, beliefs and preferences about most of the individual CDR technologies or taken positions on policy mechanisms and tax-payer support for CDR. Much of the current discourse among scientists, policy analysts and policy-makers about CDR implicitly assumes that decision-makers will exhibit unbiased, rational behaviour that weighs the costs and benefits of CDR. In this paper, we review behavioural decision theory and discuss how public reactions to CDR will be different from and more complex than that implied by rational choice theory. Given that people do not form attitudes and opinions in a vacuum, we outline how fundamental social normative principles shape important intergroup, intragroup and social network processes that influence support for or opposition to CDR technologies. We also point to key insights that may help stakeholders craft public outreach strategies that anticipate the nuances of how people evaluate the risks and benefits of CDR approaches. Finally, we outline critical research questions to understand the behavioural components of CDR to plan for an emerging public response.

Abiotic and biotic context dependency of perennial crop yield

Perennial crops in agricultural systems can increase sustainability and the magnitude of ecosystem services, but yield may depend upon biotic context, including soil mutualists, pathogens and cropping diversity. These biotic factors themselves may interact with abiotic factors such as drought. We tested whether perennial crop yield depended on soil microbes, water availability and crop diversity by testing monocultures and mixtures of three perennial crop species: a novel perennial grain (intermediate wheatgrass-Thinopyrum intermedium-- that produces the perennial grain Kernza®), a potential perennial oilseed crop (Silphium intregrifolium), and alfalfa (Medicago sativa). Perennial crop performance depended upon both water regime and the presence of living soil, most likely the arbuscular mycorrhizal (AM) fungi in the whole soil inoculum from a long term perennial monoculture and from an undisturbed native remnant prairie. Specifically, both Silphium and alfalfa strongly benefited from AM fungi. The presence of native prairie AM fungi had a greater benefit to Silphium in dry pots and alfalfa in wet pots than AM fungi present in the perennial monoculture soil. Kernza did not benefit from AM fungi. Crop mixtures that included Kernza overyielded, but overyielding depended upon inoculation. Specifically, mixtures with Kernza overyielded most strongly in sterile soil as Kernza compensated for poor growth of Silphium and alfalfa. This study identifies the importance of soil biota and the context dependence of benefits of native microbes and the overyielding of mixtures in perennial crops.

Digging Deeper for Agricultural Resources, the Value of Deep Rooting

In the quest for sustainable intensification of crop production, we discuss the option of extending the root depth of crops to increase the volume of soil exploited by their root systems. We discuss the evidence that deeper rooting can be obtained by appropriate choice of crop species, by plant breeding, or crop management and its potential contributions to production and sustainable development goals. Many studies highlight the potentials of deeper rooting, but we evaluate its contributions to sustainable intensification of crop production, the causes of the limited research into deep rooting of crops, and the research priorities to fill the knowledge gaps.

Comparative Analysis of Early Life Stage Traits in Annual and Perennial Phaseolus Crops and Their Wild Relatives

Herbaceous perennial species are receiving increased attention for their potential to provide both edible products and ecosystem services in agricultural systems. Many legumes (Fabaceae Lindl.) are of special interest due to nitrogen fixation carried out by bacteria in their roots and their production of protein-rich, edible seeds. However, herbaceous perennial legumes have yet to enter widespread use as pulse crops, and the response of wild, herbaceous perennial species to artificial selection for increased seed yield remains under investigation. Here we compare cultivated and wild accessions of congeneric annual and herbaceous perennial legume species to investigate associations of lifespan and cultivation with early life stage traits including seed size, germination, and first year vegetative growth patterns, and to assess variation and covariation in these traits. We use "cultivated" to describe accessions with a history of human planting and use, which encompasses a continuum of domestication. Analyses focused on three annual and four perennial species of the economically important genus Phaseolus. We found a significant association of both lifespan and cultivation status with seed size (weight, two-dimensional lateral area, length), node number, and most biomass traits (with cultivation alone showing additional significant associations). Wild annual and perennial accessions primarily showed only slight differences in trait values. Relative to wild forms, both cultivated annual and cultivated perennial accessions exhibited greater seed size and larger overall vegetative size, with cultivated perennials showing greater mean trait differences relative to wild accessions than cultivated annuals. Germination proportion was significantly lower in cultivated relative to wild annual accessions, while no significant difference was observed between cultivated and wild perennial germination. Regardless of lifespan and cultivation status, seed size traits were positively correlated with most vegetative traits, and all biomass traits examined here were positively correlated. This study highlights some fundamental similarities and differences between annual and herbaceous perennial legumes and provides insights into how perennial legumes might respond to artificial selection compared to annual species.

Community structure of soil fungi in a novel perennial crop monoculture, annual agriculture, and native prairie reconstruction

The use of perennial crop species in agricultural systems may increase ecosystem services and sustainability. Because soil microbial communities play a major role in many processes on which ecosystem services and sustainability depend, characterization of soil community structure in novel perennial crop systems is necessary to understand potential shifts in function and crop responses. Here, we characterized soil fungal community composition at two depths (0–10 and 10–30 cm) in replicated, long-term plots containing one of three different cropping systems: a tilled three-crop rotation of annual crops, a novel perennial crop monoculture (Intermediate wheatgrass, which produces the grain Kernza^®), and a native prairie reconstruction. The overall fungal community was similar under the perennial monoculture and native vegetation, but both were distinct from those in annual agriculture. The mutualist and saprotrophic community subsets mirrored differences of the overall community, but pathogens were similar among cropping systems. Depth structured overall communities as well as each functional group subset. These results reinforce studies showing strong effects of tillage and sampling depth on soil community structure and suggest plant species diversity may play a weaker role. Similarities in the overall and functional fungal communities between the perennial monoculture and native vegetation suggest Kernza^® cropping systems have the potential to mimic reconstructed natural systems.

Comparative Analysis of Perennial and Annual Phaseolus Seed Nutrient Concentrations

Long-term agricultural sustainability is dependent in part on our capacity to provide productive, nutritious crops that minimize the negative impacts of agriculture on the landscape. Perennial grains within an agroforestry context offers one solution: These plants produce large root systems that reduce soil erosion and simultaneously have the potential to produce nutrients to combat malnutrition. However, nutrient compositions of wild, perennial, herbaceous species, such as those related to the common bean (Phaseolus vulgaris) are not well known. In this study, seed ion and amino acid concentrations of perennial and annual Phaseolus species were quantified using ionomics and mass spectrometry. No statistical difference was observed for Zn, toxic ions (e.g., As) or essential amino acid concentrations (except threonine) between perennial and annual Phaseolus species. However, differences were observed for some nutritionally important ions. For example, Ca, Cu, Fe, Mg, Mn, and P concentrations were higher in annual species; further, ion and amino acid concentrations appear to be largely independent of each other. These results suggest variability in ion and amino acid concentrations exist in Phaseolus. As new crop candidates are considered for ecological services, nutritional quality should be optimized to maximize nutrient output of sustainable food crops.

Resources for Crop Production: Accessing the Unavailable

An acute imbalance between human population and food production is projected, partially due to increasing resource scarcity; dietary shifts and the current course of technology alone will not soon solve the problem. Natural ecosystems, typically characterized by high species richness and perennial growth habit, have solved many of the resource-acquisition problems faced by crops, making nature a likely source of insights for potential application in commercial agriculture. Further research on undomesticated plants and natural ecosystems, and the adaptations that enable them to meet their needs for N, P, and water, could change the face of commercial food production, including on marginal lands.

Competitive Analyses of the Pig Industry in Swaziland

Over recent decades, Swaziland’s pork industry has been stagnant, failing to meet the domestic demand for pork. It is only in recent years that the number of pig farmers has increased rapidly, with smallholder farmers taking the lead. However, while higher demand for pork could lead to opportunities for growth, with uncertain future markets, increased pig production capacity could subject farmers to extreme market competition and failure to sell their produce. This study used a survey and SWOT analysis to assess the current pig production and market performance of smallholder farms in Swaziland. To quantify SWOT factors, the Analytical Hierarchy Process (AHP) was used to derive priorities for subsequent formulation of potential pig production strategies that are resilient both to market and climate changes. Strategy formulation was based on Porter’s cost leadership strategy. The findings revealed that, currently, the pig industry is attractive, and that the present is probably the best time for smallholder farmers to maximize their profits. Unfortunately, the industry was found to be threatened by the expected increase in production capacity, future market competition, and the socio-environmental challenges associated with expansion. Despite this, the findings suggest that smallholder farmers can survive future market challenges by strategically using agro-industrial by-products as alternative feed ingredients to reduce production cost. The formation of farmers’ associations could benefit smallholder farmers through economies of scale, processing and product value addition, and increased access to markets, and unity could strengthen their position in the market when bargaining for better prices.