Long-term on-farm participatory maize breeding by stratified mass selection retains molecular diversity while improving agronomic performance

Multi-trait and multi-environment genomic prediction for flowering traits in maize: a deep learning approach

Maize (Zea mays L.), the third most widely cultivated cereal crop in the world, plays a critical role in global food security. To improve the efficiency of selecting superior genotypes in breeding programs, researchers have aimed to identify key genomic regions that impact agronomic traits. In this study, the performance of multi-trait, multi-environment deep learning models was compared to that of Bayesian models (Markov Chain Monte Carlo generalized linear mixed models (MCMCglmm), Bayesian Genomic Genotype-Environment Interaction (BGGE), and Bayesian Multi-Trait and Multi-Environment (BMTME)) in terms of the prediction accuracy of flowering-related traits (Anthesis-Silking Interval: ASI, Female Flowering: FF, and Male Flowering: MF). A tropical maize panel of 258 inbred lines from Brazil was evaluated in three sites (Cambira-2018, Sabaudia-2018, and Iguatemi-2020 and 2021) using approximately 290,000 single nucleotide polymorphisms (SNPs). The results demonstrated a 14.4% increase in prediction accuracy when employing multi-trait models compared to the use of a single trait in a single environment approach. The accuracy of predictions also improved by 6.4% when using a single trait in a multi-environment scheme compared to using multi-trait analysis. Additionally, deep learning models consistently outperformed Bayesian models in both single and multiple trait and environment approaches. A complementary genome-wide association study identified associations with 26 candidate genes related to flowering time traits, and 31 marker-trait associations were identified, accounting for 37%, 37%, and 22% of the phenotypic variation of ASI, FF and MF, respectively. In conclusion, our findings suggest that deep learning models have the potential to significantly improve the accuracy of predictions, regardless of the approach used and provide support for the efficacy of this method in genomic selection for flowering-related traits in tropical maize.

Advancing the science and practice of ecological nutrient management for smallholder farmers

Soil degradation is widespread in smallholder agrarian communities across the globe where limited resource farmers struggle to overcome poverty and malnutrition. This review lays out the scientific basis and practical management options for an ecologically based approach to sustainably managing soil fertility, with particular attention to smallholder subsistence systems. We seek to change the trajectory of development programs that continue to promote inorganic fertilizers and other high input strategies to resource constrained smallholders, despite ample evidence that this approach is falling short of food security goals and contributing to resource degradation. Ecological nutrient management (ENM) is an agroecological approach to managing the biogeochemical cycles that govern soil ecosystem services and soil fertility. The portfolio of ENM strategies extends beyond reliance on inorganic fertilizers and is guided by the following five principles: (1) Build soil organic matter and other nutrient reserves. (2) Minimize the size of N and P pools that are the most susceptible to loss. (3) Maximize agroecosystem capacity to use soluble, inorganic N and P. (4) Use functional and phylogenetic biodiversity to minimize bare fallows and maximize presence of growing plants. (5) Construct agroecosystem and field scale mass balances to track net nutrient flows over multiple growing seasons. Strategic increases in spatial and temporal plant species diversity is a core ENM tactic that expands agroecosystem multifunctionality to meet smallholder priorities beyond soil restoration and crop yields. Examples of ENM practices include the use of functionally designed polycultures, diversified rotations, reduced fallow periods, increased reliance on legumes, integrated crop-livestock production, and use of variety of soil amendments. These practices foster soil organic matter accrual and restoration of soil function, both of which underpin agroecosystem resilience. When ENM is first implemented, short-term yield outcomes are variable; however, over the long-term, management systems that employ ENM can increase yields, yield stability, profitability and food security. ENM rests on a solid foundation of ecosystem and biogeochemical science, and despite the many barriers imposed by current agricultural policies, successful ENM systems are being promoted by some development actors and used by smallholder farmers, with promising results.

Traditional Foods From Maize (Zea mays L.) in Europe

Maize (Zea mays L.) is one of the major crops of the world for feed, food, and industrial uses. It was originated in Central America and introduced into Europe and other continents after Columbus trips at the end of the 15th century. Due to the large adaptability of maize, farmers have originated a wide variability of genetic resources with wide diversity of adaptation, characteristics, and uses. Nowadays, in Europe, maize is mainly used for feed, but several food specialties were originated during these five centuries of maize history and became traditional food specialties. This review summarizes the state of the art of traditional foodstuffs made with maize in Southern, South-Western and South-Eastern Europe, from an historic evolution to the last research activities that focus on improving sustainability, quality and safety of food production.

Hydroxycinnamic Acids and Their Derivatives in Broa, a Traditional Ethnic Maize Bread

Maize is one of the most interesting dietary sources of hydroxycinnamic acids, widely known for their beneficial health effects, namely antioxidant properties. This work aims to identify hydroxycinnamic acids and their derivatives in broa, a Portuguese traditional ethnic maize bread, and corresponding maize flours. Soluble and insoluble phenolic fractions of diverse maize flours and corresponding broas were prepared and analysed by HPLC-DAD-MS/MS (high-performance liquid chromatography coupled with diode array detector and tandem mass spectrometry). Besides free hydroxycinnamic acids, mainly ferulic and p-coumaric acids, several structural isomers and stereoisomers of insoluble ferulic acid dehydrodimers (n = 18) and trimers (n = 11), were also identified. Hydroxycinnamic acid amides consisting of coumaroyl and feruloyl conjugates (n = 22) were present in both soluble and insoluble fractions of maize flours and breads, in different isomeric forms. A new compound was putatively identified as bis-N,N′-diferuloyl putrescine. Additionally, more complex and insoluble hydroxycinnamic acid amides, derived from ferulic acid dehydrodimers (n = 47) and trimers (n = 18), were also putatively identified for the first time, suggesting that hydroxycinnamic acid amides are also linked to maize cell walls. Since hydroxycinnamic derivatives were not only identified in maize flours, but also in broas, they can contribute to the antioxidant properties and beneficial health effects of maize-based foods.

A method for obtaining flexible broccoli varieties for sustainable agriculture

BACKGROUND

The use of high inputs in agriculture resulted in few varieties (hybrids and pure lines) used in all agricultural systems. Also varieties of vegetables, including broccoli, for organic and low-input agriculture, are almost exclusively hybrids, since there are very few specific breeding programs and varieties for sustainable agriculture systems. A strategy to overcome this issue is the adoption of specific breeding programs for developing heterogeneous varieties (i.e. synthetics, open pollinated varieties, composite cross populations and mixtures). In fact, heterogeneous varieties are able to evolve and adapt to specific agro-climatic conditions. The aim of this study was to develop a method (an Evolutionary Breeding Program, EBP) for obtaining heterogeneous varieties of broccoli and test its efficiency in developing highly diverse varieties, as needed in sustainable agriculture. A synthetic variety originated from a landrace was multiplied in different environments for 3 cycles and morpho-phenological and genetic diversity of the derived populations were assessed.

RESULTS

The presented results are the first and unique indication about the efficiency of a short-time EBP for an allogamous species like broccoli. Few morphological changes were observed among varieties multiplied in different environments with different agro-climatic conditions. This could be probably due to the initial genetic diversity of the landrace from which the populations were selected and also to the great plasticity of the crop. However, SSR data highlighted a genetic differentiation among populations multiplied for two/three years across Europe and in Central Italy, that was not so evident when considering morphological data only.

CONCLUSIONS

Few years of multiplication in different environments resulted in genetically differentiated broccoli populations that nonetheless preserved the original genetic diversity and productivity level and appear to evolve in relationship to different environments: the applied EBP is useful for developing heterogeneous materials for sustainable agriculture.

Embedding Cultivated Diversity in Society for Agro-Ecological Transition

Agroecology calls for a global approach, integrating scientific, practical, and advocacy dimensions, to redesign agricultural systems based on ecological and socio-cultural processes and emphasizing biodiversity. This review is grounded on the results of DIVERSIFOOD, a European H2020 multi-actor research project, and explores the concept of cultivated diversity using various dimensions relevant to foster sustainable organic food systems and agro-ecological transition. From the evaluation of underutilized genetic resources and forgotten crops, DIVERSIFOOD has proposed plant breeding strategies, on-farm experimentation, and statistical tools to create new populations, landraces, and organic cultivars with intra-varietal diversity. The added value of Community Seed Banks and forms of collective seed management in Europe have been described in terms of goals and activities, and their value for improving seed regulations, treaties, and genetic resources management is discussed. In the context of the current agro-food system characterized by standardization, DIVERSIFOOD raised awareness of qualities of ‘biodiverse food systems’ in which all actors have a role to play. It highlighted the critical capacity to preserve a diversity of cultural values embodied in ‘biodiverse products’, thereby involving consumers in collective strategies for reviving diversity, and empowering all actors of organic food systems to really and efficiently implement research within their farms and networks.

Maize Open-Pollinated Populations Physiological Improvement: Validating Tools for Drought Response Participatory Selection

Participatory selection—exploiting specific adaptation traits to target environments—helps to guarantees yield stability in a changing climate, in particular under low-input or organic production. The purpose of the present study was to identify reliable, low-cost, fast and easy-to-use tools to complement traditional selection for an effective participatory improvement of maize populations for drought resistance/tolerance. The morphological and eco-physiological responses to progressive water deprivation of four maize open-pollinated populations were assessed in both controlled and field conditions. Thermography and Chl a fluorescence, validated by gas exchange indicated that the best performing populations under water-deficit conditions were ‘Fandango’ and to a less extent ‘Pigarro’ (both from participatory breeding). These populations showed high yield potential under optimal and reduced watering. Under moderate water stress, ‘Bilhó’, originating from an altitude of 800 m, is one of the most resilient populations. The experiments under chamber conditions confirmed the existence of genetic variability within ‘Pigarro’ and ‘Fandango’ for drought response relevant for future populations breeding. Based on the easiness to score and population discriminatory power, the performance index (PIABS) emerges as an integrative phenotyping tool to use as a refinement of the common participatory maize selection especially under moderate water deprivation.

Crop Biodiversity: An Unfinished Magnum Opus of Nature

Crop biodiversity is one of the major inventions of humanity through the process of domestication. It is also an essential resource for crop improvement to adapt agriculture to ever-changing conditions like global climate change and consumer preferences. Domestication and the subsequent evolution under cultivation have profoundly shaped the genetic architecture of this biodiversity. In this review, we highlight recent advances in our understanding of crop biodiversity. Topics include the reduction of genetic diversity during domestication and counteracting factors, a discussion of the relationship between parallel phenotypic and genotypic evolution, the role of plasticity in genotype × environment interactions, and the important role subsistence farmers play in actively maintaining crop biodiversity and in participatory breeding. Linking genotype and phenotype remains the holy grail of crop biodiversity studies.

Setting Up Decision-Making Tools toward a Quality-Oriented Participatory Maize Breeding Program

Previous studies have reported promising differences in the quality of kernels from farmers' maize populations collected in a Portuguese region known to produce maize-based bread. However, several limitations have been identified in the previous characterizations of those populations, such as a limited set of quality traits accessed and a missing accurate agronomic performance evaluation. The objectives of this study were to perform a more detailed quality characterization of Portuguese farmers' maize populations; to estimate their agronomic performance in a broader range of environments; and to integrate quality, agronomic, and molecular data in the setting up of decision-making tools for the establishment of a quality-oriented participatory maize breeding program. Sixteen farmers' maize populations, together with 10 other maize populations chosen for comparison purposes, were multiplied in a common-garden experiment for quality evaluation. Flour obtained from each population was used to study kernel composition (protein, fat, fiber), flour's pasting behavior, and bioactive compound levels (carotenoids, tocopherols, phenolic compounds). These maize populations were evaluated for grain yield and ear weight in nine locations across Portugal; the populations' adaptability and stability were evaluated using additive main effects and multiplication interaction (AMMI) model analysis. The phenotypic characterization of each population was complemented with a molecular characterization, in which 30 individuals per population were genotyped with 20 microsatellites. Almost all farmers' populations were clustered into the same quality-group characterized by high levels of protein and fiber, low levels of carotenoids, volatile aldehydes, α- and δ-tocopherols, and breakdown viscosity. Within this quality-group, variability on particular quality traits (color and some bioactive compounds) could still be found. Regarding the agronomic performance, farmers' maize populations had low, but considerably stable, grain yields across the tested environments. As for their genetic diversity, each farmers' population was genetically heterogeneous; nonetheless, all farmers' populations were distinct from each other's. In conclusion, and taking into consideration different quality improvement objectives, the integration of the data generated within this study allowed the outline and exploration of alternative directions for future breeding activities. As a consequence, more informed choices will optimize the use of the resources available and improve the efficiency of participatory breeding activities.

Long-term on-farm participatory maize breeding by stratified mass selection retains molecular diversity while improving agronomic performance

Modern maize breeding programs gave rise to genetically uniform varieties that can affect maize's capacity to cope with increasing climate unpredictability. Maize populations, genetically more heterogeneous, can evolve and better adapt to a broader range of edaphic–climatic conditions. These populations usually suffer from low yields; it is therefore desirable to improve their agronomic performance while maintaining their valuable diversity levels. With this objective, a long‐term participatory breeding/on‐farm conservation program was established in Portugal. In this program, maize populations were subject to stratified mass selection. This work aimed to estimate the effect of on‐farm stratified mass selection on the agronomic performance, quality, and molecular diversity of two historical maize populations. Multilocation field trials, comparing the initial populations with the derived selection cycles, showed that this selection methodology led to agronomic improvement for one of the populations. The molecular diversity analysis, using microsatellites, revealed that overall genetic diversity in both populations was maintained throughout selection. The comparison of quality parameters between the initial populations and the derived selection cycles was made using kernel from a common‐garden experiment. This analysis showed that the majority of the quality traits evaluated progressed erratically over time. In conclusion, this breeding approach, through simple and low‐cost methodologies, proved to be an alternative strategy for genetic resources’ on‐farm conservation.