This study enhances our understanding of the iconic giant maize landrace (Zea mays subsp. mays) known internationally as Jala and locally as maíz de húmedo, focusing on its presence within the municipality of Jala in Nayarit state, Mexico. It examines the current geographical, environmental, and social contexts surrounding this landrace and the dominant narrative that Jala maize is only cultivated in Jala Valley for conservation purposes. The study is based on interviews with key informants, focus group discussions, questionnaires, and participatory mapping workshops with maize farmers from seven communities within the entire municipality of Jala. The study presents robust evidence that the cultivation of maíz de húmedo covers both the valley and the mountain area of the Jala municipality. It also identifies two agroecological niches in which this landrace is cultivated. Results show differences in the reasons for continuing to grow maíz de húmedo. Farmers in the mountain region emphasized cultivating it due to its strong adaptation to the local environment. In contrast, farmers in the valley highlighted tradition as the primary reason for their cultivation practices. As a valuable genetic resource for one of the world’s most important crop plants, the conservation and promotion of maíz de húmedo should be carefully considered. This study demonstrates how research integrating local expertise and participatory mapping, providing geographical context, can provide valuable, often-overlooked insights that help explain why and how to sustain and enhance the future of this landrace and the communities that cultivate it.

This study investigates the genetic basis of freezing tolerance in Tripsacum dactyloides and related subspecies as a potential source of valuable traits for improving maize agriculture. Recognizing the significant economic losses in corn yields due to frost damage, we hypothesized that northern populations of T. dactyloides are enriched for freezing tolerance alleles. 40 diverse Tripsacum accessions were collected from natural populations and long-established field collections and used to generate F1 hybrids and open-pollinated F2 families. F2 seedlings were germinated then screened within a growth chamber for freezing tolerance by exposure to freezing temperatures. Seedlings were then phenotyped by tissue survival, and extremes were pooled to create tolerant and susceptible bulks. DNA sequencing was performed on founders, F1s, and tolerant/susceptible F2 bulks. To overcome challenges in traditional SNP calling in bulked samples, we developed a regression-based approach to estimate gamete frequencies and impute allele frequencies in pooled populations. The results showed genetic diversity among Tripsacum accessions, with divergence between northern and southern populations. We tracked segregation of alleles across genomic loci, and performed a joint bulk segregant analysis, identifying 25 QTLs significantly associated with freezing tolerance. These findings highlight potential loci for freezing tolerance that could inform genetic engineering of maize. ### Competing Interest Statement The authors have declared no competing interest. USDA-ARS National Science Foundation, #1822330, #1922551

Maize (Zea mays L.) is the world's most productive grain crop and a cornerstone of global food supply. However, in temperate agricultural systems, maize exhibits 2 key anomalies. First, as a tropical species, maize cannot be planted in the cold conditions of early spring when light and natural soil nitrogen are available, resulting in a shorter growing season and creating a seasonal mismatch between nitrogen accessibility and demand. Second, maize kernel protein is a major nitrogen sink, driving fertilizer demand because of the scale of cultivation. This inefficient mismatch stems from modern maize's uses and the modest nutritional value of storage proteins. To address these anomalies, we established the Circular Economy that Reimagines Corn Agriculture initiative. Our vision requires advances in 3 research areas: (ⅰ) developing cold and frost tolerance during germination and early growth to enable the use of spring nitrogen and light resources; (ⅱ) reducing nitrogen allocation to grain by reducing low-quality storage proteins and developing alternative nitrogen sinks; and (ⅲ) stabilizing soil nitrogen by enhancing biological nitrification inhibition. We present blueprints for a nitrogen-efficient, cold-tolerant maize designed to utilize the full growing season, enabling farmers in temperate regions to fully leverage maize's C4 photosynthesis, reduce fertilizer inputs, increase yields, and minimize environmental impact.

Over the last 20 million years, the Andropogoneae tribe of grasses has evolved to dominate 17% of global land area. Domestication of these grasses in the last 10,000 years has yielded our most productive crops, including maize, sugarcane, and sorghum. The majority of Andropogoneae species, including maize, show a history of polyploidy - a condition that, while offering the evolutionary advantage of multiple gene copies, poses challenges to basic cellular processes, gene expression, and epigenetic regulation. Genomic studies of polyploidy have been limited by sparse sampling of taxa in groups with multiple polyploidy events. Here, we present 33 genome assemblies from 27 species, including chromosome-scale assemblies of maize relatives Zea and Tripsacum. In maize, the after-effects of polyploidy have been widely studied, showing reduced chromosome number, biased fractionation of duplicate genes, and transposable element (TE) expansions. While we observe these patterns within the genus Zea, 12 other polyploidy events deviate significantly. Those tetraploids and hexaploids retain elevated chromosome number, maintain nearly complete complements of duplicate genes, and have only stochastic TE amplifications. These genomes reveal variable outcomes of polyploidy, challenging simple predictions and providing a foundation for understanding its evolutionary implications in an ecologically and economically important clade.

Seed storage life in tropical areas is shortened by high humidity and temperature and the general inaccessibility to dehumidifying and refrigeration systems, resulting in rapid decreases in seed viability in storage as well as a high incidence of fungal and insect infestations. The dry chain, based on rapid and deep drying of seeds after harvest followed by packaging in moisture-proof containers, has been proposed as an effective method to maintain seed quality during medium-term storage in humid climates, even without refrigeration. In addition, seed drying with zeolite drying beads can be more effective and economical than sun or heated-air drying under these warm, humid conditions. In this paper, we review recent published literature regarding the dry chain, considering different crop species, storage environments and seed traits. In addition, we provide new original data on the application of dry chain methods and their implementation at larger scales in South Asia, Latin America and Pacific Island Countries. The clear conclusion is that the combination of reusable drying beads and waterproof storage containers enables the implementation of the dry chain in tropical climates, enhancing seed viability and quality in storage of many crop species. The dry chain approach can therefore significantly enhance seed security for farmers in many tropical countries. Finally, we propose actions and strategies that could guide further scaling-up implementation of this technology.

Aun cuando por décadas en México se han llevado a cabo esfuerzos para la conservación in situ de los maíces nativos, su fomento y protección siguen presentando desafíos y oportunidades. En este artículo exploramos dichos retos y oportunidades a través del caso del maíz raza Jala desde una perspectiva histórica, sistémica e inclusiva que permitió describir las dinámicas de pérdida y de mantenimiento que han prevalecido en las últimas décadas. Mediante un estudio que compara datos colectados con casi 20 años de diferencia sobre la raza de maíz Jala, se documentan las dinámicas que ha vivido este maíz en tres aspectos: su producción, su aprovechamiento y su valoración. Los resultados resaltan cómo los factores de mantenimiento y pérdida han cambiado y cómo nuevos retos y oportunidades han aparecido. Retos asociados a procesos de pérdida de productividad y adaptación se han vuelto relevantes, mientras oportunidades para diversificar su utilización son manifiestas. Desafíos en la integración de jóvenes para asegurar el relevo generacional se han vuelto más críticos. Así como la oportunidad de involucrar más a las mujeres que promueven el consumo local y al aprovechamiento del potencial de los mercados especializados en maíces nativos. Finalmente, el desarrollo de estrategias integrales que involucran instituciones sociales informales (como la familia) y formales (diferentes niveles de gobierno), bajo un marco legal nacional, estatal y local del maíz como patrimonio cultural, se vuelve crítico para la conservación in situ del maíz raza Jala y otras razas de maíz en México.

The most important commercial feature in popcorn (Zea mays L.) is the expansion of the starch contained in the endosperm; however, little has been studied about the underlying genetic basis of this quantitative trait, for which the development of segregating populations is required. The first step is the selection of the most appropriate contrasting parents for popping capacity to create these populations. The objectives of this study were, 1) to analyze the popping patterns of F2 populations derived from crosses between popcorn × nonpopcorn inbred lines to identify the most divergent cross for future molecular analysis in search of alleles-related to popping capacity, and 2) to estimate the number of genes responsible for popping expansion volume based on the tails of segregation. Seven biparental crosses of popcorn × non-popcorn were performed to obtain F2 populations, and those were phenotypedfor popping expansion volume. Phenotypes were analyzed by the H test, Lilliefors normality-test, Fisher’s coefficient of skewness, and kurtosis level. The number of genes estimation was made with X2 and (1/4)n tests. The popping patterns indicated that popcorn × flint corn was the most divergent cross, with the most symmetrical distribution, and therefore, the best suitable population to be used for molecular analysis. Results indicated the existence of three to five major genes related to popping expansion volume. Transgressive segregation was present in all populations, showing individuals whit a popping expansion volume higher or lower than the parental ones, suggesting that non-popcorn lines contain variation for alleles that promote popping. Keywords: Popcorn, popping expansion volume, popping patterns, transgressive segregation, Zea mays L.

Generations of farmer selection in the central Mexican highlands have produced unique maize varieties adapted to the challenges of the local environment. In addition to possessing great agronomic and cultural value, Mexican highland maize represents a good system for the study of local adaptation and acquisition of adaptive phenotypes under cultivation. In this study, we characterize a recombinant inbred line population derived from the B73 reference line and the Mexican highland maize variety Palomero Toluqueño. B73 and Palomero Toluqueño showed classic rank-changing differences in performance between lowland and highland field sites, indicative of local adaptation. Quantitative trait mapping identified genomic regions linked to effects on yield components that were conditionally expressed depending on the environment. For the principal genomic regions associated with ear weight and total kernel number, the Palomero Toluqueño allele conferred an advantage specifically in the highland site, consistent with local adaptation. We identified Palomero Toluqueño alleles associated with expression of characteristic highland traits, including reduced tassel branching, increased sheath pigmentation and the presence of sheath macrohairs. The oligogenic architecture of these three morphological traits supports their role in adaptation, suggesting they have arisen from consistent directional selection acting at distinct points across the genome. We discuss these results in the context of the origin of phenotypic novelty during selection, commenting on the role of de novo mutation and the acquisition of adaptive variation by gene flow from endemic wild relatives.

Crop landraces have unique local agroecological and societal functions and offer important genetic resources for plant breeding. Recognition of the value of landrace diversity and concern about its erosion on farms have led to sustained efforts to establish ex situ collections worldwide. The degree to which these efforts have succeeded in conserving landraces has not been comprehensively assessed. Here we modelled the potential distributions of eco-geographically distinguishable groups of landraces of 25 cereal, pulse and starchy root/tuber/fruit crops within their geographic regions of diversity. We then analysed the extent to which these landrace groups are represented in genebank collections, using geographic and ecological coverage metrics as a proxy for genetic diversity. We find that ex situ conservation of landrace groups is currently moderately comprehensive on average, with substantial variation among crops; a mean of 63% ± 12.6% of distributions is currently represented in genebanks. Breadfruit, bananas and plantains, lentils, common beans, chickpeas, barley and bread wheat landrace groups are among the most fully represented, whereas the largest conservation gaps persist for pearl millet, yams, finger millet, groundnut, potatoes and peas. Geographic regions prioritized for further collection of landrace groups for ex situ conservation include South Asia, the Mediterranean and West Asia, Mesoamerica, sub-Saharan Africa, the Andean mountains of South America and Central to East Asia. With further progress to fill these gaps, a high degree of representation of landrace group diversity in genebanks is feasible globally, thus fulfilling international targets for their ex situ conservation.

Popcorn (Zea mays L. var. Everta) is the most ancient type of cultivated maize. However, there is little known about the genetics of popping-related traits based on genotyping-by-sequencing (GBS) technology. Here, we characterized the phenotypic variation for seven popping-related traits in maize kernels among 526 CIMMYT inbred lines (CMLs). In total, 155 083 high-quality single nucleotide polymorphism (SNP) markers were identified by a GBS approach. Several trait-associated loci were detected by genome-wide association study for color, popping expansion volume, shape, pericarp, flotation index, floury/vitreous, and protein content, explaining a majority of the observed phenotypic variance, and these were validated by a diverse panel comprising 764 tropical landrace accessions. Sixty two of the identified loci were recognized to have undergone selection. On average, there was a 55.27% frequency for alleles that promote popping in CMLs. Our work not only pinpoints previously unknown loci for popping-related traits, but also reveals that many of these loci have undergone selection. Beyond establishing a new benchmark for the genetics of popcorn, our study provides a foundation for gene discovery and breeding. It also presents evidence to investigate the role of a gradual loss of popping ability as a by-product of diversification of culinary uses throughout the evolution of teosinte-to-modern maize.

BACKGROUND AND AIMSThe long-term conservation of seeds of plant genetic resources is of key importance for food security and preservation of agrobiodiversity. Nevertheless, there is scarce information available about seed longevity of many crops under germplasm bank conditions.METHODSThrough germination experiments as well as the analysis of historical monitoring data, we studied the decline in viability manifested by 1000 maize (Zea mays subsp. mays) seed accessions conserved for an average of 48 years at the CIMMYT germplasm bank, the largest maize seedbank in the world, under two cold storage conditions: an active (-3 °C; intended for seed distribution) and a base conservation chamber (-15 °C; for long-term conservation).KEY RESULTSSeed lots stored in the active chamber had a significantly lower and more variable seed germination, averaging 81.4 %, as compared with the seed lots conserved in the base chamber, averaging 92.1 %. The average seed viability detected in this study was higher in comparison with that found in other seed longevity studies on maize conserved under similar conditions. A significant difference was detected in seed germination and longevity estimates (e.g. p85 and p50) among accessions. Correlating seed longevity with seed traits and passport data, grain type showed the strongest correlation, with flint varieties being longer lived than floury and dent types.CONCLUSIONSThe more rapid loss of seed viability detected in the active chamber suggests that the seed conservation approach, based on the storage of the same seed accessions in two chambers with different temperatures, might be counterproductive for overall long-term conservation and that base conditions should be applied in both. The significant differences detected in seed longevity among accessions underscores that different viability monitoring and regeneration intervals should be applied to groups of accessions showing different longevity profiles.

Crop diversity underpins the productivity, resilience and adaptive capacity of agriculture. Loss of this diversity, termed crop genetic erosion, is therefore concerning. While alarms regarding evident declines in crop diversity have been raised for over a century, the magnitude, trajectory, drivers and significance of these losses remain insufficiently understood. We outline the various definitions, measurements, scales and sources of information on crop genetic erosion. We then provide a synthesis of evidence regarding changes in the diversity of traditional crop landraces on farms, modern crop cultivars in agriculture, crop wild relatives in their natural habitats and crop genetic resources held in conservation repositories. This evidence indicates that marked losses, but also maintenance and increases in diversity, have occurred in all these contexts, the extent depending on species, taxonomic and geographic scale, and region, as well as analytical approach. We discuss steps needed to further advance knowledge around the agricultural and societal significance, as well as conservation implications, of crop genetic erosion. Finally, we propose actions to mitigate, stem and reverse further losses of crop diversity.

Seed conservation in rural communities of low- and middle-income countries located in tropical areas is particularly problematic, due to high relative humidity that promotes insect and fungal infestations and leads to rapid losses in seed viability. Seed conservation in those areas is affected by unreliable power supplies that do not allow the use of dehumidifying and refrigeration systems recommended for the long-term storage of seeds. We tested the dry chain, i.e., initial seed drying with a reusable desiccant in the form of zeolite beads followed by seed conservation in hermetic containers, in rural communities of Guatemala (Huehuetenango Department). In this region, a network of community seed reserves (CSRs) has been established to provide a safety backup for seed and to conserve local agrobiodiversity. Using a local maize variety in three communities, we compared the dry chain with the seed conservation methodology employed in the CSRs (i.e., undried seeds in hermetic flasks) as well as with seed conservation in open storage, both in the local CSR and in a farmer’s granary. Seed conserved using the dry chain treatment maintained very high seed viability (> 80%) throughout the whole experiment (6 months) and reduced fungal and insect infestations (< 3%). In the other treatments, the viability declined significantly to an average of 52% non-viable and 19% infested seeds after 6 months of storage. The dry chain was demonstrated to be an excellent solution for enhancing seed conservation in biodiversity hotspots of tropical areas as well as for improving seed security for farmers.

The conservation of landraces is fundamental to safeguarding crop diversity, food security, and sustainable production. Jala is a special maize landrace from the region in and around the Jala Valley of Mexico that produces the largest ear and tallest plant of all maize landraces in the world. Changing socio-economic and environmental conditions in the Jala Valley could lead to the genetic erosion of the ancestral Jala landrace, which can have global consequences. This study outlines the sequence of events in the history of Jala and describes the evolution of strategies for complementary in situ and ex situ conservation of maize genetic resources that are being developed and tested by the Jala Rematriation Project. The concept of dynamic conservation is discussed and applied to the specific case of Jala . The rematriation approach could be instrumental in creating an environment that enables the dynamic conservation of maize landraces in Mexico, the primary centre of this crop’s origin and diversity, and throughout its ancestral range in the Americas.

This study describes the genetic diversity and the population structure of 66 popcorn landrace collections in a recently discovered microcenter of maize ( Zea mays L.) diversity in southern Brazil. Furthermore, we elucidate their phylogenetic relationships with a diverse panel of 575 popcorn populations from 18 countries of American Continent. The germplasm, representing distinct landraces, was genetically characterized as population bulks using single nucleotide polymorphism markers (SNPs). Five main groups were identified for the popcorn germplasm of the southern region of Brazil. This pattern was associated with phenotypic diversity in grain shape and color. The germplasm of the American Continent was structured in nine groups associated with geographical region with significant differences in terms of genetic diversity and expansion capacity or popping expansion (the formation of large flakes after the kernels explode in response to heating). The popping expansion pattern of the American groups displayed a North-South geographical continuum, in which the average values increased with geographical distance from the center of origin in Mexico. The highest averages were obtained for the Lowland groups of South America. These results raise two hypotheses: the first one is the possibility of a continuous evolution of this characteristic, which is popcorn did disperse North - South, but interbreeding with local varieties drove up the diversity of the gene pool, and at the same time allowed more efficient selection on the trait of expansion capacity. The second is the possibility of a second domestication event of Zea mays ssp. mays L., in South America, which would assume an independent origin of popcorn, but not an independent domestication of maize. Both hypotheses would be based on popcorn populations brought from Mexico by human migrations. The germplasm collected in the microcenter of diversity in southern Brazil, most of them originated in the Lowlands of South America, a part of germplasm established phylogenetic relationships closer to the popcorn populations of Brazil collected in the last century. The study contributes to improved understanding of the origin and phylogenetics of this maize group and as such to conservation of those valuable genetic resources and future breeding efforts. This is valuable genetic research which led to better insight into grouping and dispersion of studied genotypes in the target region, but also its place vis-à-vis origin and migration of popcorn genotypes in South America in general.

Understanding the genomic basis of adaptation in maize is important for gene discovery and the improvement of breeding germplasm, but much remains a mystery in spite of significant population genetics and archaeological research. Identifying the signals underpinning adaptation are challenging as adaptation often coincided with genetic drift, and the base genomic diversity of the species in massive. In this study, tGBS technology was used to genotype 1,143 diverse maize accessions including landraces collected from 20 countries and elite breeding lines of tropical lowland, highland, subtropical/midaltitude and temperate ecological zones. Based on 355,442 high‐quality single nucleotide polymorphisms, 13 genomic regions were detected as being under selection using the bottom‐up searching strategy, EigenGWAS. Of the 13 selection regions, 10 were first reported, two were associated with environmental parameters via EnvGWAS, and 146 genes were enriched. Combining large‐scale genomic and ecological data in this diverse maize panel, our study supports a polygenic adaptation model of maize and offers a framework to enhance our understanding of both the mechanistic basis and the evolutionary consequences of maize domestication and adaptation. The regions identified here are promising candidates for further, targeted exploration to identify beneficial alleles and haplotypes for deployment in maize breeding.

Understanding the causes of maize landrace loss in farmers’ field is essential to design effective conservation strategies. These strategies are necessary to ensure that genetic resources are available in the future. Previous studies have shown that this loss is caused by multiple factors. In this longitudinal study, we used a collection of 93 maize landrace accessions from Morelos, Mexico, and stored at the International Maize and Wheat Improvement Center (CIMMYT) Maize Germplasm Bank, to trace back to the original 66 donor families after 50 years and explore the causes for why they abandoned or conserved their seed lots. We used an actor-centered approach, based on interviews and focus group discussions. We adopt a Multi-Level Perspective framework to examine loss as a process, accommodating multiple causes and the interactions among them. We found that the importance of maize landrace cultivation had diminished over the last 50 years in the study area. By 2017, 13 families had conserved a total of 14 seed lots directly descended from the 1967 collection. Focus group participants identified 60 accessions that could still be found in the surrounding municipalities. Our findings showed that multiple interconnected changes in maize cultivation technologies, as well as in maize markets, other crop markets, agricultural and land policies, cultural preferences, urbanization and climate change, have created an unfavorable environment for the conservation of maize landraces. Many of these processes were location- and landrace-specific, and often led to landrace abandonment during the shift from one farmer generation to the next.

Crop wild relatives (CWR) are valuable resources for crop breeding due to their close genetic relationship to the cultivated plants and their wide genetic variation, allowing the introgression of desirable traits into the crops, such as resistance to plant pests and diseases or adaptability to climate change. Mexico is a centre of agrobiodiversity, including CWR, but climate change, and other factors, are contributing to the loss of important Mexican CWR genetic diversity. The in situ and ex situ conservation status of Mexican priority CWR were assessed through a gap analysis as part of a national CWR conservation strategy for Mexico, to ensure the long-term preservation and improve the availability of these genetic resources. A set of 310 priority CWR taxa, previously identified as part of the national CWR inventory for Mexico, were analysed. Species distribution modelling and ecogeographic diversity analyses were used to detect gaps in in situ and ex situ conservation at taxon and ecogeographic levels. Priority target sites were identified throughout the country for complementary in situ and ex situ conservation of these taxa. The results obtained allow us to make recommendations for immediate conservation actions, thus helping to mitigate the threats to Mexican agrobiodiversity and enhance both national and global food security.

The history of CGIAR and the development and implementation of the International Treaty on Plant Genetic Resources for Food and Agriculture (“Plant Treaty”) are closely intertwined. In accordance with the agreements that 11 CGIAR centers signed with the Plant Treaty’s Governing Body under Article 15 of the treaty, >730,000 accessions of crop, tree, and forage germplasm conserved in CGIAR genebanks are made available under the terms and conditions of the multilateral system of access and benefit sharing, and the CGIAR centers have transferred almost 4 million samples of plant genetic resources under the system. Many activities of CGIAR centers and their genebanks (e.g., crop enhancement, improved agronomic methods, seed system strengthening, and capacity building) are influenced by, and promote, the Plant Treaty’s objectives. The continued existence and optimal functioning of the Plant Treaty’s multilateral system of access and benefit sharing is critically important to CGIAR in the pursuit of its mission. However, the multilateral system has encountered some challenges since the Plant Treaty came into force. The successful conclusion of the ongoing process for enhancing the functioning of the multilateral system could increase monetary benefit sharing and incentives for exchanging more germplasm. In the meantime, increased efforts are necessary to promote nonmonetary benefit sharing through partnerships, technology transfer, information exchange, and capacity building. These efforts should be integrated into countries’ and organizations’ work to implement the Plant Treaty’s provisions on conservation and sustainable use of plant genetic resources, and farmers’ rights.