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Northern corn leaf blight (NCLB), caused by Setosphaeria turcica , is a major fungal disease affecting maize production in sub-Saharan Africa. Utilizing host plant resistance to mitigate yield losses associated with NCLB can serve as a cost-effective strategy. In this study, we conducted a high-resolution genome-wide association study (GWAS) in an association mapping panel and linkage mapping with three doubled haploid (DH) and three F3 populations of tropical maize. These populations were phenotyped for NCLB resistance across six hotspot environments in Kenya. Across environments and genotypes, NCLB scores ranged from 2.12 to 5.17 (on a scale of 1–9). NCLB disease severity scores exhibited significant genotypic variance and moderate-to-high heritability. From the six biparental populations, 23 quantitative trait loci (QTLs) were identified, each explaining between 2.7% and 15.8% of the observed phenotypic variance. Collectively, the detected QTLs explained 34.28%, 51.37%, 41.12%, 12.46%, 12.11%, and 14.66% of the total phenotypic variance in DH populations 1, 2, and 3 and F3 populations 4, 5, and 6, respectively. GWAS, using 337,110 high-quality single nucleotide polymorphisms (SNPs), identified 15 marker–trait associations and several putative candidate genes linked to NCLB resistance in maize. Joint linkage association mapping (JLAM) identified 37 QTLs for NCLB resistance. Using linkage mapping, JLAM, and GWAS, several QTLs were identified within the genomic region spanning 4 to 15 Mbp on chromosome 2. This genomic region represents a promising target for enhancing NCLB resistance via marker-assisted breeding. Genome-wide predictions revealed moderate correlations with mean values of 0.45, 0.44, 0.55, and 0.42 for within GWAS panel, DH pop1, DH pop2, and DH pop3, respectively. Prediction by incorporating marker-by-environment interactions did not show much improvement. Overall, our findings indicate that NCLB resistance is quantitative in nature and is controlled by few major-effect and many minor-effect QTLs. We conclude that genomic regions consistently detected across mapping approaches and populations should be prioritized for improving NCLB resistance, while genome-wide prediction results can help incorporate both major- and minor-effect genes. This study contributes to a deeper understanding of the genetic and molecular mechanisms driving maize resistance to NCLB. [ABSTRACT FROM AUTHOR]

Genotype × environment (GxE) interaction effects are one of the major challenges in identifying cultivars with stable performance across agri-environments. In this study we analysed GE interactions to identify quinoa (Chenopodium quinoa) cultivars with high and stable yields under different soil moisture regimes, representing control conditions, waterlogging and drought. Waterlogging and drought treatments were artificially induced using normoxia, a combination of hypoxia-normoxia, and 10% PEG (Polyethylene glycol) under hydroponic growth conditions, respectively. Both waterlogging and drought conditions significantly reduced the plant height (PH), number of leaves (NoL) and number of branches (NoB), stem diameter (SD), leaf area (LA) and dry weight (DW) of quinoa genotypes. The genotype, water regime, and genotype by water regime effects all significantly affected the measured quinoa traits. Based on the additive main effects and multiplicative interaction (AMMI) model for DW, the genotypes G18, Puno, Q4, 2-Want, Puno, Real1 x Ruy937 and Titicaca were found to exhibit tolerance and were stable across water regimes. A second-stage evaluation was conducted to test genotype × environment interaction effects in crop production field trials, selecting two contrasting seasons based on soil moisture conditions involving a diverse set of genotypes (58 varieties in total). Our results demonstrate significant variations in both growth and yield among the quinoa genotypes across the cropping seasons. The GGE analysis for grain yield indicate that field conditions matched to G × E under hydroponic experimental conditions and the cultivars G18, Q1, Q4, NL-3, G28, 42-Test, Atlas and 59-ALC were classified within a range of high productivity. Our findings provide a basis for understanding the mechanisms of wide adaptation, while identifying germplasm that enhances the water stress tolerance of quinoa cultivars at early growth stages. [ABSTRACT FROM AUTHOR]

Smallholder maize farming systems in sub-Saharan Africa (SSA) are vulnerable to drought-induced yield losses, which significantly impact food security and livelihoods within these communities. Mapping and characterizing genomic regions associated with water stress tolerance in tropical maize is essential for future breeding initiatives targeting this region. In this study, three biparental F3 populations composed of 753 families were evaluated in Kenya and Zimbabwe and genotyped with high-density single nucleotide polymorphism (SNP) markers. Quantitative trait loci maping was performed on these genotypes to dissect the genetic architecture for grain yield (GY), plant height (PH), ear height (EH) and anthesis-silking interval (ASI) under well-watered (WW) and water-stressed (WS) conditions. Across the studied maize populations, mean GY exhibited a range of 4.55--8.55 t/ha under WW and 1.29--5.59 t/ha under WS, reflecting a 31--59% reduction range under WS conditions. Genotypic and genotype-by-environment (G E) variances were significant for all traits except ASI. Overall broad sense heritabilities for GY were low to high (0.25--0.60). For GY, these genetic parameters were decreased under WS conditions. Linkage mapping revealed a significant difference in the number of QTLs detected, with 93 identified under WW conditions and 41 under WS conditions. These QTLs were distributed across all maize chromosomes. For GY, eight and two major effect QTLs (>10% phenotypic variation explained) were detected under WW and WS conditions, respectively. Under WS conditions, Joint Linkage Association Mapping (JLAM) identified several QTLs with minor effects for GY and revealed genomic region overlaps in the studied populations. Across the studied water regimes, five-fold cross-validation showed moderate to high prediction accuracies (0.15--0.90) for GY and other agronomic traits. Our findings demonstrate the polygenic nature of WS tolerance and highlights the immense potential of using genomic selection in improving genetic gain in maize breeding. [ABSTRACT FROM AUTHOR]

Main conclusion: Molecular mechanisms of biological rhythms provide opportunities to harness functional allelic diversity in core (and trait- or stress-responsive) oscillator networks to develop more climate-resilient and productive germplasm. The circadian clock senses light and temperature in day–night cycles to drive biological rhythms. The clock integrates endogenous signals and exogenous stimuli to coordinate diverse physiological processes. Advances in high-throughput non-invasive assays, use of forward- and inverse-genetic approaches, and powerful algorithms are allowing quantitation of variation and detection of genes associated with circadian dynamics. Circadian rhythms and phytohormone pathways in response to endogenous and exogenous cues have been well documented the model plant Arabidopsis. Novel allelic variation associated with circadian rhythms facilitates adaptation and range expansion, and may provide additional opportunity to tailor climate-resilient crops. The circadian phase and period can determine adaptation to environments, while the robustness in the circadian amplitude can enhance resilience to environmental changes. Circadian rhythms in plants are tightly controlled by multiple and interlocked transcriptional–translational feedback loops involving morning (CCA1, LHY), mid-day (PRR9, PRR7, PRR5), and evening (TOC1, ELF3, ELF4, LUX) genes that maintain the plant circadian clock ticking. Significant progress has been made to unravel the functions of circadian rhythms and clock genes that regulate traits, via interaction with phytohormones and trait-responsive genes, in diverse crops. Altered circadian rhythms and clock genes may contribute to hybrid vigor as shown in Arabidopsis, maize, and rice. Modifying circadian rhythms via transgenesis or genome-editing may provide additional opportunities to develop crops with better buffering capacity to environmental stresses. Models that involve clock gene‒phytohormone‒trait interactions can provide novel insights to orchestrate circadian rhythms and modulate clock genes to facilitate breeding of all season crops. [ABSTRACT FROM AUTHOR]

As a fundamental pillar of food security in sub-Saharan Africa (SSA), ensuring seed security is critical to empowering farmers in cultivating food and livestock feed, thereby fostering income generation from agricultural outputs. Among the crops cultivated by smallholders, legumes have the potential to deliver multifaceted benefits. Legumes are nutrient-dense and enhance soil health through their nitrogen-fixing qualities. However, in many instances, the development, release, and supply of improved legume varieties are insufficient to meet the needs of smallholder farmers in SSA. Here, we systematically reviewed the literature to (i) identify and categorize existing legume seed systems, (ii) map legume varieties available to smallholders, (iii) identify barriers hindering the adoption of various legume varieties, and (iv) identify potential strategies and opportunities for strengthening legume seed systems in SSA. Our results demonstrate the coexistence of formal and informal seed systems within legume seed supply chains in SSA, each employing unique seed distribution channels. Smallholders, however, are shown to predominantly depend on the informal seed system to source most legume seeds except for commercially available varieties. We also identified a diverse range of legume varieties available to smallholders in the region, with farmers having varying trait preferences based on crop type and gender. Notably, high yield and abiotic stress tolerance were the most preferred traits. The adoption of these varieties, however, is influenced by various factors, including lack of timely access to seeds in adequate quantities from the formal seed system, high seed costs, and limited information on new varieties. The reviewed literature highlighted that utilizing improved legume varieties had a positive effect on smallholders, leading to improved welfare, food security, dietary diversity, and income. We conclude that the effective scaling of legume systems in SSA is contingent upon the presence of supportive policy frameworks and well-established technical support structures. Packets of legume seeds within a legume germplasm and breeding program at the University of Zambia (Photo by Caitlin Breen, 2022). [ABSTRACT FROM AUTHOR]

The suboptimal productivity of maize systems in sub-Saharan Africa (SSA) is a pressing issue, with far-reaching implications for food security, nutrition, and livelihood sustainability within the affected smallholder farming communities. Dissecting the genetic basis of grain protein, starch and oil content can increase our understanding of the governing genetic systems, improve the efficacy of future breeding schemes and optimize the end-use quality of tropical maize. Here, four bi-parental maize populations were evaluated in field trials in Kenya and genotyped with mid-density single nucleotide polymorphism (SNP) markers. Genotypic (G), environmental (E) and G×E variations were found to be significant for all grain quality traits. Broad sense heritabilities exhibited substantial variation (0.18-0.68). Linkage mapping identified multiple quantitative trait loci (QTLs) for the studied grain quality traits: 13, 7, 33, 8 and 2 QTLs for oil content, protein content, starch content, grain texture and kernel weight, respectively. The colocalization of QTLs identified in our research suggests the presence of shared genetic factors or pleiotropic effects, implying that specific genomic regions influence the expression of multiple grain quality traits simultaneously. Genomic prediction accuracies were moderate to high for the studied traits. Our findings highlight the polygenic nature of grain quality traits and demonstrate the potential of genomic selection to enhance genetic gains in maize breeding. Furthermore, the identified genomic regions and single nucleotide polymorphism markers can serve as the groundwork for investigating candidate genes that regulate grain quality traits in tropical maize. This, in turn, can facilitate the implementation of marker-assisted selection (MAS) in breeding programs focused on improving grain nutrient levels. [ABSTRACT FROM AUTHOR]

Summary: In planta haploid induction (HI), which reduces the chromosome number in the progeny after fertilization, has garnered increasing attention for its significant potential in crop breeding and genetic research. Despite the identification of several natural and synthetic HI systems in different plant species, the molecular and cellular mechanisms underlying these HI systems remain largely unknown. This review synthesizes the current understanding of HI systems in plants (with a focus on genes and molecular mechanisms involved), including the molecular and cellular interactions which orchestrate the HI process. As most HI systems can function across taxonomic boundaries, we particularly discuss the evidence for conserved mechanisms underlying the process. These include mechanisms involved in preserving chromosomal integrity, centromere function, gamete communication and/or fusion, and maintenance of karyogamy. While significant discoveries and advances on haploid inducer systems have arisen over the past decades, we underscore gaps in understanding and deliberate on directions for further research for a more comprehensive understanding of in vivo HI processes in plants. [ABSTRACT FROM AUTHOR]

Agricultural sustainability faces challenges in the changing climate, particularly for rain-fed systems like those in Ethiopia. This study examines the combined impacts of climate change and soil acidity on future crop potential, focusing on Ethiopia as a case study. The EcoCrop crop suitability model was parameterized and run for four key food crops in Ethiopia (teff, maize, barley and common wheat), under current and mid-century climate conditions. To assess the impacts of soil acidification on crop suitability, a simulation study was conducted by lowering the soil pH values by 0.5, 1.0 and 1.5 and re-running the suitability model, comparing the changes in the area suitable for each crop. Our evaluation of the model, by comparing the modeled suitable areas with reference data, indicated that there was a good fit for all the four crops. Using default soil pH values, we project that there will be no significant changes in the suitability of maize, barley and wheat and an increase in the suitability of teff by the mid-century, as influenced by projected increases in rainfall in the country. Our results demonstrate a direct relationship between the lowering of soil pH and increasing losses in the area suitable for all crops, but especially for teff, barley and wheat. We conclude that soil acidification can have a strong impact on crop suitability in Ethiopia under climate change, and precautionary measures to avoid soil acidification should be a key element in the design of climate change adaptation strategies. [ABSTRACT FROM AUTHOR]

Mushrooms are a nutritionally rich and sustainably-produced food with a growing global market. Agaricus bisporus accounts for 11% of the total world mushroom production and it is the dominant species cultivated in Europe. It faces threats from pathogens that cause important production losses, including the mycoparasite Lecanicillium fungicola, the causative agent of dry bubble disease. Through quantitative real-time polymerase chain reaction (qRT-PCR), we determine the impact of L. fungicola infection on the transcription patterns of A. bisporus genes involved in key cellular processes. Notably, genes related to cell division, fruiting body development, and apoptosis exhibit dynamic transcriptional changes in response to infection. Furthermore, A. bisporus infected with L. fungicola were found to accumulate increased levels of reactive oxygen species (ROS). Interestingly, the transcription levels of genes involved in the production and scavenging mechanisms of ROS were also increased, suggesting the involvement of changes to ROS homeostasis in response to L. fungicola infection. These findings identify potential links between enhanced cell proliferation, impaired fruiting body development, and ROS-mediated defence strategies during the A. bisporus (host)–L. fungicola (pathogen) interaction, and offer avenues for innovative disease control strategies and improved understanding of fungal pathogenesis. [ABSTRACT FROM AUTHOR]

Low soil nitrogen levels, compounded by the high costs associated with nitrogen supplementation through fertilizers, significantly contribute to food insecurity, malnutrition, and rural poverty in maize-dependent smallholder communities of sub-Saharan Africa (SSA). The discovery of genomic regions associated with low nitrogen tolerance in maize can enhance selection efficiency and facilitate the development of improved varieties. To elucidate the genetic architecture of grain yield (GY) and its associated traits (anthesis-silking interval (ASI), anthesis date (AD), plant height (PH), ear position (EPO), and ear height (EH)) under different soil nitrogen regimes, four F3 maize populations were evaluated in Kenya and Zimbabwe. GY and all the traits evaluated showed significant genotypic variance and moderate heritability under both optimum and low nitrogen stress conditions. A total of 91 quantitative trait loci (QTL) related to GY (11) and other secondary traits (AD (26), PH (19), EH (24), EPO (7) and ASI (4)) were detected. Under low soil nitrogen conditions, PH and ASI had the highest number of QTLs. Furthermore, some common QTLs were identified between secondary traits under both nitrogen regimes. These QTLs are of significant value for further validation and possible rapid introgression into maize populations using markerassisted selection. Identification of many QTL with minor effects indicates genomic selection (GS) is more appropriate for their improvement. Genomic prediction within each population revealed low to moderately high accuracy under optimum and low soil N stress management. However, the accuracies were higher for GY, PH and EH under optimum compared to low soil N stress. Our findings indicate that genetic gain can be improved in maize breeding for low N stress tolerance by using GS. [ABSTRACT FROM AUTHOR]

The evolution and diversification of proteins capable of remodeling domains has been critical for transcriptional reprogramming during cell fate determination in multicellular eukaryotes. Chromatin remodeling proteins of the CHD3 family have been shown to have important and antagonistic impacts on seed development in the model plant, Arabidopsis thaliana , yet the basis of this functional divergence remains unknown. In this study, we demonstrate that genes encoding the CHD3 proteins PICKLE (PKL) and PICKLE-RELATED 2 (PKR2) originated from a duplication event during the diversification of crown Brassicaceae, and that these homologs have undergone distinct evolutionary trajectories since this duplication, with PKR2 fast evolving under positive selection, while PKL is subject to purifying selection. We find that the rapid evolution of PKR2 under positive selection reduces the encoded protein's intrinsic disorder, possibly suggesting a tertiary structure configuration which differs from that of PKL. Our whole genome transcriptome analysis in seeds of pkr2 and pkl mutants reveals that they act antagonistically on the expression of specific sets of genes, providing a basis for their differing roles in seed development. Our results provide insights into how gene duplication and neofunctionalization can lead to differing and antagonistic selective pressures on transcriptomes during plant reproduction, as well as on the evolutionary diversification of the CHD3 family within seed plants. [ABSTRACT FROM AUTHOR]

Alternative splicing (AS) is a gene regulatory mechanism modulating gene expression in multiple ways. AS is prevalent in all eukaryotes including plants. AS generates two or more mRNAs from the precursor mRNA (pre-mRNA) to regulate transcriptome complexity and proteome diversity. Advances in next-generation sequencing, omics technology, bioinformatics tools, and computational methods provide new opportunities to quantify and visualize AS-based quantitative trait variation associated with plant growth, development, reproduction, and stress tolerance. Domestication, polyploidization, and environmental perturbation may evolve novel splicing variants associated with agronomically beneficial traits. To date, pre-mRNAs from many genes are spliced into multiple transcripts that cause phenotypic variation for complex traits, both in model plant Arabidopsis and field crops. Cataloguing and exploiting such variation may provide new paths to enhance climate resilience, resource-use efficiency, productivity, and nutritional quality of staple food crops. This review provides insights into AS variation alongside a gene expression analysis to select for novel phenotypic diversity for use in breeding programs. AS contributes to heterosis, enhances plant symbiosis (mycorrhiza and rhizobium), and provides a mechanistic link between the core clock genes and diverse environmental clues. [ABSTRACT FROM AUTHOR]

Lettuce (Lactuca sativa L.) is one of the commercially important leafy vegetables worldwide. However, lettuce cultivars vary widely in their carotenoid concentrations at the time of harvest. While the carotenoid content of lettuce can depend on transcript levels of key biosynthetic enzymes, genes that can act as biomarkers for carotenoid accumulation at early stages of plant growth have not been identified. Transcriptomic and metabolomic analysis was performed on the inner and outer leaves of the six cultivars at different developmental stages to identify gene-to-metabolite networks affecting the accumulation of two key carotenoids, β-carotene and lutein. Statistical analysis, including principal component analysis, was used to better understand variations in carotenoid concentration between leaf age and cultivars. Our results demonstrate that key enzymes of carotenoid biosynthesis pathway can alter lutein and β-carotene biosynthesis across commercial cultivars. To ensure high carotenoids content in leaves, the metabolites sink from β-carotene and lutein to zeaxanthin, and subsequently, abscisic acid needs to be regulated. Based on 2–3-fold carotenoids increase at 40 days after sowing (DAS) as compared to the seedling stage, and 1.5–2-fold decline at commercial stage (60 DAS) compared to the 40 DAS stage, we conclude that the value of lettuce for human nutrition would be improved by use of less mature plants, as the widely-used commercial stage is already at plant senescence stage where carotenoids and other essential metabolites are undergoing degradation. [ABSTRACT FROM AUTHOR]

The Central American Dry Corridor (CADC) is among the most climate-vulnerable regions worldwide. Climate change, commonly referred to as a “threat multiplier” of pre-existing socioeconomic issues, already undermines rural livelihoods by reducing agricultural yields and income opportunities. This paper provides a review of climate-related migration in the CADC region while identifying the specific pathways by which climate change manifests itself as a threat multiplier to migration. Different forms of human mobility (seasonal/temporal/permanent and internal/international migration) are increasingly attempted as adaptation strategies by affected households to diversify incomes and offset climate impacts. Preferred intra-regional migrant destinations tend to be less climate-vulnerable and also less violent. Notably, climate change is not isolated from socioeconomic and political migration drivers. Erosion of rural livelihoods reduces the costs of engaging in illicit coping strategies (e.g., illegal crop production) and simultaneously favours rapid urbanisation, which is linked to (forced) gang recruitment, primarily affecting the youth. These processes contribute to extraordinarily high violence levels, which are a major push factor for migration on their own, ultimately challenging state authority. Moreover, as outmigration from the region is projected to increase, the observed securitisation of borders, particularly along the USA-Mexico border and the Mexico-Guatemala border, while unfit to limit migration attempts, make migration more desperate and dangerous, allowing organised crime to step in and exploit migration as an economic undertaking. Thus, for the CADC, the depoliticised and simplistic narrative of migration serving as adaptation must be questioned. Policy coherence and state capacity for addressing climate-security-migration nexus challenges are critical needs. [ABSTRACT FROM AUTHOR]