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  1. Abstract Background and Aims

    Nitrogen (N) is an essential macronutrient that can limit plant development and crop yield through widespread physiological and molecular impacts. In maize, N-starvation enhances biosynthesis and exudation of strigolactones (SLs) in a process reversible by nitrate addition and consequent repression of genes for SL biosynthesis.

    Methods

    In the present study, a maize mutant deficient in SL biosynthesis (zmccd8) allowed an in-depth analysis of SL contributions under low N. Both hydroponic and field conditions were used to better characterize the response of the mutant to N availability.

    Results

    The severity of responses to N-limitation by the SL-deficientzmccd8mutant extended from growth parameters to content of iron, sulfur, protein, and photosynthetic pigments, as well as pronounced impacts on expression of key genes, which could be crucial molecular target for the SL-mediated acclimatation to N shortage.

    Conclusions

    Our results demonstrate that SLs are critical for physiological acclimation to N deficiency by maize and identify central players in this action. Further contributions by iron and sulfur are implicated in the complex pathway underlying SL modulation of responses to N-deprivation, thus widening our knowledge on SL functioning and providing new hints on their potential use in agriculture.

     
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    Free, publicly-accessible full text available February 22, 2025
  2. Abstract Background

    The maize inbred line A188 is an attractive model for elucidation of gene function and improvement due to its high embryogenic capacity and many contrasting traits to the first maize reference genome, B73, and other elite lines. The lack of a genome assembly of A188 limits its use as a model for functional studies.

    Results

    Here, we present a chromosome-level genome assembly of A188 using long reads and optical maps. Comparison of A188 with B73 using both whole-genome alignments and read depths from sequencing reads identify approximately 1.1 Gb of syntenic sequences as well as extensive structural variation, including a 1.8-Mb duplication containing the Gametophyte factor1 locus for unilateral cross-incompatibility, and six inversions of 0.7 Mb or greater. Increased copy number of carotenoid cleavage dioxygenase 1 (ccd1) in A188 is associated with elevated expression during seed development. Highccd1expression in seeds together with low expression of yellow endosperm 1 (y1) reduces carotenoid accumulation, accounting for the white seed phenotype of A188. Furthermore, transcriptome and epigenome analyses reveal enhanced expression of defense pathways and altered DNA methylation patterns of the embryonic callus.

    Conclusions

    The A188 genome assembly provides a high-resolution sequence for a complex genome species and a foundational resource for analyses of genome variation and gene function in maize. The genome, in comparison to B73, contains extensive intra-species structural variations and other genetic differences. Expression and network analyses identify discrete profiles for embryonic callus and other tissues.

     
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  3. Summary

    The B vitamins provide essential co‐factors for central metabolism in all organisms. In plants, B vitamins have surprising emerging roles in development, stress tolerance and pathogen resistance. Hence, there is a paramount interest in understanding the regulation of vitamin biosynthesis as well as the consequences of vitamin deficiency in crop species. To facilitate genetic analysis of B vitamin biosynthesis and functions in maize, we have mined the UniformMu transposon resource to identify insertional mutations in vitamin pathway genes. A screen of 190 insertion lines for seed and seedling phenotypes identified mutations in biotin, pyridoxine and niacin biosynthetic pathways. Importantly, isolation of independent insertion alleles enabled genetic confirmation of genotype‐to‐phenotype associations. Because B vitamins are essential for survival, null mutations often have embryo lethal phenotypes that prevent elucidation of subtle, but physiologically important, metabolic consequences of sub‐optimal (functional) vitamin status. To circumvent this barrier, we demonstrate a strategy for refined genetic manipulation of vitamin status based on construction of heterozygotes that combine strong and hypomorphic mutant alleles. Dosage analysis ofpdx2alleles in endosperm revealed that endosperm supplies pyridoxine to the developing embryo. Similarly, a hypomorphicbio1allele enabled analysis of transcriptome and metabolome responses to incipient biotin deficiency in seedling leaves. We show that systemic pipecolic acid accumulation is an early metabolic response to sub‐optimal biotin status highlighting an intriguing connection between biotin, lysine metabolism and systemic disease resistance signaling. Seed‐stocks carrying insertions for vitamin pathway genes are available for free, public distribution via the Maize Genetics Cooperation Stock Center.

     
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  4. Free, publicly-accessible full text available September 1, 2025
  5. Nitrogen (N) fertilization has been one of the main practices used to increase yield of agricultural crops worldwide. In developed countries, N supplementation in agriculture has increased by more than 120% between the 1960s and 2020. It is estimated that N applications will continue to rise as world population is expected to grow by 3 billion people within the next 80 years. Moreover, a 56% increase in crop yield will be needed to sustain the predicted population growth. However, pollution by excess N runoff from agriculture remains a global concern. A holistic approach is thus needed to integrate knowledge of plant nitrogen use efficiency with management practices. 
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    Free, publicly-accessible full text available January 20, 2025
  6. Nearly all eukaryotes carry DNA transposons of the Robertson’s Mutator ( Mu ) superfamily, a widespread source of genome instability and genetic variation. Despite their pervasive impact on host genomes, much remains unknown about the evolution of these transposons. Transposase recognition of terminal inverted repeats (TIRs) is thought to drive and constrain coevolution of MuDR transposase genes and TIRs. To address the extent of this relationship and its impact, we compared separate phylogenies of TIRs and MuDR gene sequences from Mu elements in the maize genome. Five major clades were identified. As expected, most Mu elements were bound by highly similar TIRs from the same clade (homomorphic type). However, a subset of elements contained dissimilar TIRs derived from divergent clades. These “heteromorphs” typically occurred in multiple copies indicating active transposition in the genome. In addition, analysis of internal sequences showed that exchanges between elements having divergent TIRs produced new mudra and mudrb gene combinations. In several instances, TIR homomorphs had been regenerated within a heteromorph clade with retention of distinctive internal MuDR sequence combinations. Results reveal that recombination between divergent clades facilitates independent evolution of transposase ( mudra ), transposase-binding targets (TIRs), and capacity for insertion ( mudrb ) of active Mu elements. This mechanism would be enhanced by the preference of Mu insertions for recombination-rich regions near the 5′ ends of genes. We suggest that cycles of recombination give rise to alternating homo- and heteromorph forms that enhance the diversity on which selection for Mu fitness can operate. 
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  7. Abstract Plants release back to the atmosphere about half of the CO 2 they capture by photosynthesis. Decreasing the rate of crop respiration could therefore potentially increase yields, store more carbon in the soil and draw down atmospheric CO 2 . However, decreasing respiration rate has had very little research effort compared to increasing photosynthesis, the historically dominant metabolic paradigm for crop improvement. Conceptual and technical advances, particularly in protein turnover and directed enzyme evolution, have now opened ways to trim the large fraction of respiration that fuels proteome maintenance by lowering the breakdown and resynthesis rates of enzymes and other proteins. In addition to being theoretically possible and practicable, exploring the reduction of respiration is prudential, given that it (i) has barely yet been tried and (ii) could help meet the challenges of sustaining crop productivity and managing atmospheric carbon. 
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  8. Abstract Maize (Zea mays) kernels are the largest cereal grains, and their endosperm is severely oxygen deficient during grain fill. The causes, dynamics, and mechanisms of acclimation to hypoxia are minimally understood. Here, we demonstrate that hypoxia develops in the small, growing endosperm, but not the nucellus, and becomes the standard state, regardless of diverse structural and genetic perturbations in modern maize (B73, popcorn, sweet corn), mutants (sweet4c, glossy6, waxy), and non-domesticated wild relatives (teosintes and Tripsacum species). We also uncovered an interconnected void space at the chalazal pericarp, providing superior oxygen supply to the placental tissues and basal endosperm transfer layer. Modeling indicated a very high diffusion resistance inside the endosperm, which, together with internal oxygen consumption, could generate steep oxygen gradients at the endosperm surface. Manipulation of oxygen supply induced reciprocal shifts in gene expression implicated in controlling mitochondrial functions (23.6 kDa Heat-Shock Protein, Voltage-Dependent Anion Channel 2) and multiple signaling pathways (core hypoxia genes, cyclic nucleotide metabolism, ethylene synthesis). Metabolite profiling revealed oxygen-dependent shifts in mitochondrial pathways, ascorbate metabolism, starch synthesis, and auxin degradation. Long-term elevated oxygen supply enhanced the rate of kernel development. Altogether, evidence here supports a mechanistic framework for the establishment of and acclimation to hypoxia in the maize endosperm. 
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  9. Elucidation of maize strigolactone biosynthetic pathway has the potential for controlling the parasitic witchweed Striga . 
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  10. Abstract The maize (Zea mays) ear represents one of the most striking domestication phenotypes in any crop species, with the cob conferring an exceptional yield advantage over the ancestral form of teosinte. Remodeling of the grain-bearing surface required profound developmental changes. However, the underlying mechanisms remain unclear and can only be partly attributed to the known domestication gene Teosinte glume architecture 1 (Tga1). Here we show that a more complete conversion involves strigolactones (SLs), and that these are prominent players not only in the Tga1 phenotype but also other domestication features of the ear and kernel. Genetic combinations of a teosinte tga1 allele with three SL-related mutants progressively enhanced ancestral morphologies. The SL mutants, in addition to modulating the tga1 phenotype, also reshaped kernel-bearing pedicels and cupules in a teosinte-like manner. Genetic and molecular evidence are consistent with SL regulation of TGA1, including direct interaction of TGA1 with components of the SL-signaling system shown here to mediate TGA1 availability by sequestration. Roles of the SL network extend to enhancing maize seed size and, importantly, coordinating increased kernel growth with remodeling of protective maternal tissues. Collectively, our data show that SLs have central roles in releasing kernels from restrictive maternal encasement and coordinating other factors that increase kernel size, physical support, and their exposure on the grain-bearing surface. 
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