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Abstract In plants, embryo size is determined via interactions between metabolic and developmental signals. Maize (Zea mays) big embryo 6 (bige6) enhances embryo size while sharply reducing plant growth. Here, we show that BigE6 encodes a plastidial prephenate aminotransferase (PPA-AT), a key enzyme in the arogenate pathway for L-phenylalanine (Phe) and L-tyrosine (Tyr) biosynthesis. The maize BigE6 paralog, BigE6Like, encodes a cytosol-localized PPA-AT, revealing Phe and Tyr biosynthesis via cytosolic arogenate as a potential alternative to the known cytosolic phenylpyruvate pathway. Moreover, the single PPA-AT gene of Arabidopsis (Arabidopsis thaliana) encodes plastidial and cytosolic enzymes by alternative splicing. Transgenic rescue of a ppa-at mutant in Arabidopsis demonstrates that the plastidial PPA-AT is indispensable for seed formation due, in part, to its essential role in the female gametophyte. Leaves of bige6 maize maintained overall homeostasis for aromatic amino acids and downstream metabolites, revealing a resilience of mechanisms that scale growth to a limiting supply of Phe and Tyr. In bige6 seeds, broad perturbation of amino acid homeostasis is associated with transcriptomic upregulation of growth processes in the embryo and endosperm, implicating amino acid signaling in the regulation of embryo size. Our findings reveal the complexity and developmental dependence of growth responses to limiting amino acid biosynthesis. 

Abstract Background and AimsNitrogen (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. MethodsIn 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. ResultsThe 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. ConclusionsOur 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. 

Abstract Strigolactones are plant hormones with roles in a wide range of signaling and developmental processes. A yellow-striped maize mutant, (interveinalyellow)ivy, was determined to have low iron in tissues under normal growth conditions. The gene underlying theivymutation was mapped and identified asZmCCD8, a key enzyme in the biosynthesis of strigolactones. Under iron-replete conditions, comparison of the transcriptomes of wild-type plants and maizeccd8mutants revealed suppression of several iron-regulated genes inccd8. These genes are normally up-regulated during iron deficiency and include the key iron-regulated transcription factorIRO2as well as genes involved in the biosynthesis of iron chelators and transporters. External supply of synthetic strigolactone toivymutants alleviated chlorosis and returned iron-regulated gene expression to wild-type levels. In iron limited conditions, iron-regulated gene expression inccd8mutants responded normally, indicating that strigolactones are not required for response to externally imposed iron deficiency. However, they are required for basal expression of iron-regulated genes when adequate iron is available, highlighting a distinction between iron homeostasis during normal growth, and the iron deficiency response triggered by the lack of external available iron. The connection between strigolactones and iron homeostasis is not limited to maize, as Arabidopsisccd8mutants also show strong chlorosis when grown on medium with moderate levels of iron. This previously unappreciated role may have implications for the use of strigolactones in agricultural contexts. 

Abstract BackgroundThe 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. ResultsHere, 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. ConclusionsThe 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. 

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. 

To maintain growth and to successfully reproduce, organisms must protect key functions in specific tissues, particularly when countering pathogen invasion using internal defensive proteins that may disrupt their own developmental processes. The rice immune receptor XA21 confers race-specific resistance againstXanthomonas oryzaepv.oryzae, which causes the deadly disease bacterial leaf blight. Here, we demonstrate that XA21 is cleaved by the rhomboid-like protease OsRBL3b, likely within its transmembrane domain.OsRBL3bmRNA transcripts are preferentially expressed in rice spikelets. Rice plants expressingXa21but lacking a functionalOsRBL3bdisplayed impaired anther dehiscence and pollen viability, resulting in male sterility and yield reduction with high levels of XA21 protein present in spikelets during anthesis. In leaves,osrbl3bmutants expressing XA21 had normal levels of this resistance protein and disease immunity. This balance between reproduction and disease resistance through the specific expression of a rhomboid protease may be key to limiting the detrimental effects of an active immune response and may be useful in future for genetic improvement of crops. 

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.