Xu, F et al. 2024. iFLAS: positive-unlabeled learning facilitates full-length transcriptome-based identification and functional exploration of alternatively spliced isoforms in maize. New Phytol. :doi: 10.1111/nph.19554.
   iFLAS: positive-unlabeled learning facilitates full-length transcriptome-based identification and functional exploration of alternatively spliced isoforms in maize.

Other examples of genes exhibiting allele-specific alternative splicing: Zm00001d007470, Zm00001d034313, Zm00001d035140, Zm00001d053864, Zm00001d053865, Zm00001d017303, Zm00001d000224, Zm00001d002836, Zm00001d017303, Zm00001d020178, Zm00001d040612, Zm00001d042394, Zm00001d021822

Advances in full-length transcriptome sequencing technology have accelerated the discovery of novel splice isoforms. However, current alternative splicing (AS) tools are mainly designed for human and animal studies. The differences in AS patterns between plants and animals pose a challenge to identification and functional exploration of novel isoforms in plants. This study developed a plant-optimized full-length transcriptome analysis toolkit called iFLAS, which uses a semi-supervised machine learning approach positive-unlabeled (PU) learning to accurately identify novel isoforms and enable investigation of AS functions from multiple perspectives, such as differential AS, poly(A) tail length, and allele-specific AS (ASAS) analysis. By applying iFLAS to three full-length transcriptome sequencing datasets, this study systematically identified and functionally characterized maize (Zea mays) AS patterns. The results showed that intron retention not only introduces premature termination codons, leading to reduced expression levels of the isoforms; but also regulates the length of the 3'UTR and poly (A) tails, affecting the functional differentiation of the isoforms. In addition, different ASAS patterns were observed in the hybrid offspring of maize inbred lines B73 and Ki11, highlighting their potential value in breeding. These results highlight the extensive utilization of iFLAS in research on plant full-length transcriptome alternative splicing.

Xu, F et al. 2024. iFLAS: positive-unlabeled learning facilitates full-length transcriptome-based identification and functional exploration of alternatively spliced isoforms in maize. New Phytol. :doi: 10.1111/nph.19554.
   iFLAS: positive-unlabeled learning facilitates full-length transcriptome-based identification and functional exploration of alternatively spliced isoforms in maize.
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Wenyu Li et al. 2024. ZmMAPK6, a mitogenactivated protein kinase, regulates maize kernel weight. J Exp Bot. :doi: 10.1093/jxb/erae104.
   ZmMAPK6, a mitogenactivated protein kinase, regulates maize kernel weight.

Understanding the biological processes that contribute to grain size and weight are important for ensuring global food security. The maize Mitogen-Activated Protein Kinase 6 (ZmMAPK6), an active kinase, has previously been shown to be involved with various biotic and abiotic stresses. The authors show that changes in ZmMAPK6 expression in mutants and overexpression lines respectively decrease or increase maize grain weight and size. Increases in weight (16-23% weight increase) and size in the overexpression lines are due to increased grain-filling, resulting in more starch and protein accumulation. Transcripts involved with seed growth and development were found to be downregulated in zmmpk6-cr mutants compared to wild type. Overall, ZmMAPK6 is a promising target to explore for maize yield improvement.

Wenyu Li et al. 2024. ZmMAPK6, a mitogenactivated protein kinase, regulates maize kernel weight. J Exp Bot. :doi: 10.1093/jxb/erae104.
   ZmMAPK6, a mitogenactivated protein kinase, regulates maize kernel weight.
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Cao, SA et al. 2024. Cytoplasmic genome contributions to domestication and improvement of modern maize BMC Biology. 22:64.
   Cytoplasmic genome contributions to domestication and improvement of modern maize

The significance of cytoplasmic genomes to maize domestication and breeding is examined in this article. Cytoplasmic organelles (mitochondria, chloroplast) are important for growth and development, they are semi-autonomous (their own genome) with a constant rate of sequence changes in their genomes. All these characteristics suggest they may have an important role in domestication and improvement of maize. Cytoplasmic male sterility (CMS) of great importance in maize breeding is determined by mutations in the mitochondrial genome. The two male-fertility cytotypes (NA and NB) and the three main CMS types (CMS-C, CMS-T, and CMS-S) were examined here. Comparing the entire genome sequences of 630 related accessions of maize from North America and China, authors studied the contribution of cytoplasmic genomes in domestication and improvement of maize. According to the study’s findings, maize's cytoplasmic and nuclear genomes coevolved throughout domestication and improvement. Furthermore, the nucleotypic diversity among genes involved in photosynthesis, energy, and metabolism, have increased as a result of cytoplasmic genome evolution. The cytoplasmic variation in those genes is associated with key agronomic and reproductive traits. These new insights and considering cytoplasmic genome variation between genotypes can help in the improvement of yield stability and crop resilience of maize.

Cao, SA et al. 2024. Cytoplasmic genome contributions to domestication and improvement of modern maize BMC Biology. 22:64.
   Cytoplasmic genome contributions to domestication and improvement of modern maize
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Li, XL et al. 2024. Heat stress at the bicellular stage inhibits sperm cell development and transport into pollen tubes Plant Physiol. :doi: 10.1093/plphys/kiae087.
   Heat stress at the bicellular stage inhibits sperm cell development and transport into pollen tubes

In this article the authors have focused on understanding the development of pollen tube (male gametophyte) during the reproductive stages under heat stress. It was found that when moderate heat stress is applied to the for a period of 2 days during the uni- and bicellular stages of pollen development it severely accelerates or shortens the pollen development time and impairs the pollen germination capabilities. To get a deep understanding of this the authors set an experiment for pollinating the maize plants with heat stressed pollen and non-stressed pollen and then examine the rate of seed set through the entire cobs. These experiments suggested that the cobs pollinated with heat stressed pollens have 65% reduced seed formation compared to the control ones, suggesting that the heat stressed pollens fall into the category of non-fertile type. Further to gain insights at heat stress effects on pollen impairment based on stages i.e., uni- or bicellular morphological and biochemical experiments were performed, the findings suggests that heat stress at unicellular stage significantly effects pollen germination capabilities while the effect of heat stress at bicellular stage corresponds to affecting the sperm cell development and transport. How the sperm cell transportation ability is affected by heat stress to investigate this the mobility of the sperm cell inside the pollen tube was analyzed using α-tubulin-YFP marker line it was found that after 1 h of pollen germination and growth in vitro, about 80% non-stressed sperm cells were visible inside pollen tubes however the number was significantly reduced to 20% in case of heat-stressed conditions. Further it was found that heat-stress impacts expression of genes involved in transcription, DNA replication, RNA processing, and translation in sperm cells and this leads to mis-regulation of cell cycle control genes in the sperm cell.

Li, XL et al. 2024. Heat stress at the bicellular stage inhibits sperm cell development and transport into pollen tubes Plant Physiol. :doi: 10.1093/plphys/kiae087.
   Heat stress at the bicellular stage inhibits sperm cell development and transport into pollen tubes
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Zhong, T et al. 2024. The ZmWAKL–ZmWIK–ZmBLK1–ZmRBOH4 module provides quantitative resistance to gray leaf spot in maize Nature Genetics. :doi: 10.1038/s41588-023-01644-z.
   The ZmWAKL–ZmWIK–ZmBLK1–ZmRBOH4 module provides quantitative resistance to gray leaf spot in maize

Gray spot (GLS) is a major foliar disease of maize caused by the fungal pathogens Cercospora zeae-maydis and Cercospora zeina. Since its discovery in the United States in the 1920s, GLS has become a disease that severely affects maize yields. GLS resistance is a quantitative trait. Although more than 100 quantitative loci have been identified, the number of GLS resistance genes identified so far are very rare. In this study, a major quantitative resistance locus, qRgls1, was identified in segregating population derived from a cross between the highly GLS-resistant inbred line Y32 and GLS-susceptible inbred line Q11, this locus was able to significantly increase resistance to GLS in maize. The functional gene of this locus, ZmWAKL, was identified by fine-mapping and transgenic experiments validation, and the allele in Y32 was designated as resistant gene ZmWAKL Y , and the allele in Q11 was designated as susceptible gene ZmWAKL Q . Through further split luciferase complementation (SLC) and co-immunoprecipitation (Co-IP) experiments, it was found that ZmWAKL was able to occur homodimerization and binds to its co-receptor ZmWIK at plasma membrane to form the ZmWAKLY/ZmWIK immune complex. This complex further interacts with cytoplasmic receptor kinase ZmBLK1, which transmits the immune signals to NADPH oxidase ZmRBOH4 at plasma membrane. Upon challenge by the pathogen Cercospora zeina, the resistance gene ZmWAKL Y occurs homodimerization resulting in a rapid increase in its own phosphorylation activity, and together with ZmWIK, transmits immune signals to ZmBLK1 and then to ZmRBOH4, which triggers a ROS burst to incur innate immunity, resulting in maize disease resistance; while the susceptible gene ZmWAKL Q could not occurs homodimerization to increase its own phosphorylation activity, which impeded the signaling pathway, resulting in maize disease susceptibility. In conclusion, this study reveals the role of the maize ZmWAKL-ZmWIK-ZmBLK1-ZmRBOH4 receptor/signaling/executive module in enhancing resistance to GLS.

Zhong, T et al. 2024. The ZmWAKL–ZmWIK–ZmBLK1–ZmRBOH4 module provides quantitative resistance to gray leaf spot in maize Nature Genetics. :doi: 10.1038/s41588-023-01644-z.
   The ZmWAKL–ZmWIK–ZmBLK1–ZmRBOH4 module provides quantitative resistance to gray leaf spot in maize
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Zhou, Y et al. 2024. Genetic regulation of self-organizing azimuthal canopy orientations and their impacts on light interception in maize Plant Cell. :doi: 10.1093/plcell/koae007.
   Genetic regulation of self-organizing azimuthal canopy orientations and their impacts on light interception in maize

Increasing yields of commercial maize hybrids have been possible thanks to their improved tolerance to high plant densities. Under these circumstances plants can shade nearby plants reducing light penetration. Authors studied how maize plants adjust their canopy to tolerate the shading, finding some genotypes able to alter their azimuthal canopy orientation during development with their leaves growing in parallel to the leaves of adjacent plants. They performed a genome-wide association study on parallel canopy and on the fraction of intercepted photosynthetically active radiation. The parallel canopy trait is measured as the number or percentage of plants that are mutually parallel. They found candidate genes associated with shade avoidance syndrome and ligule development. Using mutagenesis, they demonstrated that liguleless genes (lg1, lg2, lg3) are also required for azimuthal canopy re-orientation and other normal light responses. Authors emphasize that it’s likely that pathways other than shade avoidance syndrome could also contribute to azimuthal canopy re-orientation. They also hypothesized that perception of blue light is key for the initiation of azimuthal canopy re-orientation, and this initiation signal is transduced via auxin signaling.

Zhou, Y et al. 2024. Genetic regulation of self-organizing azimuthal canopy orientations and their impacts on light interception in maize Plant Cell. :doi: 10.1093/plcell/koae007.
   Genetic regulation of self-organizing azimuthal canopy orientations and their impacts on light interception in maize
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Kumar, R et al. 2023. Genetic architecture of source-sink-regulated senescence in maize. Plant Physiol. :doi: 10.1093/plphys/kiad460.
   Genetic architecture of source-sink-regulated senescence in maize.

Source (photosynthetic organs like leaves) and sink (storage organs like ear and stalk) interactions play a critical role in regulating the senescence in maize. The important role of this interactions is obvious as activity of source determines the amount of photosynthates available for the plant growth and storage, while sink activity relates to the crop yield. However, the genetic and molecular mechanism through which source-sink interactions regulates senescence were poorly understood. Kumar et al., (2023), used a systems genetics approach to understand the mechanism of source-sink regulated senescence (SSRS) induced by preventing the pollination of maize ear. Authors performed a comprehensive time course phenotypic and transcriptomic analysis. Authors comparative analysis showed that SSRS phenotypes starts with a feedback inhibition of photosynthesis, a surge in reactive oxygen species, and the resulting endoplasmic reticulum (ER) stress results from weakened sink demand. Authors performed a multi-environmental evaluation of a biparental population and a diversity panel and identified 12 quantitative trait loci and 24 candidate genes, respectively, underlying SSRS. By combining the natural diversity and coexpression networks analyses authors identified 7 high-confidence candidate genes involved in proteolysis, photosynthesis, stress response, and protein folding. Authors showed the role of a cathepsin B like protease 4 (ccp4) in SSRS, by analysis of natural alleles in maize and heterologous analyses in Arabidopsis (Arabidopsis thaliana). Finally, authors proposed a model for SSRS regulation, and their findings provide a deeper understanding of source-sink interactions. This study offers an opportunity to modify these interactions to alter senescence program and enhance crop productivity.

Kumar, R et al. 2023. Genetic architecture of source-sink-regulated senescence in maize. Plant Physiol. :doi: 10.1093/plphys/kiad460.
   Genetic architecture of source-sink-regulated senescence in maize.
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Yan, PS et al. 2023. Biofortification of iron content by regulating a NAC transcription factor in maize Science. 382:1159-1165.
   Biofortification of iron content by regulating a NAC transcription factor in maize

The main factor contributing to anemia is iron deficiency. Increasing the iron content of foods is a fundamental, low-cost, and widespread method of improving iron malnutrition. Maize is one of the staple grains and increasing its iron content can alleviate iron deficiency anemia. However, the iron and other nutrients delivery pathways in maize kernels have been an open question. This study used 273 maize inbred lines genotype combined with transcriptome from six extreme materials to identify a candidate gene, ZmNAC78, involved in the regulation of maize kernel iron content. Kernels of transgenic maize overexpressing ZmNAC78 had significantly higher iron content, up to 70.5 mg/kg. The study further dissected the iron delivery pathways in maize kernels. ZmNAC78 was predominantly expressed in the basal endosperm transfer layer (BETL) of maize kernels and activated the expression of the metal ion transporter proteins, ZmYSL11, ZmNRAMP3, and ZmHMA8, in the BETL. Loss of function mutations showed that these metal transporter proteins play important roles in loading of iron into maize kernels, and it is clear that ZmNAC78 and metal transporter proteins together form a molecular switch to control iron delivery into maize kernels. In addition, this study also utilized the polymorphism of ZmNAC78 core promoter sequence to classify maize inbred lines into haplotype 1 with high iron content in kernel and haplotype 2 with low iron content in kernel, and used the haplotype information to breed maize varieties with higher seed iron contents and yields, which will be a feasible option for breeding high-yielding and high-iron maize in the future. In conclusion, this study reveals the iron delivery pathways in maize kernels, and also provided new ideas for dissecting nutrients delivery pathways in wheat and other cereal crops.

Yan, PS et al. 2023. Biofortification of iron content by regulating a NAC transcription factor in maize Science. 382:1159-1165.
   Biofortification of iron content by regulating a NAC transcription factor in maize
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Yuan, Y et al. 2024. Decoding the gene regulatory network of endosperm differentiation in maize Nat Commun. 15:34.
   Decoding the gene regulatory network of endosperm differentiation in maize

The authors analyzed the transcriptome of the developing maize (Zea mays) endosperm during cell differentiation using single-cell transcriptomics. By analyzing 17,022 single cells and the expression of 25,365 genes from 6 to 7 days after pollination, authors identified 12 clusters corresponding to five cell types, and revealed their temporal gene expression patterns. Results revealed heterogeneity of the endosperm composition and complex expression patterns across and withing cell types. Authors combined transcriptomic data with DNA-binding profiles of 161 transcription factors (TF) differentially expressed between cell types to construct a gene regulatory network. This comprehensive network contained 181 regulons, defined as TF with their direct-binding targets, that were mapped to the different cell types to identify specific cell- type regulators. This study generated valuable information for understanding maize endosperm development, a framework that can be applied to other maize tissues, and a web interface to enable researchers to easily navigate the expression and regulatory network atlas of this study (https://www.maize-endosperm.cn).

Early seed developmental stages provide dynamics resource to understand the regulatory function of genes expressed in specific tissue types. Maize endosperm provides an excellent model for developmental and molecular studies considering its size and storage space. The study focused on single cell transcriptomics of maize endosperm during early developmental stage when the cells undergo robust differentiation. A transcriptomic resource of 17,022 single cells was generated between developmental stages 6 to 7 days after pollination (DAP). The authors analyzed the expression of 25,365 genes during the active growth stage of 6 to 7 DAP, that colonizes 12 clusters showing spatial and temporal expression pattern. Endosperm being triploid in nature defines the heterogeneous nature, and so was the expression of the genes within the differentiating cells. Further in the study the authors identified 161 transcription factors (TFs) differentially expressed and analyzed their DNA binding motifs between different cell clusters and constructed a gene regulatory network (GRN), identifying 181 regulons (hub genes) suggesting direct interactions to specific cell types. The regulon map generated in this article corresponding to specific cell clusters in developing endosperm provides a valuable resource to understand the role of important regulators in tissue specific manner during early stages maize endosperm development.

Yuan, Y et al. 2024. Decoding the gene regulatory network of endosperm differentiation in maize Nat Commun. 15:34.
   Decoding the gene regulatory network of endosperm differentiation in maize
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Liu, X-Y et al. 2024. Maize requires Embryo defective27 for embryogenesis and seedling development Plant Physiol. :doi: 10.1093/plphys/kiae010.
   Maize requires Embryo defective27 for embryogenesis and seedling development

The maize mutant embryo defective27 (emb27) was identified using the UniformMu mutagenesis population and found to encode the chloroplast-localized ribosomal protein RPS13. The kernels of the emb27 mutant make normal endosperm but have defects in embryo development, while a second weaker allele emb27-2, makes normal kernels but has albino seedlings due to chloroplast defects. The authors find that transcription level of Emb27 is correlated with normal embryogenesis with a minimum threshold of 6% of wild-type and that expression is likely modulated by genetic background. In addition, emb27 mutants have defects in plastid ribosome assembly and chloroplast protein translation. The emb27-1 allele and other plastid-translation-deficient mutants have splicing defects in plastid transcripts, further indicating defects in plastid translation. Altogether these data suggest a model where nuclear encoded Emb27 is expressed, translated, and imported into the plastid where it facilitates assembly of chloroplast ribosomes and translation of chloroplast proteins. Severe reduction in Emb27 transcript levels lead to embryo lethality through a hypothesized retrograde signal, providing insight into the role of plastid translation in regulating maize embryogenesis.

Liu, X-Y et al. 2024. Maize requires Embryo defective27 for embryogenesis and seedling development Plant Physiol. :doi: 10.1093/plphys/kiae010.
   Maize requires Embryo defective27 for embryogenesis and seedling development
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Yang, N et al. 2023. Two teosintes made modern maize. Science 282: 6674
   Two teosintes made modern maize

Structured Abstract: INTRODUCTION AND RATIONALE: The drastic morphological differences between maize and its wild relatives gave rise to more than a century of debate about its origins. Today, the most widely accepted model is also the simplest—maize was domesticated once from the wild annual grass Zea mays ssp. parviglumis in the lowlands of southwest Mexico. More recently, however, genomic surveys of traditional maize varieties in both Mexico and South America have identified evidence for gene flow from a second wild relative, Zea mays ssp. mexicana, a weedy annual grass adapted to the central Mexican highlands. These results, combined with long-standing archaeological evidence of hybridization, challenge the sufficiency of a simple model of a single origin. RESULTS: To elucidate the genetic contributions of Zea mays ssp. mexicana to maize, we analyzed >1000 wild and domesticated genomes, including 338 newly sequenced traditional varieties. We found ubiquitous evidence for admixture between maize and Zea mays ssp. mexicana, including in ancient samples from North and South America, diverse traditional varieties, and even modern inbred lines. These results are mirrored in a genotyping survey of >5000 traditional varieties representing maize diversity across the Americas. The only maize sample surveyed that lacks strong evidence for admixture with Zea mays ssp. mexicana is a single ancient South American sample N16, dating to ~5500 years before present. We next fit graphs of population history to our data, revealing multiple admixture events in the history of modern maize. On the basis of these results, we propose a new model of maize origins, which posits that, some 4000 years after domestication, maize hybridized with Zea mays ssp. mexicana in the highlands of central Mexico. The resulting admixed maize then spread across the Americas, replacing or hybridizing with preexisting populations. The timing of this secondary dispersal is roughly coincident with archaeological data showing a transition to a staple maize diet in regions across Mesoamerica. We then explored variation in ancestry along the maize genome. We found that 15 to 25% of the genome could be attributed to Zea mays ssp. mexicana ancestry. We identified regions in which Zea mays ssp. mexicana alleles had reached high frequency in maize, presumably as a result of positive selection. We investigated one of these adaptive introgressions in more detail, using CRISPR-Cas9 knockout mutants and overexpression lines to demonstrate the role of the circadian clock gene ZmPRR37a in determining flowering time under long-day conditions. Our results suggest that introgression at this locus may have facilitated the adaptation of maize to higher latitudes. Finally, we explored the contributions of Zea mays ssp. mexicana alleles to phenotypic variation in maize. Admixture mapping identified at least 25 loci in modern inbred lines where highland teosinte ancestry associates with phenotypes of agronomic importance, from oil content to kernel size and disease resistance, as well as a large effect locus associated with cob diameter in traditional maize varieties. We then modeled the additive genetic variance of each phenotype, allowing us to estimate that Zea mays ssp. mexicana admixture explained a meaningful proportion of the additive genetic variation for many traits, including 25% of the variation for the number of kernels per row and nearly 50% of some disease phenotypes. CONCLUSION: Our extensive population and quantitative genetic analysis of domesticated maize and its wild relatives uncovered a substantial role for two different wild taxa in making modern maize. We propose a new model for the origin of maize that can explain both genetic and archaeological data, and we show how variation in Zea mays ssp. mexicana is a key component of maize diversity, both at individual loci and for genetic variation underlying agronomic traits. Our model raises a number of questions about how and why a secondary spread of maize may have occurred, but we speculate that the timing of admixture suggests a possible direct role for hybridization between maize and Zea mays ssp. mexicana in improving early domesticated forms of maize, helping to transform it into the staple crop we know today. Editor’s summary: Domestication of plants and animals is often characterized by selection for specific traits interspersed with introduction of new desirable traits from wild relatives. Yang et al. examined genetic data from more than 1000 varieties of maize and related species to clarify the complex origins of this agricultural staple. They found evidence that after initial domestication, introgression from a relative of domesticated maize, Zea mays ssp. mexicana, occurred in the highlands of Mexico before propagating across Central America. Alleles from this wild relative affect photoperiodicity and flowering time, which suggests that traits from Zea mays ssp. mexicana may have been beneficial during domestication. These results demonstrate the importance of broad sampling in elucidating the history of domesticates. —Corinne Simonti

See also: https://www.science.org/content/article/scientists-thought-they-understood-maizes-origins-they-were-missing-something-big

This paper proposes a new model of the origin of maize, and discovers two completely different species of Zea mays ssp. Parviglumis and Zea mays ssp. Mexicana are the ancestors of modern maize, revising the hypothesis that maize originated from Zea mays ssp. Parviglumis. (Qiang Ning, Editorial Board Comment December 2023)

Hypotheses about the origin of maize have centered on its domestication from the lowland teosinte Zea mays spp. parviglumis, however this model fails to incorporate evidence that suggests a more complex origin. Using 338 newly sequenced traditional Mexican maize varieties, archaeological samples, modern US varieties and traditional Chinese varieties, the authors found evidence of admixture with the highland Zea mays spp. mexicana. Variation in the mexicana admixture may have resulted in 1) the reduction of genetic load and 2) adaptation to higher latitudes. Admixture from teosinte also contributes to phenotypic variation in agronomic traits such as cold tolerance, cob size, and flowering time in modern maize. Altogether these data suggest a new model where introgression from mexicana contributed to a secondary spread of maize after its initial domestication. (Aimee Uyehara, Editorial Board Comment December 2023 and January 2024)

Understanding the domestication of maize is of great interest for the scientific community as it provides guidance for the introgression of new diversity and key adaptation traits into cultivated maize. It was believed maize domestication occurred from the annual grass zea mays spp. Parviglumis in the lowlands of southwest Mexico; however, evidence has raised suggesting gene flow from a second wild relative zea mays spp. mexicana, a weedy annual grass from the central Mexican high lands. This in combination with archeological evidence suggest a single origin of domesticated maize might not be possible. For the above-mentioned reasons, the authors analyzed a large number of genomes from wild and domesticated (>1000) maize, as well as maize varieties (>5000) representing the diversity across the Americas to elucidate the contribution of mexicana to maize domestication. Authors observed strong evidence of admixture with 15-25% of maize genome originating from mexicana. Suggesting domesticated maize hybridized with mexicana 4000 years after domestication and spread across America replacing or hybridizing with preexisting populations. In addition, they demonstrated the role of the circadian clock gene ZmPRR37a in determining flowering time under long-day conditions via CRISPR-Cas9 knockout and overexpression experiments. The introgression of this locus from mexicana likely facilitated adaptation of maize to higher latitudes. Mexicana also contributed other alleles associated with cob diameter, oil content, kernel size, and disease resistance. This new evidence and model suggest a key role of the hybridization with mexicana in the domestication of maize and highlight key adaptation loci. (Diana Escamilla Sanchez, Editorial Board Comment January 2024)

Yang, N et al. 2023. Two teosintes made modern maize. Science 282: 6674
   Two teosintes made modern maize
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Lisa Thoenen et al. 2023. Bacterial tolerance to host-exuded specialized metabolites structures the maize root microbiome. Proc Natl Acad Sci, USA. 120:e2310134120.
   Bacterial tolerance to host-exuded specialized metabolites structures the maize root microbiome.

The effect of microbes in determining the plant health and nutrient acquisition from soil is well known concept. However, the signaling mechanism responsible for establishing the interaction of microbes with plant roots especially maize are less understood. Various studies have shown that maize roots secrete benzoxazinoids (BXs), a bioactive metabolite in the root exudates which could structure the maize root microbiome. Here in this study Thoenen et al. (2023), reveal that one of the major determinants of root conization is tolerance of microbes to plant specialized metabolites. Authors established a representative collection of maize root bacteria (MRB) and tested their tolerance against BXs. There experiment showed the compound- and strain dependent inhibition of bacterial growth. They also showed that tolerance to BXs compounds depend on cell wall structure of bacterial strain with Gram-positive MRB isolates were more tolerant compared to the gram-negative ones. This study alludes to specific and important role of BXs in controlling the root colonization and could have role in deciding the positive and negative associations. In conclusion, this study can be helpful in designing of microbial composition suitable for a specific host like maize or other species for enhancing the nutrient utilization.

Lisa Thoenen et al. 2023. Bacterial tolerance to host-exuded specialized metabolites structures the maize root microbiome. Proc Natl Acad Sci, USA. 120:e2310134120.
   Bacterial tolerance to host-exuded specialized metabolites structures the maize root microbiome.
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Yin, P et al. 2023. Cytokinin signaling promotes salt tolerance by modulating shoot chloride exclusion in maize. Molecular Plant.
   Cytokinin signaling promotes salt tolerance by modulating shoot chloride exclusion in maize.

Ion toxicity caused by soil salinization is one of the major environmental factors that harms crop yield as well as quality. A list of genes regulating Na+ uptake and transport have been cloned from different crops, but the molecular mechanism and genetic basis of the regulation of Cl- uptake and transport are still unclear. In this study, an A-type response regulator, ZmRR1, was identified from transgenic maize lines tested for salt tolerance, which negatively regulates maize salt tolerance by negatively regulating the cytokinin signaling pathway. On the basis of this result, the molecular mechanism by which cytokinin promotes salt tolerance in maize through the regulation of Cl- transport was elucidated. Under salt stress, ZmRR1 protein levels decreased and its inhibition of ZmHP2, a positive regulator of cytokinin signaling, was deregulated, and then ZmHP2-mediated cytokinin signaling up-regulated the expression of ZmMATE29 (encoding a vesicle-localized protein that can translocate Cl-), which, in turn, promotes salt tolerance in maize by compartmentalizing Cl- into vacuoles of root cortex cells in order to reduce the transport of Cl- from roots to the shoots. In addition, this study also analyzed the natural variation that affect ZmRR1 function through GWAS of 311 maize inbred lines seedling biomass phenotypes and candidate gene association analysis, and found that a non-synonymous SNP (SNP307-T) enhanced the interaction between ZmRR1 and ZmHP2. As a result, the ZmHP2-dependent up-regulation of ZmMATE29 expression under salt stress is blocked, resulting in excessive Cl- being transported from the roots to the shoots, making the SNP307-T inbred line more sensitive to salt stress than the SNP307-C inbred line. This locus provides a new target site for the improvement of salt tolerance in maize.

Yin, P et al. 2023. Cytokinin signaling promotes salt tolerance by modulating shoot chloride exclusion in maize. Molecular Plant.
   Cytokinin signaling promotes salt tolerance by modulating shoot chloride exclusion in maize.
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Chen, ZL et al. 2023. Genetic dissection of cis-regulatory control of ZmWUSCHEL1 expression by type-B RESPONSE REGULATORS. Plant Physiol. :doi: 10.1093/plphys/kiad652.
   Genetic dissection of cis-regulatory control of ZmWUSCHEL1 expression by type-B RESPONSE REGULATORS.

Gene expression caused by modification of Cis-regulatory regions is one of the important aspects in evolution and domestication of modern cultivated maize. However, the in plants impact of cis-regulatory control on transcriptional regulation and immediate observed phenotype is challenging. WUSCHEL (WUS) a homeobox transcription factor is known to regulate the shoot meristem biology and young ear development in maize. Hybridization and domestication events have resulted in generation of duplicated gene copies in crops and so in case of maize Barren inflorescence 3 (Bif3) mutant. The mutant Bif3 carries a duplicated copy of ZmWUS1 named ZmWUS-B and the duplicated copy was found to be associated with increased meristem inflorescence. The proximal promoter region of the WUS has 84bp non-coding sequence and is evolutionally conserved. A 69bp fragment of the stretch carries a Type-B RR (Response Regulators) motif (AGATAT). Interestingly this region was found duplicated in a 119bp ZmWUS1-B enhancer region resulting in three repeated AGATAT motifs, flanked by 69-bp fragment. To determine the function of the AGATAT motifs in ZmWUS1-B CRISPR-Cas9 deletion experiments were designed. Multiple editing events generated targeting 69bp conserved nucleotide sequence (CNS) and Type-B RR motifs impact the expression of ZmWUS1-B in consequent ear development. The Cas9 homozygous mutants suggested an expression threshold of ZmWUS1 affecting inflorescence meristem function. To further determine the threshold limit transactivation dual luciferase assay in maize protoplast was done with 444bp region proximal promoter of ZmWUS1. It was found that increased number of AGATAT core motifs result in linear additive effects om ZmWUS1 expression levels. However, the effect tends to weaken and does not produce meaningful impact from distance apart. The ZmWUS1 significantly affects inflorescence development and at the same time applies threshold of buffering capacity for overexpression.

Chen, ZL et al. 2023. Genetic dissection of cis-regulatory control of ZmWUSCHEL1 expression by type-B RESPONSE REGULATORS. Plant Physiol. :doi: 10.1093/plphys/kiad652.
   Genetic dissection of cis-regulatory control of ZmWUSCHEL1 expression by type-B RESPONSE REGULATORS.
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