Project description:The annual Zea mays ssp. mexicana L. is a member of teosinte, a wild relative of the Zea mays spp. mays L. This subspecies has strong growth and regeneration ability, high tiller numbers, high protein and lysine content as well as resistance to many fungal diseases, and it can be effectively used in maize improvement. In this study, we reported a Zea mays ssp. mexicana L. transcriptome by merging data from untreated control (CK), cold (4°C) and drought (PEG2000, 20%) treated plant samples. A total of 251,145 transcripts (N50 = 1,269 bp) and 184,280 unigenes (N50 = 923 bp) were predicted, which code for homologs of near 47% of the published maize proteome. Under cold conditions, 2,232 and 817 genes were up-regulated and down-regulated, respectively, while fewer genes were up-regulated (532) and down-regulated (82) under drought stress, indicating that Zea mays ssp. mexicana L. is more sensitive to the applied cold rather than to the applied drought stresses. Functional enrichment analyses identified many common or specific biological processes and gene sets in response to drought and cold stresses. The ABA dependent pathway, trehalose synthetic pathway and the ICE1-CBF pathway were up-regulated by both stresses. GA associated genes have been shown to differentially regulate the responses to cold in close subspecies in Zea mays. These findings and the identified functional genes can provide useful clues for improving abiotic stress tolerance of maize.
Project description:Background:Health risks arising from heavy metal pollution have attracted global attention. As a result, many studies on the accumulation of heavy metals in soil-plant systems have performed human health risk assessments. Objectives:We aimed to examine the ability of Zea mays (maize) to accumulate heavy metals and assess the bioaccumulation factor (BAF) by collecting, collating, and analyzing data on heavy metal concentrations in Zea mays. Methods:This study reviewed the accumulation of five selected heavy metals, cadmium (Cd), chromium (Cr), lead (Pb), copper (Cu), and zinc (Zn) in soil and the corresponding BAF of Zea mays grown on those soils using a systematic search of peer-reviewed scientific journals. A total of 27 research works were reviewed after screening 52 articles for subject matter relevancy, including dumpsites, industrially polluted soils, inorganically fertilized soils, mining sites, smelting sites, municipal wastewater irrigated soils, and a battery waste dumpsite. Results:Among the reviewed sites, concentrations of Cd and Cr were highest at a tin mining site, where prolonged mining, mineral processing and other production activities contributed heavy metal pollution in the soil. The soil at a battery waste dumpsite exhibited the highest Pb concentration, while the soil at a Zn smelting site presented the highest concentration of Zn. The highest soil Cu concentration was found in an area where sewage irrigation had been carried out over a long period. The BAF of the five heavy metals in Zea mays increased with the metal concentrations in the soil. The BAF of Cd, Cr, Pb, Cu, and Zn in Zea mays from the study areas fall within the ranges of 0-0.95, 0-1.89, 0-1.20, 0.011-0.99, and 0.03-0.99, respectively. Cadmium and Zn had the highest bioconcentration factors values in maize plants, likely due to their higher mobility rate compared to the other heavy metals. Conclusions:The study concluded that Zea mays is capable of accumulating high amounts of heavy metals, although accumulation of these heavy metals is influenced by multiple factors including soil texture, cation exchange capacity, root exudation and especially soil pH and chemical forms of the heavy metals. Zea mays should not be planted on metal-contaminated soils because of its potential to act as a hyperaccumulator. Competing Interests:The authors declare no competing financial interests.
Project description:Zea mays is an economically important crop, but its molecular mechanism of flowering remains largely uncharacterized. The gene, SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1), integrates multiple flowering signals to regulate floral transition in Arabidopsis. In this study, ZmSOC1 was isolated from Zea mays. Sequence alignment and phylogenetic analysis demonstrated that the ZmSOC1 protein contained a highly conserved MADS domain and a typical SOC1 motif. ZmSOC1 protein was localized in the nucleus in protoplasts and showed no transcriptional activation activity in yeast cells. ZmSOC1 was highly expressed in maize reproductive organs, including filaments, ear and endosperm, but expression was very low in embryos; on the other hand, the abiotic stresses could repress ZmSOC1 expression. Overexpression of ZmSOC1 resulted in early flowering in Arabidopsis through increasing the expression of AtLFY and AtAP1. Overall, these results suggest that ZmSOC1 is a flowering promoter in Arabidopsis.
Project description:Purple acid phosphatases (PAPs) play an important role in plant phosphorus nutrition, both by liberating phosphorus from organic sources in the soil and by modulating distribution within the plant throughout growth and development. Furthermore, members of the PAP protein family have been implicated in a broader role in plant mineral homeostasis, stress responses and development. We have identified 33 candidate PAP encoding gene models in the maize (Zea mays ssp. mays var. B73) reference genome. The maize Pap family includes a clear single-copy ortholog of the Arabidopsis gene AtPAP26, shown previously to encode both major intracellular and secreted acid phosphatase activities. Certain groups of PAPs present in Arabidopsis, however, are absent in maize, while the maize family contains a number of expansions, including a distinct radiation not present in Arabidopsis. Analysis of RNA-sequencing based transcriptome data revealed accumulation of maize Pap transcripts in multiple plant tissues at multiple stages of development, and increased accumulation of specific transcripts under low phosphorus availability. These data suggest the maize PAP family as a whole to have broad significance throughout the plant life cycle, while highlighting potential functional specialization of individual family members.
Project description:Maize was domesticated from lowland teosinte (Zea mays ssp. parviglumis), but the contribution of highland teosinte (Zea mays ssp. mexicana, hereafter mexicana) to modern maize is not clear. Here, two genomes for Mo17 (a modern maize inbred) and mexicana are assembled using a meta-assembly strategy after sequencing of 10 lines derived from a maize-teosinte cross. Comparative analyses reveal a high level of diversity between Mo17, B73, and mexicana, including three Mb-size structural rearrangements. The maize spontaneous mutation rate is estimated to be 2.17 × 10-8 ~3.87 × 10-8 per site per generation with a nonrandom distribution across the genome. A higher deleterious mutation rate is observed in the pericentromeric regions, and might be caused by differences in recombination frequency. Over 10% of the maize genome shows evidence of introgression from the mexicana genome, suggesting that mexicana contributed to maize adaptation and improvement. Our data offer a rich resource for constructing the pan-genome of Zea mays and genetic improvement of modern maize varieties.
Project description:RNA-sequencing (RNA-seq) enables in-depth exploration of transcriptomes, but typical sequencing depth often limits its comprehensiveness. In this study, we generated nearly 3 billion RNA-Seq reads, totaling 341 Gb of sequence, from a Zea mays seedling sample. At this depth, a near complete snapshot of the transcriptome was observed consisting of over 90% of the annotated transcripts, including lowly expressed transcription factors. A novel hybrid strategy combining de novo and reference-based assemblies yielded a transcriptome consisting of 126,708 transcripts with 88% of expressed known genes assembled to full-length. We improved current annotations by adding 4,842 previously unannotated transcript variants and many new features, including 212 maize transcripts, 201 genes, 10 genes with undocumented potential roles in seedlings as well as maize lineage specific gene fusion events. We demonstrated the power of deep sequencing for large transcriptome studies by generating a high quality transcriptome, which provides a rich resource for the research community.
Project description:Stress memory refers to the observation that an initial, sub-lethal stress alters plants' responses to subsequent stresses. Previous transcriptome analyses of maize seedlings exposed to a repeated dehydration stress has revealed the existence of transcriptional stress memory in Zea mays. Whether drought-related physiological responses also display memory and how transcriptional memory translates into physiological memory are fundamental questions that are still unanswered. Using a systems-biology approach we investigate whether/how transcription memory responses established in the genome-wide analysis of Z. mays correlate with 14 physiological parameters measured during a repeated exposure of maize seedlings to dehydration stress. Co-expression network analysis revealed ten gene modules correlating strongly with particular physiological processes, and one module displaying strong, yet divergent, correlations with several processes suggesting involvement of these genes in coordinated responses across networks. Two processes key to the drought response, stomatal conductance and non-photochemical quenching, displayed contrasting memory patterns that may reflect trade-offs related to metabolic costs versus benefits of cellular protection. The main contribution of this study is the demonstration of coordinated changes in transcription memory responses at the genome level and integrated physiological responses at the cellular level upon repetitive stress exposures. The results obtained by the network-based systems analysis challenge the commonly held view that short-term physiological responses to stress are primarily mediated biochemically.
Project description:RNA-directed DNA methylation (RdDM) in plants is a well-characterized example of RNA interference-related transcriptional gene silencing. To determine the relationships between RdDM and heterochromatin in the repeat-rich maize (Zea mays) genome, we performed whole-genome analyses of several heterochromatic features: dimethylation of lysine 9 and lysine 27 (H3K9me2 and H3K27me2), chromatin accessibility, DNA methylation, and small RNAs; we also analyzed two mutants that affect these processes, mediator of paramutation1 and zea methyltransferase2.
Project description:Background:The spread of maize cultivation to the highlands of central Mexico was accompanied by substantial introgression from the endemic wild teosinte Zea mays ssp. mexicana, prompting the hypothesis that the transfer of beneficial variation facilitated local adaptation. Methods:We used whole-genome sequence data to map regions of Zea mays ssp. mexicana introgression in three Mexican highland maize individuals. We generated a genetic linkage map and performed Quantitative Trait Locus mapping in an F2 population derived from a cross between lowland and highland maize individuals. Results:Introgression regions ranged in size from several hundred base pairs to Megabase-scale events. Gene density within introgression regions was comparable to the genome as a whole, and over 1,000 annotated genes were located within introgression events. Quantitative Trait Locus mapping identified a small number of loci linked to traits characteristic of Mexican highland maize. Discussion:Although there was no strong evidence to associate quantitative trait loci with regions of introgression, we nonetheless identified many Mexican highland alleles of introgressed origin that carry potentially functional sequence variants. The impact of introgression on stress tolerance and yield in the highland environment remains to be fully characterized.