Florigen-Encoding Genes of Day-Neutral and Photoperiod-Sensitive Maize Are Regulated by Different Chromatin Modifications at the Floral Transition

Finding the right balance: The enduring role of florigens during cereal inflorescence development and their influence on fertility

Flowering is a vital process in a plant's lifecycle and variation for flowering-time has helped cereals adapt to diverse environments. Much cereal research has focused on understanding how flowering signals, or florigens, regulate the floral transition and timing of ear emergence. However, flowering genes also perform an enduring role during inflorescence development, with genotypes that elicit a weaker flowering signal producing more elaborately branched inflorescences with extra floret-bearing spikelets. While this outcome indicates that variable expression of flowering genes could boost yield potential, further analysis has shown that dampened florigen levels can compromise fertility, negating the benefit of extra grain-producing sites. Here, we discuss ways that florigens contribute to early and late inflorescence development, including their influence on branch/spikelet architecture and fertility. We propose that a deeper understanding of the role for florigens during inflorescence development could be used to balance the effects of florigens throughout flowering to improve productivity.

Sorghum bicolor INDETERMINATE1 is a conserved primary regulator of flowering

Introduction

A fundamental developmental switch for plants is transition from vegetative to floral growth, which integrates external and internal signals. INDETERMINATE1 (Id1) family proteins are zinc finger transcription factors that activate flowering in grasses regardless of photoperiod. Mutations in maize Id1 and rice Id1 (RID1) cause very late flowering. RID1 promotes expression of the flowering activator genes Early Heading Date1 (Ehd1) and Heading date 1 (Hd1), a rice homolog of CONSTANS (CO).

Methods and results

Mapping of two recessive late flowering mutants from a pedigreed sorghum EMS mutant library identified two distinct mutations in the Sorghum bicolor Id1 (SbId1) homolog, mutant alleles named sbid1-1 and sbid1-2. The weaker sbid1-1 allele caused a 35 day delay in reaching boot stage in the field, but its effect was limited to 6 days under greenhouse conditions. The strong sbid1-2 allele delayed boot stage by more than 60 days in the field and under greenhouse conditions. When sbid1-1 and sbid1-2 were combined, the delayed flowering phenotype remained and resembled that of sbid1-2, confirming late flowering was due to loss of SbId1 function. Evaluation of major flowering time regulatory gene expression in sbid1-2 showed that SbId1 is needed for expression of floral activators, like SbCO and SbCN8, and repressors, like SbPRR37 and SbGhd7.

Discussion

These results demonstrate a conserved role for SbId1 in promotion of flowering in sorghum, where it appears to be critical to allow expression of most major flowering regulatory genes.

INDETERMINATE1-mediated expression of FT family genes is required for proper timing of flowering in Brachypodium distachyon

The transition to flowering is a major developmental switch in plants. In many temperate grasses, perception of indicators of seasonal change, such as changing day-length and temperature, leads to expression of FLOWERING LOCUS T1 (FT1) and FT-Like (FTL) genes that are essential for promoting the transition to flowering. However, little is known about the upstream regulators of FT1 and FTL genes in temperate grasses. Here, we characterize the monocot-specific gene INDETERMINATE1 (BdID1) in Brachypodium distachyon and demonstrate that BdID1 is a regulator of FT family genes. Mutations in ID1 impact the ability of the short-day (SD) vernalization, cold vernalization, and long-day (LD) photoperiod pathways to induce certain FTL genes. BdID1 is required for upregulation of FTL9 (FT-LIKE9) expression by the SD vernalization pathway, and overexpression of FTL9 in an id1 background can partially restore the delayed flowering phenotype of id1. We show that BdID1 binds in vitro to the promoter region of FTL genes suggesting that ID1 directly activates FTL expression. Transcriptome analysis shows that BdID1 is required for FT1, FT2, FTL12, and FTL13 expression under inductive LD photoperiods, indicating that BdID1 is a regulator of the FT gene family. Moreover, overexpression of FT1 in the id1 background results in rapid flowering similar to overexpressing FT1 in the wild type, demonstrating that BdID1 is upstream of FT family genes. Interestingly, ID1 negatively regulates a previously uncharacterized FTL gene, FTL4, and we show that FTL4 is a repressor of flowering. Thus, BdID1 is critical for proper timing of flowering in temperate grasses.

Novel insights into maize (Zea mays) development and organogenesis for agricultural optimization

In maize, intrinsic hormone activities and sap fluxes facilitate organogenesis patterning and plant holistic development; these hormone movements should be a primary focus of developmental biology and agricultural optimization strategies. Maize (Zea mays) is an important crop plant with distinctive life history characteristics and structural features. Genetic studies have extended our knowledge of maize developmental processes, genetics, and molecular ecophysiology. In this review, the classical life cycle and life history strategies of maize are analyzed to identify spatiotemporal organogenesis properties and develop a definitive understanding of maize development. The actions of genes and hormones involved in maize organogenesis and sex determination, along with potential molecular mechanisms, are investigated, with findings suggesting central roles of auxin and cytokinins in regulating maize holistic development. Furthermore, investigation of morphological and structural characteristics of maize, particularly node ubiquity and the alternate attachment pattern of lateral organs, yields a novel regulatory model suggesting that maize organ initiation and subsequent development are derived from the stimulation and interaction of auxin and cytokinin fluxes. Propositions that hormone activities and sap flow pathways control organogenesis are thoroughly explored, and initiation and development processes of distinctive maize organs are discussed. Analysis of physiological factors driving hormone and sap movement implicates cues of whole-plant activity for hormone and sap fluxes to stimulate maize inflorescence initiation and organ identity determination. The physiological origins and biogenetic mechanisms underlying maize floral sex determination occurring at the tassel and ear spikelet are thoroughly investigated. The comprehensive outline of maize development and morphogenetic physiology developed in this review will enable farmers to optimize field management and will provide a reference for de novo crop domestication and germplasm improvement using genome editing biotechnologies, promoting agricultural optimization.

The battle of crops against drought: Genetic dissection and improvement

With ongoing global climate change, water scarcity-induced drought stress remains a major threat to agricultural productivity. Plants undergo a series of physiological and morphological changes to cope with drought stress, including stomatal closure to reduce transpiration and changes in root architecture to optimize water uptake. Combined phenotypic and multi-omics studies have recently identified a number of drought-related genetic resources in different crop species. The functional dissection of these genes using molecular techniques has enriched our understanding of drought responses in crops and has provided genetic targets for enhancing resistance to drought. Here, we review recent advances in the cloning and functional analysis of drought resistance genes and the development of technologies to mitigate the threat of drought to crop production.

The evening complex promotes maize flowering and adaptation to temperate regions

Maize (Zea mays) originated in southern Mexico and has spread over a wide latitudinal range. Maize expansion from tropical to temperate regions has necessitated a reduction of its photoperiod sensitivity. In this study, we cloned a quantitative trait locus (QTL) regulating flowering time in maize and show that the maize ortholog of Arabidopsis thaliana EARLY FLOWERING3, ZmELF3.1, is the causal locus. We demonstrate that ZmELF3.1 and ZmELF3.2 proteins can physically interact with ZmELF4.1/4.2 and ZmLUX1/2, to form evening complex(es; ECs) in the maize circadian clock. Loss-of-function mutants for ZmELF3.1/3.2 and ZmLUX1/2 exhibited delayed flowering under long-day and short-day conditions. We show that EC directly represses the expression of several flowering suppressor genes, such as the CONSTANS, CONSTANS-LIKE, TOC1 (CCT) genes ZmCCT9 and ZmCCT10, ZmCONSTANS-LIKE 3, and the PSEUDORESPONSE REGULATOR (PRR) genes ZmPRR37a and ZmPRR73, thus alleviating their inhibition, allowing florigen gene expression and promoting flowering. Further, we identify two closely linked retrotransposons located in the ZmELF3.1 promoter that regulate the expression levels of ZmELF3.1 and may have been positively selected during postdomestication spread of maize from tropical to temperate regions during the pre-Columbian era. These findings provide insights into circadian clock-mediated regulation of photoperiodic flowering in maize and new targets of genetic improvement for breeding.

ZmCCT10-relayed photoperiod sensitivity regulates natural variation in the arithmetical formation of male germinal cells in maize

Extensive mutational screening studies have documented genes regulating anther and pollen development. Knowledge concerning how formation of male germinal cell is arithmetically controlled in natural populations, under different environmental conditions, is lacking. We counted pollen number within a single anther and a maize-teosinte BC₂ S₃ recombinant inbred line population to identify ZmCCT10 as a major determinant of pollen number variation. ZmCCT10 was originally identified as a photoperiod-sensitive negative regulator of flowering. ZmCCT10 inactivation, after transposon insertion within its promoter, is proposed to have accelerated maize spread toward higher latitudes, thus allowing temperate maize to flower under long-day conditions. We showed that the active ZmCCT10 allele decreased pollen formation. As different active and inactive ZmCCT10 alleles have been found in natural maize populations, this represents the first report of a gene controlling pollen number in a crop natural population. These findings suggest that higher pollen number, which provides a competitive advantage in open-pollinated populations, may have been one of the major driving forces for the selection of an inactive ZmCCT10 allele during tropical maize domestication. We provide evidence that ZmCCT10 has opposite effects on cell proliferation of archesporial and tapetum cells and it modulates expression of key regulators during early anther development.

SDG102, a H3K36-Methyltransferase-Encoding Gene, Plays Pleiotropic Roles in Growth and Development of Maize (Zea mays L.)

Although histone lysine methylation has been studied in thale cress (Arabidopsis thaliana (L.) Heynh.) and rice (Oryza sativa L.) in recent years, its function in maize (Zea mays L.) remains poorly characterized. To better understand the function of histone lysine methylation in maize, SDG102, a H3 lysine 36 (H3K36) methylase, was chosen for functional characterization using overexpressed and knockout transgenic plants. SDG102-deficiency in maize caused multiple phenotypes including yellow leaves in seedlings, late-flowering, and increased adult plant height, while the overexpression of SDG102 led to reduced adult plant height. The key flowering genes, ZCN8/ZCN7 and MADS4/MADA67, were downregulated in SDG102-deficient plants. Chromatin immunoprecipitation (ChIP) experiments showed that H3 lysine 36 trimethylation (H3K36me3) levels were reduced at these loci. Perturbation of SDG102 expression caused the misexpression of multiple genes. Interestingly, the overexpression or knockout of SDG102 also led to genome-wide decreases and increases in the H3K36me3 levels, respectively. Together, our results suggest that SDG102 is a methyltransferase that catalyzes the trimethylation of H3K36 of many genes across the maize genome, which are involved in multiple biological processes including those controlling flowering time.

Major niche transitions in Pooideae correlate with variation in photoperiodic flowering and evolution of CCT domain genes

The external cues that trigger timely flowering vary greatly across tropical and temperate plant taxa, the latter relying on predictable seasonal fluctuations in temperature and photoperiod. In the grass family (Poaceae) for example, species of the subfamily Pooideae have become specialists of the northern temperate hemisphere, generating the hypothesis that their progenitor evolved a flowering response to long days from a short-day or day-neutral ancestor. Sampling across the Pooideae, we found support for this hypothesis, and identified several secondary shifts to day-neutral flowering and one to short-day flowering in a tropical highland clade. To explain the proximate mechanisms for the secondary transition back to short-day-regulated flowering, we investigated the expression of CCT domain genes, some of which are known to repress flowering in cereal grasses under specific photoperiods. We found a shift in CONSTANS 1 and CONSTANS 9 expression that coincides with the derived short-day photoperiodism of our exemplar species Nassella pubiflora. This sets up the testable hypothesis that trans- or cis-regulatory elements of these CCT domain genes were the targets of selection for major niche shifts in Pooideae grasses.

A gene regulatory network for tiller development mediated by Tin8 in maize

The complex gene regulatory network underlying tiller development in maize remains largely unknown. Here we identified two major quantitative trait loci for tiller number, Tin8 on chromosome 8 and the previously known Tb1 on chromosome 1, in a population derived from a teosinte-maize cross. Map-based cloning and association mapping revealed that Tin8, corresponding to Zcn8 encoding a phosphatidylethanolamine-binding-related kinase, is down-regulated in transcription, which results in decreased tiller number. A strong interaction between Tin8 and the key gen Tb1 was detected for tiller number. Further RNA-seq analysis showed that the expression of 13 genes related to tiller development was controlled by Tin8. Our results support the existence of a complex gene regulatory network for the outgrowth of the tiller bud in maize, in which Zcn8 controls 13 tiller-related genes, including four genes for hormonal responses. In particular, Zcn8 represses Gt1, D14, and Tru1 through the interaction with Tb1.

RID1 sets rice heading date by balancing its binding with SLR1 and SDG722

Rice (Oryza sativa) is a major crop that feeds billions of people, and its yield is strongly influenced by flowering time (heading date). Loss of RICE INDETERMINATE1 (RID1) function causes plants not to flower; thus, RID1 is considered a master switch among flowering-related genes. However, it remains unclear whether other proteins function together with RID1 to regulate rice floral transition. Here, we revealed that the chromatin accessibility and H3K9ac, H3K4me3, and H3K36me3 levels at Heading date 3a (Hd3a) and RICE FLOWERING LOCUS T1 (RFT1) loci were significantly reduced in rid1 mutants. Notably, RID1 interacted with SET DOMAIN GROUP PROTEIN 722 (SDG722), a methyltransferase. We determined that SDG722 affects the global level of H3K4me2/3 and H3K36me2/3, and promotes flowering primarily through the Early heading date1-Hd3a/RFT1 pathway. We further established that rice DELLA protein SLENDER RICE1 (SLR1) interacted with RID1 to inhibit its transactivation activity, that SLR1 suppresses rice flowering, and that messenger RNA and protein levels of SLR1 gradually decrease with plant growth. Furthermore, SLR1 competed with SDG722 for interaction with RID1. Overall, our results establish that interplay between RID1, SLR1, and SDG722 feeds into rice flowering-time control.

Epigenetics and its role in effecting agronomical traits

Climate-resilient crops with improved adaptation to the changing climate are urgently needed to feed the growing population. Hence, developing high-yielding crop varieties with better agronomic traits is one of the most critical issues in agricultural research. These are vital to enhancing yield as well as resistance to harsh conditions, both of which help farmers over time. The majority of agronomic traits are quantitative and are subject to intricate genetic control, thereby obstructing crop improvement. Plant epibreeding is the utilisation of epigenetic variation for crop development, and has a wide range of applications in the field of crop improvement. Epigenetics refers to changes in gene expression that are heritable and induced by methylation of DNA, post-translational modifications of histones or RNA interference rather than an alteration in the underlying sequence of DNA. The epigenetic modifications influence gene expression by changing the state of chromatin, which underpins plant growth and dictates phenotypic responsiveness for extrinsic and intrinsic inputs. Epigenetic modifications, in addition to DNA sequence variation, improve breeding by giving useful markers. Also, it takes epigenome diversity into account to predict plant performance and increase crop production. In this review, emphasis has been given for summarising the role of epigenetic changes in epibreeding for crop improvement.

Coordinative regulation of plants growth and development by light and circadian clock

The circadian clock, known as an endogenous timekeeping system, can integrate various cues to regulate plant physiological functions for adapting to the changing environment and thus ensure optimal plant growth. The synchronization of internal clock with external environmental information needs a process termed entrainment, and light is one of the predominant entraining signals for the plant circadian clock. Photoreceptors can detect and transmit light information to the clock core oscillator through transcriptional or post-transcriptional interactions with core-clock components to sustain circadian rhythms and regulate a myriad of downstream responses, including photomorphogenesis and photoperiodic flowering which are key links in the process of growth and development. Here we summarize the current understanding of the molecular network of the circadian clock and how light information is integrated into the circadian system, especially focus on how the circadian clock and light signals coordinately regulate the common downstream outputs. We discuss the functions of the clock and light signals in regulating photoperiodic flowering among various crop species.

Phosphorylation-mediated signalling in flowering: prospects and retrospects of phosphoproteomics in crops

Protein phosphorylation is a major post-translational modification, regulating protein function, stability, and subcellular localization. To date, annotated phosphorylation data are available mainly for model organisms and humans, despite the economic importance of crop species and their large kinomes. Our understanding of the phospho-regulation of flowering in relation to the biology and interaction between the pollen and pistil is still significantly lagging, limiting our knowledge on kinase signalling and its potential applications to crop production. To address this gap, we bring together relevant literature that were previously disconnected to present an overview of the roles of phosphoproteomic signalling pathways in modulating molecular and cellular regulation within specific tissues at different morphological stages of flowering. This review is intended to stimulate research, with the potential to increase crop productivity by providing a platform for novel molecular tools.

Large-scale reconstruction of chromatin structures of maize temperate and tropical inbred lines

Maize is a model plant species often used for genetics and genomics research because of its genetic diversity. There are prominent morphological, genetic, and epigenetic variations between tropical and temperate maize lines. However, the genome-wide chromatin conformations of these two maize types remain unexplored. We applied a Hi-C approach to compare the genome-wide chromatin interactions between temperate inbred line D132 and tropical line CML288. A reconstructed maize three-dimensional genome model revealed the spatial segregation of the global A and B compartments. The A compartments contain enriched genes and active epigenome marks, whereas the B compartments are gene-poor, transcriptionally silent chromatin regions. Whole-genome analyses indicated that the global A compartment content of CML288 was 3.12% lower than that of D132. Additionally, global and A/B sub-compartments were associated with differential gene expression and epigenetic changes between two inbred lines. About 25.3% of topologically associating domains (TADs) were determined to be associated with complex domain-level modifications that induced transcriptional changes, indicative of a large-scale reorganization of chromatin structures between the inbred maize lines. Furthermore, differences in chromatin interactions between the two lines correlated with epigenetic changes. These findings provide a solid foundation for the wider plant community to further investigate the genome-wide chromatin structures in other plant species.

Flowering time regulation model revisited by pooled sequencing of mass selection populations

Maize is one of the most broadly cultivated crops throughout the world, and flowering time is a major adaptive trait for its diffusion. The biggest challenge in understanding maize flowering genetic architecture is that the trait is confounded with population structure. To eliminate the effect, we revisited the flower time genetic network by using a tropical maize population Pop32, which was under mass selection for adaptation to early flowering time in China for six generations from tropical to temperate regions. The days to anthesis (DTA) of the initial (Pop32C0), intermedia (Pop32C3), and final population (Pop32C5) was 90.77, 84.63, and 79.72 days on average, respectively. To examine the genetic mechanism and identify the genetic loci underlying this rapid change in flowering time of Pop32, we bulked 30 individuals from C0, C3, and C5 to conduct the whole genome sequencing. And we finally identified 4,973,810 high-quality single nucleotide polymorphisms (SNPs) and 6,517 genes with allele frequency significantly changed during the artificial improvement process. We speculate that these genes might participate in the adaptive improvement process and control flowering time. To identify the candidate genes for flowering time from the gene set with allele frequency changed, we carried out weighted gene co-expression network analysis (WGCNA), and identified four co-expression modules that highly associated with the flowering time development, as well as constructed the co-expression network of key flowering time genes. Gene Ontology (GO) enrichment analysis revealed that the GO terms photosynthesis/light reaction, carbohydrate binding, auxin mediated signaling pathway, response to temperature stimulus that are closely connected with flowering time. Furthermore, targeted GWAS revealed the genes are significantly connected with the flowering time. qRT-PCR of four candidate genes GRMZM2G019879, GRMZM2G055905, GRMZM2G058158, and GRMZM2G171365 showed that their expression level is similar to the flowering time genes, which playing a key role in maize flowering time transition. This study revealed that the changes of flowering time in mass selection process may be strongly associated with the variations of allele frequency changes, and we identified some important candidate genes for flowering time, which will provide a new insight for the rapid improvement of maize important agronomic traits and promote the gene cloning of maize flowering time.

dlf1 promotes floral transition by directly activating ZmMADS4 and ZmMADS67 in the maize shoot apex

The floral transition of the maize (Zea mays ssp. mays) shoot apical meristem determines leaf number and flowering time, which are key traits influencing local adaptation and yield potential. dlf1 (delayed flowering1) encodes a basic leucine zipper protein that interacts with the florigen ZCN8 to mediate floral induction in the shoot apex. However, the mechanism of how dlf1 promotes floral transition remains largely unknown. We demonstrate that dlf1 underlies qLB7-1, a quantitative trait locus controlling leaf number and flowering time that was identified in a BC₂ S₃ population derived from a cross between maize and its wild ancestor, teosinte (Zea mays ssp. parviglumis). Transcriptome sequencing and chromatin immunoprecipitation sequencing demonstrated that DLF1 binds the core promoter of two AP1/FUL subfamily MADS-box genes, ZmMADS4 and ZmMADS67, to activate their expression. Knocking out ZmMADS4 and ZmMADS67 both increased leaf number and delayed flowering, indicating that they promote the floral transition. Nucleotide diversity analysis revealed that dlf1 and ZmMADS67 were targeted by selection, suggesting that they may have played important roles in maize flowering time adaptation. We show that dlf1 promotes maize floral transition by directly activating ZmMADS4 and ZmMADS67 in the shoot apex, providing novel insights into the mechanism of maize floral transition.

Maize adaptation across temperate climates was obtained via expression of two florigen genes

Expansion of the maize growing area was central for food security in temperate regions. In addition to the suppression of the short-day requirement for floral induction, it required breeding for a large range of flowering time that compensates the effect of South-North gradients of temperatures. Here we show the role of a novel florigen gene, ZCN12, in the latter adaptation in cooperation with ZCN8. Strong eQTLs of ZCN8 and ZCN12, measured in 327 maize lines, accounted for most of the genetic variance of flowering time in platform and field experiments. ZCN12 had a strong effect on flowering time of transgenic Arabidopsis thaliana plants; a path analysis showed that it directly affected maize flowering time together with ZCN8. The allelic composition at ZCN QTLs showed clear signs of selection by breeders. This suggests that florigens played a central role in ensuring a large range of flowering time, necessary for adaptation to temperate areas.

Understanding Past, and Predicting Future, Niche Transitions based on Grass Flowering Time Variation

Since their origin in the early Cretaceous, grasses have diversified across every continent on Earth, with a handful of species (rice [Oryza sativa], maize [Zea mays], and wheat [Triticum aestivum]) providing most of the caloric intake of contemporary humans and their livestock. The ecological dominance of grasses can be attributed to a number of physiological innovations, many of which contributed to shifts from closed to open habitats that incur daily (e.g. tropical mountains) and/or seasonal extremes in temperature (e.g. temperate/continental regions) and precipitation (e.g. tropical savannas). In addition to strategies that allow them to tolerate or resist periodically stressful environments, plants can adopt escape behaviors by modifying the relative timing of distinct development phases. Flowering time is one of these behaviors that can also act as a postzygotic barrier to reproduction and allow temporal partitioning of resources to promote coexistence. In this review, we explore what is known about the phylogenetic pattern of flowering control in grasses, and how this relates to broad- and fine-scale niche transitions within the family. We then synthesize recent findings on the genetic basis of flowering time evolution as a way to begin deciphering why certain aspects of flowering are seemingly so conserved, and what the implications of this are for future adaptation under climate change.

Dark response genes: a group of endogenous pendulum/timing players in maize?

MAIN CONCLUSION

Maize has a set of dark response genes, expression of which is influenced by multiple factor and varies with maize inbred lines but without germplasm specificity. The response to photoperiod is a common biological issue across the species kingdoms. Dark is as important as light in photoperiod. However, further in-depth understanding of responses of maize (Zea mays) to light and dark transition under photoperiod is hindered due to the lack of understanding of dark response genes. With multiple public "-omic" datasets of temperate and tropical/subtropical maize, 16 maize dark response genes, ZmDRGs, were found and had rhythmic expression under dark and light-dark cycle. ZmDRGs 6-8 were tandemly duplicated. ZmDRGs 2, 13, and 14 had a chromosomal collinearity with other maize genes. ZmDRGs 1-11 and 13-16 had copy-number variations. ZmDRGs 2, 9, and 16 showed 5'-end sequence deletion mutations. Some ZmDRGs had chromatin interactions and underwent DNA methylation and/or m6A mRNA methylation. Chromosomal histones associated with 15 ZmDRGs were methylated and acetylated. ZmDRGs 1, 2, 4, 9, and 13 involved photoperiodic phenotypes. ZmDRG16 was within flowering-related QTLs. ZmDRGs 1, 3, and 6-11 were present in cis-acting expression QTLs (eQTLs). ZmDRGs 1, 4, 6-9, 11, 12, and 14-16 showed co-expression with other maize genes. Some of ZmDRG-encoded ZmDRGs showed obvious differences in abundance and phosphorylation.

CONCLUSION

Sixteen ZmDRGs 1-16 are associated with the dark response of maize. In the process of post-domestication and/or breeding, the ZmDRGs undergo the changes without germplasm specificity, including epigenetic modifications, gene copy numbers, chromatin interactions, and deletion mutations. In addition to effects by these factors, ZmDRG expression is influenced by promoter elements, cis-acting eQTLs, and co-expression networks.

Epigenomic landscape and epigenetic regulation in maize

Epigenetic regulation has been implicated in the control of multiple agronomic traits in maize. Here, we review current advances in our understanding of epigenetic regulation, which has great potential for improving agronomic traits and the environmental adaptability of crops. Epigenetic regulation plays vital role in the control of complex agronomic traits. Epigenetic variation could contribute to phenotypic diversity and can be used to improve the quality and productivity of crops. Maize (Zea mays L.), one of the most widely cultivated crops for human food, animal feed, and ethanol biofuel, is a model plant for genetic studies. Recent advances in high-throughput sequencing technology have made possible the study of epigenetic regulation in maize on a genome-wide scale. In this review, we discuss recent epigenetic studies in maize many achieved by Chinese research groups. These studies have explored the roles of DNA methylation, posttranslational modifications of histones, chromatin remodeling, and noncoding RNAs in the regulation of gene expression in plant development and environment response. We also provide our future prospects for manipulating epigenetic regulation to improve crops.

ZmMADS69 functions as a flowering activator through the ZmRap2.7-ZCN8 regulatory module and contributes to maize flowering time adaptation

Flowering time is a major determinant of the local adaptation of plants. Although numerous loci affecting flowering time have been mapped in maize, their underlying molecular mechanisms and roles in adaptation remain largely unknown. Here, we report the identification and characterization of MADS-box transcription factor ZmMADS69 that functions as a flowering activator through the ZmRap2.7-ZCN8 regulatory module and contributes to adaptation. We show that ZmMADS69 underlies a quantitative trait locus controlling the difference in flowering time between maize and its wild ancestor, teosinte. Maize ZmMADS69 allele is expressed at a higher level at floral transition and confers earlier flowering than the teosinte allele under long days and short days. Overexpression of ZmMADS69 causes early flowering, while a transposon insertion mutant of ZmMADS69 exhibits delayed flowering. ZmMADS69 shows pleiotropic effects for multiple traits of agronomic importance. ZmMADS69 functions upstream of the flowering repressor ZmRap2.7 to downregulate its expression, thereby relieving the repression of the florigen gene ZCN8 and causing early flowering. Population genetic analyses showed that ZmMADS69 was a target of selection and may have played an important role as maize spread from the tropics to temperate zones. Our findings provide important insights into the regulation and adaptation of flowering time.

Over-expression of the photoperiod response regulator ZmCCT10 modifies plant architecture, flowering time and inflorescence morphology in maize

Maize originated as a tropical plant that required short days to transition from vegetative to reproductive development. ZmCCT10 [CO, CONSTANS, CO-LIKE and TIMING OF CAB1 (CCT) transcription factor family] is a regulator of photoperiod response and was identified as a major QTL controlling photoperiod sensitivity in maize. We modulated expression of ZmCCT10 in transgenic maize using two constitutive promoters with different expression levels. Transgenic plants over expressing ZmCCT10 with either promoter were delayed in their transition from vegetative to reproductive development but were not affected in their switch from juvenile-to-adult vegetative growth. Strikingly, transgenic plants containing the stronger expressing construct had a prolonged period of vegetative growth accompanied with dramatic modifications to plant architecture that impacted both vegetative and reproductive traits. These plants did not produce ears, but tassels were heavily branched. In more than half of the transgenic plants, tassels were converted into a branched leafy structure resembling phyllody, often composed of vegetative plantlets. Analysis of expression modules controlling the floral transition and meristem identity linked these networks to photoperiod dependent regulation, whereas phase change modules appeared to be photoperiod independent. Results from this study clarified the influence of the photoperiod pathway on vegetative and reproductive development and allowed for the fine-tuning of the maize flowering time model.

Distinct gene networks modulate floral induction of autonomous maize and photoperiod-dependent teosinte

Temperate maize was domesticated from its tropical ancestor, teosinte. Whereas temperate maize is an autonomous day-neutral plant, teosinte is an obligate short-day plant that requires uninterrupted long nights to induce flowering. Leaf-derived florigenic signals trigger reproductive growth in both teosinte and temperate maize. To study the genetic mechanisms underlying floral inductive pathways in maize and teosinte, mRNA and small RNA genome-wide expression analyses were conducted on leaf tissue from plants that were induced or not induced to flower. Transcriptome profiles reveal common differentially expressed genes during floral induction, but a comparison of candidate flowering time genes indicates that photoperiod and autonomous pathways act independently. Expression differences in teosinte are consistent with the current paradigm for photoperiod-induced flowering, where changes in circadian clock output trigger florigen production. Conversely, differentially expressed genes in temperate maize link carbon partitioning and flowering, but also show altered expression of circadian clock genes that are distinct from those altered upon photoperiodic induction in teosinte. Altered miRNA399 levels in both teosinte and maize suggest a novel common connection between flowering and phosphorus perception. These findings provide insights into the molecular mechanisms underlying a strengthened autonomous pathway that enabled maize growth throughout temperate regions.

The Importance of Being on Time: Regulatory Networks Controlling Photoperiodic Flowering in Cereals

Flowering is the result of the coordination between genetic information and environmental cues. Gene regulatory networks have evolved in plants in order to measure diurnal and seasonal variation of day length (or photoperiod), thus aligning the reproductive phase with the most favorable season of the year. The capacity of plants to discriminate distinct photoperiods classifies them into long and short day species, depending on the conditions that induce flowering. Plants of tropical origin and adapted to short day lengths include rice, maize, and sorghum, whereas wheat and barley were originally domesticated in the Fertile Crescent and are considered long day species. In these and other crops, day length measurement mechanisms have been artificially modified during domestication and breeding to adapt plants to novel areas, to the extent that a wide diversity of responses exists within any given species. Notwithstanding the ample natural and artificial variation of day length responses, some of the basic molecular elements governing photoperiodic flowering are widely conserved. However, as our understanding of the underlying mechanisms improves, it becomes evident that specific regulators exist in many lineages that are not shared by others, while apparently conserved components can be recruited to novel functions during evolution.

Flowering Time-Regulated Genes in Maize Include the Transcription Factor ZmMADS1

Flowering time (FTi) control is well examined in the long-day plant Arabidopsis (Arabidopsis thaliana), and increasing knowledge is available for the short-day plant rice (Oryza sativa). In contrast, little is known in the day-neutral and agronomically important crop plant maize (Zea mays). To learn more about FTi and to identify novel regulators in this species, we first compared the time points of floral transition of almost 30 maize inbred lines and show that tropical lines exhibit a delay in flowering transition of more than 3 weeks under long-day conditions compared with European flint lines adapted to temperate climate zones. We further analyzed the leaf transcriptomes of four lines that exhibit strong differences in flowering transition to identify new key players of the flowering control network in maize. We found strong differences among regulated genes between these lines and thus assume that the regulation of FTi is very complex in maize. Especially genes encoding MADS box transcriptional regulators are up-regulated in leaves during the meristem transition. ZmMADS1 was selected for functional studies. We demonstrate that it represents a functional ortholog of the central FTi integrator SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) of Arabidopsis. RNA interference-mediated down-regulation of ZmMADS1 resulted in a delay of FTi in maize, while strong overexpression caused an early-flowering phenotype, indicating its role as a flowering activator. Taken together, we report that ZmMADS1 represents a positive FTi regulator that shares an evolutionarily conserved function with SOC1 and may now serve as an ideal stating point to study the integration and variation of FTi pathways also in maize.

Genetic Architecture of Flowering Phenology in Cereals and Opportunities for Crop Improvement

Cereal crop species including bread wheat (Triticum aestivum L.), barley (Hordeum vulgare L.), rice (Oryza sativa L.), and maize (Zea mays L.) provide the bulk of human nutrition and agricultural products for industrial use. These four cereals are central to meet future demands of food supply for an increasing world population under a changing climate. A prerequisite for cereal crop production is the transition from vegetative to reproductive and grain-filling phases starting with flower initiation, a key developmental switch tightly regulated in all flowering plants. Although studies in the dicotyledonous model plant Arabidopsis thaliana build the foundations of our current understanding of plant phenology genes and regulation, the availability of genome assemblies with high-confidence sequences for rice, maize, and more recently bread wheat and barley, now allow the identification of phenology-associated gene orthologs in monocots. Together with recent advances in next-generation sequencing technologies, QTL analysis, mutagenesis, complementation analysis, and RNA interference, many phenology genes have been functionally characterized in cereal crops and conserved as well as functionally divergent genes involved in flowering were found. Epigenetic and other molecular regulatory mechanisms that respond to environmental and endogenous triggers create an enormous plasticity in flowering behavior among cereal crops to ensure flowering is only induced under optimal conditions. In this review, we provide a summary of recent discoveries of flowering time regulators with an emphasis on four cereal crop species (bread wheat, barley, rice, and maize), in particular, crop-specific regulatory mechanisms and genes. In addition, pleiotropic effects on agronomically important traits such as grain yield, impact on adaptation to new growing environments and conditions, genetic sequence-based selection and targeted manipulation of phenology genes, as well as crop growth simulation models for predictive crop breeding, are discussed.