The FT-like ZCN8 Gene Functions as a Floral Activator and Is Involved in Photoperiod Sensitivity in Maize

The genome of Aechmea fasciata provides insights into the evolution of tank epiphytic habits and ethylene-induced flowering

Aechmea fasciata is one of the most popular bromeliads and bears a water-impounding tank with a vase-like rosette. The tank habit is a key innovation that has promoted diversity among bromeliads. To reveal the genomic basis of tank habit formation and ethylene-induced flowering, we sequenced the genome of A. fasciata and assembled 352 Mb of sequences into 24 chromosomes. Comparative genomic analysis showed that the chromosomes experienced at least two fissions and two fusions from the ancestral genome of A. fasciata and Ananas comosus. The gibberellin receptor gene GID1C-like was duplicated by a segmental duplication event. This duplication may affect GA signalling and promote rosette expansion, which may permit water-impounding tank formation. During ethylene-induced flowering, AfFTL2 expression is induced and targets the EIN3 binding site 'ATGTAC' by AfEIL1-like. The data provided here will serve as an important resource for studying the evolution and mechanisms underlying flowering time regulation in bromeliads.

Association mapping across a multitude of traits collected in diverse environments in maize

Classical genetic studies have identified many cases of pleiotropy where mutations in individual genes alter many different phenotypes. Quantitative genetic studies of natural genetic variants frequently examine one or a few traits, limiting their potential to identify pleiotropic effects of natural genetic variants. Widely adopted community association panels have been employed by plant genetics communities to study the genetic basis of naturally occurring phenotypic variation in a wide range of traits. High-density genetic marker data-18M markers-from 2 partially overlapping maize association panels comprising 1,014 unique genotypes grown in field trials across at least 7 US states and scored for 162 distinct trait data sets enabled the identification of of 2,154 suggestive marker-trait associations and 697 confident associations in the maize genome using a resampling-based genome-wide association strategy. The precision of individual marker-trait associations was estimated to be 3 genes based on a reference set of genes with known phenotypes. Examples were observed of both genetic loci associated with variation in diverse traits (e.g., above-ground and below-ground traits), as well as individual loci associated with the same or similar traits across diverse environments. Many significant signals are located near genes whose functions were previously entirely unknown or estimated purely via functional data on homologs. This study demonstrates the potential of mining community association panel data using new higher-density genetic marker sets combined with resampling-based genome-wide association tests to develop testable hypotheses about gene functions, identify potential pleiotropic effects of natural genetic variants, and study genotype-by-environment interaction.

Fine Mapping and Functional Research of Key Genes for Photoperiod Sensitivity in Maize

Maize is native to the tropics and is very sensitive to photoperiod. Planting in temperate regions with increased hours of daylight always leads to late flowering, sterility, leggy plants, and increased numbers of maize leaves. This phenomenon severely affects the utilization of tropical maize germplasm resources. The sensitivity to photoperiod is mainly reflected in differences in plant height (PH), ear height (EH), total leaf number (LN), leaf number under ear (LE), silking stage (SS), and anthesis stage (AT) in the same variety under different photoperiod conditions. These differences are more pronounced for varieties that are more sensitive to photoperiod. In the current study, a high-density genetic map was constructed from a recombinant inbred line (RIL) population containing 209 lines to map the quantitative trait loci (QTL) for photoperiod sensitivity of PH, EH, LN, LE, SS, and AT. A total of 39 QTL were identified, including three consistent major QTL. We identified candidate genes in the consensus major QTL region by combined analysis of transcriptome data, and after enrichment by GO and KEGG, we identified a total of four genes (Zm00001d006212, Zm00001d017241, Zm00001d047761, and Zm00001d047632) enriched in the plant circadian rhythm pathway (KEGG:04712). We analyzed the expression levels of these four genes, and the analysis results showed that there were significant differences in response under different photoperiod conditions for three of them (Zm00001d047761, Zm00001d006212 and Zm00001d017241). The results of functional verification showed that the expression patterns of genes rhythmically oscillated, which can affect the length of the hypocotyl and the development of the shoot apical meristem. We also found that the phenotypes of the positive plants were significantly different from the control plants when they overexpressed the objective gene or when it was knocked out, and the expression period, phase, and amplitude of the target gene also shifted. The objective gene changed its own rhythmic oscillation period, phase, and amplitude with the change in the photoperiod, thereby regulating the photoperiod sensitivity of maize. These results deepen our understanding of the genetic structure of photoperiod sensitivity and lay a foundation for further exploration of the regulatory mechanism of photoperiod sensitivity.

Linkage mapping combined with GWAS revealed the genetic structural relationship and candidate genes of maize flowering time-related traits

BACKGROUND

Flowering time is an important agronomic trait of crops and significantly affects plant adaptation and seed production. Flowering time varies greatly among maize (Zea mays) inbred lines, but the genetic basis of this variation is not well understood. Here, we report the comprehensive genetic architecture of six flowering time-related traits using a recombinant inbred line (RIL) population obtained from a cross between two maize genotypes, B73 and Abe2, and combined with genome-wide association studies to identify candidate genes that affect flowering time.

RESULTS

Our results indicate that these six traits showed extensive phenotypic variation and high heritability in the RIL population. The flowering time of this RIL population showed little correlation with the leaf number under different environmental conditions. A genetic linkage map was constructed by 10,114 polymorphic markers covering the whole maize genome, which was applied to QTL mapping for these traits, and identified a total of 82 QTLs that contain 13 flowering genes. Furthermore, a combined genome-wide association study and linkage mapping analysis revealed 17 new candidate genes associated with flowering time.

CONCLUSIONS

In the present study, by using genetic mapping and GWAS approaches with the RIL population, we revealed a list of genomic regions and candidate genes that were significantly associated with flowering time. This work provides an important resource for the breeding of flowering time traits in maize.

Bioengineering and Molecular Biology of Miscanthus

Miscanthus is a perennial wild plant that is vital for the production of paper and roofing, as well as horticulture and the development of new high-yielding crops in temperate climates. Chromosome-level assembly of the ancient tetraploid genome of miscanthus chromosomes is reported to provide resources that can link its chromosomes to related diploid sorghum and complex polyploid sugarcane. Analysis of Miscanthus sinensis and Miscanthus sacchariflorus showed intense mixing and interspecific hybridization and documented the origin of a high-yielding triploid bioenergetic plant, Miscanthus × giganteus. The Miscanthus genome expands comparative genomics functions to better understand the main abilities of Andropogoneae herbs. Miscanthus × giganteus is widely regarded as a promising lignocellulosic biomass crop due to its high-biomass yield, which does not emit toxic compounds into the environment, and ability to grow in depleted lands. The high production cost of lignocellulosic bioethanol limits its commercialization. The main components that inhibit the enzymatic reactions of fermentation and saccharification are lignin in the cell wall and its by-products released during the pre-treatment stage. One approach to overcoming this barrier could be to genetically modify the genes involved in lignin biosynthesis, manipulating the lignin content and composition of miscanthus.

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.

Circadian-period variation underlies the local adaptation of photoperiodism in the short-day plant Lemna aequinoctialis

Phenotypic variation is the basis for trait adaptation via evolutionary selection. However, the driving forces behind quantitative trait variations remain unclear owing to their complexity at the molecular level. This study focused on the natural variation of the free-running period (FRP) of the circadian clock because FRP is a determining factor of the phase phenotype of clock-dependent physiology. Lemna aequinoctialis in Japan is a paddy field duckweed that exhibits a latitudinal cline of critical day length (CDL) for short-day flowering. We collected 72 strains of L. aequinoctialis and found a significant correlation between FRPs and locally adaptive CDLs, confirming that variation in the FRP-dependent phase phenotype underlies photoperiodic adaptation. Diel transcriptome analysis revealed that the induction timing of an FT gene is key to connecting the clock phase to photoperiodism at the molecular level. This study highlights the importance of FRP as a variation resource for evolutionary adaptation.

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Natural variation of flowering/circadian traits in a paddy-field duckweed is studied.

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Critical day length for flowering of the duckweed in Japan shows a latitudinal cline.

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A negative correlation between critical day length and circadian period was found.

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An FT gene responding to lengthening of the dark period was isolated.

Impacts of RNA Mobility Signals on Virus Induced Somatic and Germline Gene Editing

Viral vectors are being engineered to deliver CRISPR/Cas9 components systemically in plants to induce somatic or heritable site-specific mutations. It is hypothesized that RNA mobility signals facilitate entry of viruses or single guide RNAs (sgRNAs) into the shoot apical meristem where germline mutations can occur. Our objective was to understand the impact of RNA mobility signals on virus-induced somatic and germline gene editing in Nicotiana benthamiana and Zea mays. Previously, we showed that foxtail mosaic virus (FoMV) expressing sgRNA induced somatic mutations in N. benthamiana and Z. mays expressing Cas9. Here, we fused RNA mobility signals to sgRNAs targeting the genes encoding either N. benthamiana phytoene desaturase (PDS) or Z. mays high affinity potassium transporter 1 (HKT1). Addition of Arabidopsis thaliana Flowering Locus T (AtFT) and A. thaliana tRNA-Isoleucine (AttRNAIle) did not improve FoMV-induced somatic editing, and neither were sufficient to facilitate germline mutations in N. benthamiana. Maize FT homologs, Centroradialus 16 (ZCN16) and ZCN19, as well as AttRNAIle were found to aid somatic editing in maize but did not enable sgRNAs delivered by FoMV to induce germline mutations. Additional viral guide RNA delivery systems were assessed for somatic and germline mutations in N. benthamiana with the intention of gaining a better understanding of the specificity of mobile signal-facilitated germline editing. Potato virus X (PVX), barley stripe mosaic virus (BSMV), and tobacco rattle virus (TRV) were included in this comparative study, and all three of these viruses delivering sgRNA were able to induce somatic and germline mutations. Unexpectedly, PVX, a potexvirus closely related to FoMV, expressing sgRNA alone induced biallelic edited progeny, indicating that mobility signals are dispensable in virus-induced germline editing. These results show that PVX, BSMV, and TRV expressing sgRNA all have an innate ability to induce mutations in the germline. Our results indicate that mobility signals alone may not be sufficient to enable virus-based delivery of sgRNAs using the viruses, FoMV, PVX, BSMV, and TRV into cell types that result in germline mutations.

Comparative analysis of buds transcriptome and identification of two florigen gene AkFTs in Amorphophallus konjac

Leaves and flowers of Amorphophallus konjac do not develop simultaneously thus unique features can be elucidated through study of flowering transformation in A. konjac. In this study, transcriptome libraries of A. konjac leaf buds (LB) and flower buds (FB) were constructed followed by high-throughput sequencing. A total of 68,906 unigenes with an average length of 920 bp were obtained after library assembly. Out of these genes, 24,622 unigenes had annotation information. A total of 6859 differentially expressed genes (DEGs) were identified through differential expression analysis using LB as control. Notably, 2415 DEGs were upregulated whereas 4444 DEGs were downregulated in the two transcriptomes. Go and KEGG analysis showed that the DEGs belonged to 44 functional categories and were implicated in 98 metabolic pathways and 38 DEGs involved in plant hormone signal transduction. Several genes were mined that may be involved in A. konjac flower bud differentiation and flower organ development. Eight DEGs were selected for verification of RNA-seq results using qRT-PCR analysis. Two FLOWERING LOCUS T (FT) genes named AkFT1 and AkFT2 were identified though homologous analysis may be the florigen gene implicated in modulation of A. konjac flowering. These genes were significantly upregulated in flower buds compared with the expression levels on leaf buds. Overexpression of AkFT genes though heterologous expression in Arabidopsis showed that the transgenics flowered at a very early stage relative to wild type plants. These findings indicate that AkFT1 and AkFT2 function as regulation genes in A. konjac flowering development and the two genes may present similar functions during flowering transition.

A transposon insertion drove the loss of natural seed shattering during foxtail millet domestication

Loss of seed shattering was a key step during cereal domestication, and it greatly facilitated seed harvest of the staple cereal foxtail millet (Setaria italica) because the cereal has very small seeds. However, the genetic basis for this loss has been largely unknown. Here, we combined comparative and association mapping to identify an 855-bp Harbinger transposable element insertion in the second exon of the foxtail millet gene shattering1 (sh1) that was responsible for the loss of seed shattering. The sh1 gene encodes zinc finger and YABBY domains. The insert prevents transcription of the second exon, causing partial loss of the zinc finger domain and then loss of natural seed shattering. Specifically, sh1 functions as a transcription repressor and represses the transcription of genes associated with lignin synthesis in the abscission zone, including CAD2. The diversity of sh1 is highly reduced in foxtail millet, consistent with either a severe domestication bottleneck or a selective sweep. Phylogenetic analysis of sh1 further revealed a single origin of foxtail millet in China. Our results support the theories that transposons were the most active factors in genome evolution driving loss of natural seed shattering during foxtail millet domestication and that sh1 underwent parallel selection during domestication across different cereal species.

Analysis of the PEBP gene family and identification of a novel FLOWERING LOCUS T orthologue in sugarcane

Sugarcane (Saccharum spp.) is an important economic crop for both sugar and biomass, the yields of which are negatively affected by flowering. The molecular mechanisms controlling flowering in sugarcane are nevertheless poorly understood. RNA-seq data analysis and database searches have enabled a comprehensive description of the PEBP gene family in sugarcane. It is shown to consist of at least 13 FLOWERING LOCUS T (FT)-like genes, two MOTHER OF FT AND TFL (MFT)-like genes, and four TERMINAL FLOWER (TFL)-like genes. As expected, these genes all show very high homology to their corresponding genes in Sorghum, and also to FT-like, MFT-like, and TFL-like genes in maize, rice, and Arabidopsis. Functional analysis in Arabidopsis showed that the sugarcane ScFT3 gene can rescue the late flowering phenotype of the Arabidopsis ft-10 mutant, whereas ScFT5 cannot. High expression levels of ScFT3 in leaves of short day-induced sugarcane plants coincided with initial stages of floral induction in the shoot apical meristem as shown by histological analysis of meristem dissections. This suggests that ScFT3 is likely to play a role in floral induction in sugarcane; however, other sugarcane FT-like genes may also be involved in the flowering process.

A B73×Palomero Toluqueño mapping population reveals local adaptation in Mexican highland maize

Generations of farmer selection in the central Mexican highlands have produced unique maize varieties adapted to the challenges of the local environment. In addition to possessing great agronomic and cultural value, Mexican highland maize represents a good system for the study of local adaptation and acquisition of adaptive phenotypes under cultivation. In this study, we characterize a recombinant inbred line population derived from the B73 reference line and the Mexican highland maize variety Palomero Toluqueño. B73 and Palomero Toluqueño showed classic rank-changing differences in performance between lowland and highland field sites, indicative of local adaptation. Quantitative trait mapping identified genomic regions linked to effects on yield components that were conditionally expressed depending on the environment. For the principal genomic regions associated with ear weight and total kernel number, the Palomero Toluqueño allele conferred an advantage specifically in the highland site, consistent with local adaptation. We identified Palomero Toluqueño alleles associated with expression of characteristic highland traits, including reduced tassel branching, increased sheath pigmentation and the presence of sheath macrohairs. The oligogenic architecture of these three morphological traits supports their role in adaptation, suggesting they have arisen from consistent directional selection acting at distinct points across the genome. We discuss these results in the context of the origin of phenotypic novelty during selection, commenting on the role of de novo mutation and the acquisition of adaptive variation by gene flow from endemic wild relatives.

The Genetic and Hormonal Inducers of Continuous Flowering in Orchids: An Emerging View

Orchids are the flowers of magnetic beauty. Vivid and attractive flowers with magnificent shapes make them the king of the floriculture industry. However, the long-awaited flowering is a drawback to their market success, and therefore, flowering time regulation is the key to studies about orchid flower development. Although there are some rare orchids with a continuous flowering pattern, the molecular regulatory mechanisms are yet to be elucidated to find applicable solutions to other orchid species. Multiple regulatory pathways, such as photoperiod, vernalization, circadian clock, temperature and hormonal pathways are thought to signalize flower timing using a group of floral integrators. This mini review, thus, organizes the current knowledge of floral time regulators to suggest future perspectives on the continuous flowering mechanism that may help to plan functional studies to induce flowering revolution in precious orchid species.

Photoperiod Control of Plant Growth: Flowering Time Genes Beyond Flowering

Fluctuations in environmental conditions greatly influence life on earth. Plants, as sessile organisms, have developed molecular mechanisms to adapt their development to changes in daylength, or photoperiod. One of the first plant features that comes to mind as affected by the duration of the day is flowering time; we all bring up a clear image of spring blossom. However, for many plants flowering happens at other times of the year, and many other developmental aspects are also affected by changes in daylength, which range from hypocotyl elongation in Arabidopsis thaliana to tuberization in potato or autumn growth cessation in trees. Strikingly, many of the processes affected by photoperiod employ similar gene networks to respond to changes in the length of light/dark cycles. In this review, we have focused on developmental processes affected by photoperiod that share similar genes and gene regulatory networks.

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.

Genome-wide analysis of deletions in maize population reveals abundant genetic diversity and functional impact

Two read depth methods were jointly used in next-generation sequencing data to identify deletions in maize population. GWAS by deletions were analyzed for gene expression pattern and classical traits, respectively. Many studies have confirmed that structural variation (SV) is pervasive throughout the maize genome. Deletion is one type of SV that may impact gene expression and cause phenotypic changes in quantitative traits. In this study, two read count approaches were used to analyze the deletions in the whole-genome sequencing data of 270 maize inbred lines. A total of 19,754 deletion windows overlapped 12,751 genes, which were unevenly distributed across the genome. The deletions explained population structure well and correlated with genomic features. The deletion proportion of genes was determined to be negatively correlated with its expression. The detection of gene expression quantitative trait loci (eQTL) indicated that local eQTL were fewer but had larger effects than distant ones. The common associated genes were related to basic metabolic processes, whereas unique associated genes with eQTL played a role in the stress or stimulus responses in multiple tissues. Compared with the eQTL detected by SNPs derived from the same sequencing data, 89.4% of the associated genes could be detected by both markers. The effect of top eQTL detected by SNPs was usually larger than that detected by deletions for the same gene. A genome-wide association study (GWAS) on flowering time and plant height illustrated that only a few loci could be consistently captured by SNPs, suggesting that combining deletion and SNP for GWAS was an excellent strategy to dissect trait architecture. Our findings will provide insights into characteristic and biological function of genome-wide deletions in maize.

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.

Comprehensive Effects of Flowering Locus T-Mediated Stem Growth in Tobacco

In flowering plants, Flowering locus T (FT) encodes a major florigen. It is a key flowering hormone in controlling flowering time and has a wide range of effects on plant development. Although the mechanism by which FT promotes flowering is currently clearly understood, comprehensive effects of the FT gene on plant growth have not been evaluated. Therefore, the effects of FT on vegetative growth need to be explored for a complete understanding of the molecular functions of the FT gene. In this study, the Jatropha curcas L. FT gene was overexpressed in tobacco (JcFT^OE) in order to discover multiple aspects and related mechanisms of how the FT gene affects plant development. In JcFT^OE plants, root, stem, and leaf development was strongly affected. Stem tissues were selected for further transcriptome analysis. In JcFT^OE plants, stem growth was affected because of changes in the nucleus, cytoplasm, and cell wall. In the nucleus of JcFT^OE plants, the primary effect was to weaken all aspects of DNA replication, which ultimately affected the cell cycle and cell division. The number of stem cells decreased significantly in JcFT^OE plants, which decreased the thickness and height of tobacco stems. In the cell wall of JcFT^OE plants, hemicellulose and cellulose contents increased, with the increase in hemicellulose associated with up-regulation of xylan synthase-related genes expression. In the cytoplasm of JcFT^OE plants, the primary effects were on biogenesis of ribonucleoprotein complexes, photosynthesis, carbohydrate biosynthesis, and the cytoskeleton. In addition, in the cytoplasm of JcFT^OE plants, there were changes in certain factors of the core oscillator, expression of many light-harvesting chlorophyll a/b binding proteins was down-regulated, and expression of fructose 1,6-bisphosphatase genes was up-regulated to increase starch content in tobacco stems. Changes in the xylem and phloem of JcFT^OE plants were also identified, and in particular, xylem development was affected by significant increases in expression of irregular xylem genes.

Identification of ZmNF-YC2 and its regulatory network for maize flowering time

Flowering time is an important agronomic trait that determines the distribution and adaptation of plants. The accurate prediction of flowering time in elite germplasm is critical for maize breeding. However, the molecular mechanisms underlying the photoperiod response remain elusive in maize. Here we cloned the flowering time-controlling gene, ZmNF-YC2, by map-based cloning and confirmed that ZmNF-YC2 is the nuclear transcription factor Y subunit C-2 protein and a positive regulator of flowering time in maize under long-day conditions. Our results show that ZmNF-YC2 promotes the expression of ZmNF-YA3. ZmNF-YA3 negatively regulates the transcription of ZmAP2. ZmAP2 suppresses the expression of ZMM4 to delay flowering time. We then developed a gene regulatory model of flowering time in maize using ZmNF-YC2, ZmNF-YA3, ZmAP2, ZMM4, and other key genes. The cascading regulation by ZmNF-YC2 of maize flowering time has not been reported in other species.

Combining QTL-seq and linkage mapping to uncover the genetic basis of single vs. paired spikelets in the advanced populations of two-ranked maize×teosinte

BACKGROUND

Teosinte ear bears single spikelet, whereas maize ear bears paired spikelets, doubling the number of grains in each cupulate during maize domestication. In the past 20 years, genetic analysis of single vs. paired spikelets (PEDS) has been stagnant. A better understanding of genetic basis of PEDS could help fine mapping of quantitative trait loci (QTL) and cloning of genes.

RESULTS

In this study, the advanced mapping populations (BC₃F₂ and BC₄F₂) of maize × teosinte were developed by phenotypic recurrent selection. Four genomic regions associated with PEDS were detected using QTL-seq, located on 194.64-299.52 Mb, 0-162.80 Mb, 12.82-97.17 Mb, and 125.06-157.01 Mb of chromosomes 1, 3, 6, and 8, respectively. Five QTL for PEDS were identified in the regions of QTL-seq using traditional QTL mapping. Each QTL explained 1.12-38.05% of the phenotypic variance (PVE); notably, QTL qPEDS3.1 with the average PVE of 35.29% was identified in all tests. Moreover, 14 epistatic QTL were detected, with the total PVE of 47.57-66.81% in each test. The QTL qPEDS3.1 overlapped with, or was close to, one locus of 7 epistatic QTL. Near-isogenic lines (NILs) of QTL qPEDS1.1, qPEDS3.1, qPEDS6.1, and qPEDS8.1 were constructed. All individuals of NIL-qPEDS6.1(MT1) and NIL-qPEDS8.1(MT1) showed paired spikelets (PEDS = 0), but the flowering time was 7 days shorter in the NIL-qPEDS8.1(MT1). The ratio of plants with PEDS > 0 was low (1/18 to 3/18) in the NIL-qPEDS1.1(MT1) and NIL-qPEDS3.1(MT1), maybe due to the epistatic effect.

CONCLUSION

Our results suggested that major QTL, minor QTL, epistasis and photoperiod were associated with the variation of PEDS, which help us better understand the genetic basis of PEDS and provide a genetic resource for fine mapping of QTL.

A Daylength Recognition Model of Photoperiodic Flowering

The photoperiodic flowering pathway is crucial for plant development to synchronize internal signaling events and external seasons. One hundred years after photoperiodic flowering was discovered, the underlying core signaling network has been elucidated in model plants such as Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), and soybean (Glycine max). Here, we review the progress made in the photoperiodic flowering area and summarize previously accepted photoperiodic flowering models. We then introduce a new model based on daylength recognition by florigen. By determining the expression levels of the florigen gene, this model can assess the mechanism of daylength sensing and crop latitude adaptation. Future applications of this model under the constraints of global climate change are discussed.

ZmCCT regulates photoperiod-dependent flowering and response to stresses in maize

BACKGROUND

Appropriate flowering time is very important to the success of modern agriculture. Maize (Zea mays L.) is a major cereal crop, originated in tropical areas, with photoperiod sensitivity. Which is an important obstacle to the utilization of tropical/subtropical germplasm resources in temperate regions. However, the study on the regulation mechanism of photoperiod sensitivity of maize is still in the early stage. Although it has been previously reported that ZmCCT is involved in the photoperiod response and delays maize flowering time under long-day conditions, the underlying mechanism remains unclear.

RESULTS

Here, we showed that ZmCCT overexpression delays flowering time and confers maize drought tolerance under LD conditions. Implementing the Gal4-LexA/UAS system identified that ZmCCT has a transcriptional inhibitory activity, while the yeast system showed that ZmCCT has a transcriptional activation activity. DAP-Seq analysis and EMSA indicated that ZmCCT mainly binds to promoters containing the novel motifs CAAAAATC and AAATGGTC. DAP-Seq and RNA-Seq analysis showed that ZmCCT could directly repress the expression of ZmPRR5 and ZmCOL9, and promote the expression of ZmRVE6 to delay flowering under long-day conditions. Moreover, we also demonstrated that ZmCCT directly binds to the promoters of ZmHY5, ZmMPK3, ZmVOZ1 and ZmARR16 and promotes the expression of ZmHY5 and ZmMPK3, but represses ZmVOZ1 and ZmARR16 to enhance stress resistance. Additionally, ZmCCT regulates a set of genes associated with plant development.

CONCLUSIONS

ZmCCT has dual functions in regulating maize flowering time and stress response under LD conditions. ZmCCT negatively regulates flowering time and enhances maize drought tolerance under LD conditions. ZmCCT represses most flowering time genes to delay flowering while promotes most stress response genes to enhance stress tolerance. Our data contribute to a comprehensive understanding of the regulatory mechanism of ZmCCT in controlling maize flowering time and stress response.

Combined QTL mapping and association study reveals candidate genes for leaf number and flowering time in maize

KEY MESSAGE

Twelve QTL for flowering and leaf number were detected. The ZmWRKY14Hap4 could increase leaf number, flowering time and biomass yield which are promising for silage maize breeding. Silage maize, one of the most important feedstock for ruminants, is widely grown from temperate regions to the tropics. Flowering time and leaf number are two significantly correlated traits and important for the quality, adaptation and biomass yield of silage maize. In this study, a recombinant inbred line population consisting of 215 individuals and an association panel of 369 inbred lines were analysed in field conditions in three locations for 2 consecutive years, and five, four and three quantitative trait loci for the total leaf number, days to anthesis (DTA) and silking (DTS) were detected, which could explain 48.55, 35.37 and 34.22% of total phenotypic variation, respectively. Association analysis of qLN10 on chromosome 10 found that ZmWRKY14 was the candidate gene for leaf number, whose expression level was negatively correlated with the leaf number. There are five haplotypes for ZmWRKY14, and haplotype 4 could significantly increase flowering time, leaf number and biomass yield, but has no obvious influence on ear weight. The optimal allelic combination of ZmWRKY14 and ZCN8 could further increase leaf number and biomass yield. The results will provide important genetic information for silage maize breeding.

LightGBM: accelerated genomically designed crop breeding through ensemble learning

LightGBM is an ensemble model of decision trees for classification and regression prediction. We demonstrate its utility in genomic selection-assisted breeding with a large dataset of inbred and hybrid maize lines. LightGBM exhibits superior performance in terms of prediction precision, model stability, and computing efficiency through a series of benchmark tests. We also assess the factors that are essential to ensure the best performance of genomic selection prediction by taking complex scenarios in crop hybrid breeding into account. LightGBM has been implemented as a toolbox, CropGBM, encompassing multiple novel functions and analytical modules to facilitate genomically designed breeding in crops.

Opposite response of maize ZmCCT to photoperiod due to transposon jumping

The new 4.2-kb transposable insertion in the intron of ZmCCT reversely responded relative to the known 5.1-kb transposable insertion to photoperiods between low- and high-latitude regions. Flowering time is a key trait for cereal adaptation that is controlled by a complex genetic background in maize. The effect of multiple alleles from a quantitative trait locus (QTL) on flowering time remains largely unknown. Here, we fine-mapped a major QTL for flowering time on maize chromosome 10 corresponding to ZmCCT, where a new allele with a 4.2-kilobase (kb) transposable insertion was present in the intron. The known allele with a 5.1-kb transposon insertion in the promoter of ZmCCT enhances flowering in high-latitude regions, but has no effect on flowering time in low-latitude regions in comparison with the null allele lacking this insertion. However, our new allele with a 4.2-kb insertion reduced flowering in the low-latitude region, but produced unchanged flowering time in the high-latitude region relative to the 5.1-kb transposable insertion. Transcription analysis revealed that the new allele with 4.2-kb insertion versus the 5.1-kb insertion repressed and unchanged the transcription of ZmCCT in the low- and high-latitude regions, respectively. Thus, the allele with the 4.2-kb transposable insertion showed a completely opposite response to photoperiods between these two regions. Phylogenetic analysis revealed that the 4.2-kb transposable insertion in the two Northern flint corns originated from tropical maize. RNA-seq analysis and dual-luciferase transient expression assays further identified a conserved gene regulation network of ZmCCT between maize and rice, in which ZmCCT directly repressed the transcription of the florigen gene ZCN8 via ZmEhd1. Our results suggest that transposable elements play an important role in maize adaptation.

Dissecting the Genetic Basis of Flowering Time and Height Related-Traits Using Two Doubled Haploid Populations in Maize

In the field, maize flowering time and height traits are closely linked with yield, planting density, lodging resistance, and grain fill. To explore the genetic basis of flowering time and height traits in maize, we investigated six related traits, namely, days to anthesis (AD), days to silking (SD), the anthesis-silking interval (ASI), plant height (PH), ear height (EH), and the EH/PH ratio (ER) in two locations for two years based on two doubled haploid (DH) populations. Based on the two high-density genetic linkage maps, 12 and 22 quantitative trait loci (QTL) were identified, respectively, for flowering time and height-related traits. Of these, ten QTLs had overlapping confidence intervals between the two populations and were integrated into three consensus QTLs (qFT_YZ1a, qHT_YZ5a, and qHT_YZ7a). Of these, qFT_YZ1a, conferring flowering time, is located at 221.1-277.0 Mb on chromosome 1 and explained 10.0-12.5% of the AD and SD variation, and qHT_YZ5a, conferring height traits, is located at 147.4-217.3 Mb on chromosome 5 and explained 11.6-15.3% of the PH and EH variation. These consensus QTLs, in addition to the other repeatedly detected QTLs, provide useful information for further genetic studies and variety improvements in flowering time and height-related traits.

Finding Needles in a Haystack: Using Geo-References to Enhance the Selection and Utilization of Landraces in Breeding for Climate-Resilient Cultivars of Upland Cotton (Gossypium hirsutum L.)

The genetic uniformity of cultivated cotton as a consequence of domestication and modern breeding makes it extremely vulnerable to abiotic challenges brought about by major climate shifts. To sustain productivity amidst worsening agro-environments, future breeding objectives need to seriously consider introducing new genetic variation from diverse resources into the current germplasm base of cotton. Landraces are genetically heterogeneous, population complexes that have been primarily selected for their adaptability to specific localized or regional environments. This makes them an invaluable genetic resource of novel allelic diversity that can be exploited to enhance the resilience of crops to marginal environments. The utilization of cotton landraces in breeding programs are constrained by the phenology of the plant and the lack of phenotypic information that can facilitate efficient selection of potential donor parents for breeding. In this review, the genetic value of cotton landraces and the major challenges in their utilization in breeding are discussed. Two strategies namely Focused Identification of Germplasm Strategy and Environmental Association Analysis that have been developed to effectively screen large germplasm collections for accessions with adaptive traits using geo-reference-based, mathematical modelling are highlighted. The potential applications of both approaches in mining available cotton landrace collections are also presented.

An integrated framework reinstating the environmental dimension for GWAS and genomic selection in crops

Identifying mechanisms and pathways involved in gene-environment interplay and phenotypic plasticity is a long-standing challenge. It is highly desirable to establish an integrated framework with an environmental dimension for complex trait dissection and prediction. A critical step is to identify an environmental index that is both biologically relevant and estimable for new environments. With extensive field-observed complex traits, environmental profiles, and genome-wide single nucleotide polymorphisms for three major crops (maize, wheat, and oat), we demonstrated that identifying such an environmental index (i.e., a combination of environmental parameter and growth window) enables genome-wide association studies and genomic selection of complex traits to be conducted with an explicit environmental dimension. Interestingly, genes identified for two reaction-norm parameters (i.e., intercept and slope) derived from flowering time values along the environmental index were less colocalized for a diverse maize panel than for wheat and oat breeding panels, agreeing with the different diversity levels and genetic constitutions of the panels. In addition, we showcased the usefulness of this framework for systematically forecasting the performance of diverse germplasm panels in new environments. This general framework and the companion CERIS-JGRA analytical package should facilitate biologically informed dissection of complex traits, enhanced performance prediction in breeding for future climates, and coordinated efforts to enrich our understanding of mechanisms underlying phenotypic variation.

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.

Joint analysis of days to flowering reveals independent temperate adaptations in maize

Domesticates are an excellent model for understanding biological consequences of rapid climate change. Maize (Zea mays ssp. mays) was domesticated from a tropical grass yet is widespread across temperate regions today. We investigate the biological basis of temperate adaptation in diverse structured nested association mapping (NAM) populations from China, Europe (Dent and Flint) and the United States as well as in the Ames inbred diversity panel, using days to flowering as a proxy. Using cross-population prediction, where high prediction accuracy derives from overall genomic relatedness, shared genetic architecture, and sufficient diversity in the training population, we identify patterns in predictive ability across the five populations. To identify the source of temperate adapted alleles in these populations, we predict top associated genome-wide association study (GWAS) identified loci in a Random Forest Classifier using independent temperate-tropical North American populations based on lines selected from Hapmap3 as predictors. We find that North American populations are well predicted (AUC equals 0.89 and 0.85 for Ames and USNAM, respectively), European populations somewhat well predicted (AUC equals 0.59 and 0.67 for the Dent and Flint panels, respectively) and that the Chinese population is not predicted well at all (AUC is 0.47), suggesting an independent adaptation process for early flowering in China. Multiple adaptations for the complex trait days to flowering in maize provide hope for similar natural systems under climate change.

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.

Inter-species functional compatibility of the Theobroma cacao and Arabidopsis FT orthologs: 90 million years of functional conservation of meristem identity genes

BACKGROUND

In angiosperms the transition to flowering is controlled by a complex set of interacting networks integrating a range of developmental, physiological, and environmental factors optimizing transition time for maximal reproductive efficiency. The molecular mechanisms comprising these networks have been partially characterized and include both transcriptional and post-transcriptional regulatory pathways. Florigen, encoded by FLOWERING LOCUS T (FT) orthologs, is a conserved central integrator of several flowering time regulatory pathways. To characterize the molecular mechanisms involved in controlling cacao flowering time, we have characterized a cacao candidate florigen gene, TcFLOWERING LOCUS T (TcFT). Understanding how this conserved flowering time regulator affects cacao plant's transition to flowering could lead to strategies to accelerate cacao breeding.

RESULTS

BLAST searches of cacao genome reference assemblies identified seven candidate members of the CENTRORADIALIS/TERMINAL FLOWER1/SELF PRUNING gene family including a single florigen candidate. cDNA encoding the predicted cacao florigen was cloned and functionally tested by transgenic genetic complementation in the Arabidopsis ft-10 mutant. Transgenic expression of the candidate TcFT cDNA in late flowering Arabidopsis ft-10 partially rescues the mutant to wild-type flowering time. Gene expression studies reveal that TcFT is spatially and temporally expressed in a manner similar to that found in Arabidopsis, specifically, TcFT mRNA is shown to be both developmentally and diurnally regulated in leaves and is most abundant in floral tissues. Finally, to test interspecies compatibility of florigens, we transformed cacao tissues with AtFT resulting in the remarkable formation of flowers in tissue culture. The morphology of these in vitro flowers is normal, and they produce pollen that germinates in vitro with high rates.

CONCLUSION

We have identified the cacao CETS gene family, central to developmental regulation in angiosperms. The role of the cacao's single FT-like gene (TcFT) as a general regulator of determinate growth in cacao was demonstrated by functional complementation of Arabidopsis ft-10 late-flowering mutant and through gene expression analysis. In addition, overexpression of AtFT in cacao resulted in precocious flowering in cacao tissue culture demonstrating the highly conserved function of FT and the mechanisms controlling flowering in cacao.

A novel deletion in FLOWERING LOCUS T modulates flowering time in winter oilseed rape

A novel structural variant was discovered in the FLOWERING LOCUS T orthologue BnaFT.A02 by long-read sequencing. Nested association mapping in an elite winter oilseed rape population revealed that this 288 bp deletion associates with early flowering, putatively by modification of binding-sites for important flowering regulation genes. Perfect timing of flowering is crucial for optimal pollination and high seed yield. Extensive previous studies of flowering behavior in Brassica napus (canola, rapeseed) identified mutations in key flowering regulators which differentiate winter, semi-winter and spring ecotypes. However, because these are generally fixed in locally adapted genotypes, they have only limited relevance for fine adjustment of flowering time in elite cultivar gene pools. In crosses between ecotypes, the ecotype-specific major-effect mutations mask minor-effect loci of interest for breeding. Here, we investigated flowering time in a multiparental mapping population derived from seven elite winter oilseed rape cultivars which are fixed for major-effect mutations separating winter-type rapeseed from other ecotypes. Association mapping revealed eight genomic regions on chromosomes A02, C02 and C03 associating with fine modulation of flowering time. Long-read genomic resequencing of the seven parental lines identified seven structural variants coinciding with candidate genes for flowering time within chromosome regions associated with flowering time. Segregation patterns for these variants in the elite multiparental population and a diversity set of winter types using locus-specific assays revealed significant associations with flowering time for three deletions on chromosome A02. One of these was a previously undescribed 288 bp deletion within the second intron of FLOWERING LOCUS T on chromosome A02, emphasizing the advantage of long-read sequencing for detection of structural variants in this size range. Detailed analysis revealed the impact of this specific deletion on flowering-time modulation under extreme environments and varying day lengths in elite, winter-type oilseed rape.

The interplay of phloem-mobile signals in plant development and stress response

Plants integrate a variety of biotic and abiotic factors for optimal growth in their given environment. While some of these responses are local, others occur distally. Hence, communication of signals perceived in one organ to a second, distal part of the plant and the coordinated developmental response require an intricate signaling system. To do so, plants developed a bipartite vascular system that mediates the uptake of water, minerals, and nutrients from the soil; transports high-energy compounds and building blocks; and traffics essential developmental and stress signals. One component of the plant vasculature is the phloem. The development of highly sensitive mass spectrometry and molecular methods in the last decades has enabled us to explore the full complexity of the phloem content. As a result, our view of the phloem has evolved from a simple transport path of photoassimilates to a major highway for pathogens, hormones and developmental signals. Understanding phloem transport is essential to comprehend the coordination of environmental inputs with plant development and, thus, ensure food security. This review discusses recent developments in its role in long-distance signaling and highlights the role of some of the signaling molecules. What emerges is an image of signaling paths that do not just involve single molecules but rather, quite frequently an interplay of several distinct molecular classes, many of which appear to be transported and acting in concert.

Beyond Arabidopsis: BBX Regulators in Crop Plants

B-box proteins represent diverse zinc finger transcription factors and regulators forming large families in various plants. A unique domain structure defines them—besides the highly conserved B-box domains, some B-box (BBX) proteins also possess CCT domain and VP motif. Based on the presence of these specific domains, they are mostly classified into five structural groups. The particular members widely differ in structure and fulfill distinct functions in regulating plant growth and development, including seedling photomorphogenesis, the anthocyanins biosynthesis, photoperiodic regulation of flowering, and hormonal pathways. Several BBX proteins are additionally involved in biotic and abiotic stress response. Overexpression of some BBX genes stimulates various stress-related genes and enhanced tolerance to different stresses. Moreover, there is evidence of interplay between B-box and the circadian clock mechanism. This review highlights the role of BBX proteins as a part of a broad regulatory network in crop plants, considering their participation in development, physiology, defense, and environmental constraints. A description is also provided of how various BBX regulators involved in stress tolerance were applied in genetic engineering to obtain stress tolerance in transgenic crops.

Developmental genetics of maize vegetative shoot architecture

More than 1.1 billion tonnes of maize grain were harvested across 197 million hectares in 2019 (FAOSTAT 2020). The vast global productivity of maize is largely driven by denser planting practices, higher yield potential per area of land, and increased yield potential per plant. Shoot architecture, the three-dimensional structural arrangement of the above-ground plant body, is critical to maize grain yield and biomass. Structure of the shoot is integral to all aspects of modern agronomic practices. Here, the developmental genetics of the maize vegetative shoot is reviewed. Plant architecture is ultimately determined by meristem activity, developmental patterning, and growth. The following topics are discussed: shoot apical meristem, leaf architecture, axillary meristem and shoot branching, and intercalary meristem and stem activity. Where possible, classical and current studies in maize developmental genetics, as well as recent advances leveraged by "-omics" analyses, are highlighted within these sections.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01208-1.

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.

Genome-wide member identification, phylogeny and expression analysis of PEBP gene family in wheat and its progenitors

The phosphatidylethanolamine binding protein (PEBP) family comprises ancient proteins found throughout the biosphere that play an important role in plant growth and development, flowering, seed development and dormancy. However, not all PEBP genes have been identified or analyzed in common wheat (Triticum aestivum L.) and its progenitors. In this study, we identified the PEBP genes in common wheat, Triticum dicoccoides, Triticum urartu and Aegilops tauschii by searching whole genome sequences, and characterized these genes by phylogenetic and transcriptome analyses. A total of 76, 38, 16 and 22 PEBP genes were identified in common wheat, T. dicoccoides, T. urartu and Ae. tauschii, respectively. Phylogenetic analysis classified the PEBP genes into four subfamilies (PEBP-like, MFT-like, TFL-like and FT-like); the PEBP-like subfamily was identified as a new subfamily with genes in this subfamily were conserved in plants. Group 2, 3 and 5 chromosomes of common wheat and its progenitors contained more PEBP genes than other chromosomes. The PEBP genes were conserved in wheat during evolution, and tandem duplication played a more important role in the amplification of PEBP genes than segmental duplication. Furthermore, transcriptome analysis revealed that PEBP genes showed tissue/organ-specific expression profiles and some PEBP genes were induced to express by biotic stresses. Quantitative real-time PCR (qRT-PCR) analysis revealed that seven randomly selected PEBP genes expressed differently during seed germination under cold, drought, flood, heat and salt stress treatments, and five of these genes (TaPEBP1, TaPEBP5, TaPEBP9, TaPEBP66 and TaPEBP69) showed significantly higher expression under different stress treatments, indicating that these genes play important roles during seed germination under stress conditions.

CRISPR/Cas9-mediated knockout and overexpression studies reveal a role of maize phytochrome C in regulating flowering time and plant height

Maize is a major staple crop widely used for food, feedstocks and industrial products. Shade-avoidance syndrome (SAS), which is triggered when plants sense competition of light from neighbouring vegetation, is detrimental for maize yield production under high-density planting conditions. Previous studies have shown that the red and far-red photoreceptor phytochromes are responsible for perceiving the shading signals and triggering SAS in Arabidopsis; however, their roles in maize are less clear. In this study, we examined the expression patterns of ZmPHYC1 and ZmPHYC2 and found that ZmPHYC1, but not ZmPHYC2, is highly expressed in leaves and is regulated by the circadian clock. Both ZmPHYC1 and ZmPHYC2 proteins are localized to both the nucleus and cytoplasm under light conditions and both of them can interact with themselves or with ZmPHYBs. Heterologous expression of ZmPHYCs can complement the Arabidopsis phyC-2 mutant under constant red light conditions and confer an attenuated SAS in Arabidopsis in response to shading. Double knockout mutants of ZmPHYC1 and ZmPHYC2 created using the CRISPR/Cas9 technology display a moderate early-flowering phenotype under long-day conditions, whereas ZmPHYC2 overexpression plants exhibit a moderately reduced plant height and ear height. Together, these results provided new insight into the function of ZmPHYCs and guidance for breeding high-density tolerant maize cultivars.

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.

Gene editing applications to modulate crop flowering time and seed dormancy

Gene editing technologies such as CRISPR/Cas9 have been used to improve many agricultural traits, from disease resistance to grain quality. Now, emerging research has used CRISPR/Cas9 and other gene editing technologies to target plant reproduction, including major areas such as flowering time and seed dormancy. Traits related to these areas have important implications for agriculture, as manipulation of flowering time has multiple applications, including tailoring crops for regional adaptation and improving yield. Moreover, understanding seed dormancy will enable approaches to improve germination upon planting and prevent pre-harvest sprouting. Here, we summarize trends and recent advances in using gene editing to gain a better understanding of plant reproduction and apply the resulting information for crop improvement.

Adaptive introgression from maize has facilitated the establishment of teosinte as a noxious weed in Europe

Global trade has considerably accelerated biological invasions. The annual tropical teosintes, the closest wild relatives of maize, were recently reported as new agricultural weeds in two European countries, Spain and France. Their prompt settlement under climatic conditions differing drastically from that of their native range indicates rapid genetic evolution. We performed a phenotypic comparison of French and Mexican teosintes under European conditions and showed that only the former could complete their life cycle during maize cropping season. To test the hypothesis that crop-to-wild introgression triggered such rapid adaptation, we used single nucleotide polymorphisms to characterize patterns of genetic variation in French, Spanish, and Mexican teosintes as well as in maize germplasm. We showed that both Spanish and French teosintes originated from Zea mays ssp. mexicana race "Chalco," a weedy teosinte from the Mexican highlands. However, introduced teosintes differed markedly from their Mexican source by elevated levels of genetic introgression from the high latitude Dent maize grown in Europe. We identified a clear signature of divergent selection in a region of chromosome 8 introgressed from maize and encompassing ZCN8, a major flowering time gene associated with adaptation to high latitudes. Moreover, herbicide assays and sequencing revealed that French teosintes have acquired herbicide resistance via the introgression of a mutant herbicide-target gene (ACC1) present in herbicide-resistant maize cultivars. Altogether, our results demonstrate that adaptive crop-to-wild introgression has triggered both rapid adaptation to a new climatic niche and acquisition of herbicide resistance, thereby fostering the establishment of an emerging noxious weed.

Adaptation to novel environments during crop diversification

In the context of the global challenge of climate change, mitigation strategies are needed to adapt crops to novel environments. The main goal to address this is an understanding of the genetic basis of crop adaptation to different agro-ecological conditions. The movement of crops during the Colombian Exchange that started with the travels of Columbus in 1492 is an example of rapid adaptation to novel environments. Many diversification-related traits have been characterised in multiple crop species, and association-mapping analyses have identified loci involved in these. Here, we present an overview of current knowledge regarding the molecular basis related to the complex patterns of crop adaptation and dissemination, particularly outside their centres of origin. Investigation of the genomic basis of crop expansion offers a powerful contribution to the development of tools to identify and exploit valuable genetic diversity and to improve and design novel resilient crop varieties.

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.

Characterization of DvSSJ1 transcripts targeting the smooth septate junction (SSJ) of western corn rootworm (Diabrotica virgifera virgifera)

Transgenic maize plants expressing dsRNA targeting western corn rootworm (WCR, Diabrotica virgifera virgifera) DvSSJ1 mRNA, a Drosophila snakeskin (ssk) ortholog, show insecticidal activity and significant plant protection from WCR damage. The gene encodes a membrane protein associated with the smooth sepate junction (SSJ) which is required for intestinal barrier function. To understand the active RNA form that leads to the mortality of WCR larvae by DvSSJ1 RNA interference (RNAi), we characterized transgenic plants expressing DvSSJ1 RNA transcripts targeting WCR DvSSJ1 mRNA. The expression of the silencing cassette results in the full-length transcript of 901 nucleotides containing a 210 bp inverted fragment of the DvSSJ1 gene, the formation of a double-stranded RNA (dsRNA) transcript and siRNAs in transgenic plants. Our artificial diet-feeding study indicates that dsRNAs greater than or equal to approximately 60 base-pairs (bp) are required for DvSSJ1 insecticidal activity. Impact of specificity of dsRNA targeting DvSSJ1 mRNA on insecticidal activities was also evaluated in diet bioassay, which showed a single nucleotide mutation can have a significant impact or abolish diet activities against WCR. These results provide insights as to the functional forms of plant-delivered dsRNA for the protection of transgenic maize from WCR feeding damage and information contributing to the risk assessment of transgenic maize expressing insecticidal dsRNA.

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.

High-Throughput CRISPR/Cas9 Mutagenesis Streamlines Trait Gene Identification in Maize

Maize (Zea mays) is one of the most important crops in the world. However, few agronomically important maize genes have been cloned and used for trait improvement, due to its complex genome and genetic architecture. Here, we integrated multiplexed CRISPR/Cas9-based high-throughput targeted mutagenesis with genetic mapping and genomic approaches to successfully target 743 candidate genes corresponding to traits relevant for agronomy and nutrition. After low-cost barcode-based deep sequencing, 412 edited sequences covering 118 genes were precisely identified from individuals showing clear phenotypic changes. The profiles of the associated gene-editing events were similar to those identified in human cell lines and consequently are predictable using an existing algorithm originally designed for human studies. We observed unexpected but frequent homology-directed repair through endogenous templates that was likely caused by spatial contact between distinct chromosomes. Based on the characterization and interpretation of gene function from several examples, we demonstrate that the integration of forward and reverse genetics via a targeted mutagenesis library promises rapid validation of important agronomic genes for crops with complex genomes. Beyond specific findings, this study also guides further optimization of high-throughput CRISPR experiments in plants.

Identification and characterization of PEBP family genes reveal CcFT8 a probable candidate for photoperiod insensitivity in C. cajan

Understanding the molecular mechanism underlying photoperiod sensitivity will play a crucial role in extending the cropping area of Cajanus cajan, a photoperiod sensitive major grain legume of India and Africa. In flowering plants, Flowering locus T (FT) gene is involved in the production of florigen molecule which is essential for induction of flowering, influenced largely by the duration of photoperiod. To understand the structural and regulatory nature of this gene, a genome-wide survey was carried out, revealing the presence of 13 PEBP (FT) family genes in C. cajan. Based on the gene expression profiling of 13 PEBP genes across the 30 tissues of C. cajan, CcFT6 and CcFT8 were found to be probable Flowering locus T genes responsible for the production of florigen as both of them showed expression in reproductive leaf. Expression analysis in photoperiod sensitive, MAL3 genotype revealed that CcFT6 is upregulated under SD. However, in photoperiod insensitive genotype (ICP20338) CcFT6 and CcFT8 were upregulated in SD and LD, respectively. Hence, in ICP20338 under SD, flowering induction occurs with the involvement of CcFT6 while under LD, flowering induction seems to be associated with the expression of CcFT8. CcFT6 was found to be expressed only under favourable photoperiodic condition (SD) in both MAL3 and ICP20338 and may be regulated through a photoperiod dependent pathway. The presence of additional florigen producing gene, CcFT8 in ICP20338 which has the ability to flower in a photoperiod independent manner under LD conditions might provide some clues on its photoperiod insensitive nature. This study will provide a detailed characterization of the genes involved in photoperiodic regulation of flowering in C. cajan.