The myb-homologous P gene controls phlobaphene pigmentation in maize floral organs by directly activating a flavonoid biosynthetic gene subset

Trait association and prediction through integrative k-mer analysis

Genome-wide association study (GWAS) with single nucleotide polymorphisms (SNPs) has been widely used to explore genetic controls of phenotypic traits. Alternatively, GWAS can use counts of substrings of length k from longer sequencing reads, k-mers, as genotyping data. Using maize cob and kernel color traits, we demonstrated that k-mer GWAS can effectively identify associated k-mers. Co-expression analysis of kernel color k-mers and genes directly found k-mers from known causal genes. Analyzing complex traits of kernel oil and leaf angle resulted in k-mers from both known and candidate genes. A gene encoding a MADS transcription factor was functionally validated by showing that ectopic expression of the gene led to less upright leaves. Evolution analysis revealed most k-mers positively correlated with kernel oil were strongly selected against in maize populations, while most k-mers for upright leaf angle were positively selected. In addition, genomic prediction of kernel oil, leaf angle, and flowering time using k-mer data resulted in a similarly high prediction accuracy to the standard SNP-based method. Collectively, we showed k-mer GWAS is a powerful approach for identifying trait-associated genetic elements. Further, our results demonstrated the bridging role of k-mers for data integration and functional gene discovery.

Molecular mechanisms underlying gene regulatory variation of maize metabolic traits

Variation in gene expression levels is pervasive among individuals and races or varieties, and has substantial agronomic consequences, for example, by contributing to hybrid vigor. Gene expression level variation results from mutations in regulatory sequences (cis) and/or transcription factor (TF) activity (trans), but the mechanisms underlying cis- and/or trans-regulatory variation of complex phenotypes remain largely unknown. Here, we investigated gene expression variation mechanisms underlying the differential accumulation of the insecticidal compounds maysin and chlorogenic acid in silks of widely used maize (Zea mays) inbreds, B73 and A632. By combining transcriptomics and cistromics, we identified 1,338 silk direct targets of the maize R2R3-MYB TF Pericarp color1 (P1), consistent with it being a regulator of maysin and chlorogenic acid biosynthesis. Among these P1 targets, 464 showed allele-specific expression (ASE) between B73 and A632 silks. Allelic DNA-affinity purification sequencing identified 34 examples in which P1 allelic specific binding (ASB) correlated with cis-expression variation. From previous yeast one-hybrid studies, we identified 9 TFs potentially implicated in the control of P1 targets, with ASB to 83 out of 464 ASE genes (cis) and differential expression of 4 out of 9 TFs between B73 and A632 silks (trans). These results provide a molecular framework for understanding universal mechanisms underlying natural variation of gene expression levels, and how the regulation of metabolic diversity is established.

OsMYB14, an R2R3-MYB transcription factor, regulates plant height through the control of hormone metabolism in rice

Plant growth must be regulated throughout the plant life cycle. The myeloblastosis (MYB) transcription factor (TF) family is one of the largest TF families and is involved in metabolism, lignin biosynthesis, and developmental processes. Here, we showed that OsMYB14, a rice R2R3-MYB TF, was expressed in leaves and roots, especially in rice culm and panicles, and that it localized to the nucleus. Overexpression of OsMYB14 (OsMYB14-ox) in rice resulted in a 30% reduction in plant height compared to that of the wild type (WT), while the height of the osmyb14-knockout (osmyb14-ko) mutant generated using the CRISPR/Cas9 system was not significantly different. Microscopic observations of the first internode revealed that the cell size did not differ significantly among the lines. RNA sequencing analysis revealed that genes associated with plant development, regulation, lipid metabolism, carbohydrate metabolism, and gibberellin (GA) and auxin metabolic processes were downregulated in the OsMYB14-ox line. Hormone quantitation revealed that inactive GA19 accumulated in OsMYB14-ox but not in the WT or knockout plants, suggesting that GA20 generation was repressed. Indole-3-acetic acid (IAA) and IAA-aspartate accumulated in OsMYB14-ox and osmyb14-ko, respectively. Indeed, real-time PCR analysis revealed that the expression of OsGA20ox1, encoding GA20 oxidase 1, and OsGH3-2, encoding IAA-amido synthetase, was downregulated in OsMYB14-ox and upregulated in osmyb14-ko. A protein-binding microarray revealed the presence of a consensus DNA-binding sequence, the ACCTACC-like motif, in the promoters of the OsGA20ox1 and GA20ox2 genes. These results suggest that OsMYB14 may act as a negative regulator of biological processes affecting plant height in rice by regulating GA biosynthesis and auxin metabolism.

The White Clover TrMYB33-TrSAMS1 Module Contributes to Drought Tolerance by Modulation of Spermidine Biosynthesis via an ABA-Dependent Pathway

Spermidine is well known to accumulate in plants exposed to drought, but the regulatory network associated with its biosynthesis and accumulation and the underlying molecular mechanisms remain unclear. Here, we demonstrated that the Trifolium repens TrMYB33 relayed the ABA signal to modulate drought-induced spermidine production by directly regulating the expression of TrSAMS1, which encodes an S-adenosylmethionine synthase. This gene was identified by transcriptome and expression analysis in T. repens. TrSAMS1 overexpression and its pTRV-VIGS-mediated silencing demonstrated that TrSAMS1 is a positive regulator of spermidine synthesis and drought tolerance. TrMYB33 was identified as an interacting candidate through yeast one-hybrid library screening with the TrSAMS1 promoter region as the bait. TrMYB33 was confirmed to bind directly to the predicted TAACCACTAACCA (the TAACCA MYB binding site is repeated twice in tandem) within the TrSAMS1 promoter and to act as a transcriptional activator. Additionally, TrMYB33 contributed to drought tolerance by regulating TrSAMS1 expression and modulating spermidine synthesis. Additionally, we found that spermidine accumulation under drought stress depended on ABA and that TrMYB33 coordinated ABA-mediated upregulation of TrSAMS1 and spermidine accumulation. This study elucidated the role of a T. repens MYB33 homolog in modulating spermidine biosynthesis. The further exploitation and functional characterization of the TrMYB33-TrSAMS1 regulatory module can enhance our understanding of the molecular mechanisms responsible for spermidine accumulation during drought stress.

Tandemly duplicated MYB genes are functionally diverged in the regulation of anthocyanin biosynthesis in soybean

Gene duplications have long been recognized as a driving force in the evolution of genes, giving rise to novel functions. The soybean (Glycine max) genome is characterized by a large number of duplicated genes. However, the extent and mechanisms of functional divergence among these duplicated genes in soybean remain poorly understood. In this study, we revealed that 4 MYB genes (GmMYBA5, GmMYBA2, GmMYBA1, and Glyma.09g235000)-presumably generated by tandem duplication specifically in the Phaseoleae lineage-exhibited a stronger purifying selection in soybean compared to common bean (Phaseolus vulgaris). To gain insights into the diverse functions of these tandemly duplicated MYB genes in anthocyanin biosynthesis, we examined the expression, transcriptional activity, induced metabolites, and evolutionary history of these 4 MYB genes. Our data revealed that Glyma.09g235000 is a pseudogene, while the remaining 3 MYB genes exhibit strong transcriptional activation activity, promoting anthocyanin biosynthesis in different soybean tissues. GmMYBA5, GmMYBA2, and GmMYBA1 induced anthocyanin accumulation by upregulating the expression of anthocyanin pathway-related genes. Notably, GmMYBA5 showed a lower capacity for gene induction compared to GmMYBA2 and GmMYBA1. Metabolomics analysis further demonstrated that GmMYBA5 induced distinct anthocyanin accumulation in Nicotiana benthamiana leaves and soybean hairy roots compared to GmMYBA2 and GmMYBA1, suggesting their functional divergence leading to the accumulation of different metabolites accumulation following gene duplication. Together, our data provide evidence of functional divergence within the MYB gene cluster following tandem duplication, which sheds light on the potential evolutionary directions of gene duplications during legume evolution.

An ARF gene mutation creates flint kernel architecture in dent maize

Dent and flint kernel architectures are important characteristics that affect the physical properties of maize kernels and their grain end uses. The genes controlling these traits are unknown, so it is difficult to combine the advantageous kernel traits of both. We found mutation of ARFTF17 in a dent genetic background reduces IAA content in the seed pericarp, creating a flint-like kernel phenotype. ARFTF17 is highly expressed in the pericarp and encodes a protein that interacts with and inhibits MYB40, a transcription factor with the dual functions of repressing PIN1 expression and transactivating genes for flavonoid biosynthesis. Enhanced flavonoid biosynthesis could reduce the metabolic flux responsible for auxin biosynthesis. The decreased IAA content of the dent pericarp appears to reduce cell division and expansion, creating a shorter, denser kernel. Introgression of the ARFTF17 mutation into dent inbreds and hybrids improved their kernel texture, integrity, and desiccation, without affecting yield.

Auxin response factors fine-tune lignin biosynthesis in response to mechanical bending in bamboo

Lignin contributes to plant mechanical properties during bending loads. Meanwhile, phytohormone auxin controls various plant biological processes. However, the mechanism of auxin's role in bending-induced lignin biosynthesis was unclear, especially in bamboo, celebrated for its excellent deformation stability. Here, we reported that auxin response factors (ARF) 3 and ARF6 from Moso bamboo (Phyllostachys edulis (Carrière) J. Houz) directly regulate lignin biosynthesis pathway genes, and affect lignin biosynthesis in bamboo. Auxin and lignin exhibited asymmetric distribution patterns, and auxin promoted lignin biosynthesis in response to bending loads in bamboo. Employing transcriptomic and weighted gene co-expression network analysis approach, we discovered that expression patterns of ARF3 and ARF6 strongly correlated with lignin biosynthesis genes. ARF3 and ARF6 directly bind to the promoter regions of 4-coumarate: coenzyme A ligase (4CL3, 4CL7, and 4CL9) or caffeoyl-CoA O-methyltransferase (CCoAOMT2) genes, pivotal to lignin biosynthesis, and activate their expressions. Notably, the efficacy of this binding hinges on auxin levels. Alternation of the expressions of ARF3 and ARF6 substantially altered lignin accumulation in transgenic bamboo. Collectively, our study shed light on bamboo lignification genetics. Auxin signaling could directly modulate lignin biosynthesis genes to impact plant lignin content.

Transcriptional regulation of tomato fruit ripening

An intrinsic and genetically determined ripening program of tomato fruits often depends upon the appropriate activation of tissue- and stage-specific transcription factors in space and time. The past two decades have yielded considerable progress in detailing these complex transcriptional as well as hormonal regulatory circuits paramount to fleshy fruit ripening. This non-linear ripening process is strongly controlled by the MADS-box and NOR family of proteins, triggering a transcriptional response associated with the progression of fruit ripening. Deepening insights into the connection between MADS-RIN and plant hormones related transcription factors, such as ERFs and ARFs, further conjugates the idea that several signaling units work in parallel to define an output fruit ripening transcriptome. Besides these TFs, the role of other families of transcription factors such as MYB, GLK, WRKY, GRAS and bHLH have also emerged as important ripening regulators. Other regulators such as EIN and EIL proteins also determine the transcriptional landscape of ripening fruits. Despite the abundant knowledge of the complex spectrum of ripening networks in the scientific domain, identifying more ripening effectors would pave the way for a better understanding of fleshy fruit ripening at the molecular level. This review provides an update on the transcriptional regulators of tomato fruit ripening.

Transcribed enhancer sequences are required for maize p1 paramutation

Paramutation is a transfer of heritable silencing states between interacting endogenous alleles or between endogenous alleles and homologous transgenes. Prior results demonstrated that paramutation occurs at the P1-rr (red pericarp and red cob) allele of the maize p1 (pericarp color 1) gene when exposed to a transgene containing a 1.2-kb enhancer fragment (P1.2) of P1-rr. The paramutable P1-rr allele undergoes transcriptional silencing resulting in a paramutant light-pigmented P1-rr' state. To define more precisely the sequences required to elicit paramutation, the P1.2 fragment was further subdivided, and the fragments transformed into maize plants and crossed with P1-rr. Analysis of the progeny plants showed that the sequences required for paramutation are located within a ∼600-bp segment of P1.2 and that this segment overlaps with a previously identified enhancer that is present in 4 direct repeats in P1-rr. The paramutagenic segment is transcribed in both the expressed P1-rr and the silenced P1-rr'. Transcription is sensitive to α-amanitin, indicating that RNA polymerase II mediates most of the transcription of this sequence. Although transcription within the paramutagenic sequence was similar in all tested genotypes, small RNAs were more abundant in the silenced P1-rr' epiallele relative to the expressed P1-rr allele. In agreement with prior results indicating the association of RNA-mediated DNA methylation in p1 paramutation, DNA blot analyses detected increased cytosine methylation of the paramutant P1-rr' sequences homologous to the transgenic P1.2 subfragments. Together these results demonstrate that the P1-rr enhancer repeats mediate p1 paramutation.

Genetic analysis of pericarp pigmentation variation in Corn Belt dent maize

The US standard for maize commercially grown for grain specifies that yellow corn can contain at maximum 5% corn of other colors. Inbred parents of commercial hybrids typically have clear pericarp, but transgressive segregants in breeding populations can display variation in pericarp pigmentation. We identified 10 doubled haploid biparental populations segregating for pigmented pericarp and evaluated qualitative genetic models using chi-square tests of observed and expected frequencies. Pigmentation ranged from light to dark brown color, and pigmentation intensity was quantitatively measured across 1,327 inbred lines using hue calculated from RGB pixel values. Genetic mapping was used to identify loci associated with pigmentation intensity. For 9 populations, pigmentation inheritance best fit a hypothesis of a 2- or 3-gene epistatic model. Significant differences in pigment intensity were observed across populations. W606S-derived inbred lines with the darkest pericarp often had clear glumes, suggesting the presence of a novel P1-rw allele, a hypothesis supported by a significant quantitative trait locus peak at P1. A separate quantitative trait locus region on chromosome 2 between 221.64 and 226.66 Mbp was identified in LH82-derived populations, and the peak near p1 was absent. A genome-wide association study using 416 inbred lines from the Wisconsin Diversity panel with full genome resequencing revealed 4 significant associations including the region near P1. This study supports that pericarp pigmentation among dent maize inbreds can arise by transgressive segregation when pigmentation in the parental generation is absent and is partially explained by functional allelic variation at the P1 locus.

Sugar Signals and R2R3-MYBs Participate in Potassium-Repressed Anthocyanin Accumulation in Radish

Anthocyanin biosynthesis in plants is influenced by a wide range of environmental factors, such as light, temperature and nutrient availability. In this study, we revealed that the potassium-repressed anthocyanin accumulation in radish hypocotyls was associated with altered sugar distribution and sugar signaling pathways rather than changes in oxidative stress status. Sugar-feeding experiments suggested a hexokinase-independent glucose signal acted as a major contributor in regulating anthocyanin biosynthesis, transport and regulatory genes at the transcriptional level. Several R2R3-MYBs were identified as anthocyanin-related MYBs. Phylogenetic and protein sequence analyses suggested that RsMYB75 met the criteria of subgroup 6 MYB activator, while RsMYB39 and RsMYB82 seemed to be a non-canonical MYB anthocyanin activator and repressor, respectively. Through yeast-one-hybrid, dual-luciferase and transient expression assays, we confirmed that RsMYB39 strongly induced the promoter activity of anthocyanin transport-related gene RsGSTF12, while RsMYB82 significantly reduced anthocyanin biosynthesis gene RsANS1 expression. Molecular models are proposed in the discussion, allowing speculation on how these novel RsMYBs may regulate the expression levels of anthocyanin-related structural genes. Together, our data evidenced the strong impacts of potassium on sugar metabolism and signaling and its regulation of anthocyanin accumulation through different sugar signals and R2R3-MYBs in a hierarchical regulatory system.

An LcMYB111-LcHY5 Module Differentially Activates an LcFLS Promoter in Different Litchi Cultivars

Flavonol synthase (FLS) is the crucial enzyme of the flavonol biosynthetic pathways, and its expression is tightly regulated in plants. In our previous study, two alleles of LcFLS,LcFLS-A and LcFLS-B, have been identified in litchi, with extremely early-maturing (EEM) cultivars only harboring LcFLS-A, while middle-to-late-maturing (MLM) cultivars only harbor LcFLS-B. Here, we overexpressed both LcFLS alleles in tobacco, and transgenic tobacco produced lighter-pink flowers and showed increased flavonol levels while it decreased anthocyanin levels compared to WT. Two allelic promoters of LcFLS were identified, with EEM cultivars only harboring proLcFLS-A, while MLM cultivars only harbor proLcFLS-B. One positive and three negative R2R3-MYB transcription regulators of LcFLS expression were identified, among which only positive regulator LcMYB111 showed a consistent expression pattern with LcFLS, which both have higher expression in EEM than that of MLM cultivars. LcMYB111 were further confirmed to specifically activate proLcFLS-A with MYB-binding element (MBE) while being unable to activate proLcFLS-B with mutated MBE (MBEm). LcHY5 were also identified and can interact with LcMYB111 to promote LcFLS expression. Our study elucidates the function of LcFLS and its differential regulation in different litchi cultivars for the first time.

KIPEs3: Automatic annotation of biosynthesis pathways

Flavonoids and carotenoids are pigments involved in stress mitigation and numerous other processes. Both pigment classes can contribute to flower and fruit coloration. Flavonoid aglycones and carotenoids are produced by a pathway that is largely conserved across land plants. Glycosylations, acylations, and methylations of the flavonoid aglycones can be species-specific and lead to a plethora of biochemically diverse flavonoids. We previously developed KIPEs for the automatic annotation of biosynthesis pathways and presented an application on the flavonoid aglycone biosynthesis. KIPEs3 is an improved version with additional features and the potential to identify not just the core biosynthesis players, but also candidates involved in the decoration steps and in the transport of flavonoids. Functionality of KIPEs3 is demonstrated through the analysis of the flavonoid biosynthesis in Arabidopsis thaliana Nd-1, Capsella grandiflora, and Dioscorea dumetorum. We demonstrate the applicability of KIPEs to other pathways by adding the carotenoid biosynthesis to the repertoire. As a technical proof of concept, the carotenoid biosynthesis was analyzed in the same species and Daucus carota. KIPEs3 is available as an online service to enable access without prior bioinformatics experience. KIPEs3 facilitates the automatic annotation and analysis of biosynthesis pathways with a consistent and high quality in a large number of plant species. Numerous genome sequencing projects are generating a huge amount of data sets that can be analyzed to identify evolutionary patterns and promising candidate genes for biotechnological and breeding applications.

Exploring the Relationship Between Pattern-Triggered Immunity and Quantitative Resistance to Xanthomonas vasicola pv. vasculorum in Maize

Bacterial leaf streak (BLS) of maize is an emerging foliar disease of maize in the Americas. It is caused by the gram-negative nonvascular bacterium Xanthomonas vasicola pv. vasculorum. There are no chemical controls available for BLS, and thus, host resistance is crucial for managing X. vasicola pv. vasculorum. The objective of this study was to examine the genetic determinants of resistance to X. vasicola pv. vasculorum in maize, as well as the relationship between other defense-related traits and BLS resistance. Specifically, we examined the correlations among BLS severity, severity for three fungal diseases, flg-22 response, hypersensitive response, and auricle color. We conducted quantitative trait locus (QTL) mapping for X. vasicola pv. vasculorum resistance using the maize recombinant inbred line population Z003 (B73 × CML228). We detected three QTLs for BLS resistance. In addition to the disease resistance QTL, we detected a single QTL for auricle color. We observed significant, yet weak, correlations among BLS severity, levels of pattern-triggered immunity response and leaf flecking. These results will be useful for understanding resistance to X. vasicola pv. vasculorum and mitigating the impact of BLS on maize yields.

Insights into the functional characterization of DIR proteins through genome-wide in silico and evolutionary studies: a systematic review

Dirigent proteins (DIRs) are a new class of proteins that were identified during the 8-8' lignan biosynthetic pathway and involves the formation of ( +) or ( -)-pinoresinol through stereoselective coupling from E-coniferyl alcohol. These proteins are known to play a vital role in the development and stress response in plants. Various studies have reported the functional and structural characterization of dirigent gene family in different plants using in silico approaches. Here, we have summarized the importance of dirigent proteins in plants and their role in plant stress tolerance by analyzing the genome-wide analysis including gene structure, mapping of chromosomes, phylogenetic evolution, conserved motifs, gene structure, and gene duplications in important plants. Overall, this review would help to compare and clarify the molecular and evolutionary characteristics of dirigent gene family in different plants.

Impact of High Light Intensity and Low Temperature on the Growth and Phenylpropanoid Profile of Azolla filiculoides

Exposure to high light intensity (HL) and cold treatment (CT) induces reddish pigmentation in Azolla filiculoides, an aquatic fern. Nevertheless, how these conditions, alone or in combination, influence Azolla growth and pigment synthesis remains to be fully elucidated. Likewise, the regulatory network underpinning the accumulation of flavonoids in ferns is still unclear. Here, we grew A. filiculoides under HL and/or CT conditions for 20 days and evaluated the biomass doubling time, relative growth rate, photosynthetic and non-photosynthetic pigment contents, and photosynthetic efficiency by chlorophyll fluorescence measurements. Furthermore, from the A. filiculoides genome, we mined the homologs of MYB, bHLH, and WDR genes, which form the MBW flavonoid regulatory complex in higher plants, to investigate their expression by qRT-PCR. We report that A. filiculoides optimizes photosynthesis at lower light intensities, regardless of the temperature. In addition, we show that CT does not severely hamper Azolla growth, although it causes the onset of photoinhibition. Coupling CT with HL stimulates the accumulation of flavonoids, which likely prevents irreversible photoinhibition-induced damage. Although our data do not support the formation of MBW complexes, we identified candidate MYB and bHLH regulators of flavonoids. Overall, the present findings are of fundamental and pragmatic relevance to Azolla's biology.

Fusion gene 4CL-CCR promotes lignification in tobacco suspension cells

KEY MESSAGE

The fusion gene 4CL-CCR promotes lignification and activates lignin-related MYB expression in tobacco but inhibits auxin-related gene expression and hinders the auxin absorption of cells. Given the importance of lignin polymers in plant growth and their industrial value, it is necessary to investigate how plants synthesize monolignols and regulate the level of lignin in cell walls. In our previous study, expression of the Populus tomentosa fusion gene 4CL-CCR significantly promoted the production of 4-hydroxycinnamyl alcohols. However, the function of 4CL-CCR in organisms remains poorly understood. In this study, the fusion gene 4CL-CCR was heterologously expressed in tobacco suspension cells. We found that the transgenic suspension cells exhibited lignification earlier. Furthermore, 4CL-CCR significantly reduced the content of phenolic acids and increased the content of aldehydes in the medium, which led to an increase in lignin deposition. Moreover, transcriptome results showed that the genes related to lignin synthesis, such as PAL, 4CL, CCoAOMT and CAD, were significantly upregulated in the 4CL-CCR group. The expression of genes related to auxin, such as ARF3, ARF5 and ARF6, was significantly downregulated. The downregulation of auxin affected the expression of transcription factor MYBs. We hypothesize that the upregulated genes MYB306 and MYB315 are involved in the regulation of cell morphogenesis and lignin biosynthesis and eventually enhance lignification in tobacco suspension cells. Our findings provide insight into the function of 4CL-CCR in lignification and how secondary cell walls are formed in plants.

CRISPR/Cas9-induced modification of the conservative promoter region of VRN-A1 alters the heading time of hexaploid bread wheat

In cereals, the vernalization-related gene network plays an important role in regulating the transition from the vegetative to the reproductive phase to ensure optimal reproduction in a temperate climate. In hexaploid bread wheat (Triticum aestivum L.), the spring growth habit is associated with the presence of at least one dominant locus of VERNALIZATION 1 gene (VRN-1), which usually differs from recessive alleles due to mutations in the regulatory sequences of the promoter or/and the first intron. VRN-1 gene is a key regulator of floral initiation; various combinations of dominant and recessive alleles, especially VRN-A1 homeologs, determine the differences in the timing of wheat heading/flowering. In the present study, we attempt to expand the types of VRN-A1 alleles using CRISPR/Cas9 targeted modification of the promoter sequence. Several mono- and biallelic changes were achieved within the 125-117 bp upstream sequence of the start codon of the recessive vrn-A1 gene in plants of semi-winter cv. 'Chinese Spring'. New mutations stably inherited in subsequent progenies and transgene-free homozygous plants carrying novel VRN-A1 variants were generated. Minor changes in the promoter sequence, such as 1-4 nucleotide insertions/deletions, had no effect on the heading time of plants, whereas the CRISPR/Cas9-mediated 8 bp deletion between -125 and -117 bp of the vrn-A1 promoter shortened the time of head emergence by up to 2-3 days. Such a growth habit was consistently observed in homozygous mutant plants under nonvernalized cultivation using different long day regimes (16, 18, or 22 h), whereas the cold treatment (from two weeks and more) completely leveled the effect of the 8 bp deletion. Importantly, comparison with wild-type plants showed that the implemented alteration has no negative effects on main yield characteristics. Our results demonstrate the potential to manipulate the heading time of wheat through targeted editing of the VRN-A1 gene promoter sequence on an otherwise unchanged genetic background.

Genetic Dissection of Phosphorus Use Efficiency and Genotype-by-Environment Interaction in Maize

Genotype-by-environment interaction (G-by-E) is a common but potentially problematic phenomenon in plant breeding. In this study, we investigated the genotypic performance and two measures of plasticity on a phenotypic and genetic level by assessing 234 maize doubled haploid lines from six populations for 15 traits in seven macro-environments with a focus on varying soil phosphorus levels. It was found intergenic regions contributed the most to the variation of phenotypic linear plasticity. For 15 traits, 124 and 31 quantitative trait loci (QTL) were identified for genotypic performance and phenotypic plasticity, respectively. Further, some genes associated with phosphorus use efficiency, such as Zm00001eb117170, Zm00001eb258520, and Zm00001eb265410, encode small ubiquitin-like modifier E3 ligase were identified. By significantly testing the main effect and G-by-E effect, 38 main QTL and 17 interaction QTL were identified, respectively, in which MQTL38 contained the gene Zm00001eb374120, and its effect was related to phosphorus concentration in the soil, the lower the concentration, the greater the effect. Differences in the size and sign of the QTL effect in multiple environments could account for G-by-E. At last, the superiority of G-by-E in genomic selection was observed. In summary, our findings will provide theoretical guidance for breeding P-efficient and broadly adaptable varieties.

Intracellular infection by symbiotic bacteria requires the mitotic kinase AURORA1

The subcellular events occurring in cells of legume plants as they form transcellular symbiotic-infection structures have been compared with those occurring in premitotic cells. Here, we demonstrate that Aurora kinase 1 (AUR1), a highly conserved mitotic regulator, is required for intracellular infection by rhizobia in Medicago truncatula. AUR1 interacts with microtubule-associated proteins of the TPXL and MAP65 families, which, respectively, activate and are phosphorylated by AUR1, and localizes with them within preinfection structures. MYB3R1, a rhizobia-induced mitotic transcription factor, directly regulates AUR1 through two closely spaced, mitosis-specific activator cis elements. Our data are consistent with a model in which the MYB3R1-AUR1 regulatory module serves to properly orient preinfection structures to direct the transcellular deposition of cell wall material for the growing infection thread, analogous to its role in cell plate formation. Our findings indicate that the eukaryotically conserved MYB3R1-TPXL-AUR1-MAP65 mitotic module was conscripted to support endosymbiotic infection in legumes.

Complex chromosomal rearrangements induced by transposons in maize

Eukaryotic genomes are large and complex, and gene expression can be affected by multiple regulatory elements and their positions within the dynamic chromatin architecture. Transposable elements are known to play important roles in genome evolution, yet questions remain as to how transposable elements alter genome structure and affect gene expression. Previous studies have shown that genome rearrangements can be induced by Reversed Ends Transposition involving termini of Activator and related transposable elements in maize and other plants. Here, we show that complex alleles can be formed by the rapid and progressive accumulation of Activator-induced duplications and rearrangements. The p1 gene enhancer in maize can induce ectopic expression of the nearby p2 gene in pericarp tissue when placed near it via different structural rearrangements. By screening for p2 expression, we identified and studied 5 cases in which multiple sequential transposition events occurred and increased the p1 enhancer copy number. We see active p2 expression due to multiple copies of the p1 enhancer present near p2 in all 5 cases. The p1 enhancer effects are confirmed by the observation that loss of p2 expression is correlated with transposition-induced excision of the p1 enhancers. We also performed a targeted Chromosome Conformation Capture experiment to test the physical interaction between the p1 enhancer and p2 promoter region. Together, our results show that transposon-induced rearrangements can accumulate rapidly and progressively increase genetic variation important for genomic evolution.

TDTHub, a web server tool for the analysis of transcription factor binding sites in plants

Transcriptional regulation underlies most developmental programs and physiological responses to environmental changes in plants. Transcription factors (TFs) play a key role in the regulation of gene expression by binding specifically to short DNA sequences in the regulatory regions of genes: the TF binding sites (TFBSs). In recent years, several bioinformatic tools have been developed to detect TFBSs in candidate genes, either by de novo prediction or by directly mapping experimentally known TFBSs. However, most of these tools contain information for only a few species or require multi-step procedures, and are not always intuitive for non-experienced researchers. Here we present TFBS-Discovery Tool Hub (TDTHub), a web server for quick and intuitive studies of transcriptional regulation in plants. TDTHub uses pre-computed TFBSs in 40 plant species and allows the choice of two mapping algorithms, providing a higher versatility. Besides the main TFBS enrichment tool, TDTHub includes additional tools to assist in the analysis and visualization of data. In order to demonstrate the effectiveness of TDTHub, we analyzed the transcriptional regulation of the anthocyanin biosynthesis pathway. We also analyzed the transcriptional cascades in response to jasmonate and wounding in Arabidopsis and tomato (Solanum lycopersicum), respectively. In these studies, TDTHub helped to verify the most relevant TF nodes and to propose new ones with a prominent role in these pathways. TDTHub is available at http://acrab.cnb.csic.es/TDTHub/, and it will be periodically upgraded and expanded for new species and gene annotations.

Excision and reinsertion of Ac macrotransposons in maize

Eukaryotic Macrotransposons (MTns) can be formed by 2 nearby elements flanking a segment of host DNA. The maize Ac transposon can form Ac::MTns, but little is known about Ac::MTn transposition activities. Here, we studied 3 Ac::MTns at the maize p1 locus, each of which is composed of a segment of maize p1 genomic DNA (up to 15 kb) bounded by a fractured Ac element (fAc, 2039 bp), and a full-length Ac element in direct orientation. The resulting Ac::MTns are of 16, 16.5, and 22 kb total length. From these 3 Ac::MTns, we identified 10 independent cases of macrotransposition, and observed similar features of transposition between Ac::MTn and standard Ac/Ds, including characteristic excision footprints and insertion target site duplications. Nine out of the 10 Ac::MTn reinsertion targets were genetically linked to the donor sites, another similarity with Ac/Ds standard transposition. We also identified a MTn-like structure in the maize B73 reference genome and 5 NAM founder lines. The MTn in diverse lines is flanked by target site duplications, confirming the historic occurrence of MTn transposition during genome evolution. Our results show that Ac::MTns are capable of mobilizing segments of DNA long enough to include a typical full-length plant gene and in theory could erode gene colinearity in syntenic regions during plant genome evolution.

EbMYBP1, a R2R3-MYB transcription factor, promotes flavonoid biosynthesis in Erigeron breviscapus

Erigeron breviscapus, a traditional Chinese medicinal plant, is enriched in flavonoids that are beneficial to human health. While we know that R2R3-MYB transcription factors (TFs) are crucial to flavonoid pathway, the transcriptional regulation of flavonoid biosynthesis in E. breviscapus has not been fully elucidated. Here, EbMYBP1, a R2R3-MYB transcription factor, was uncovered as a regulator involved in the regulation of flavonoid accumulation. Transcriptome and metabolome analysis revealed that a large group of genes related to flavonoid biosynthesis were significantly changed, accompanied by significantly increased concentrations of the flavonoid in EbMYBP1-OE transgenic tobacco compared with the wild-type (WT). In vitro and in vivo investigations showed that EbMYBP1 participated in flavonoid biosynthesis, acting as a nucleus-localized transcriptional activator and activating the transcription of flavonoid-associated genes like FLS, F3H, CHS, and CHI by directly binding to their promoters. Collectively, these new findings are advancing our understanding of the transcriptional regulation that modulates the flavonoid biosynthesis.

Molecular components associated with the regulation of flavonoid biosynthesis

Flavonoids exhibit amazing structural diversity and play different roles in plants. Besides, these compounds have been associated with several health benefits in humans. Several exogenous and endogenous cues, for example, light, temperature, nutrient status, and phytohormones have been reported as modulators of biosynthesis and accumulation of flavonoids. Thus, multiple hormones and stress-related signaling pathways are involved in the regulation of gene expression associated with this pathway. The transcriptional regulators belonging to the MYB and bHLH family transcription factors are well documented as the direct regulators of the structural genes associated with flavonoid biosynthesis. Recent studies also suggest that some of these factors are regulated by molecular components involved in stress and hormone signaling pathways. Adapter proteins for transcriptional activation or repression via recruitment of co-activators and co-repressors, respectively, E2 ubiquitin ligases, miRNA processing complex, and DNA methylation/demethylation factors have been recently discovered in various plants to play key roles in fine-tuning flavonoids synthesis. In the present review, we aim to provide comprehensive information about the role of different factors in the regulation of flavonoid biosynthesis. Besides, we describe the potential upstream regulators involved in the regulation of flavonoid biosynthesis within the context of available information. To sum up, the present review furnishes an updated account of signal transduction pathways modulating the biosynthesis of flavonoids.

Identification and Expression Analysis of R2R3-MYB Family Genes Associated with Salt Tolerance in Cyclocarya paliurus

R2R3-MYB transcription factors are most abundant in the MYB superfamily, while the R2R3-MYB genes play an important role in plant growth and development, especially in response to environmental stress. Cyclocarya paliurus is a multifunction tree species, and the existing resources cannot meet the requirement for its leaf production and medical use. Therefore, lands with some environmental stresses would be potential sites for developing C. paliurus plantations. However, the function of R2R3-MYB genes in C.paliurus in response to environmental stress remains unknown. In this study, to identify the roles of R2R3-MYB genes associated with salt stress response, 153 CpaMYB genes and their corresponding protein sequences were identified from the full-length transcriptome. Based on the comparison with MYB protein sequences of Arabidopsis thaliana, 69 R2R3-MYB proteins in C. paliurus were extracted for further screening combined with conserved functional domains. Furthermore, the MYB family members were analyzed from the aspects of protein sequences alignment, evolution, motif prediction, promoter cis-acting element analysis, and gene differential expression under different salt treatments using both a pot experiment and hydroponic experiment. The results showed that the R2R3-MYB genes of C.paliurus conserved functional domains, whereas four R2R3-MYB genes that might respond to salt stress via regulating plant hormone signals were identified in this study. This work provides a basis for further functional characterization of R2R3-MYB TFs in C. paliurus.

CmMYB9a activates floral coloration by positively regulating anthocyanin biosynthesis in chrysanthemum

KEY MESSAGE

An R2R3-MYB transcription factor, CmMYB9a, activates floral coloration in chrysanthemum by positively regulating CmCHS, CmDFR and CmFNS, but inhibiting the expression of CmFLS. Chrysanthemum is one of the most popular ornamental plants worldwide. Flavonoids, such as anthocyanins, flavones, and flavonols, are important secondary metabolites for coloration and are involved in many biological processes in plants, like petunia, snapdragon, Gerbera hybrida, as well as chrysanthemum. However, the metabolic regulation of flavonoids contributing to chrysanthemum floral coloration remains largely unexplored. Here, an R2R3-MYB transcription factor, CmMYB9a, was found to be involved in flavonoid biosynthesis. Phylogenetic analysis and amino acid sequence analysis suggested that CmMYB9a belonged to subgroup 7. Transient overexpression of CmMYB9a in flowers of chrysanthemum cultivar 'Anastasia Pink' upregulated the anthocyanin-related and flavone-related genes and downregulated CmFLS, which led to the accumulation of anthocyanins and flavones. We further demonstrated that CmMYB9a independently activates the expression of CmCHS, CmDFR and CmFNS, but inhibits the expression of CmFLS. Overexpression of CmMYB9a in tobacco resulted in increased anthocyanins and decreased flavonols in the petals by upregulating NtDFR and downregulating NtFLS. These results suggest that CmMYB9a facilitates metabolic flux into anthocyanin and flavone biosynthesis. Taken together, this study functionally characterizes the role of CmMYB9a in regulating the branched pathways of flavonoids in chrysanthemum flowers.

Genome-Wide Association Study of Root Mealiness and Other Texture-Associated Traits in Cassava

Cassava breeders have made significant progress in developing new genotypes with improved agronomic characteristics such as improved root yield and resistance against biotic and abiotic stresses. However, these new and improved cassava (Manihot esculenta Crantz) varieties in cultivation in Nigeria have undergone little or no improvement in their culinary qualities; hence, there is a paucity of genetic information regarding the texture of boiled cassava, particularly with respect to its mealiness, the principal sensory quality attribute of boiled cassava roots. The current study aimed at identifying genomic regions and polymorphisms associated with natural variation for root mealiness and other texture-related attributes of boiled cassava roots, which includes fibre, adhesiveness (ADH), taste, aroma, colour, and firmness. We performed a genome-wide association (GWAS) analysis using phenotypic data from a panel of 142 accessions obtained from the National Root Crops Research Institute (NRCRI), Umudike, Nigeria, and a set of 59,792 high-quality single nucleotide polymorphisms (SNPs) distributed across the cassava genome. Through genome-wide association mapping, we identified 80 SNPs that were significantly associated with root mealiness, fibre, adhesiveness, taste, aroma, colour and firmness on chromosomes 1, 4, 5, 6, 10, 13, 17 and 18. We also identified relevant candidate genes that are co-located with peak SNPs linked to these traits in M. esculenta. A survey of the cassava reference genome v6.1 positioned the SNPs on chromosome 13 in the vicinity of Manes.13G026900, a gene recognized as being responsible for cell adhesion and for the mealiness or crispness of vegetables and fruits, and also known to play an important role in cooked potato texture. This study provides the first insights into understanding the underlying genetic basis of boiled cassava root texture. After validation, the markers and candidate genes identified in this novel work could provide important genomic resources for use in marker-assisted selection (MAS) and genomic selection (GS) to accelerate genetic improvement of root mealiness and other culinary qualities in cassava breeding programmes in West Africa, especially in Nigeria, where the consumption of boiled and pounded cassava is low.

Genome-Wide Identification and Expression Analysis of R2R3-MYB Family Genes Associated with Petal Pigment Synthesis in Liriodendron

The MYB transcription factor family is one of the largest families in plants, and its members have various biological functions. R2R3-MYB genes are involved in the synthesis of pigments that yield petal colors. Liriodendron plants are widely cultivated as ornamental trees owing to their peculiar leaves, tulip-like flowers, and colorful petals. However, the mechanism underlying petal coloring in this species is unknown, and minimal information about MYB genes in Liriodendron is available. Herein, this study aimed to discern gene(s) involved in petal coloration in Liriodendron via genome-wide identification, HPLC, and RT-qPCR assays. In total, 204 LcMYB superfamily genes were identified in the Liriodendron chinense genome, and 85 R2R3-MYB genes were mapped onto 19 chromosomes. Chromosome 4 contained the most (10) R2R3-MYB genes, and chromosomes 14 and 16 contained the fewest (only one). MEME analysis showed that R2R3-MYB proteins in L. chinense were highly conserved and that their exon-intron structures varied. The HPLC results showed that three major carotenoids were uniformly distributed in the petals of L. chinense, while lycopene and β-carotene were concentrated in the orange band region in the petals of Liriodendron tulipifera. Furthermore, the expression profiles via RT-qPCR assays revealed that four R2R3-MYB genes were expressed at the highest levels at the S3P/S4P stage in L. tulipifera. This result combined with the HPLC results showed that these four R2R3-MYB genes might participate in carotenoid synthesis in the petals of L. tulipifera. This work laid a cornerstone for further functional characterization of R2R3-MYB genes in Liriodendron plants.

Methyl jasmonate elicits distinctive hydrolyzable tannin, flavonoid, and phyto-oxylipin responses in pomegranate (Punica granatum L.) leaves

Transcriptome and biochemical analyses suggested that, while suppression of multiple flavonoids and anthocyanins occurs at least partially at the transcriptional level, increased biosynthesis of non-jasmonate phyto-oxylipins is likely controlled non-transcriptionally. Methyl jasmonate (MeJA) produced in plants can mediate their response to environmental stresses. Exogenous application of MeJA has also shown to activate signaling pathways and induce phytoalexin accumulation in many plant species. To understand how pomegranate plants respond biochemically to environmental stresses, metabolite analysis was conducted in pomegranate leaves subjected to MeJA application and revealed unique changes in hydrolyzable tannins, flavonoids, and phyto-oxylipins. Additionally, transcriptome and real-time qPCR analyses of mock- and MeJA-treated pomegranate leaves identified differentially expressed metabolic genes and transcription factors that are potentially involved in the control of hydrolyzable tannin, flavonoid, and phyto-oxylipin pathways. Molecular, biochemical, and bioinformatic characterization of the only lipoxygenase with sustained, MeJA-induced expression showed that it is capable of oxidizing polyunsaturated fatty acids, though not located in the subcellular compartment where non-jasmonate (non-JA) phyto-oxylipins were produced. These results collectively suggested that while the broad suppression of flavonoids and anthocyanins is at least partially controlled at the transcriptional level, the induced biosynthesis of non-JA phyto-oxylipins is likely not regulated transcriptionally. Overall, a better understanding of how pomegranate leaves respond to environmental stresses will not only promote plant health and productivity, but also have an impact on human health as fruits produced by pomegranate plants are a rich source of nutritional compounds.

Playing with colours: genetics and regulatory mechanisms for anthocyanin pathway in cereals

Cereals form the most important source of energy in our food. Currently, demand for coloured food grains is significantly increasing globally because of their antioxidant properties and enhanced nutritional value. Coloured grains of major and minor cereals are due to accumulation of secondary metabolites like carotenoids and flavonoids such as anthocyanin, proanthocyanin, phlobaphenes in pericarp, aleurone, lemma, testa or seed coat of grains. Differential accumulation of colour in grains is regulated by several regulatory proteins and enzymes involved in flavonoid and caroteniod biosynthesis. MYB and bHLH gene family members are the major regulators of these pathways. Genes for colour across various cereals have been extensively studied; however, only a few functional and allele-specific markers to be utilized directly in breeding programmes are reported so far. In this review, while briefly discussing the well studied and explored carotenoid pathway, we focus on a much more complex anthocyanin pathway that is found across cereals. The genes and their orthologs that are responsible for encoding key regulators of anthocyanin biosynthesis are discussed. This review also focuses on the genetic factors that influence colour change in different cereal crops, and the available/reported markers that can be used in breeding programs for utilizing this pathway for enhancing food and nutritional security.

Maize unstable factor for orange1 is essential for endosperm development and carbohydrate accumulation

Maize (Zea mays L.) Ufo1-1 is a spontaneous dominant mutation of the unstable factor for orange1 (ufo1). We recently cloned ufo1, which is a Poaceae-specific gene highly expressed during seed development in maize. Here, we have characterized Ufo1-1 and a loss-of-function Ds insertion allele (ufo1-Dsg) to decipher the role of ufo1 in maize. We found that both ufo1 mutant alleles impact sugars and hormones, and have defects in the basal endosperm transfer layer (BETL) and adjacent cell types. The Ufo1-1 BETL had reduced cell elongation and cell wall ingrowth, resulting in cuboidal shaped transfer cells. In contrast, the ufo1-Dsg BETL cells showed a reduced overall size with abnormal wall ingrowth. Expression analysis identified the impact of ufo1 on several genes essential for BETL development. The overexpression of Ufo1-1 in various tissues leads to ectopic phenotypes, including abnormal cell organization and stomata subsidiary cell defects. Interestingly, pericarp and leaf transcriptomes also showed that as compared with wild type, Ufo1-1 had ectopic expression of endosperm development-specific genes. This study shows that Ufo1-1 impacts the expression patterns of a wide range of genes involved in various developmental processes.

OsMYB3 is a R2R3-MYB gene responsible for anthocyanin biosynthesis in black rice

Black rice is a rare type of rice germplasm with various health benefits that are largely attributed to anthocyanin pigment accumulation in the pericarps. The anthocyanin biosynthesis in plant tissues is activated mainly by the MBW complexes, consisting of three types of transcription factors R2R3-MYB, bHLH, and WDR. In black rice, the bHLH and WDR components regulating anthocyanin biosynthesis in pericarps have been characterized, while the R2R3-MYB factor remains unknown. By examining the expression correlation between all putative rice MYB genes and anthocyanin biosynthesis-related genes based on transcriptome data of pericarps in combination with further molecular and genetic analysis, we proved that OsMYB3 (LOC_Os03g29614) was the determinant R2R3-MYB gene for anthocyanin biosynthesis in rice pericarps. The expression level of OsMYB3 in pericarps of black rice was significantly higher than that of white rice. The knockout of OsMYB3 in a black rice variety caused significant downregulation of 19 anthocyanin metabolites and many other flavonoids in grains. Our research deepens the understanding of regulatory system for anthocyanin biosynthesis in rice pericarps and provides implications for breeding black rice varieties with high anthocyanin level.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01244-x.

Transposon-induced inversions activate gene expression in the maize pericarp

Chromosomal inversions can have considerable biological and agronomic impacts including disrupted gene function, change in gene expression, and inhibited recombination. Here, we describe the molecular structure and functional impact of six inversions caused by Alternative Transpositions between p1 and p2 genes responsible for floral pigmentation in maize. In maize line p1-wwB54, the p1 gene is null and the p2 gene is expressed in anther and silk but not in pericarp, making the kernels white. By screening for kernels with red pericarp, we identified inversions in this region caused by transposition of Ac and fractured Ac (fAc) transposable elements. We hypothesize that these inversions place the p2 gene promoter near a p1 gene enhancer, thereby activating p2 expression in kernel pericarp. To our knowledge, this is the first report of multiple recurrent inversions that change the position of a gene promoter relative to an enhancer to induce ectopic expression in a eukaryote.

Chromosome-level genome assembly of a regenerable maize inbred line A188

BACKGROUND

The maize inbred line A188 is an attractive model for elucidation of gene function and improvement due to its high embryogenic capacity and many contrasting traits to the first maize reference genome, B73, and other elite lines. The lack of a genome assembly of A188 limits its use as a model for functional studies.

RESULTS

Here, we present a chromosome-level genome assembly of A188 using long reads and optical maps. Comparison of A188 with B73 using both whole-genome alignments and read depths from sequencing reads identify approximately 1.1 Gb of syntenic sequences as well as extensive structural variation, including a 1.8-Mb duplication containing the Gametophyte factor1 locus for unilateral cross-incompatibility, and six inversions of 0.7 Mb or greater. Increased copy number of carotenoid cleavage dioxygenase 1 (ccd1) in A188 is associated with elevated expression during seed development. High ccd1 expression in seeds together with low expression of yellow endosperm 1 (y1) reduces carotenoid accumulation, accounting for the white seed phenotype of A188. Furthermore, transcriptome and epigenome analyses reveal enhanced expression of defense pathways and altered DNA methylation patterns of the embryonic callus.

CONCLUSIONS

The A188 genome assembly provides a high-resolution sequence for a complex genome species and a foundational resource for analyses of genome variation and gene function in maize. The genome, in comparison to B73, contains extensive intra-species structural variations and other genetic differences. Expression and network analyses identify discrete profiles for embryonic callus and other tissues.

Myb10-D confers PHS-3D resistance to pre-harvest sprouting by regulating NCED in ABA biosynthesis pathway of wheat

Pre-harvest sprouting (PHS), the germination of grain before harvest, is a serious problem resulting in wheat yield and quality losses. Here, we mapped the PHS resistance gene PHS-3D from synthetic hexaploid wheat to a 2.4 Mb presence-absence variation (PAV) region and found that its resistance effect was attributed to the pleiotropic Myb10-D by integrated omics and functional analyses. Three haplotypes were detected in this PAV region among 262 worldwide wheat lines and 16 Aegilops tauschii, and the germination percentages of wheat lines containing Myb10-D was approximately 40% lower than that of the other lines. Transcriptome and metabolome profiling indicated that Myb10-D affected the transcription of genes in both the flavonoid and abscisic acid (ABA) biosynthesis pathways, which resulted in increases in flavonoids and ABA in transgenic wheat lines. Myb10-D activates 9-cis-epoxycarotenoid dioxygenase (NCED) by biding the secondary wall MYB-responsive element (SMRE) to promote ABA biosynthesis in early wheat seed development stages. We revealed that the newly discovered function of Myb10-D confers PHS resistance by enhancing ABA biosynthesis to delay germination in wheat. The PAV harboring Myb10-D associated with grain color and PHS will be useful for understanding and selecting white grained PHS resistant wheat cultivars.

Population genomics and haplotype analysis in spelt and bread wheat identifies a gene regulating glume color

The cloning of agriculturally important genes is often complicated by haplotype variation across crop cultivars. Access to pan-genome information greatly facilitates the assessment of structural variations and rapid candidate gene identification. Here, we identified the red glume 1 (Rg-B1) gene using association genetics and haplotype analyses in ten reference grade wheat genomes. Glume color is an important trait to characterize wheat cultivars. Red glumes are frequent among Central European spelt, a dominant wheat subspecies in Europe before the 20th century. We used genotyping-by-sequencing to characterize a global diversity panel of 267 spelt accessions, which provided evidence for two independent introductions of spelt into Europe. A single region at the Rg-B1 locus on chromosome 1BS was associated with glume color in the diversity panel. Haplotype comparisons across ten high-quality wheat genomes revealed a MYB transcription factor as candidate gene. We found extensive haplotype variation across the ten cultivars, with a particular group of MYB alleles that was conserved in red glume wheat cultivars. Genetic mapping and transient infiltration experiments allowed us to validate this particular MYB transcription factor variants. Our study demonstrates the value of multiple high-quality genomes to rapidly resolve copy number and haplotype variations in regions controlling agriculturally important traits.

MYB-Mediated Regulation of Anthocyanin Biosynthesis

Anthocyanins are natural water-soluble pigments that are important in plants because they endow a variety of colors to vegetative tissues and reproductive plant organs, mainly ranging from red to purple and blue. The colors regulated by anthocyanins give plants different visual effects through different biosynthetic pathways that provide pigmentation for flowers, fruits and seeds to attract pollinators and seed dispersers. The biosynthesis of anthocyanins is genetically determined by structural and regulatory genes. MYB (v-myb avian myeloblastosis viral oncogene homolog) proteins are important transcriptional regulators that play important roles in the regulation of plant secondary metabolism. MYB transcription factors (TFs) occupy a dominant position in the regulatory network of anthocyanin biosynthesis. The TF conserved binding motifs can be combined with other TFs to regulate the enrichment and sedimentation of anthocyanins. In this study, the regulation of anthocyanin biosynthetic mechanisms of MYB-TFs are discussed. The role of the environment in the control of the anthocyanin biosynthesis network is summarized, the complex formation of anthocyanins and the mechanism of environment-induced anthocyanin synthesis are analyzed. Some prospects for MYB-TF to modulate the comprehensive regulation of anthocyanins are put forward, to provide a more relevant basis for further research in this field, and to guide the directed genetic modification of anthocyanins for the improvement of crops for food quality, nutrition and human health.

Linking anthocyanin diversity, hue, and genetics in purple corn

While maize with anthocyanin-rich pericarp (purple corn) is rising in popularity as a source of natural colorant for foods and beverages, information on color range and stability-factors associated with anthocyanin decorations and compositional profiles-is currently limited. Furthermore, to maximize the scalability and meet growing demands, both anthocyanin concentrations and agronomic performance must improve in purple corn varieties. Using the natural anthocyanin diversity present in a purple corn landrace, Apache Red, we generated a population with variable flavonoid profiles-flavanol-anthocyanin condensed forms (0-83%), acylated anthocyanins (2-72%), pelargonidin-derived anthocyanins (5-99%), C-glycosyl flavone co-pigments up to 1904 µg/g, and with anthocyanin content up to 1598 µg/g. Each aspect of the flavonoid profiles was found to play a role in either the resulting extract hue or intensity. With genotyping-by-sequencing of this population, we mapped aspects of the flavonoid profile. Major quantitative trait loci (QTLs) for anthocyanin type were found near loci previously identified only in aleurone-pigmented maize varieties [Purple aleurone1 (Pr1) and Anthocyanin acyltransferase1 (Aat1)]. A QTL near P1 (Pericarp color1) was found for both flavone content and flavanol-anthocyanin condensed forms. A significant QTL associated with peonidin-derived anthocyanins near a candidate S-adenosylmethionine-dependent methyltransferase was also identified, warranting further investigation. Mapping total anthocyanin content produced signals near Aat1, the aleurone-associated bHLH R1 (Colored1), the plant color-associated MYB, Pl1 (Purple plant1), the aleurone-associated recessive intensifier, In1 (Intensifier1), and several previously unidentified candidates. This population represents one of the most anthocyanin diverse pericarp-pigmented maize varieties characterized to date. Moreover, the candidates identified here will serve as branching points for future research studying the genetic and molecular processes determining anthocyanin profile in pericarp.

MdMYB114 regulates anthocyanin biosynthesis and functions downstream of MdbZIP4-like in apple fruit

Anthocyanins, a major class of compounds derived from the flavonoid pathway, are important pigments of apple fruit. They can also prevent certain diseases and are beneficial to human health. Fruit pigmentation is a key quality trait that influences consumer preference; therefore, it is of great importance to investigate its regulatory mechanism. Here, we identified a MYB transcription factor (TF), MdMYB114, whose transcript level increased in the skin of the deep red apple fruit. It was determined to belong to the R2R3-MYB TF family and was localized in the nucleus. MdMYB114 overexpression led to anthocyanin accumulation in apple calli. MdMYB114 was not able to form an MBW complex but could enhance anthocyanin biosynthesis and transport by directly binding to the promoters of MdANS, MdUFGT, and MdGST to promote their expression. In addition, multiple assays revealed that MdbZIP4-like, a basic leucine-zipper TF, could directly bind to the MdMYB114 promoter to enhance its expression. Taken collectively, our results provide evidence that MdMYB114 is a positive regulator of anthocyanin biosynthesis and transport and it functions downstream of MdbZIP4-like in apple fruit.

Characterization of Maize Near-Isogenic Lines With Enhanced Flavonoid Expression to Be Used as Tools in Diet-Health Complexity

Increasing incidence of chronic diseases in the 21st century has emphasized the importance of developing crops with enhanced nutritional value. Plant-based diets are associated with reduced incidence of many chronic diseases. The growing population and increased food demand have prioritized the development of high-yielding commercial crop varieties at the expense of natural flavors as well as health-benefiting compounds including polyphenols. Flavonoids are a large subfamily of polyphenols abundant in the plant kingdom with known health-promoting effects, making them a promising trait to be re-introduced into elite lines. Given the vast array of flavonoids and the complexity of plant food metabolome interactions, it is difficult to identify with certainty the specific class(es) of flavonoids in the food matrix that are anti-inflammatory. To address this, we have developed four maize near-isogenic lines (NILs); a line that lacked both anthocyanins and phlobaphenes, a second NIL containing phlobaphenes, a third line had anthocyanins, and a fourth line that contained both anthocyanins and phlobaphenes. The phytochemical profiles and the antioxidant potential of the NILs were characterized. The accumulation of anthocyanins and phlobaphenes contributed significantly to antioxidant capacity compared to maize lines that lacked one or both of the compounds (p < 0.05). Pilot study showed that intake of flavonoid-rich maize diets were able to alleviate experimental colitis in mice. These NILs offer novel materials combining anthocyanins and phlobaphenes and can be used as powerful tools to investigate the disease-preventive effects of specific flavonoid compound in diet/feeding experiments.

Contribution of phenylpropanoid metabolism to plant development and plant-environment interactions

Phenylpropanoid metabolism is one of the most important metabolisms in plants, yielding more than 8,000 metabolites contributing to plant development and plant-environment interplay. Phenylpropanoid metabolism materialized during the evolution of early freshwater algae that were initiating terrestrialization and land plants have evolved multiple branches of this pathway, which give rise to metabolites including lignin, flavonoids, lignans, phenylpropanoid esters, hydroxycinnamic acid amides, and sporopollenin. Recent studies have revealed that many factors participate in the regulation of phenylpropanoid metabolism, and modulate phenylpropanoid homeostasis when plants undergo successive developmental processes and are subjected to stressful environments. In this review, we summarize recent progress on elucidating the contribution of phenylpropanoid metabolism to the coordination of plant development and plant-environment interaction, and metabolic flux redirection among diverse metabolic routes. In addition, our review focuses on the regulation of phenylpropanoid metabolism at the transcriptional, post-transcriptional, post-translational, and epigenetic levels, and in response to phytohormones and biotic and abiotic stresses.

Identification of MBW Complex Components Implicated in the Biosynthesis of Flavonoids in Woodland Strawberry

Flavonoids belong to the family of polyphenolic secondary metabolites and contribute to fruit quality traits. It has been shown that MBW complexes (MYB-bHLH-WD40) regulate the flavonoids biosynthesis in different plants, but only a limited number of MBW complexes have been identified in strawberry species in general. In this study, we identified 112 R2R3-MYB proteins in woodland strawberry; 12 of them were found to have potential functions in regulating flavonoids biosynthesis by phylogenetic analysis. qRT-PCR assays showed that FvMYB3, FvMYB9, FvMYB11, FvMYB22, FvMYB64, and FvMYB105 mostly expressed at green stage of fruit development, aligned with proanthocyanidins accumulation; FvMYB10 and FvMYB41 showed higher expression levels at turning and ripe stages, aligned with anthocyanins accumulation. These results suggest that different MYBs might be involved in flavonoids biosynthesis at specific stages. Furthermore, FvMYB proteins were demonstrated to interact with FvbHLH proteins and induce expression from the promoters of CHS2 and DFR2 genes, which encode key enzymes in flavonoids biosynthesis. The co-expression of FvMYB and FvbHLH proteins in strawberry fruits also promoted the accumulation of proanthocyanidins. These findings confirmed and provided insights into the biofunction of MBW components in the regulation of flavonoid biosynthesis in woodland strawberry.

The FUSED LEAVES1-ADHERENT1 regulatory module is required for maize cuticle development and organ separation

All aerial epidermal cells in land plants are covered by the cuticle, an extracellular hydrophobic layer that provides protection against abiotic and biotic stresses and prevents organ fusion during development. Genetic and morphological analysis of the classic maize adherent1 (ad1) mutant was combined with genome-wide binding analysis of the maize MYB transcription factor FUSED LEAVES1 (FDL1), coupled with transcriptional profiling of fdl1 mutants. We show that AD1 encodes an epidermally-expressed 3-KETOACYL-CoA SYNTHASE (KCS) belonging to a functionally uncharacterized clade of KCS enzymes involved in cuticular wax biosynthesis. Wax analysis in ad1 mutants indicates that AD1 functions in the formation of very-long-chain wax components. We demonstrate that FDL1 directly binds to CCAACC core motifs present in AD1 regulatory regions to activate its expression. Over 2000 additional target genes of FDL1, including many involved in cuticle formation, drought response and cell wall organization, were also identified. Our results identify a regulatory module of cuticle biosynthesis in maize that is conserved across monocots and eudicots, and highlight previously undescribed factors in lipid metabolism, transport and signaling that coordinate organ development and cuticle formation.

JA-Responsive Transcription Factor SmMYB97 Promotes Phenolic Acid and Tanshinone Accumulation in Salvia miltiorrhiza

Phenolic acids and tanshinones are active principles in Salvia miltiorrhiza Bunge administered for cardiovascular and cerebrovascular diseases. Jasmonic acid (JA) promotes secondary metabolite accumulation, but the regulatory mechanism is unknown in S. miltiorrhiza. We identified and characterized the JA-responsive gene SmMYB97. Multiple sequence alignment and phylogenetic tree analyses showed that SmMYB97 was clustered with AtMYB11, AtMYB12, and ZmP1 in the subgroup S7 regulating flavonol biosynthesis. SmMYB97 was highly expressed in S. miltiorrhiza leaves and induced by methyl jasmonate (MeJA). SmMYB97 was localized in the nucleus and had strong transcriptional activation activity. SmMYB97 overexpression increased phenolic acid and tanshinone biosynthesis and upregulated the genes implicated in these processes. Yeast one-hybrid and transient transcriptional activity assays disclosed that SmMYB97 binds the PAL1, TAT1, CPS1, and KSL1 promoter regions. SmJAZ8 interacts with SmMYB97 and downregulates the genes that it controls. This study partially clarified the regulatory network of MeJA-mediated secondary metabolite biosynthesis in S. miltiorrhiza.

Transcription Factors Rc and OsVP1 Coordinately Regulate Preharvest Sprouting Tolerance in Red Pericarp Rice

Red pericarp associates with seed dormancy or preharvest sprouting (PHS) tolerance in crops. To identify this association's molecular mechanism, a PHS mutant Osviviparous1 (Osvp1) was characterized in rice and crossed with Kasalath, a red pericarp cultivar with Rc (red coleoptiles) genotype. Among the dehulled seeds of F₂ progenies, RcRcvp1vp1 seeds performed a lower PHS rate than rcrcvp1vp1 seeds and showed shallower pigmentation than RcRcVP1VP1 seeds. Kasalath and SL9 (an RcRcVP1VP1 substitution line with Nipponbare background) showed more ABA sensitivity than the Nipponbare (rcrcVP1VP1) by the germination assay, and the transcriptional abundance of ABA signal genes OsABI2, OsSnRK2, OsVP1, ABI5, and especially OsVP1 increased in the red pericarp line SL9. Moreover, OsVP1 can directly bind Rc (bHLH) promoter by yeast one-hybrid, which activates Rc and OsLAR expression in red pericarp rice. Furthermore, a luciferase complementation imaging assay showed that OsVP1 interacts with transcriptions factors Rc and OsC1. These results indicate that OsVP1 promotes proanthocyanidin accumulation through the interaction among OsVP1, Rc, and OsC1 and then increases the plant's ABA sensitivity and PHS resistance.

Ectopic Expression of a Maize Gene Is Induced by Composite Insertions Generated Through Alternative Transposition

Transposable elements (TEs) are DNA sequences that can mobilize and proliferate throughout eukaryotic genomes. Previous studies have shown that in plant genomes, TEs can influence gene expression in various ways, such as inserting in introns or exons to alter transcript structure and content, and providing novel promoters and regulatory elements to generate new regulatory patterns. Furthermore, TEs can also regulate gene expression at the epigenetic level by modifying chromatin structure, changing DNA methylation status, and generating small RNAs. In this study, we demonstrated that Ac/fractured Ac (fAc) TEs are able to induce ectopic gene expression by duplicating and shuffling enhancer elements. Ac/fAc elements belong to the hAT family of class II TEs. They can undergo standard transposition events, which involve the two termini of a single transposon, or alternative transposition events that involve the termini of two different nearby elements. Our previous studies have shown that alternative transposition can generate various genome rearrangements such as deletions, duplications, inversions, translocations, and composite insertions (CIs). We identified >50 independent cases of CIs generated by Ac/fAc alternative transposition and analyzed 10 of them in detail. We show that these CIs induced ectopic expression of the maize pericarp color 2 (p2) gene, which encodes a Myb-related protein. All the CIs analyzed contain sequences including a transcriptional enhancer derived from the nearby p1 gene, suggesting that the CI-induced activation of p2 is affected by mobilization of the p1 enhancer. This is further supported by analysis of a mutant in which the CI is excised and p2 expression is lost. These results show that alternative transposition events are not only able to induce genome rearrangements, but also generate CIs that can control gene expression.