Cleistogamous flowering in barley arises from the suppression of microRNA-guided HvAP2 mRNA cleavage

Identification of microRNAs and their target genes associated with chasmogamous and cleistogamous flower development in Viola prionantha

MAIN CONCLUSION

Differentially expressed microRNAs were found associated with the development of chasmogamous and cleistogamous flowers in Viola prionantha, revealing potential roles of microRNAs in the developmental evolution of dimorphic flowers. In Viola prionantha, chasmogamous (CH) flowers are induced by short daylight, while cleistogamous (CL) flowers are triggered by long daylight. How environmental factors and microRNAs (miRNAs) affect dimorphic flower formation remains unknown. In this study, small RNA sequencing was performed on CH and CL floral buds at different developmental stages in V. prionantha, differentially expressed miRNAs (DEmiRNAs) were identified, and their target genes were predicted. In CL flowers, Viola prionantha miR393 (vpr-miR393a/b) and vpr-miRN3366 were highly expressed, while in CH flowers, vpr-miRN2005, vpr-miR172e-2, vpr-miR166m-3, vpr-miR396f-2, and vpr-miR482d-2 were highly expressed. In the auxin-activated signaling pathway, vpr-miR393a/b and vpr-miRN2005 could target Vpr-TIR1/AFB and Vpr-ARF2, respectively, and other DEmiRNAs could target genes involved in the regulation of transcription, e.g., Vpr-AP2-7. Moreover, Vpr-UFO and Vpr-YAB5, the main regulators in petal and stamen development, were co-expressed with Vpr-TIR1/AFB and Vpr-ARF2 and showed lower expression in CL flowers than in CH flowers. Some V. prionantha genes relating to the stress/defense responses were co-expressed with Vpr-TIR1/AFB, Vpr-ARF2, and Vpr-AP2-7 and highly expressed in CL flowers. Therefore, in V. prionantha, CH-CL flower development may be regulated by the identified DEmiRNAs and their target genes, thus providing the first insight into the formation of dimorphic flowers in Viola.

A guide to barley mutants

BACKGROUND

Mutants have had a fundamental impact upon scientific and applied genetics. They have paved the way for the molecular and genomic era, and most of today's crop plants are derived from breeding programs involving mutagenic treatments.

RESULTS

Barley (Hordeum vulgare L.) is one of the most widely grown cereals in the world and has a long history as a crop plant. Barley breeding started more than 100 years ago and large breeding programs have collected and generated a wide range of natural and induced mutants, which often were deposited in genebanks around the world. In recent years, an increased interest in genetic diversity has brought many historic mutants into focus because the collections are regarded as valuable resources for understanding the genetic control of barley biology and barley breeding. The increased interest has been fueled also by recent advances in genomic research, which provided new tools and possibilities to analyze and reveal the genetic diversity of mutant collections.

CONCLUSION

Since detailed knowledge about phenotypic characters of the mutants is the key to success of genetic and genomic studies, we here provide a comprehensive description of mostly morphological barley mutants. The review is closely linked to the International Database for Barley Genes and Barley Genetic Stocks ( bgs.nordgen.org ) where further details and additional images of each mutant described in this review can be found.

Accumulation of mutations in the AP2 homoeologs causes suppression of anther extrusion with altered spike and culm development in hexaploid wheat

Cleistogamy or closed flowering is a widely used trait in barley (Hordeum vulgare) breeding because it reduces the risk of fungal infection in florets at anthesis. Cleistogamy in barley is caused by a point mutation within the microRNA172 (miR172) target site of the Cly1 gene, which encodes the Apetala2 (AP2) transcription factor. Because cleistogamy is not apparent in cultivars of hexaploid wheat (Triticum aestivum), a strategy to develop cleistogamous wheat was proposed by inducing point mutations in all three AP2 homoeologs, which are the wheat orthologs of barley Cly1. In this study, we investigated the effects of miR172 target site mutations on wheat cleistogamy using double mutants by combining three previously obtained mutant alleles (AP2-A1, D1 and D2) in a near-isogenic background. The AP2-D2 allele had the greatest effect on reducing the anther extrusion rate and lodicule size compared with the other two mutant alleles. The double mutant containing the AP2-A1 and AP2-D2 alleles had a much greater suppression of anther extrusion by reducing the lodicule size than the single AP2-D2 mutant, suggesting cumulative effects of the two mutant alleles. In addition, both single and double mutants exhibited compact spikes and shorter plant heights due to reduced rachis and culm internodes in the upper parts. The presence or absence of the wild-type AP2-B homoeolog had no significant effect on phenotype. This study provides insights into the cumulative effects of mutant AP2 alleles in suppressing open flowering and provides a basis for further research on the development of complete cleistogamy in hexaploid wheat.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01458-9.

An overview of floral regulatory genes in annual and perennial plants

The floral initiation in angiosperms is a complex process influenced by endogenous and exogenous signals. With this approach, we aim to provide a comprehensive review to integrate this complex floral regulatory process and summarize the regulatory genes and their functions in annuals and perennials. Seven primary paths leading to flowering have been discovered in Arabidopsis under several growth condition that include; photoperiod, ambient temperature, vernalization, gibberellins, autonomous, aging and carbohydrates. These pathways involve a series of interlinked signaling pathways that respond to both internal and external signals, such as light, temperature, hormones, and developmental cues, to coordinate the expression of genes that are involved in flower development. Among them, the photoperiodic pathway was the most important and conserved as some of the fundamental loci and mechanisms are shared even by closely related plant species. The activation of floral regulatory genes such as FLC, FT, LFY, and SOC1 that determine floral meristem identity and the transition to the flowering stage result from the merging of these pathways. Recent studies confirmed that alternative splicing, antisense RNA and epigenetic modification play crucial roles by regulating the expression of genes related to blooming. In this review, we documented recent progress in the floral transition time in annuals and perennials, with emphasis on the specific regulatory mechanisms along with the application of various molecular approaches including overexpression studies, RNA interference and Virus-induced flowering. Furthermore, the similarities and differences between annual and perennial flowering will aid significant contributions to the field by elucidating the mechanisms of perennial plant development and floral initiation regulation.

Organ-enriched gene expression during floral morphogenesis in wild barley

Floral morphology varies considerably between dicots and monocots. The ABCDE model explaining how floral organ development is controlled was formulated using core eudicots and applied to grass crops. Barley (Hordeum. vulgare) has unique floral morphogenesis. Wild barley (H. vulgare ssp. spontaneum), which is the immediate ancestor of cultivated barley (H. vulgare ssp. vulgare), contains a rich reservoir of genetic diversity. However, the wild barley genes involved in floral organ development are still relatively uncharacterized. In this study, we generated an organ-specific transcriptome atlas for wild barley floral organs. Genome-wide transcription profiles indicated that 22 838 protein-coding genes were expressed in at least one organ. These genes were grouped into seven clusters according to the similarities in their expression patterns. Moreover, 5619 genes exhibited organ-enriched expression, 677 of which were members of 47 transcription factor families. Gene ontology analyses suggested that the functions of the genes with organ-enriched expression influence the biological processes in floral organs. The co-expression regulatory network showed that the expression of 690 genes targeted by MADS-box proteins was highly positively correlated with the expression of ABCDE model genes during floral morphogenesis. Furthermore, the expression of 138 genes was specific to the wild barley OUH602 genome and not the Morex genome; most of these genes were highly expressed in the glume, awn, lemma, and palea. This study revealed the global gene expression patterns underlying floral morphogenesis in wild barley. On the basis of the study findings, a molecular mechanism controlling floral morphology in barley was proposed.

Mutations within the miR172 target site of wheat AP2 homoeologs regulate lodicule size and rachis internode length

Closed fertilization in flowers, or cleistogamy, reduces the risk of fungal infection in Triticeae crops. In barley (Hordeum vulgare), cleistogamy is determined by a single recessive gene, cly1, which results from a single nucleotide polymorphism within the microRNA172 target site of the Apetala2 (AP2) transcription factor gene. The recessive cly1 allele negatively regulates the development of lodicules, keeping florets closed at anthesis. However, cleistogamy is not evident in hexaploid wheat (Triticum aestivum) cultivars. This study aimed at identifying mutations in wheat AP2 orthologs by ethyl methane sulfonate-induced mutagenesis and high-resolution melt analysis. Although flowers of AP2 mutants induced in the A and D genomes opened at anthesis, their lodicule size was significantly smaller, especially in the direction of depth, than that of wild-type plants. One of the mutants that carried a nucleotide replacement in AP2 from the D genome produced a compact spike caused by a substantial decrease in rachis internode length, analogous to the barley dense spike. Cleistogamous hexaploid wheat might be generated by combining effective mutant alleles of AP2-homoeologous genes.

Identification of candidate genes responsible for chasmogamy in wheat

BACKGROUND

The flowering biology of wheat plants favours self-pollination which causes obstacles in wheat hybrid breeding. Wheat flowers can be divided into two groups, the first one is characterized by flowering and pollination within closed flowers (cleistogamy), while the second one possesses the ability to open flowers during processes mentioned above (chasmogamy). The swelling of lodicules is involved in the flowering of cereals and among others their morphology, calcium and potassium content differentiate between cleistogamic and non-cleistogamous flowers. A better understanding of the chasmogamy mechanism can lead to the development of tools for selection of plants with the desired outcrossing rate. To learn more, the sequencing of transcriptomes (RNA-Seq) and Representational Difference Analysis products (RDA-Seq) were performed to investigate the global transcriptomes of wheat lodicules in two highly chasmogamous (HCH, Piko and Poezja) and two low chasmogamous (LCH, Euforia and KWS Dacanto) varieties at two developmental stages-pre-flowering and early flowering.

RESULTS

The differentially expressed genes were enriched in five, main pathways: "metabolism", "organismal systems", "genetic information processing", "cellular processes" and "environmental information processing", respectively. Important genes with opposite patterns of regulation between the HCH and LCH lines have been associated with the lodicule development i.e. expression levels of MADS16 and MADS58 genes may be responsible for quantitative differences in chasmogamy level in wheat.

CONCLUSIONS

We conclude that the results provide a new insight into lodicules involvement in the wheat flowering process. This study generated important genomic information to support the exploitation of the chasmogamy in wheat hybrid breeding programs.

MicroRNA172b-5p/trehalose-6-phosphate synthase module stimulates trehalose synthesis and microRNA172b-3p/AP2-like module accelerates flowering in barley upon drought stress

MicroRNAs (miRNAs) are major regulators of gene expression during plant development under normal and stress conditions. In this study, we analyzed the expression of 150 conserved miRNAs during drought stress applied to barley ready to flower. The dynamics of miRNAs expression was also observed after rewatering. Target messenger RNA (mRNAs) were experimentally identified for all but two analyzed miRNAs, and 41 of the targets were not reported before. Drought stress applied to barley induced accelerated flowering coordinated by a pair of two differently expressed miRNAs originating from a single precursor: hvu-miR172b-3p and hvu-miR172b-5p. Increased expression of miRNA172b-3p during drought leads to the downregulation of four APETALA2(AP2)-like genes by their mRNA cleavage. In parallel, the downregulation of the miRNA172b-5p level results in an increased level of a newly identified target, trehalose-6-phosphate synthase, a key enzyme in the trehalose biosynthesis pathway. Therefore, drought-treated plants have higher trehalose content, a known osmoprotectant, whose level is rapidly dropping after watering. In addition, trehalose-6-phosphate, an intermediate of the trehalose synthesis pathway, is known to induce flowering. The hvu-miRNA172b-5p/trehalose-6-phosphate synthase and hvu-miRNA172b-3p/AP2-like create a module leading to osmoprotection and accelerated flowering induction during drought.

Form follows function in Triticeae inflorescences

Grass inflorescences produce grains, which are directly connected to our food. In grass crops, yields are mainly affected by grain number and weight; thus, understanding inflorescence shape is crucially important for cereal crop breeding. In the last two decades, several key genes controlling inflorescence shape have been elucidated, thanks to the availability of rich genetic resources and powerful genomics tools. In this review, we focus on the inflorescence architecture of Triticeae species, including the major cereal crops wheat and barley. We summarize recent advances in our understanding of the genetic basis of spike branching, and spikelet and floret development in the Triticeae. Considering our changing climate and its impacts on cereal crop yields, we also discuss the future orientation of research.

Engineered Cleistogamy in Camelina sativa for bioconfinement

Camelina sativa is a self-pollinating and facultative outcrossing oilseed crop. Genetic engineering has been used to improve camelina yield potential for altered fatty acid composition, modified protein profiles, improved seed and oil yield, and enhanced drought resistance. The deployment of transgenic camelina in the field posits high risks related to the introgression of transgenes into non-transgenic camelina and wild relatives. Thus, effective bioconfinement strategies need to be developed to prevent pollen-mediated gene flow (PMGF) from transgenic camelina. In the present study, we overexpressed the cleistogamy (i.e. floral petal non-openness)-inducing PpJAZ1 gene from peach in transgenic camelina. Transgenic camelina overexpressing PpJAZ1 showed three levels of cleistogamy, affected pollen germination rates after anthesis but not during anthesis, and caused a minor silicle abortion only on the main branches. We also conducted field trials to examine the effects of the overexpressed PpJAZ1 on PMGF in the field, and found that the overexpressed PpJAZ1 dramatically inhibited PMGF from transgenic camelina to non-transgenic camelina under the field conditions. Thus, the engineered cleistogamy using the overexpressed PpJAZ1 is a highly effective bioconfinement strategy to limit PMGF from transgenic camelina, and could be used for bioconfinement in other dicot species.

Molecular Links between Flowering and Abiotic Stress Response: A Focus on Poaceae

Extreme temperatures, drought, salinity and soil pollution are the most common types of abiotic stresses crops can encounter in fields; these variations represent a general warning to plant productivity and survival, being more harmful when in combination. Plant response to such conditions involves the activation of several molecular mechanisms, starting from perception to signaling, transcriptional reprogramming and protein modifications. This can influence the plant's life cycle and development to different extents. Flowering developmental transition is very sensitive to environmental stresses, being critical to reproduction and to agricultural profitability for crops. The Poacee family contains some of the most widespread domesticated plants, such as wheat, barley and rice, which are commonly referred to as cereals and represent a primary food source. In cultivated Poaceae, stress-induced modifications of flowering time and development cause important yield losses by directly affecting seed production. At the molecular level, this reflects important changes in gene expression and protein activity. Here, we present a comprehensive overview on the latest research investigating the molecular pathways linking flowering control to osmotic and temperature extreme conditions in agronomically relevant monocotyledons. This aims to provide hints for biotechnological strategies that can ensure agricultural stability in ever-changing climatic conditions.

Transcriptomic heterochrony and completely cleistogamous flower development in the mycoheterotrophic orchid Gastrodia

Cleistogamy, in which plants can reproduce via self-fertilization within permanently closed flowers, has evolved in > 30 angiosperm lineages; however, consistent with Darwin's doubts about its existence, complete cleistogamy - the production of only cleistogamous flowers - has rarely been recognized. Thus far, the achlorophyllous orchid genus, Gastrodia, is the only known genus with several plausible completely cleistogamous species. Here, we analyzed the floral developmental transcriptomes of two recently evolved, completely cleistogamous Gastrodia species and their chasmogamous sister species to elucidate the possible changes involved in producing common cleistogamous traits. The ABBA-BABA test did not support introgression and protein sequence convergence as evolutionary mechanisms leading to cleistogamy, leaving convergence in gene expression as a plausible mechanism. Regarding transcriptomic differentiation, the two cleistogamous species had common modifications in the expression of developmental regulators, exhibiting a gene family-wide signature of convergent expression changes in MADS-box genes. Our transcriptomic pseudotime analysis revealed a prolonged juvenile state and eventual maturation, a heterochronic pattern consistent with partial neoteny, in cleistogamous flower development. These findings indicate that transcriptomic partial neoteny, arising from changes in the expression of conserved developmental regulators, might have contributed to the rapid and repeated evolution of cleistogamous flowers in Gastrodia.

What Do We Know about Barley miRNAs?

Plant miRNAs are powerful regulators of gene expression at the post-transcriptional level, which was repeatedly proved in several model plant species. miRNAs are considered to be key regulators of many developmental, homeostatic, and immune processes in plants. However, our understanding of plant miRNAs is still limited, despite the fact that an increasing number of studies have appeared. This systematic review aims to summarize our current knowledge about miRNAs in spring barley (Hordeum vulgare), which is an important agronomical crop worldwide and serves as a common monocot model for studying abiotic stress responses as well. This can help us to understand the connection between plant miRNAs and (not only) abiotic stresses in general. In the end, some future perspectives and open questions are summarized.

A small chromosomal inversion mediated by MITE transposons confers cleistogamy in Brassica napus

Cleistogamy, self-pollination within closed flowers, can help maintain seed purity, accelerate breeding speed, and aid in the development of ornamental flowers. However, the mechanism underlying petal closing/opening behavior remains elusive. Here, we found that a Brassica napus petal closing/opening behavior was inherited in a Mendelian manner. Fine mapping and positional cloning experiments revealed that the Mendelian factor originated from a short (29.8 kb) inversion mediated by BnDTH9 miniature inverted-repeat transposable elements (MITEs) on chromosome C03. This inversion led to tissue-specific gene promoter exchange between BnaC03.FBA (BnaC03G0156800ZS encoding an F-Box-associated domain-containing protein) and BnaC03.EFO1 (BnaC03G0157400ZS encoding an EARLY FLOWERING BY OVEREXPRESSION 1 protein) positioned near the respective inversion breakpoints. Our genetic transformation work demonstrated that the cleistogamy originated from high tissue-specific expression of the BnaC03.FBA gene caused by promoter changes due to the MITE-mediated inversion. BnaC03.FBA is involved in the formation of an SCF (Skp1-Cullin-F-box) complex, which participates in ubiquitin-mediated protein targeting for degradation through the ubiquitin 26S-proteasome system. Our results shed light on a molecular model of petal-closing behavior.

Roles of microRNAs in abiotic stress response and characteristics regulation of plant

MicroRNAs (miRNAs) are a class of non-coding endogenous small RNAs (long 20-24 nucleotides) that negatively regulate eukaryotes gene expression at post-transcriptional level via cleavage or/and translational inhibition of targeting mRNA. Based on the diverse roles of miRNA in regulating eukaryotes gene expression, research on the identification of miRNA target genes has been carried out, and a growing body of research has demonstrated that miRNAs act on target genes and are involved in various biological functions of plants. It has an important influence on plant growth and development, morphogenesis, and stress response. Recent case studies indicate that miRNA-mediated regulation pattern may improve agronomic properties and confer abiotic stress resistance of plants, so as to ensure sustainable agricultural production. In this regard, we focus on the recent updates on miRNAs and their targets involved in responding to abiotic stress including low temperature, high temperature, drought, soil salinity, and heavy metals, as well as plant-growing development. In particular, this review highlights the diverse functions of miRNAs on achieving the desirable agronomic traits in important crops. Herein, the main research strategies of miRNAs involved in abiotic stress resistance and crop traits improvement were summarized. Furthermore, the miRNA-related challenges and future perspectives of plants have been discussed. miRNA-based research lays the foundation for exploring miRNA regulatory mechanism, which aims to provide insights into a potential form of crop improvement and stress resistance breeding.

The Qc5 Allele Increases Wheat Bread-Making Quality by Regulating SPA and SPR

Common wheat (Triticum aestivum L.) is an important food crop with a unique processing quality. The Q gene positively regulates the processing quality of wheat, but the underlying mechanism remains unclear. Here, a new Q allele (Q^c5) responsible for compact spikes and good bread performance was identified. Compared with the Q allele widely distributed in modern common wheat cultivars, Q^c5 had a missense mutation outside the miRNA172-binding site. This missense mutation led to a more compact messenger RNA (mRNA) secondary structure around the miRNA172-binding region, resulting in increased Q^c5 expression during the spike development stage and a consequent increase in spike density. Furthermore, this missense mutation weakened the physical interaction between Q^c5 and storage protein activator (SPA) in seeds and suppressed the expression of storage protein repressor (SPR). These changes increased the grain protein content and improved the bread-making quality of wheat. In conclusion, a missense mutation increases Q expression because of the resulting highly folded mRNA secondary structure around the miRNA172-binding site. Furthermore, this mutation improves the bread-making quality of wheat by repressing the expression of SPR and influencing the physical interaction between Q and SPA. These findings provide new insights into the miRNA172-directed regulation of gene expression, with implications for wheat breeding.

microRNAs and Their Roles in Plant Development

Small RNAs are short non-coding RNAs with a length ranging between 20 and 24 nucleotides. Of these, microRNAs (miRNAs) play a distinct role in plant development. miRNAs control target gene expression at the post-transcriptional level, either through direct cleavage or inhibition of translation. miRNAs participate in nearly all the developmental processes in plants, such as juvenile-to-adult transition, shoot apical meristem development, leaf morphogenesis, floral organ formation, and flowering time determination. This review summarizes the research progress in miRNA-mediated gene regulation and its role in plant development, to provide the basis for further in-depth exploration regarding the function of miRNAs and the elucidation of the molecular mechanism underlying the interaction of miRNAs and other pathways.

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.

Identification of microRNAs Responding to Aluminium, Cadmium and Salt Stresses in Barley Roots

Plants are frequently exposed to various abiotic stresses, including aluminum, cadmium and salinity stress. Barley (Hordeum vulgare) displays wide genetic diversity in its tolerance to various abiotic stresses. In this study, small RNA and degradome libraries from the roots of a barley cultivar, Golden Promise, treated with aluminum, cadmium and salt or controls were constructed to understand the molecular mechanisms of microRNAs in regulating tolerance to these stresses. A total of 525 microRNAs including 198 known and 327 novel members were identified through high-throughput sequencing. Among these, 31 microRNAs in 17 families were responsive to these stresses, and Gene Ontology (GO) analysis revealed that their targeting genes were mostly highlighted as transcription factors. Furthermore, five (miR166a, miR166a-3p, miR167b-5p, miR172b-3p and miR390), four (MIR159a, miR160a, miR172b-5p and miR393) and three (miR156a, miR156d and miR171a-3p) microRNAs were specifically responsive to aluminum, cadmium and salt stress, respectively. Six miRNAs, i.e., miR156b, miR166a-5p, miR169a, miR171a-5p, miR394 and miR396e, were involved in the responses to the three stresses, with different expression patterns. A model of microRNAs responding to aluminum, cadmium and salt stresses was proposed, which may be helpful in comprehensively understanding the mechanisms of microRNAs in regulating stress tolerance in barley.

A novel mutant allele at the Cleistogamy 1 locus in barley

A chasmogamous mutant was induced by exposing a cleistogamous cultivar to sodium azide. The altered cly1 sequence in the mutant was not in the miR172 binding site, as is the case in other known cleistogamous alleles, but rather in a region encoding one of the gene product's two AP2 domains. The genetic basis of cleistogamy (in which pollination occurs before the flower opens) in barley is centered on the Cleistogamy 1 locus (cly1). The sequence of the microRNA (miR172)-targeting site in the gene, which belongs to the APETALA2 family, differs between cleistogamous and chasmogamous cultivars at a single nucleotide position, resulting in the differential ability of the lodicules to swell. Here, mutagenesis of the barley cultivar 'Misato Golden' (which carries the cly1.b allele), achieved using sodium azide, was used to induce a change from cleistogamy to chasmogamy (non-cleistogamous flowering). The cly1 coding sequence in the selected mutant differed from that of cly1.b by two non-synonymous mutations, one of which was responsible for an altered residue in one of the AP2 domains present in the Cly1 protein. Although there was no difference in the miR172 targeting site between cly1.b and the novel allele (designated cly1.b3), the mutant's lodicules' ability to swell was indistinguishable from that observed in cultivars carrying the chasmogamous allele Cly1.a. The phenotype of cly1.b3/cly1.b, cly1.b3/cly1.b2 and cly1.b3/cly1.c heterozygotes indicated that cly1.b3 is recessive or incompletely dominant with respect to these alleles.

Circular RNAs Repertoire and Expression Profile during Brassica rapa Pollen Development

Circular RNAs (circRNAs) are covalently closed RNA molecules generated by the back-splicing of exons from linear precursor mRNAs. Though various linear RNAs have been shown to play important regulatory roles in many biological and developmental processes, little is known about the role of their circular counterparts. In this study, we performed high-throughput RNA sequencing to delineate the expression profile and potential function of circRNAs during the five stages of pollen development in Brassica rapa. A total of 1180 circRNAs were detected in pollen development, of which 367 showed stage-specific expression patterns. Functional enrichment and metabolic pathway analysis showed that the parent genes of circRNAs were mainly involved in pollen-related molecular and biological processes such as mitotic and meiotic cell division, DNA processes, protein synthesis, protein modification, and polysaccharide biosynthesis. Moreover, by predicting the circRNA–miRNA network from our differentially expressed circRNAs, we found 88 circRNAs with potential miRNA binding sites, suggesting their role in post-transcriptional regulation of the genes. Finally, we confirmed the back-splicing sites of nine selected circRNAs using divergent primers and Sanger sequencing. Our study presents the systematic analysis of circular RNAs during pollen development and forms the basis of future studies for unlocking complex gene regulatory networks underpinning reproduction in flowering plants.

Comprehensive Mechanism of Gene Silencing and Its Role in Plant Growth and Development

Gene silencing is a negative feedback mechanism that regulates gene expression to define cell fate and also regulates metabolism and gene expression throughout the life of an organism. In plants, gene silencing occurs via transcriptional gene silencing (TGS) and post-transcriptional gene silencing (PTGS). TGS obscures transcription via the methylation of 5' untranslated region (5'UTR), whereas PTGS causes the methylation of a coding region to result in transcript degradation. In this review, we summarized the history and molecular mechanisms of gene silencing and underlined its specific role in plant growth and crop production.

Analysis of barley mutants ert-c.1 and ert-d.7 reveals two loci with additive effect on plant architecture

Both mutant ert-c.1 and ert-d.7 carry T2-T3 translocations in the Ert-c gene. Principal coordinate analyses revealed the translocation types and translocation breakpoints. Mutant ert-d.7 is an Ert-c Ert-d double mutant. Mutations in the Ert-c and Ert-d loci are among the most common barley mutations affecting plant architecture. The mutants have various degrees of erect and compact spikes, often accompanied with short and stiff culms. In the current study, complementation tests, linkage mapping, principal coordinate analyses and fine mapping were conducted. We conclude that the original ert-d.7 mutant does not only carry an ert-d mutation but also an ert-c mutation. Combined, mutations in Ert-c and Ert-d cause a pyramid-dense spike phenotype, whereas mutations in only Ert-c or Ert-d give a pyramid and dense phenotype, respectively. Associations between the Ert-c gene and T2-T3 translocations were detected in both mutant ert-c.1 and ert-d.7. Different genetic association patterns indicate different translocation breakpoints in these two mutants. Principal coordinate analysis based on genetic distance and screening of recombinants from all four ends of polymorphic regions was an efficient way to narrow down the region of interest in translocation-involved populations. The Ert-c gene was mapped to the marker interval of 2_0801to1_0224 on 3HL near the centromere. The results illuminate a complex connection between two single genes having additive effects on barley spike architecture and will facilitate the identification of the Ert-c and Ert-d genes.

APETALA2 functions as a temporal factor together with BLADE-ON-PETIOLE2 and MADS29 to control flower and grain development in barley

Cereal grain develops from fertilised florets. Alterations in floret and grain development greatly influence grain yield and quality. Despite this, little is known about the underlying genetic control of these processes, especially in key temperate cereals such as barley and wheat. Using a combination of near-isogenic mutant comparisons, gene editing and genetic analyses, we reveal that HvAPETALA2 (HvAP2) controls floret organ identity, floret boundaries, and maternal tissue differentiation and elimination during grain development. These new roles of HvAP2 correlate with changes in grain size and HvAP2-dependent expression of specific HvMADS-box genes, including the B-sister gene, HvMADS29. Consistent with this, gene editing demonstrates that HvMADS29 shares roles with HvAP2 in maternal tissue differentiation. We also discovered that a gain-of-function HvAP2 allele masks changes in floret organ identity and grain size due to loss of barley LAXATUM.A/BLADE-ON-PETIOLE2 (HvBOP2) gene function. Taken together, we reveal novel pleiotropic roles and regulatory interactions for an AP2-like gene controlling floret and grain development in a temperate cereal.

Overcoming barriers to the registration of new plant varieties under the DUS system

Distinctness, Uniformity and Stability (DUS) is an intellectual property system introduced in 1961 by the International Union for the Protection of New Varieties of Plants (UPOV) for safeguarding the investment and rewarding innovation in developing new plant varieties. Despite the rapid advancement in our understanding of crop biology over the past 60 years, the DUS system has changed little and is still largely dependent upon a set of morphological traits for testing candidate varieties. As the demand for more plant varieties increases, the barriers to registration of new varieties become more acute and thus require urgent review to the system. To highlight the challenges and remedies in the current system, we evaluated a comprehensive panel of 805 UK barley varieties that span the entire history of DUS testing. Our findings reveal the system deficiencies such as inconsistencies in DUS traits across environments, limitations in DUS trait combinatorial space, and inadequacies in currently available DUS markers. We advocate the concept of genomic DUS and provide evidence for a shift towards a robust genomics-enabled registration system for new crop varieties.

The genome of Cleistogenes songorica provides a blueprint for functional dissection of dimorphic flower differentiation and drought adaptability

Cleistogenes songorica (2n = 4x = 40) is a desert grass with a unique dimorphic flowering mechanism and an ability to survive extreme drought. Little is known about the genetics underlying drought tolerance and its reproductive adaptability. Here, we sequenced and assembled a high-quality chromosome-level C. songorica genome (contig N50 = 21.28 Mb). Complete assemblies of all telomeres, and of ten chromosomes were derived. C. songorica underwent a recent tetraploidization (~19 million years ago) and four major chromosomal rearrangements. Expanded genes were significantly enriched in fatty acid elongation, phenylpropanoid biosynthesis, starch and sucrose metabolism, and circadian rhythm pathways. By comparative transcriptomic analysis we found that conserved drought tolerance related genes were expanded. Transcription of CsMYB genes was associated with differential development of chasmogamous and cleistogamous flowers, as well as drought tolerance. Furthermore, we found that regulation modules encompassing miRNA, transcription factors and target genes are involved in dimorphic flower development, validated by overexpression of CsAP2_9 and its targeted miR172 in rice. Our findings enable further understanding of the mechanisms of drought tolerance and flowering in C. songorica, and provide new insights into the adaptability of native grass species in evolution, along with potential resources for trait improvement in agronomically important species.

Molecular Control of Carpel Development in the Grass Family

Carpel is the ovule-bearing female reproductive organ of flowering plants and is required to ensure its protection, an efficient fertilization, and the development of diversified types of fruits, thereby it is a vital element of most food crops. The origin and morphological changes of the carpel are key to the evolution and adaption of angiosperms. Progresses have been made in elucidating the developmental mechanisms of carpel establishment in the model eudicot plant Arabidopsis thaliana, while little and fragmentary information is known in grasses, a family that includes many important crops such as rice (Oryza sativa), maize (Zea mays), barley (Hordeum vulgare), and wheat (Triticum aestivum). Here, we highlight recent advances in understanding the mechanisms underlying potential pathways of carpel development in grasses, including carpel identity determination, morphogenesis, and floral meristem determinacy. The known role of transcription factors, hormones, and miRNAs during grass carpel formation is summarized and compared with the extensively studied eudicot model plant Arabidopsis. The genetic and molecular aspects of carpel development that are conserved or diverged between grasses and eudicots are therefore discussed.

Precise Genome Editing in miRNA Target Site via Gene Targeting and Subsequent Single-Strand-Annealing-Mediated Excision of the Marker Gene in Plants

Gene targeting (GT) enables precise genome modification-e.g., the introduction of base substitutions-using donor DNA as a template. Combined with clean excision of the selection marker used to select GT cells, GT is expected to become a standard, generally applicable, base editing system. Previously, we demonstrated marker excision via a piggyBac transposon from GT-modified loci in rice. However, piggyBac-mediated marker excision has the limitation that it recognizes only the sequence TTAA. Recently, we proposed a novel and universal precise genome editing system consisting of GT with subsequent single-strand annealing (SSA)-mediated marker excision, which has, in principle, no limitation of target sequences. In this study, we introduced base substitutions into the microRNA miR172 target site of the OsCly1 gene-an ortholog of the barley Cleistogamy1 gene involved in cleistogamous flowering. To ensure efficient SSA, the GT vector harbors 1.2-kb overlapped sequences at both ends of a selection marker. The frequency of positive-negative selection-mediated GT using the vector with overlapped sequences was comparable with that achieved using vectors for piggyBac-mediated marker excision without overlapped sequences, with the frequency of SSA-mediated marker excision calculated as ~40% in the T0 generation. This frequency is thought to be adequate to produce marker-free cells, although it is lower than that achieved with piggyBac-mediated marker excision, which approaches 100%. To date, introduction of precise substitutions in discontinuous multiple bases of a targeted gene using base editors and the prime editing system based on CRISPR/Cas9 has been quite difficult. Here, using GT and our SSA-mediated marker excision system, we succeeded in the precise base substitution not only of single bases but also of artificial discontinuous multiple bases in the miR172 target site of the OsCly1 gene. Precise base substitution of miRNA target sites in target genes using this precise genome editing system will be a powerful tool in the production of valuable crops with improved traits.

Highly Conserved Evolution of Aquaporin PIPs and TIPs Confers Their Crucial Contribution to Flowering Process in Plants

Flowering is the key process for the sexual reproduction in seed plants. In gramineous crops, the process of flowering, which includes the actions of both glume opening and glume closing, is directly driven by the swelling and withering of lodicules due to the water flow into and out of lodicule cells. All these processes are considered to be controlled by aquaporins, which are the essential transmembrane proteins that facilitate the transport of water and other small molecules across the biological membranes. In the present study, the evolution of aquaporins and their contribution to flowering process in plants were investigated via an integration of genome-wide analysis and gene expression profiling. Across the barley genome, we found that HvTIP1;1, HvTIP1;2, HvTIP2;3, and HvPIP2;1 were the predominant aquaporin genes in lodicules and significantly upregulated in responding to glume opening and closing, suggesting the importance of them in the flowering process of barley. Likewise, the putative homologs of the above four aquaporin genes were also abundantly expressed in lodicules of the other monocots like rice and maize and in petals of eudicots like cotton, tobacco, and tomato. Furthermore, all of them were mostly upregulated in responding to the process of floret opening, indicating a conserved function of these aquaporin proteins in plant flowering. The phylogenetic analysis based on the OneKP database revealed that the homologs of TIP1;1, TIP1;2, TIP2;3, and PIP2;1 were highly conserved during the evolution, especially in the angiosperm species, in line with their conserved function in controlling the flowering process. Taken together, it could be concluded that the highly evolutionary conservation of TIP1;1, TIP1;2, TIP2;3 and PIP2;1 plays important roles in the flowering process for both monocots and eudicots.

A Universal System of CRISPR/Cas9-Mediated Gene Targeting Using All-in-One Vector in Plants

Homologous recombination-mediated genome editing, also called gene targeting (GT), is an essential technique that allows precise modification of a target sequence, including introduction of point mutations, knock-in of a reporter gene, and/or swapping of a functional domain. However, due to its low frequency, it has been difficult to establish GT approaches that can be applied widely to a large number of plant species. We have developed a simple and universal clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)-mediated DNA double-strand break (DSB)-induced GT system using an all-in-one vector comprising a CRISPR/Cas9 expression construct, selectable marker, and GT donor template. This system enabled introduction of targeted point mutations with non-selectable traits into several target genes in both rice and tobacco. Since it was possible to evaluate the GT frequency on endogenous target genes precisely using this system, we investigated the effect of treatment with Rad51-stimulatory compound 1 (RS-1) on the frequency of DSB-induced GT. GT frequency was slightly, but consistently, improved by RS-1 treatment in both target plants.

Increased expression of the MALE STERILITY1 transcription factor gene results in temperature-sensitive male sterility in barley

Understanding the control of fertility is critical for crop yield and breeding; this is particularly important for hybrid breeding to capitalize upon the resultant hybrid vigour. Different hybrid breeding systems have been adopted; however, these are challenging and crop specific. Mutants with environmentally reversible fertility offer valuable opportunities for hybrid breeding. The barley HvMS1 gene encodes a PHD-finger transcription factor that is expressed in the anther tapetum, which is essential for pollen development and causes complete male sterility when overexpressed in barley. This male sterility is due at least in part to indehiscent anthers resulting from incomplete tapetum degeneration, failure of anther opening, and sticky pollen under normal growth conditions (15 °C). However, dehiscence and fertility are restored when plants are grown at temperatures >20 °C, or when transferred to >20 °C during flowering prior to pollen mitosis I, with transfer at later stages unable to rescue fertility in vivo. As far as we are aware, this is the first report of thermosensitive male sterility in barley. This offers opportunities to understand the impact of temperature on pollen development and potential applications for environmentally switchable hybrid breeding systems; it also provides a 'female' male-sterile breeding tool that does not need emasculation to facilitate backcrossing.

In silico prediction of human genes as potential targets for rice miRNAs

BACKGROUND

Exogenous microRNAs (miRNAs) enter the human body through food, and their effects on metabolic processes can be considerable. It is important to determine which miRNAs from plants affect the expression of human genes and the extent of their influence.

METHOD

The binding sites of 738Oryza sativa miRNAs (osa-miRNAs) that interact with 17 508 mRNAs of human genes were determined using the MirTarget program.

RESULT

The characteristics of the binding of 46 single osa-miRNAs to 86 mRNAs of human genes with a value of free energy (ΔG) interaction equal 94%-100% from maximum ΔG were established. The findings showed that osa-miR2102-5p, osa-miR5075-3p, osa-miR2097-5p, osa-miR2919 targeted the largest number of genes at 38, 36, 23, 19 sites, respectively. mRNAs of 86 human genes were identified as targets for 93 osa-miRNAs of all family osa-miRNAs with ΔG values equal 94%-98% from maximum ΔG. Each miRNA of the osa-miR156-5p, osa-miR164-5p, osa-miR168-5p, osa-miR395-3p, osa-miR396-3p, osa-miR396-5p, osa-miR444-3p, osa-miR529-3p, osa-miR1846-3p, osa-miR2907-3p families had binding sites in mRNAs of several human target genes. The binding sites of osa-miRNAs in mRNAs of the target genes for each family of osa-miRNAs were conserved when compared to flanking nucleotide sequences.

CONCLUSION

Target mRNA human genes of osa-miRNAs are also candidate genes of cancer, cardiovascular and neurodegenerative diseases.

Cloning and molecular characterization of Triticum aestivum ornithine amino transferase (TaOAT) encoding genes

BACKGROUND

Ornithine aminotransferase (OAT, EC:2.6.1.13), alternatively known as ornithine delta aminotransferase (δOAT), is a pyridoxal phosphate (PLP)-dependent enzyme involved in the conversion of ornithine into glutamyl-5-semi-aldehyde (GSA) and vice versa. Up till now, there has been no study on OAT in wheat despite the success of its isolation from rice, maize, and sorghum. This study focuses on identification and molecular characterization of OAT in wheat.

RESULTS

In total, three homeologous OAT genes in wheat genome were found on chromosome group 5, named as TaOAT-5AL, TaOAT-5BL, and TaOAT-5DL. Sequence alignment between gDNA and its corresponding cDNA obtained a total of ten exons and nine introns. A phylogenetic tree was constructed and results indicated that OATs shared highly conserved domains between monocots and eudicots, which was further illustrated by using WebLogo to generate a sequence logo. Further subcellular localization analysis indicated that they functioned in mitochondria. Protein-protein interactions supported their role in proline biosynthesis through interactions with genes, such as delta 1-pyrroline-5-carboxylate synthetase (P5CS) and pyrroline-5-carboxylate reductase (P5CR), involved in the proline metabolic pathway. Promoter analysis exposed the presence of several stress responsive elements, implying their involvement in stress regulation. Expression profiling illustrated that TaOAT was highly induced in the wheat plants exposed to drought or salt stress condition. Upregulated expression of TaOATs was observed in stamens and at the heading stage. A potential role of TaOAT genes during floret development was also revealed. Furthermore, the transgenic plants overexpressing TaOAT showed enhanced tolerance to drought stress by increasing proline accumulation. In addition, salt tolerance of the transgenic plants was also enhanced.

CONCLUSION

TaOATs genes were involved in proline synthesis and nitrogen remobilization because they interacted with genes related to proline biosynthesis enzymes and arginine catabolism. In addition, TaOAT genes had a role in abiotic stress tolerance and a potential role in floret development. The results of this study may propose future research in the improvement of wheat resistance to abiotic stresses.

The Critical Role of miRNAs in Regulation of Flowering Time and Flower Development

Flowering is an important biological process for plants that ensures reproductive success. The onset of flowering needs to be coordinated with an appropriate time of year, which requires tight control of gene expression acting in concert to form a regulatory network. MicroRNAs (miRNAs) are non-coding RNAs known as master modulators of gene expression at the post-transcriptional level. Many different miRNA families are involved in flowering-related processes such as the induction of floral competence, floral patterning, and the development of floral organs. This review highlights the diverse roles of miRNAs in controlling the flowering process and flower development, in combination with potential biotechnological applications for miRNAs implicated in flower regulation.

Of floral fortune: tinkering with the grain yield potential of cereal crops

Enhancing the yield potential and stability of small-grain cereals, such as wheat (Triticum sp.), rice (Oryza sativa), and barley (Hordeum vulgare), is a priority for global food security. Over the last several decades, plant breeders have increased grain yield mainly by increasing the number of grains produced in each inflorescence. This trait is determined by the number of spikelets per spike and the number of fertile florets per spikelet. Recent genetic and genomic advances in cereal grass species have identified the molecular determinants of grain number and facilitated the exchange of information across genera. In this review, we focus on the genetic basis of inflorescence architecture in Triticeae crops, highlighting recent insights that have helped to improve grain yield by, for example, reducing the preprogrammed abortion of floral organs. The accumulating information on inflorescence development can be harnessed to enhance grain yield by comparative trait reconstruction and rational design to boost the yield potential of grain crops.

Identification of microRNAs in developing wheat grain that are potentially involved in regulating grain characteristics and the response to nitrogen levels

BACKGROUND

MicroRNAs (miRNAs) play crucial roles in the regulation of plant development and growth, but little information is available concerning their roles during grain development under different nitrogen (N) application levels. Our objective was to identify miRNAs related to the regulation of grain characteristics and the response to different N fertilizer conditions.

RESULTS

A total of 79 miRNAs (46 known and 33 novel miRNAs) were identified that showed significant differential expression during grain development under both high nitrogen (HN) and low nitrogen (LN) treatments. The miRNAs that were significantly upregulated early in grain development target genes involved mainly in cell differentiation, auxin-activated signaling, and transcription, which may be associated with grain size; miRNAs abundant in the middle and later stages target genes mainly involved in carbohydrate and nitrogen metabolism, transport, and kinase activity and may be associated with grain filling. Additionally, we identified 50 miRNAs (22 known and 28 novel miRNAs), of which 11, 9, and 39 were differentially expressed between the HN and LN libraries at 7, 17, and 27 days after anthesis (DAA). The miRNAs that were differentially expressed in response to nitrogen conditions target genes involved mainly in carbohydrate and nitrogen metabolism, the defense response, and transport as well as genes that encode ubiquitin ligase. Only one novel miRNA (PC-5p-2614_215) was significantly upregulated in response to LN treatment at all three stages, and 21 miRNAs showed significant differential expression between HN and LN conditions only at 27 DAA. We therefore propose a model for target gene regulation by miRNAs during grain development with N-responsive patterns.

CONCLUSIONS

The potential targets of the identified miRNAs are related to various biological processes, such as carbohydrate/nitrogen metabolism, transcription, cellular differentiation, transport, and defense. Our results indicate that miRNA-mediated networks, via posttranscriptional regulation, play crucial roles in grain development and the N response, which determine wheat grain weight and quality. Our study provides useful information for future research of regulatory mechanisms that focus on improving grain yield and quality.

APETALA 2-like genes AP2L2 and Q specify lemma identity and axillary floral meristem development in wheat

The spikelet is the basic unit of the grass inflorescence. In tetraploid (Triticum turgidum) and hexaploid wheat (Triticum aestivum), the spikelet is a short indeterminate branch with two proximal sterile bracts (glumes) followed by a variable number of florets, each including a bract (lemma) with an axillary flower. Varying levels of miR172 and/or its target gene Q (AP2L5) result in gradual transitions of glumes to lemmas, and vice versa. Here, we show that AP2L5 and its related paralog AP2L2 play critical and redundant roles in the specification of axillary floral meristems and lemma identity. AP2L2, also targeted by miR172, displayed similar expression profiles to AP2L5 during spikelet development. Loss-of-function mutants in both homeologs of AP2L2 (henceforth ap2l2) developed normal spikelets, but ap2l2 ap2l5 double mutants generated spikelets with multiple empty bracts before transitioning to florets. The coordinated nature of these changes suggest an early role of these genes in floret development. Moreover, the flowers of ap2l2 ap2l5 mutants showed organ defects in paleas and lodicules, including the homeotic conversion of lodicules into carpels. Mutations in the miR172 target site of AP2L2 were associated with reduced plant height, more compact spikes, promotion of lemma-like characters in glumes and smaller lodicules. Taken together, our results show that the balance in the expression of miR172 and AP2-like genes is crucial for the correct development of spikelets and florets, and that this balance has been altered during the process of wheat and barley (Hordeum vulgare) domestication. The manipulation of this regulatory module provides an opportunity to modify spikelet architecture and improve grain yield.

Besides and Beyond Flowering: Other roles of EuAP2 Genes in Plant Development

EuAP2 genes are well-known for their role in flower development, a legacy of the founding member of this subfamily of transcription factors, whose mutants lacked petals in Arabidopsis. However, studies of euAP2 genes in several species have accumulated evidence highlighting the diverse roles of euAP2 genes in other aspects of plant development. Here, we emphasize other developmental roles of euAP2 genes in various species and suggest a shift from regarding euAP2 genes as just flowering genes to consider the global role they may be playing in plant development. We hypothesize that their almost universal expression profile and pleiotropic effects of their mutation suggest their involvement in fundamental plant development processes.

Identification of consistent QTL with large effect on anther extrusion in doubled haploid populations developed from spring wheat accessions in German Federal ex situ Genebank

Novel large-effect consistent QTL for anther extrusion (AE) to improve cross-pollination were mapped in doubled haploid populations derived from IPK gene bank spring wheat accessions. TaAP2-D, an ortholog of Cleistogamy1 in barley, is a likely candidate gene for AE in wheat. To establish a robust hybrid wheat breeding system, male lines harboring alleles that promote outcrossing should be developed. In this study, we developed two doubled haploid (DH) populations of hexaploid spring wheat (Triticum aestivum L.) by crossing accessions taken from IPK gene bank. In both populations, the phenotypic data of anther extrusion (AE) based on three years of field trials showed a wide variation and approximated a normal distribution. Both populations were genotyped with a 15 k Infinium single nucleotide polymorphism (SNP) array resulting in 3567 and 3457 polymorphic SNP markers for DH population-1 and DH population-2, respectively. Composite interval mapping identified quantitative trait loci (QTL) on chromosomes 1D, 2D, 4A, 4B, 5A, 5D, 6A, and 6B; with consistent QTL (that are identified in all the years) on chromosome 4A in DH population-1, and on chromosomes 2D and 6B in DH population-2. The consistent QTL explained 17.2%, 32.9%, and 12.3% of the phenotypic variances, respectively. Genic scan of the chromosome 2D-QTL showed that the wheat gene TaAP2-D, an ortholog of Cleistogamy1 which promotes AE via swelling of the lodicules in barley, lies within the QTL region. A diagnostic marker was developed for TaAP2-D that showed co-segregation with the AE phenotype. This study shows the use of gene bank diversity reservoir to find alleles which are otherwise difficult to detect in elite populations. The identification of large-effect consistent QTL for AE is expected to help form efficient male parental lines suitable for hybrid wheat seed production and serve as a source for map-based cloning.

Profiling miRNA expression in photo-thermo-sensitive male genic sterility line (PTGMS) PA64S under high and low temperature

Peiai64S (PA64S) is a photo-thermo-sensitive genic male sterile line (PTGMS), with wide application in hybrid seed production in rice (Oryza sativa L.). Micro-RNAs are 21-24 nt, endogenously expressed small RNAs that have been characterized in various developmental stages of rice, but none have been studied with respect to the regulation of TGMS in rice. Here, we employed high-throughput sequencing to identify expression profiles of miRNAs in the anthers of PA64S at high (PA64S-H) and low temperature (PA64S-L). Two small RNA libraries from PA64S-H and PA64-L anthers were sequenced, and 263 known and 321 novel candidate miRNAs were identified. Based on the number of sequencing reads, a total of 133 known miRNAs were found to be differentially expressed between PA64S-H and PA64S-L. Target prediction showed that the target genes encode MYB and TCP transcription factors, and bHLH proteins. These target genes are related to pollen development and male sterility, suggesting that miRNA/targets may play roles in regulating TGMS in rice. Further, starch and sucrose metabolism pathways, sphingolipid metabolism, arginine and proline metabolism, and plant hormone signal transduction pathways were enriched by KEGG pathway annotation. These findings contribute to our understanding of the role of miRNAs during anther development and TGMS occurrence in rice.

Genome-wide exploration and characterization of miR172/euAP2 genes in Brassica napus L. for likely role in flower organ development

BACKGROUND

APETALA2-like genes encode plant-specific transcription factors, some of which possess one microRNA172 (miR172) binding site. The miR172 and its target euAP2 genes are involved in the process of phase transformation and flower organ development in many plants. However, the roles of miR172 and its target AP2 genes remain largely unknown in Brassica napus (B. napus).

RESULTS

In this study, 19 euAP2 and four miR172 genes were identified in the B. napus genome. A sequence analysis suggested that 17 euAP2 genes were targeted by Bna-miR172 in the 3' coding region. EuAP2s were classified into five major groups in B.napus. This classification was consistent with the exon-intron structure and motif organization. An analysis of the nonsynonymous and synonymous substitution rates revealed that the euAP2 genes had gone through purifying selection. Whole genome duplication (WGD) or segmental duplication events played a major role in the expansion of the euAP2 gene family. A cis-regulatory element (CRE) analysis suggested that the euAP2s were involved in the response to light, hormones, stress, and developmental processes including circadian control, endosperm and meristem expression. Expression analysis of the miR172-targeted euAP2s in nine different tissues showed diverse spatiotemporal expression patterns. Most euAP2 genes were highly expressed in the floral organs, suggesting their specific functions in flower development. BnaAP2-1, BnaAP2-5 and BnaTOE1-2 had higher expression levels in late-flowering material than early-flowering material based on RNA-seq and qRT-PCR, indicating that they may act as floral suppressors.

CONCLUSIONS

Overall, analyses of the evolution, structure, tissue specificity and expression of the euAP2 genes were peformed in B.napus. Based on the RNA-seq and experimental data, euAP2 may be involved in flower development. Three euAP2 genes (BnaAP2-1, BnaAP2-5 and BnaTOE1-2) might be regarded as floral suppressors. The results of this study provide insights for further functional characterization of the miR172 /euAP2 module in B.napus.

iTRAQ-based quantitative proteome analysis reveals metabolic changes between a cleistogamous wheat mutant and its wild-type wheat counterpart

Background

Wheat is one of the most important staple crops worldwide. Fusarium head blight (FHB) severely affects wheat yield and quality. A novel bread wheat mutant, ZK001, characterized as cleistogamic was isolated from a non-cleistogamous variety Yumai 18 (YM18) through static magnetic field mutagenesis. Cleistogamy is a promising strategy for controlling FHB. However, little is known about the mechanism of cleistogamy in wheat.

Methods

We performed a FHB resistance test to identify the FHB infection rate of ZK001. We also measured the agronomic traits of ZK001 and the starch and total soluble sugar contents of lodicules in YM18 and ZK001. Finally, we performed comparative studies at the proteome level between YM18 and ZK001 based on the proteomic technique of isobaric tags for relative and absolute quantification.

Results

The infection rate of ZK001 was lower than that of its wild-type and Aikang 58. The abnormal lodicules of ZK001 lost the ability to push the lemma and palea apart during the flowering stage. Proteome analysis showed that the main differentially abundant proteins (DAPs) were related to carbohydrate metabolism, protein transport, and calcium ion binding. These DAPs may work together to regulate cellular homeostasis, osmotic pressure and the development of lodicules. This hypothesis is supported by the analysis of starch, soluble sugar content in the lodicules as well as the results of Quantitative reverse transcription polymerase chain reaction.

Conclusions

Proteomic analysis has provided comprehensive information that should be useful for further research on the lodicule development mechanism in wheat. The ZK001 mutant is optimal for studying flower development in wheat and could be very important for FHB resistant projects via conventional crossing.

Genetic and Molecular Control of Floral Organ Identity in Cereals

Grasses represent a major family of monocots comprising mostly cereals. When compared to their eudicot counterparts, cereals show a remarkable morphological diversity. Understanding the molecular basis of floral organ identity and inflorescence development is crucial to gain insight into the grain development for yield improvement purposes in cereals, however, the exact genetic mechanism of floral organogenesis remains elusive due to their complex inflorescence architecture. Extensive molecular analyses of Arabidopsis and other plant genera and species have established the ABCDE floral organ identity model. According to this model, hierarchical combinatorial activities of A, B, C, D, and E classes of homeotic genes regulate the identity of different floral organs with partial conservation and partial diversification between eudicots and cereals. Here, we review the developmental role of A, B, C, D, and E gene classes and explore the recent advances in understanding the floral development and subsequent organ specification in major cereals with reference to model plants. Furthermore, we discuss the evolutionary relationships among known floral organ identity genes. This comparative overview of floral developmental genes and associated regulatory factors, within and between species, will provide a thorough understanding of underlying complex genetic and molecular control of flower development and floral organ identity, which can be helpful to devise innovative strategies for grain yield improvement in cereals.

Genome-wide association mapping in a diverse spring barley collection reveals the presence of QTL hotspots and candidate genes for root and shoot architecture traits at seedling stage

BACKGROUND

Adaptation to drought-prone environments requires robust root architecture. Genotypes with a more vigorous root system have the potential to better adapt to soils with limited moisture content. However, root architecture is complex at both, phenotypic and genetic level. Customized mapping panels in combination with efficient screenings methods can resolve the underlying genetic factors of root traits.

RESULTS

A mapping panel of 233 spring barley genotypes was evaluated for root and shoot architecture traits under non-stress and osmotic stress. A genome-wide association study elucidated 65 involved genomic regions. Among them were 34 root-specific loci, eleven hotspots with associations to up to eight traits and twelve stress-specific loci. A list of candidate genes was established based on educated guess. Selected genes were tested for associated polymorphisms. By this, 14 genes were identified as promising candidates, ten remained suggestive and 15 were rejected. The data support the important role of flowering time genes, including HvPpd-H1, HvCry2, HvCO4 and HvPRR73. Moreover, seven root-related genes, HERK2, HvARF04, HvEXPB1, PIN5, PIN7, PME5 and WOX5 are confirmed as promising candidates. For the QTL with the highest allelic effect for root thickness and plant biomass a homologue of the Arabidopsis Trx-m3 was revealed as the most promising candidate.

CONCLUSIONS

This study provides a catalogue of hotspots for seedling growth, root and stress-specific genomic regions along with candidate genes for future potential incorporation in breeding attempts for enhanced yield potential, particularly in drought-prone environments. Root architecture is under polygenic control. The co-localization of well-known major genes for barley development and flowering time with QTL hotspots highlights their importance for seedling growth. Association analysis revealed the involvement of HvPpd-H1 in the development of the root system. The co-localization of root QTL with HERK2, HvARF04, HvEXPB1, PIN5, PIN7, PME5 and WOX5 represents a starting point to explore the roles of these genes in barley. Accordingly, the genes HvHOX2, HsfA2b, HvHAK2, and Dhn9, known to be involved in abiotic stress response, were located within stress-specific QTL regions and await future validation.

Transcriptomics Identifies Modules of Differentially Expressed Genes and Novel Cyclotides in Viola pubescens

Viola is a large genus with worldwide distribution and many traits not currently exemplified in model plants including unique breeding systems and the production of cyclotides. Here we report de novo genome assembly and transcriptomic analyses of the non-model species Viola pubescens using short-read DNA sequencing data and RNA-Seq from eight diverse tissues. First, V. pubescens genome size was estimated through flow cytometry, resulting in an approximate haploid genome of 455 Mbp. Next, the draft V. pubescens genome was sequenced and assembled resulting in 264,035,065 read pairs and 161,038 contigs with an N50 length of 3,455 base pairs (bp). RNA-Seq data were then assembled into tissue-specific transcripts. Together, the DNA and transcript data generated 38,081 ab initio gene models which were functionally annotated based on homology to Arabidopsis thaliana genes and Pfam domains. Gene expression was visualized for each tissue via principal component analysis and hierarchical clustering, and gene co-expression analysis identified 20 modules of tissue-specific transcriptional networks. Some of these modules highlight genetic differences between chasmogamous and cleistogamous flowers and may provide insight into V. pubescens' mixed breeding system. Orthologous clustering with the proteomes of A. thaliana and Populus trichocarpa revealed 8,531 sequences unique to V. pubescens, including 81 novel cyclotide precursor sequences. Cyclotides are plant peptides characterized by a stable, cyclic cystine knot motif, making them strong candidates for drug scaffolding and protein engineering. Analysis of the RNA-Seq data for these cyclotide transcripts revealed diverse expression patterns both between transcripts and tissues. The diversity of these cyclotides was also highlighted in a maximum likelihood protein cladogram containing V. pubescens cyclotides and published cyclotide sequences from other Violaceae and Rubiaceae species. Collectively, this work provides the most comprehensive sequence resource for Viola, offers valuable transcriptomic insight into V. pubescens, and will facilitate future functional genomics research in Viola and other diverse plant groups.

Target-mimicry based diminution of miRNA167 reinforced flowering-time phenotypes in tobacco via spatial-transcriptional biases of flowering-associated miRNAs

Evolutionarily conserved microRNAs such as miR156, miR159, miR167 and miR172 tightly regulate the extensive array of gene expression during flowering in plants, through instant and long-term alterations in the expression of their target genes. Here we employed a novel target-mimicry approach for the diminution of auxin signalling regulator miRNA167 by developing mimic-transgenic lines in tobacco, to investigate the transcriptional biases of flowering-associated miRNAs in apical and floral meristematic tissues and their phenotypic implications. Recorded morpho-alterations such as uneven flowering-time phenotypes, anomalous floral organ formation, and large variations in the seed forming characteristics permitted us to determine the consequence of the extent of miR167 expression diminution accompanying the transcriptional biases of interrelated miRNAs. We demonstrate that percent diminution of miR167 gene expression is proportionally associated with both early and late flowering-time phenotypes in mimic lines. Also, the associated miRNAs, miR156, miR159, and miR172 showed >90% transcriptional diminution in at least 'early-flowering' miR167 mimic lines. On contrary, low percentages of their respective diminution were recorded in 'late-flowering' lines. Evidently, the misexpression of miR156, miR159, and miR172 led to the over-expression of their respective target genes SPL9, AtMYB33-like and AP2 genes in mimic lines which resulted in assorted phenotypes. We describe the scope of spatial regulation of these microRNAs in floral bud tissues of mimic lines which showed negative- or very low (<25%) misexpression levels in early/late-flowering lines highlighting their roles in the acquisition of flowering mechanism. To our knowledge, this study represents the first characterization of transcriptional biases of flowering associated miRNAs in miR167-mimic lines and certainly augments our understanding of the importance of microRNA-mediated regulation of flowering in plants.

The APETALA2-Like Transcription Factor SUPERNUMERARY BRACT Controls Rice Seed Shattering and Seed Size

The elimination of seed shattering was a crucial event during crop domestication. Improving and fine-tuning the regulation of this process will further enhance grain yield by avoiding seed losses during crop production. In this work, we identified the loss-of-shattering mutant suppression of shattering1 (ssh1) through a screen of mutagenized wild rice (Oryza rufipogon) introgression lines with naturally high shattering. Using the MutMap approach and transformation experiments, we isolated a genetic factor for seed shattering, SSH1, which is an allele of SUPERNUMERARY BRACT (SNB), a gene encoding a plant-specific APETALA2-like transcription factor. A C-to-A point mutation in the ninth intron of SNB altered the splicing of its messenger RNA, causing the reduced shattering of the ssh1 mutant by altering the development of the abscission layer and vascular bundle at the junction between the seed and the pedicel. Our data suggest that SNB positively regulates the expression of two rice REPLUMLESS orthologs, qSH1 and SH5 In addition, the ssh1 mutant had larger seeds and a higher grain weight, resulting from its increased elongation of the glume longitudinal cells. The further identification of favorable SNB alleles will be valuable for improving rice seed shattering and grain yield using molecular breeding strategies.

miR172 Regulates both Vegetative and Reproductive Development in the Perennial Woody Plant Jatropha curcas

Jatropha curcas is a promising feedstock for biofuel production because its oil is highly suitable for processing bio-jet fuels and biodiesel. However, Jatropha exhibits a long juvenile stage in subtropical areas. miR172, a conserved small non-protein-coding RNA molecule with 21 nucleotides, regulates a wide range of developmental processes. To date, however, no studies have examined the function of miR172 in Jatropha. There are five miR172 precursors encoding two mature miR172s in Jatropha, which are expressed in all tissues, with the highest expression level in leaves, and the levels are up-regulated with age. Overexpression of JcmiR172a resulted in early flowering, abnormal flowers, and altered leaf morphology in transgenic Arabidopsis and Jatropha. The expression levels of miR172 target genes were down-regulated, and the flower identity genes were up-regulated in the JcmiR172a-overexpressing transgenic plants. Interestingly, we showed that JcmiR172 might be involved in regulation of stem vascular development through manipulating the expression of cellulose and lignin biosynthesis genes. Overexpression of JcmiR172a enhanced xylem development and reduced phloem and pith development. This study helped elucidate the functions of miR172 in perennial plants, a known age-related miRNA involved in the regulation of perennial plant phase change and organ development.

Marker-trait associations in two-rowed spring barley accessions from Kazakhstan and the USA

In this study, phenotyping and single nucleotide polymorphism (SNP) genotyping data of 272 accessions of two-rowed spring barley from the USA along with 94 accessions from Kazakhstan were assessed in field trials at six breeding organizations in Kazakhstan to evaluate the performance of the USA samples over three years (2009-2011). The average grain yield over the six locations was not significantly higher in Kazakh accessions in comparison to the USA samples. Twenty four samples from Montana, Washington, the USDA station in Aberdeen Idaho, and the Anheuser-Busch breeding programs showed heavier average yield than the local standard cultivar "Ubagan". Principal Coordinate analysis based on two sets of SNP data suggested that Kazakh accessions were closest to the USA accessions among eight groups of samples from different parts of the World, and within five US barley origin groups the samples from Montana and Washington perfectly matched six groups of Kazakh breeding origins. A genome-wide association study (GWAS) using data from eighteen field trials allowed the identification of ninety one marker-trait associations (MTA) in two or more environments for nine traits, including key characters such as heading time (HT), number of kernels per spike (NKS), and thousand grain weight (TGW). Our GWAS allowed the identification of eight MTA for HT and NKS, and sixteen MTA for TGW, when those MTA were linked to mapped SNPs. Based on comparisons of chromosomal positions of MTA identified in this study, and positions of known genes and quantitative trait loci for HT, NKS and TGW, it was suggested that MTA for HT on chromosome 2H (at 158.2 cM, 11_21414), MTA for NKS on 5H (at 118.6 cM, 11_20298), and two MTA for TGW on chromosome 4H (at 94.7 cM, 12_30718, and at 129.3 cM, 11_20013) were potentially new associations in barley. GWAS suggested that six MTA for HT, including two on chromosome 1H, two on chromosome 3H, and one each on chromosomes 4H and 6H, had useful pleiotropic effects for improving barley spike traits.