HvPG1 and ECA1: two genes activated transcriptionally in the transition of barley microspores from the gametophytic to the embryogenic pathway

DNA authentication of brewery products: basic principles and methodological approaches

Beer DNA authentication is the process of authentication by identification of barley malt Hordeum vulgare or its substitutes, as well as hops and yeast. The method is based on molecular genetic analysis of residual quantities of nucleic acids extracted from the cellular debris of the final product. The aim of the study was to analyse scientific and methodical approaches to extraction of residual quantities of beer raw materials nucleic acids and beer DNA authentication for their later application in determining brewing products authenticity. The technological level discloses the method of DNA extraction from wines, modified for extraction of nucleic acids from beer samples. The method includes the following characteristic peculiarities: stage enzymatic hydrolysis of polysaccharides and polypeptides of dissolved lyophilisate, multiple sedimentation and resursuspension of nucleoproteid complex, RNA removal followed by DNA extraction by organic solvents, and additional DNA purification by magnetic particle adsorption. This review presents the analysis of genetic targets used as molecular markers for gene identification of malting barley varieties and beer DNA authentication. We also provided the interpretation of PCR analysis of Hordeum vulgare varieties and samples of commercial beer. Data on SSR- and SNP-markers of Hordeum vulgare nuclear DNA, used for barley varieties identification and potentially suitable for beer DNA authentication, are also presented. We also analysed genetic targets used in malting barley substitute detection, as well as hops and yeast identification in beer. Data on correlation of amplified DNA targets with beer quality indicators were systematised.

RWP-RK domain-containing transcription factors control cell differentiation during female gametophyte development in Arabidopsis

The formation of gametes is a prerequisite for any sexually reproducing organism in order to complete its life cycle. In plants, female gametes are formed in a multicellular tissue, the female gametophyte or embryo sac. Although the events leading to the formation of the female gametophyte have been morphologically characterized, the molecular control of embryo sac development remains elusive. We used single and double mutants as well as cell-specific marker lines to characterize a novel class of gene regulators in Arabidopsis thaliana, the RWP-RK domain-containing (RKD) transcription factors. Morphological and histological analyses were conducted using confocal laser scanning and differential interference contrast microscopy. Gene expression and transcriptome analyses were performed using quantitative reverse transcription-PCR and RNA sequencing, respectively. Our results showed that RKD genes are expressed during distinct stages of embryo sac development. Morphological analysis of the mutants revealed severe distortions in gametophyte polarity and cell differentiation. Transcriptome analysis revealed changes in the expression of several gametophyte-specific gene families (RKD2 and RKD3) and ovule development-specific genes (RKD3), and identified pleiotropic effects on phytohormone pathways (RKD5). Our data provide novel insight into the regulatory control of female gametophyte development. RKDs are involved in the control of cell differentiation and are required for normal gametophytic development.

Microspore embryogenesis in wheat: new marker genes for early, middle and late stages of embryo development

Microspore embryogenesis involves reprogramming of the pollen immature cell towards embryogenesis. We have identified and characterized a collection of 14 genes induced along different morphological phases of microspore-derived embryo development in wheat (Triticum aestivum L.) anther culture. SERKs and FLAs genes previously associated with somatic embryogenesis and reproductive tissues, respectively, were also included in this analysis. Genes involved in signalling mechanisms such as TaTPD1-like and TAA1b, and two glutathione S-transferase (GSTF2 and GSTA2) were induced when microspores had acquired a 'star-like' morphology or had undergone the first divisions. Genes associated with control of plant development and stress response (TaNF-YA, TaAGL14, TaFLA26, CHI3, XIP-R; Tad1 and WALI6) were activated before exine rupture. When the multicellular structures have been released from the exine, TaEXPB4, TaAGP31-like and an unknown embryo-specific gene TaME1 were induced. Comparison of gene expression, between two wheat cultivars with different response to anther culture, showed that the profile of genes activated before exine rupture was shifted to earlier stages in the low responding cultivar. This collection of genes constitutes a value resource for study mechanism of intra-embryo communication, early pattern formation, cell wall modification and embryo differentiation.

Microspore embryogenesis: establishment of embryo identity and pattern in culture

The developmental plasticity of plants is beautifully illustrated by the competence of the immature male gametophyte to change its developmental fate from pollen to embryo development when exposed to stress treatments in culture. This process, referred to as microspore embryogenesis, is widely exploited in plant breeding, but also provides a unique system to understand totipotency and early cell fate decisions. We summarize the major concepts that have arisen from decades of cell and molecular studies on microspore embryogenesis and put these in the context of recent experiments, as well as results obtained from the study of pollen and zygotic embryo development.

Microspore embryogenesis: establishment of embryo identity and pattern in culture

The developmental plasticity of plants is beautifully illustrated by the competence of the immature male gametophyte to change its developmental fate from pollen to embryo development when exposed to stress treatments in culture. This process, referred to as microspore embryogenesis, is widely exploited in plant breeding, but also provides a unique system to understand totipotency and early cell fate decisions. We summarize the major concepts that have arisen from decades of cell and molecular studies on microspore embryogenesis and put these in the context of recent experiments, as well as results obtained from the study of pollen and zygotic embryo development.

A molecular and proteomic investigation of proteins rapidly released from triticale pollen upon hydration

Analysis of Triticale (×Triticosecale Wittmack cv. AC Alta) mature pollen proteins quickly released upon hydration was performed using two-dimensional gel electrophoresis followed by mass spectrometry. A total of 17 distinct protein families were identified and these included expansins, profilins, and various enzymes, many of which are pollen allergens. The corresponding genes were obtained and expression studies revealed that the majority of these genes were only expressed in developing anthers and pollen. Some genes including glucanase, glutathione peroxidase, glutaredoxin, and a profilin were found to be widely expressed in different reproductive and vegetative tissues. Group 11 pollen allergens, polygalacturonase, and actin depolymerizing factor were characterized for the first time in the Triticeae. This study represents a distinctive combination of proteomic and molecular analyses of the major cereal pollen proteins released upon hydration and therefore at the forefront of pollen-stigma interactions.

Atypical DNA methylation of genes encoding cysteine-rich peptides in Arabidopsis thaliana

BACKGROUND

In plants, transposons and non-protein-coding repeats are epigenetically silenced by CG and non-CG methylation. This pattern of methylation is mediated in part by small RNAs and two specialized RNA polymerases, termed Pol IV and Pol V, in a process called RNA-directed DNA methylation. By contrast, many protein-coding genes transcribed by Pol II contain in their gene bodies exclusively CG methylation that is independent of small RNAs and Pol IV/Pol V activities. It is unclear how the different methylation machineries distinguish between transposons and genes. Here we report on a group of atypical genes that display in their coding region a transposon-like methylation pattern, which is associated with gene silencing in sporophytic tissues.

RESULTS

We performed a methylation-sensitive amplification polymorphism analysis to search for targets of RNA-directed DNA methylation in Arabidopsis thaliana and identified several members of a gene family encoding cysteine-rich peptides (CRPs). In leaves, the CRP genes are silent and their coding regions contain dense, transposon-like methylation in CG, CHG and CHH contexts, which depends partly on the Pol IV/Pol V pathway and small RNAs. Methylation in the coding region is reduced, however, in the synergid cells of the female gametophyte, where the CRP genes are specifically expressed. Further demonstrating that expressed CRP genes lack gene body methylation, a CRP4-GFP fusion gene under the control of the constitutive 35 S promoter remains unmethylated in leaves and is transcribed to produce a translatable mRNA. By contrast, a CRP4-GFP fusion gene under the control of a CRP4 promoter fragment acquires CG and non-CG methylation in the CRP coding region in leaves similar to the silent endogenous CRP4 gene.

CONCLUSIONS

Unlike CG methylation in gene bodies, which does not dramatically affect Pol II transcription, combined CG and non-CG methylation in CRP coding regions is likely to contribute to gene silencing in leaves because loss of this methylation in synergid cells is associated with CRP gene expression. We discuss this unusual methylation pattern and its alteration in synergid cells as well as the possible retrogene origin and evolutionary significance of CRP genes that are methylated like transposons.

Characterization of genomic sequence showing strong association with polyembryony among diverse Citrus species and cultivars, and its synteny with Vitis and Populus

Polyembryony, in which multiple somatic nucellar cell-derived embryos develop in addition to the zygotic embryo in a seed, is common in the genus Citrus. Previous genetic studies indicated polyembryony is mainly determined by a single locus, but the underlying molecular mechanism is still unclear. As a step towards identification and characterization of the gene or genes responsible for nucellar embryogenesis in Citrus, haplotype-specific physical maps around the polyembryony locus were constructed. By sequencing three BAC clones aligned on the polyembryony haplotype, a single contiguous draft sequence consisting of 380 kb containing 70 predicted open reading frames (ORFs) was reconstructed. Single nucleotide polymorphism genotypes detected in the sequenced genomic region showed strong association with embryo type in Citrus, indicating a common polyembryony locus is shared among widely diverse Citrus cultivars and species. The arrangement of the predicted ORFs in the characterized genomic region showed high collinearity to the genomic sequence of chromosome 4 of Vitis vinifera and linkage group VI of Populus trichocarpa, suggesting that the syntenic relationship among these species is conserved even though V. vinifera and P. trichocarpa are non-apomictic species. This is the first study to characterize in detail the genomic structure of an apomixis locus determining adventitious embryony.

Haploids in flowering plants: origins and exploitation

The first haploid angiosperm, a dwarf form of cotton with half the normal chromosome complement, was discovered in 1920, and in the ninety years since then such plants have been identified in many other species. They can occur either spontaneously or can be induced by modified pollination methods in vivo, or by in vitro culture of immature male or female gametophytes. Haploids represent an immediate, one-stage route to homozygous diploids and thence to F(1) hybrid production. The commercial exploitation of heterosis in such F(1) hybrids leads to the development of hybrid seed companies and subsequently to the GM revolution in agriculture. This review describes the range of techniques available for the isolation or induction of haploids and discusses their value in a range of areas, from fundamental research on mutant isolation and transformation, through to applied aspects of quantitative genetics and plant breeding. It will also focus on how molecular methods have been used recently to explore some of the underlying aspects of this fascinating developmental phenomenon.