A 5‐year vision for Annals of Applied Biology

Epigenetic changes including DNA and histone methylation may reorganise the nuclear architecture during in vitro culture. The states of methylation resulting from in vitro cultures are often related to control the somatic embryogenesis and regeneration process via modulating gene expression. By changing the methylation profile, it is possible to alter gene expression which may be applicable to produce large number of high quality planting materials or to improve agronomic traits leading to crop improvement. Understanding the molecular mechanisms of methylation alterations and acquisition of developmental cell fate during in vitro cultures can help in the development of strategies to enhance the embryogenic capability and totipotency in recalcitrant plant species and genotypes. Moreover, the methylation profile may also be useful to adapt crops under adverse environment as the plants undergo through various stresses during in vitro cultures. In this article, we review the literature on the role of DNA and histone methylation in plant variation and discuss the potential of targeted epigenetic variation for crop improvement.     

Somaclonal variation in embryogenic cultures of silver fir (Abies alba Mill.)

Abstract

The somaclonal variation analysis was conducted on callus of 57 lines obtained by the method of somatic embryogenesis from six zygotic embryos (with different genotypes) of silver fir (Abies alba Mill.) located in two mountain regions in the south of Poland. The somaclonal variation at the DNA level was estimated using RAPD markers and the data produced were used to estimate the level of similarity using Jaccard’s coefficient. For RAPD analysis, 24 ten‐nucleotide primers from the groups OPA, OPB and OPG were used. Two genotypes deriving from Krynica and My?lenice showed high genetic similarity (Jaccard’s coefficient 0.74 and 0.83), which provides a substantial chance for producing firs with the parental genotype. The remaining four genotypes showed somaclonal variation (average Jaccard’s coefficient approx. 0.5). The significance in variation of the research sites was ascertained by the ANOVA statistical test, which showed the impact of genotype, type of medium and phytohormones included in it on the variation among the fir lines bred in vitro. The somaclonal variation data in silver fir could be useful for its propagation through in vitro culture, and in generating detailed genetic maps of this species.     

Linear landscape elements in an Austrian viticultural landscape have limited effects on spatial patterns of plant genetic diversity

Background: The Wachau region along the river Danube in eastern Austria represents one of central Europe's hotspots of plant and animal species diversity. One of the typical landscape elements is vineyards, mostly established as linear elements on terraces along the slopes, with a characteristic and species-rich flora and fauna on terrace slopes lying between the cultivated terraces.

Aims: We addressed the question of how the genetic variation of four plant species of open grassland vegetation types is distributed. We asked if levels and distribution of genetic diversity of the plant species Aster amellus, Gentianella aspera, Pulsatilla grandis, and Stachys recta were correlated with geographic distances along the terrace slopes.

Methods: The dominant inherited molecular marker system random amplified polymorphic DNA (RAPD ) was used to estimate and compare the distribution of genetic diversity of the four selected species.

Results: We found only low levels of correlation of the distribution of genetic variation with linear geographic patterns and obtained indirect evidence for high levels of gene flow between adjacent terrace slopes.

Conclusions: We found that genetic diversity parameters of the four target species did not mirror the pattern of linear landscape elements, indicating that gene flow acts efficiently against the linear distribution of genetic variation.     

Somatic embryogenesis and shoot regeneration from leaf derived callus of Hypericum perforatum var. angustifolium (sin. Fröhlich) Borkh

Abstract

The development of in vitro regeneration systems for Hypericum perforatum var. angustifolium (sin. Fröhlich) Borkh, a medicinal plant used for treating neurological disorders, is described. For the first time in this variety, somatic embryogenesis and shoot regeneration were induced from leaf-derived callus. Well-formed plantlets were obtained through both shoot regeneration and somatic embryogenesis, with separate morphogenetic programmes. Proembryogenic masses were obtained in liquid MS and B5 media supplemented with 5.8 μM 2,4-D, 1.34 μM NAA, and 1.16 μM Kin; after being transferred onto hormone-free medium, they formed whitish and spherical structures that subsequently developed into the heart and torpedo stages.

On MS agarized medium containing thidiazuron (TDZ) at different concentrations (3, 6, 9, 12 μM) combined with 2 μM IBA, only shoot regeneration, and not somatic embryogenesis, was obtained. The mean number of shoots increased significantly when the concentration of TDZ was 3 μM.     

Interspecific somatic hybrids between Solanum bulbocastanum and S. tuberosum and their haploidization for potato breeding

Protoplast fusion between incongruent Solanum bulbocastanum and S. tuberosum haploids was accomplished to produce hybrids combining elite traits from both parents. We identified 11 somatic hybrids out of 42 regenerants analyzed through ISSR markers. Some hybrids had loss or gain of fragments compared to the parents, likely due to rearrangements and deletions of chromosome segments after fusion, and/or to somaclonal variation during hybrid regeneration. Increased heterotic vigor for some traits as well as high diversity was observed as the effect of both ploidy and fusion combination. Microsporogenesis analysis indicated the occurrence of multivalent configurations and several meiotic abnormalities, such as chromosomes bridges and various spindle orientations. Since all hybrids were sterile, in vitro anther culture was employed for haploidization as a possible strategy to overcome barriers to hybridizations. Haploids were obtained from all the tetraploid S. bulbocastanum (+) S. tuberosum somatic hybrids tested, although with differences in both the number of embryos per 100 anthers cultured and the number of differentiated green plantlets. This is the first report on the successful production of haploid plants from S. bulbocastanum (+) S. tuberosum hybrids.     

Chromosomes tell half of the story: the correlation between karyotype rearrangements and genetic diversity in sedges,a group with holocentric chromosomes

Chromosome rearrangements may affect the rate and patterns of gene flow within species, through reduced fitness of structural heterozygotes or by reducing recombination rates in rearranged areas of the genome. While the effects of chromosome rearrangements on gene flow have been studied in a wide range of organisms with monocentric chromosomes, the effects of rearrangements in holocentric chromosomes—chromosomes in which centromeric activity is distributed along the length of the chromosome—have not. We collected chromosome number and molecular genetic data in Carex scoparia, an eastern North American plant species with holocentric chromosomes and highly variable karyotype (2n = 56–70). There are no deep genetic breaks within C. scoparia that would suggest cryptic species differentiation. However, genetic distance between individuals is positively correlated with chromosome number difference and geographic distance. A positive correlation is also found between chromosome number and genetic distance in the western North American C. pachystachya (2n = 74–81). These findings suggest that geographic distance and the number of karyotype rearrangements separating populations affect the rate of gene flow between those populations. This is the first study to quantify the effects of holocentric chromosome rearrangements on the partitioning of intraspecific genetic variance.     

Progress in the genomics and genome-wide study of sake yeast

ABSTRACT

Completion of the whole genome sequence of a laboratory yeast strain Saccharomyces cerevisiae in 1996 ushered in the development of genome-wide experimental tools and accelerated subsequent genetic study of S. cerevisiae. The study of sake yeast also shared the benefit of such tools as DNA microarrays, gene disruption-mutant collections, and others. Moreover, whole genome analysis of representative sake yeast strain Kyokai no. 7 was performed in the late 2000s, and enabled comparative genomics between sake yeast and laboratory yeast, resulting in some notable finding for of sake yeast genetics. Development of next-generation DNA sequencing and bioinformatics also drastically changed the field of the genetics, including for sake yeast. Genomics and the genome-wide study of sake yeast have progressed under these circumstances during the last two decades, and are summarized in this article.

Abbreviations: AFLP: amplified fragment length polymorphism; CGH: comparative genomic hybridization; CNV: copy number variation; DMS: dimethyl succinate; DSW: deep sea water; LOH: loss of heterozygosity; NGS: next generation sequencer; QTL: quantitative trait loci; QTN: quantitative trait nucleotide; SAM: S-adenosyl methionine; SNV: single nucleotide variation     

Peroxidase activity in non-embryogenic and embryogenic calli and in developing somatic embryos of white fir (Abies concolor Gord. et Glend)

ABSTRACT

Peroxidase activity was monitored during somatic embryogenesis of white fir (Abies concolor Gord. et Glend) starting from a non-embryogenic callus. Results revealed profound differences between non-embryogenic and embryogenic calli with an elevated level of enzyme activity in non-embryogenic ones. Precotyledonary, early cotyledonary and late cotyledonary stages of somatic embryogenesis were characterized by a substantially reduced peroxidase activity compared to callus tissues and regenerated plantlets. Changes in peroxidase activity are as a rule paralleled by variation in isoenzyme composition. The utility of the enzyme in the induction stage of somatic embryogenesis in white fir is proposed.     

Next Generation Sequencing of Acute Myeloid Leukemia: Influencing Prognosis

Background

Epilepsy is genetically complex neurological disorder affecting millions of people of different age groups varying in its type and severity. Copy number variants (CNVs) are key players in the genetic etiology of numerous neurodevelopmental disorders and prior findings also revealed that chromosomal aberrations are more susceptible against the pathogenesis of epilepsy. Novel technologies, such as array comparative genomic hybridization (array-CGH), may help to uncover the pathogenic CNVs in patients with epilepsy.

Results

This study was carried out by high density whole genome array-CGH analysis with blood DNA samples from a cohort of 22 epilepsy patients to search for CNVs associated with epilepsy. Pathogenic rearrangements which include 6p12.1 microduplications in 5 patients covering a total region of 99.9kb and 7q32.3 microdeletions in 3 patients covering a total region of 63.9kb were detected. Two genes BMP5 and PODXL were located in the predicted duplicated and deleted regions respectively. Furthermore, these CNV findings were confirmed by qPCR.

Conclusion

We have described, for the first time, several novel CNVs/genes implicated in epilepsy in the Saudi population. These findings enable us to better describe the genetic variations in epilepsy, and could provide a foundation for understanding the critical regions of the genome which might be involved in the development of epilepsy.

     

Methylation patterns revealed by MSAP profiling in genetically stable somatic embryogenic cultures of <Emphasis Type="Italic">Ocotea catharinensis</Emphasis> (Lauraceae)

Ocotea catharinensis is a rare tree species indigenous to the Atlantic rainforest of South America. In spite of its value as a hardwood species, it is in danger of extinction. The species erratically produces seeds showing irregular flowering and slow growth. Therefore, plants are not easily replaced. Tissue culture-based techniques are commonly used for obtaining living material for tree propagation and in vitro preservation. Therefore, a high-frequency somatic embryogenic system was developed for the species. In the present work, the genetic fidelity of cell aggregates and somatic embryos at various stages of in vitro development of O. catharinensis was investigated using RAPD and AFLP markers. Both analyses confirmed the absence of genetic variation in all developmental stages of O. catharinensis embryogenic cultures, verifying that the in vitro system is genetically stable. The cultures were also analyzed for their methylation profiles at 5′-CCGG-3′ sites by identifying methylation-sensitive amplification polymorphisms. Some of these markers differentiated cell aggregates from embryo bodies. The sequencing of ten MSAP markers revealed that four sequences showed significant similarity to genes encoding plant proteins. Particularly, the predicted amino acid sequence of the fragment designated as OcEaggHMttc155 was similar to the enzyme 1–aminocyclopropane-1-carboxylate oxidase (ACO), which is involved in the biosynthesis of ethylene, and its expression was reported to occur from the beginning to the intermediate stages of plant embryo development. Here, we suggest that this enzyme is possibly involved in the control of the earliest stages of somatic embryogenesis of O. catharinensis, and an approach to study ACO expression during somatic embryogenesis is proposed.     

Somatic Polyploid Petals: Regeneration Offers New Roads for Breeding Belgian Pot Azaleas

Bud sporting, the consequence of sudden variations in gene expression of somatic cells, leads to the occurrence of phenotypically altered shoots in many vegetatively propagated plant species. In ornamentals, such as azalea (Rhododendron simsii), flower colour bud sports are appreciated as a valuable additional source of variation, and it is evident that both genetic and epigenetic mechanisms are involved in the creation of the whole colour range. Flowers exhibiting two-coloured petals, i.e. the margin is coloured differently than the central zone, characterize one of the sport types, namely picotees. This particular sporting type contributes to the enlargement of the available variation not only because of its coloration pattern but interestingly displays somatic polyploidy in its petals. The differently coloured petal margin is tetraploid while the rest of the corolla, as well as the entire plant are diploid. Aiming at introducing polyploidy in the completely diploid breeding collection, in vitro regeneration of tetraploid petal marginal tissue was performed. This led to the production of the first induced tetraploid Belgian azalea. The markedly increased robustness of the flowers as well as their polyploid status is exceptionally interesting for breeding programs.     

Mapping of homoeologous chromosome exchanges influencing quantitative trait variation in Brassica napus

Genomic rearrangements arising during polyploidization are an important source of genetic and phenotypic variation in the recent allopolyploid crop Brassica napus. Exchanges among homoeologous chromosomes, due to interhomoeologue pairing, and deletions without compensating homoeologous duplications are observed in both natural B. napus and synthetic B. napus. Rearrangements of large or small chromosome segments induce gene copy number variation (CNV) and can potentially cause phenotypic changes. Unfortunately, complex genome restructuring is difficult to deal with in linkage mapping studies. Here, we demonstrate how high‐density genetic mapping with codominant, physically anchored SNP markers can detect segmental homoeologous exchanges (HE) as well as deletions and accurately link these to QTL. We validated rearrangements detected in genetic mapping data by whole‐genome resequencing of parental lines along with cytogenetic analysis using fluorescence in situ hybridization with bacterial artificial chromosome probes (BAC‐FISH) coupled with PCR using primers specific to the rearranged region. Using a well‐known QTL region influencing seed quality traits as an example, we confirmed that HE underlies the trait variation in a DH population involving a synthetic B. napus trait donor, and succeeded in narrowing the QTL to a small defined interval that enables delineation of key candidate genes.     

Identification of candidate genes for nicotine withdrawal in C57BL/6J × DBA/2J recombinant inbred mice

Nicotine is the reinforcing ingredient in tobacco. Following chronic exposure, sudden cessation of nicotine use produces negative symptoms of withdrawal that contribute to dependence. The molecular mechanisms underlying nicotine withdrawal behaviors, however, are poorly understood. Using recombinant inbred mice, chronic nicotine was delivered by minipump and withdrawal induced using mecamylamine. Somatic signs of withdrawal, and anxiety-like behavior using elevated plus maze, were then assessed. Interval mapping was used to identify associations between genetic variation and withdrawal behaviors, and with basal gene expression. Differential gene expression following nicotine exposure and withdrawal was also assessed in progenitor mice using microarrays. Quantitative trait loci mapping identified chromosome intervals with significant genetic associations to somatic signs of withdrawal or withdrawal-induced anxiety-like behavior. Using bioinformatics, and association with basal gene expression in nucleus accumbens, we implicated Rb1, Bnip3l, Pnma2, Itm2b, and Kif13b as candidate genes for somatic signs of withdrawal, and Galr1, which showed trans-regulation from a region of chromosome 14 that was associated with somatic signs of withdrawal. Candidate genes within the chromosome 9 region associated with anxiety-like withdrawal behavior included Dixdc1, Ncam1, and Sorl1. Bioinformatics identified six genes that were also significantly associated with nicotine or alcohol traits in recent human genome-wide association studies. Withdrawal-associated somatic signs and anxiety-like behavior had strong non-overlapping genetic associations, respectively, with regions of chromosome 14 and chromosome 9. Genetic, behavioral and gene expression correlations, and bioinformatics analysis identified several candidate genes that may represent novel molecular targets for modulating nicotine withdrawal symptoms.     

Effect arylamine N-acetyltransferase 1 on morphology,adhesion, migration,and invasion of MDA-MB-231 cells: role of matrix metalloproteinases and integrin αV

ABSTRACT

Reducted arylamine N-acetyltransferase (NAT1) in breast cancers is associated with poor patient survival. NAT1 has also been associated with changes in cancer cell survival and invasion both in vitro and in vivo. Here, we report the effects of NAT1 in cancer cell invasion by addressing its role in adherence, migration, and invasion in vitro. The NAT1 gene was deleted in MDA-MB-231, HT-29 and HeLa cells using CRISPR/Cas9 gene editing. Loss of NAT1 increased adherence to collagen in all three cell-lines but migration was unaffected. NAT1 deletion decreased invasion and induced changes to cell morphology. These effects were independent of matrix metalloproteinases but were related to integrin ITGαV expression. The data suggest NAT1 is important in adhesion and invasion through integrin expression.     

Morphological,cytological and molecular characterization of a novel symmetric somatic hybrid between N. tabacum and N. glauca

Abstract

By using the protoplast fusion technique, we have obtained 44 regenerated plants, phenotypically different and distinct from their parents, among which we have identified a fertile symmetric somatic hybrid, designated as TG-32, between N. tabacum var. Gexin No.1 and N. glauca. The morphology, fertility, chromosome number and nuclear constitution of the somatic hybrid have been studied in detail. Unlike other asymmetric interspecific somatic hybrids, the chromosome number of the symmetric somatic hybrid is 72, equal to the sum of chromosomes of both parents. The TG-32 plant has flowers similar to those of N. tabacum, but with petals similar to those of N. glauca. Interestingly the offspring of TG-32 vary in seed production ability with temperature, and produce more seeds under a relatively low temperature. Two SCAR markers were used to evaluate genetic variability and structure. The hybrid amplified the expected fragment, but the parents showed only one of two markers. This experimental result supports the hypothesis of the co-existence of two parental genomes in the somatic hybrid.     

Brazilian red propolis extract enhances expression of antioxidant enzyme genes in vitro and in vivo

ABSTRACT

Brazilian red propolis reportedly has reactive oxygen species (ROS) scavenging effects in vitro, but the cellular mechanisms remain unclear. In the present study, the effects of an ethanol extract of Brazilian red propolis (EERP) on the Nrf2-ARE intracellular antioxidant pathway were examined in vitro and in vivo. EERP and its constituents transactivated the reporter gene through the ARE sequence and enhanced the expression of Nrf2-regulated genes in HEK293 cells. It also increased Nrf2 protein in the nucleus, which was partially inhibited by kinase inhibitors. Furthermore, EERP suppressed ROS generation and cytotoxicity induced by tert-butyl hydroperoxide. In vivo, orally administered EERP increased the expression of Nrf2-regulated genes in mice liver. These results suggest that EERP is a potential resource for preventing oxidative stress-related diseases as an Nrf2 inducer.     

Network-based cancer genomic data integration for pattern discovery

Background

Next-generation sequencing (NGS) has profoundly changed the approach to genetic/genomic research. Particularly, the clinical utility of NGS in detecting mutations associated with disease risk has contributed to the development of effective therapeutic strategies. Recently, comprehensive analysis of somatic genetic mutations by NGS has also been used as a new approach for controlling the quality of cell substrates for manufacturing biopharmaceuticals. However, the quality evaluation of cell substrates by NGS largely depends on the limit of detection (LOD) for rare somatic mutations. The purpose of this study was to develop a simple method for evaluating the ability of whole-exome sequencing (WES) by NGS to detect mutations with low allele frequency. To estimate the LOD of WES for low-frequency somatic mutations, we repeatedly and independently performed WES of a reference genomic DNA using the same NGS platform and assay design. LOD was defined as the allele frequency with a relative standard deviation (RSD) value of 30% and was estimated by a moving average curve of the relation between RSD and allele frequency.

Results

Allele frequencies of 20 mutations in the reference material that had been pre-validated by droplet digital PCR (ddPCR) were obtained from 5, 15, 30, or 40 G base pair (Gbp) sequencing data per run. There was a significant association between the allele frequencies measured by WES and those pre-validated by ddPCR, whose p-value decreased as the sequencing data size increased. By this method, the LOD of allele frequency in WES with the sequencing data of 15 Gbp or more was estimated to be between 5 and 10%.

Conclusions

For properly interpreting the WES data of somatic genetic mutations, it is necessary to have a cutoff threshold of low allele frequencies. The in-house LOD estimated by the simple method shown in this study provides a rationale for setting the cutoff.

     

Genetic variability of invasive species,Fallopia convolvulus (Polygonaceae) in Iran

Abstract

Fallopia (Polygonaceae) as a noxious weed contains 17 species in the world out of which three species occur in Iran with invasive distribution. F. convolvulus growing in wide range of soil types causes significant problems for native ecosystems of river banks. In this study, we have examined genetic variability in F. convolvulus for the first time in Iran. Ten Inter Simple Sequence Repeats (ISSR) markers were used to study the genetic variability on 11 populations of this species. Genetic diversity parameters, genetic distance and gene flow were determined. Genetic variation at inter- and intra-population level was evaluated by different methods. AMOVA and structure analyses revealed high genetic diversity within populations. Mantel test revealed a significant correlation between genetic and geographic distances. Between populations a limited gene flow was observed. It is concluded that local adaptation, low gene exchange and genetic drift can affect genetic diversity of F. convolvulus. Despite self-compatibility of this species, it is proposed that outcrossing may occur because of higher genetic variation among populations of this taxon.     

Gene expression during the male gametophytic phase

Abstract

In recent years a number of experimental findings have indicated that in higher plants the gametophytic phase is able to express its own genetic information, a large part of which it shares with the sporophytic generation. Quantitative estimates of haploid and haplodiploid gene expression have been obtained by mRNA and isozyme analysis in several plant species: 60-70% of the genes are expressed in both pollen and plant, about 10% are pollen-specific, and 20% represent the sporophytic domain. Moreover, it has been demonstrated that stage-specific genes are expressed in the gametophytic generation: at least two sets of genes are activated during pollen development, others are expressed only in the postshedding period, during germination and tube growth. Studies have been made to ascertain the role played by gametophyte-expressed genes in pollen development; the in vivo and in vitro pollen tube growth rate has been revealed to be controlled by the gametophyte genome itself. Differential effects of specific chromosomal deficiencies on the development of maize pollen grains have indicated that components of normal microspore development are controlled by genes located in specific parts of the genome. For single gene analysis, gene transfer can be used; on the contrary, for traits with a multifactorial genetic control, direct proof of gene expression both in the gametophytic and the sporophytic generation can be obtained when selection is applied to the pollen population of a hybrid plant, and response to selection is observed in the resulting sporophytic progeny. Response to selection, applied at different stages of the gametophytic phase, has been described in the sporophytic progeny and this with regard to many adaptive traits; thus the phenomenon can have an important bearing on the genetic structure of natural populations and on higher plant evolution, it can also be used as a breeding tool to increase the efficiency of conventional selection methods.     

Spring phenology shows genetic variation among and within populations in seedlings of Scots pine (Pinus sylvestris L.) in the Scottish Highlands

Background: Genetic differentiation in phenotypic traits is often observed among forest tree populations, but less is known about patterns of adaptive variation within populations. Such variation is expected to enhance the survival likelihood of extant populations under climate change.

Aims: Scots pine (Pinus sylvestris) occurs over a spatially and temporally heterogeneous landscape in Scotland. Our goal was to examine whether populations had differentiated genetically in timing of bud flush in response to spatial heterogeneity and whether variation was also maintained within populations.

Methods: Two common-garden studies, involving maternal families of seedlings from 21 native pinewoods, were established and variation in the trait was measured at the beginning of the second growing season.

Results: Populations showed genetic differences in the trait correlated with the length of growing season at their site of origin, but the majority of variation was observed within populations. Populations also differed in their levels of variation in the trait; a pattern that may be influenced by spatial variation in the extent of temporal climate variability.

Conclusions: Our findings suggest that populations have adapted to their home environments and that they also have substantial ability to adapt in situ to changes in growing season length.