1,721,089 research outputs found
Genomics applied to the analysis of flowering time, abiotic stress tolerance and disease resistance: a review of what we have learned in lolium spp
Full text linkFlowering time, abiotic stress tolerance and disease resistance are important agronomic traits of forage species like Lolium spp. Understanding the genetic control of these traits is enabled by the combination of genomic tools with conventional breeding techniques. Flowering time in this genus represents a complex trait due to the differences in the primary induction requirements among the species. In total, 36 QTLs (Quantitative Trait Locus) were identified across all seven linkage groups of Italian and perennial ryegrass involved in the flowering pathways, with several putative orthologous/homologous genes that have been characterized in other major crops. From the perspective of climate change, abiotic stress tolerance has become an essential feature; many QTLs that are involved in the control of plant responses have been identified, and transcriptional studies focusing on drought tolerance reported several DEGs (Differentially Expressed Genes) involved in carbon and lipid metabolism and signal transduction. Due to the incidence of microbial diseases, QTLs useful to developing cultivars resistant to bacterial wilt (Xanthomonas translucens pv. graminis), ryegrass crown rust (Puccinia coronata f. sp. Lolii) and gray leaf spot (Magnaporthe grisea/oryzae) have been mapped in both L. perenne and L. multiflorum populations. Due to the great importance of Lolium species, especially as forage crops, additional information about the three aforementioned agronomic traits is needed
Author Correction: Uncovering the sources of DNA found on the Turin Shroud
Full text linkAn amendment to this paper has been published and can be accessed via a link at the top of the paper
ANNOTATION AND EXPRESSION OF FDM-LIKE GENES IN SEXUAL AND APOMICTIC MODEL SPECIES
Full text linkAposporous apomixis is a reproductive strategy that leads to seed production by avoiding
female sporogenesis and, eventually, fertilization. In this peculiar reproductive strategy, embryo and
endosperm are formed from unreduced gametes developing from somatic cells belonging to the
ovule nucellus. Recently gained information on ovule gene expression in the apomictic model
species Hypericum perforatum L. demonstrated that a few genes involved in the RNA-directed
DNA methylation pathway (RdDM) are differentially expressed in ovules collected from apomictic
accessions at pre-meiotic stages. In A. thaliana, the protein Involved in De Novo 2 (IDN2), together
with members of the gene family Factors of DNA Methylation (FDM1, FDM2), acts downstream of
the RdDM. In this pathway, IDN2/FDM complex are recruited to the chromatin by the ra-siRNAPol V transcript duplex, and then bind the un-methylated DNA to promote DNA methylation of
both transposons and protein coding genes. Remarkably, the knock-out of genes involved in the
RdDM in sexually reproducing species such as A. thaliana and Z. mays results in phenotypes
mimicking early events of aposporous apomixis. Taken together, these findings let us to
hypothesize that RNA-directed DNA methylation might be involved in correct patterning of cell
fate determination in the ovule in sexual and apomictic species. This research focuses on genes
belonging to the gene family known as Factors of DNA Methylation (FDM1-5) and their closely
related IDN2 (Involved in De Novo 2). Our research aim is a better understanding of roles played
by these genes in the frame of ovule cell fate determination and gametes formation.
Bioinformatics analyses were performed in order to identify and annotate all gene family
members expressed in H. perforatum ovules. Gene expression differences between pistils collected
from sexual and apomictic accessions were confirmed by qPCR and ISH. Correlated experiments
were performed by taking advantage of mutant lines available for A. thaliana. IDN2 and FDM1-5
knockout lines were analyzed for alterations in total seed set and plant habits. Mutant lines
displayed overlapping phenotypes, including the reduction of seed set. Overall, our phenotypic data
are in line with a sporophytic effect resulting in the ovule abortion in A. thaliana. GUS reporter
lines were adopted to visualize the FDM promoter activity in ovules at different developmental time
points. Furthermore, the development of a protocol suitable for whole-mount qPCR assays allowed
rapid and reliable quantification of gene expression in micro-dissected ovules. Our results elucidate
the role of FDM and IDN2 genes in both sexual and apomicts plants and add new factors affecting
the complex events involved in ovule and gametes formation that should be further investigated
Molecular Characterization and Genetic Structure Evaluation of Breeding Populations of Fennel (Foeniculum vulgare Mill.)
Full text linkFennel, or Foeniculum vulgare Mill., is an important horticultural crop belonging to the Apiaceae family that is cultivated worldwide and used in the agri-food sector and for pharmaceutical preparations. Breeding strategies in this species usually involve three parental lines, including two maternal lines (one cytoplasmic male-sterile line and an ideotype representative maintainer line) that are crossed to obtain an ideotype representative of the cytoplasmic male-sterile line and one paternal line, used as a pollinator in crosses with the progeny of the derived maternal lines. From this cross, F1 hybrid progenies are obtained, which are characterized by high levels of heterozygosity and hybrid vigor. In this study, over 450 plants, representing 8 breeding populations and their respective 3 parental and 1 progeny line, were genotyped by means of codominant molecular markers. The 12 highly polymorphic microsatellites enabled the analyses of the genetic variability, distinctiveness and stability of each breeding line. Moreover, the genetic structure of the core collection was investigated, which, together with the homozygosity, gene flow and genetic similarity results, allowed the identification of unsuitable lines to be used in breeding plans due to their low homozygosity (10.4% in the pollinator line of population 7). Moreover, the Bayesian reconstruction of the core collection’s genetic structure, based on the codominant markers used, allowed us to confirm the distinctiveness results obtained from the genetic similarity investigation and the computed gene flow estimates. Among these, a trend in hybrid heterozygosity was also observed, that increased when the genetic similarity between the respective parental lines decreased. Thus, this research proposes a suitable method for genotyping fennel populations in pre-and post-breeding approaches, such as marker-assisted breeding or breeding line distinctiveness and stability verifications
Genetic diversity and stand structure of neighboring white willow (Salix alba L.) populations along fragmented riparian corridors: a case study
Full text linkRemnant riparian woodlands have an important landscape function, due to their ability to act as ecological corridors. In this study we used molecular markers to assess the genetic variation occurring within and between spontaneous white willow (Salix alba L.) riparian woodlands. Our main goal was to evaluate the extent to which the fragmentation of a woodland corridor along a heavily impacted river in northeastern Italy and stand structural conditions may have affected the population genetics. Although having different structures, the three examined white willow stands showed high estimates of genetic similarity, as well as low genetic differentiation between them, indicating that they shared a similar gene pool and that the stands could result from a common set of individual genotypes, and should be regarded as metapopulations. The magnitude of genetic diversity within each of the stands and genetic differentiation between them, despite their high sexual reproductive capacity associated with a highly marked gene flow, suggest that these stands are dynamic and capable of adaptive responses to possible changes in their fluvial environment. However, the factors influencing genetic diversity should be interpreted from a long-term perspective. Fluvial geomorphic patterns in regulated rivers may be modified to a degree that could lead to changes in dispersal processes, sexual reproduction vs. asexual propagation, and hence genetic diversity
Apomeiosis in Poa pratensis L. and Medicago sativa L.
No full textRegnum Vegetabile Volume 147.
A series of monographs in plant systematics, from the International Association for
Plant Taxonomy
Hormone profiles and antioxidant activity of cultivated and wild tomato seedlings under low-temperature stress
Full text linkLow temperature is a major limiting factor for the growth and reproduction of some plant species, such as tomato. So far, few studies have been conducted on the effects of low temperature, and the mechanisms of plants’ response to this type of stress is not fully clear. In the current study, the effects of low, nonfreezing temperature (10◦ C for three days) on the hormone content, antioxidant activity, and expression patterns of cold-related genes in the leaves of cold-tolerant species (Solanum habrochaites Accession ‘LA1777′ ) and cold-susceptible species (Solanum lycopersicum cultivar ‘Moneymaker’) were investigated. Low temperature increased the abscisic acid (ABA) content in both tomato species, while the content of zeatin-type cytokinins (ZT) increased in the cold-tolerant species. However, the content of indole-3-acetic acid (IAA) and gibberellic acid (GA) reduced in response to low temperature in susceptible species. Accordingly, cytokinin (CK) is identified as an important hormone associated with low-temperature stress in tomato. In addition, our results indicate that the C-repeat/DRE binding factor 1 (CBF1) gene is less induced in response to low temperature in tomato, although transcription of the inducer of CBF expression 1 (ICE1) gene was upregulated under low temperature in both tomato species. It seems that ICE1 may modulate cold-regulated (COR) genes in a CBF-independent way. In addition, in response to low temperature, the malondialdehyde (MDA) level and membrane stability index (MSI) increased in the susceptible species, indicating that low temperature induces oxidative stress. Additionally, we found that glutathione peroxidase is highly involved in reactive oxygen species (ROS) scavenging induced by low temperature, and antioxidants are more induced in tolerant species. Overall, our results suggest that sub-optimal temperatures promote oxidative stress in tomato and CK is introduced as a factor related to the response to low temperature that requires deeper attention in future breeding programs of tomato
TRANSCRIPTOMIC ANALYSIS OF OVULE-SPECIFIC CELL LINEAGES TO IDENTIFY GENES RELATED TO APOSPOROUS APOMIXIS IN HYPERICUM PERFORATUM L.
Full text linkThe medicinal plant St. John’s wort (Hypericum perforatum L.) is an attractive model system
for the study of aposporous apomixis. The key biological features of apomixis in this species are the
by-passing of meiosis, the differentiation of aposporous initials into embryo sacs containing
unreduced egg cells, their autonomous development in functional embryos without fertilization, and
the formation of viable endosperm either via fertilization-independent means or following
fertilization with a sperm nucleus. The aim of this research is to define gene expression changes
occurring in the nucellar cell types of the ovules primarily involved in the differentiation of the
megaspore mother cells and aposporous initials. To this end, a laser-capture microdissection
approach was adopted in combination with the RNA-seq technology in order to restrict the frame of
our investigations to a specific portion of the ovule, i.e. the nucellus, at developmental stages
preceding the differentiation of aposporous initials. Overall, our gene expression analysis identified
270 and 81 unigenes that were found significantly up- and down-regulated between ovules collected
from sexual and apomictic accessions. Ontological annotation of differentially expressed genes
indicated that genes up-regulated in apomictic ovules were significantly enriched in ontological
terms related to the RNA-directed DNA polymerase activity and the RNA binding. Among these
genes, several actors of the RdDM pathway were found, suggesting that the phenotypic expression
of early events of aposporous apomixis is associated to changes in de novo DNA methylation
mediated by small RNAs. Furthermore, as deregulation of single components of the sexual
developmental pathway is believed to be a trigger of the apomictic reproductive program, genes
involved in sporogenesis, gametogenesis and response to hormonal stimuli were annotated and
investigated in great detail. The expression analysis of candidate genes was performed not only by
Real-Time qPCR but also by ISH assays in order to verify the temporal and spatial expression
patterns of selected transcripts in the ovule. Finally, the activity of specific genes in relation to
embryo sac and/or embryo formation was investigated by using A. thaliana knock-out lines.
Overall, our data suggest that phenotypic expression of aposporous apomixis is concomitant with
the modulation of key genes involved in the sexual reproductive pathway, hormones and other
actors likely playing a crucial role in the RNA-directed DNA methylation pathway
Impact of genomic and transcriptomic resources on apiaceae crop breeding strategies
Full text linkThe Apiaceae taxon is one of the most important families of flowering plants and includes thousands of species used for food, flavoring, fragrance, medical and industrial purposes. This study had the specific intent of reviewing the main genomics and transcriptomic data available for this family and their use for the constitution of new varieties. This was achieved starting from the description of the main reproductive systems and barriers, with particular reference to cytoplasmic (CMS) and nuclear (NMS) male sterility. We found that CMS and NMS systems have been discovered and successfully exploited for the development of varieties only in Foeniculum vulgare, Daucus carota, Apium graveolens and Pastinaca sativa; whereas, strategies to limit self-pollination have been poorly considered. Since the constitution of new varieties benefits from the synergistic use of marker-assisted breeding in combination with conventional breeding schemes, we also analyzed and discussed the available SNP and SSR marker datasets (20 species) and genomes (8 species). Furthermore, the RNA-seq studies aimed at elucidating key pathways in stress tolerance or biosynthesis of the metabolites of interest were limited and proportional to the economic weight of each species. Finally, by aligning 53 plastid genomes from as many species as possible, we demonstrated the precision offered by the super barcoding approach to reconstruct the phylogenetic relationships of Apiaceae species. Overall, despite the impressive size of this family, we documented an evident lack of molecular data, especially because genomic and transcriptomic resources are circumscribed to a small number of species. We believe that our contribution can help future studies aimed at developing molecular tools for boosting breeding programs in crop plants of the Apiaceae family
Annotation and Expression of IDN2-like and FDM-like genes in sexual and aposporous hypericum perforatum L. Accessions
Full text linkThe protein IDN2, together with the highly similar interactors FDM1 and FDM2, is required for RNA-directed DNA methylation (RdDM) and siRNA production. Epigenetic regulation of gene expression is required to restrict cell fate determination in A. thaliana ovules. Recently, three transcripts sharing high similarity with the A. thaliana IDN2 and FDM1-2 were found to be differentially expressed in ovules of apomictic Hypericum perforatum L. accessions. To gain further insight into the expression and regulation of these genes in the context of apomixis, we investigated genomic, transcriptional and functional aspects of the gene family in this species. The H. perforatum genome encodes for two IDN2-like and 7 FDM-like genes. Differential and heterochronic expression of FDM4-like genes was found in H. perforatum pistils. The involvement of these genes in reproduction and seed development is consistent with the observed reduction of the seed set and high variability in seed size in A. thaliana IDN2 and FDM-like knockout lines. Differential expression of IDN2-like and FDM-like genes in H. perforatum was predicted to affect the network of potential interactions between these proteins. Furthermore, pistil transcript levels are modulated by cytokinin and auxin but the effect operated by the two hormones depends on the reproductive phenotype
- …
