95 publications from this institution
The potential of alternative oxidase (AOX) genes to develop functional markers for plant breeding programs has been emphasized. In this sense, it is essential to have a reliable classification system, which could aid in the selection of candidate AOX genes from...
The nuclear-encoded plastid terminal oxidase gene (PTOX) is present in photosynthetic species and functions in the oxidation of the plastoquinone pool. It plays an important role on chlororespiration, chromorespiration and carotenoid biosynthesis. Here, we show short-term early response of carrot PTOX (DcPTOX) in leaves of two carrot inbred lines upon chilling. Analysis of the complete gene confirmed DcPTOX as a single gene and revealed an exceptionally large genomic sequence (9422bp) in comparison to other species, comprising nine exons interrupted by eight introns. In silico analysis based on data from whole genome sequencing projects discovered that some plant species present two PTOX genes. A search for sequence variability at genomic level was performed in the heterogeneous, ancient carrot cultivar ‘Rotin’. DcPTOX revealed intron length polymorphisms (ILPs) in intron 2, due to the occurrence of two insertion/deletions (InDels) events. Prediction of pre-miRNA sequences in intronic regions of DcPTOX showed two putative locations coding for putative miRNAs, one located at intron 2 and other located at intron 6. Both putative miRNAs revealed high homology with miRNAs described in Glycine max (gma-miR1520p) and Oryza sativa (osa-miR5494), respectively. Plant disease resistance genes were identified as miRNAs target genes.
Functional markers for stress tolerance can be used in plant breeding to identify genotypes with high yield stabilities under various conditions. Thus, a good marker should show a strong correlation with favourable adaptive plant behaviour. The efficient reprogramming of target cells for yield determination is currently considered to be the most important step towards defining abiotic stress tolerance. In this Opinion article, we propose a role for the alternative oxidase (AOX) gene as a marker for genetic variation in cell reprogramming and yield stability. Evidence to support this idea comes from the metabolic role of alternative respiration under stress, the link between AOX activity and differential growth, and the single nucleotide polymorphism recently observed in AOX genes. We propose an innovative, interdisciplinary and global research strategy for future experimentation on AOX genes that could have an application in plant breeding.
AOX gene family in motion marks in-born efficiency of respiration adjustment; can serve for primer screening, genotype ranking, in vitro-plant discriminati
Backgroung Selection of reference genes (RGs) for normalization of PCR-gene expression data includes two crucial steps: determination of the among-sample transcriptionally more stable genes and subsequent choosing of the most suitable genes as internal controls. Both steps can be carried-out through generally accepted strategies each having different strengths and weaknesses. The present study proposes to reinforce normalization of gene expression data by integrating and adding analytical revision at critical steps of those accepted procedures. Especially crucial is to counterbalance a higher representative number of RGs with a correspondent increase in their average transcriptional instability or a generalised co-expression trend among the samples. This methodological study used in vitro olive adventitious rooting as an experimental system, since the underlying morphogenetic process -wich is common to diverse species- is still not completely understood. Results Firstly, RG candidates were ranked according to transcriptional stability following a simple statistical method that reduces biasing effects of concomitant, systematic biological variations associated to experimental conditions, such as the variations caused by gene co-regulation. Those types of systematic co-variation are unconsidered by several popular ad hoc informatics programmes. To select the adequate genes among those already ranked, an algorithm of one of the ad hoc informatics programmes (GeNorm) was adapted to allow partial automatization of RG selection for any strategy of transcriptional-gene stability ordering. In order to delve into the resulting possible RG sets suitability for inter-assay comparisons and technical-error compensation, separate statistics were formulated. The achieved results were compared with those obtained by standard stability ranking methods. Finally, a double evaluation was performed to accurately contrast two choice RG sets. The whole strategy was applied to a panel considering several independent factors, but the suitability of the obtained putative RG sets was tested for cases restricted to fewer variables. H2B , OUB and ACT are valid for normalization in transcriptional studies on olive microshoot rooting when comparing treatments, time points and assays. Conclusions The set of genes identified as internal reference is now available for wider expression studies on any target gene in similar biological systems. The overall methodology aims to constitute a guide for general application.
Genome fingerprinting by random amplified polymorphic DNA (RAPD) is a subject for critical discussion. Reproducibility of the method is often hampered by its high sensitivity to experimental and technical conditions and generation of a fingerprint pattern is highly determined by competition between primer binding sites in the genome of interist. Nevertheless, under standardized conditions, the especially high sensitivity of genome organisation to RAPD analysis may particularly offer the chance to reveal differential changes in genome organisation using markers. To test this hypothesis, RAPD fingerprints were performed on a primary culture and on different tissues and organs of carrot plants, including leaves of different ages. Polymorphic RAPD bands were discovered that were dependent on the regulation of cell division-growth, displayed tissue specificity or depended on the age of the tissue. The differential RAPD fingerprints were reproducible and occurred with different individual plants of similar genotypes. The observed polymorphism was obviously based on quantitative variation in the target genomes. Also, the putative loss of variable bands could be traced back to quantitative polymorphism by varying primer or template concentration.
Growth rates of plant tissues depend on both the respiration rate and the efficiency with which carbon is incorporated into new structural biomass. Calorespirometric measurement of respiratory heat and CO2 rates, from which both efficiency and growth rate can be calculated, is a well established method for determining the effects of rapid temperature changes on the respiratory and growth properties of plant tissues. The effect of the alternative oxidase/cytochrome oxidase activity ratio on efficiency is calculated from first principles. Data on the temperature dependence of the substrate carbon conversion efficiency are tabulated. These data show that epsilon is maximum and approximately constant through the optimum growth temperature range and decreases rapidly as temperatures approach temperature limits to growth. The width of the maximum and the slopes of decreasing epsilon at high and low temperatures vary greatly with species, cultivars and accessions.
Functional marker (FM) development across plant species requires common allelic sequences that affect phenotypic variation in the same way. The identification of orthologous genes showing the same function across species could indicate conservation of functional...
No abstract is provided for this article.
The methylation and amplification pattern of genomic DNA of carrot root expiants (Daucus carota L.) undergoes transitory changes during the cultural cycle.
By definition, the domestication process leads to an overall reduction of crop genetic diversity. This lead to the current search of genomic regions in wild crop relatives (CWR), an important task for modern carrot breeding. Nowadays massive sequencing possibilities can allow for discovery of novel genetic resources in wild populations, but this quest could be aided by the use of a surrogate gene (to first identify and prioritize novel wild populations for increased sequencing effort). Alternative oxidase (AOX) gene family seems to be linked to all kinds of abiotic and biotic stress reactions in various organisms and thus have the potential to be used in the identification of CWR hotspots of environment-adapted diversity. High variability of DcAOX1 was found in populations of wild carrot sampled across a West-European environmental gradient. Even though no direct relation was found with the analyzed climatic conditions or with physical distance, population differentiation exists and results mainly from the polymorphisms associated with DcAOX1 exon 1 and intron 1. The relatively high number of amino acid changes and the identification of several unusually variable positions (through a likelihood ratio test), suggests that DcAOX1 gene might be under positive selection. However, if positive selection is considered, it only acts on some specific populations (i.e. is in the form of adaptive differences in different population locations) given the observed high genetic diversity. We were able to identify two populations with higher levels of differentiation which are promising as hot spots of specific functional diversity.
