1,721,321 research outputs found
New genetic achievements on gametophytic self-incompatibility of fruit trees
No full textSelf-incompatibility is a crucial aspect of the reproductive biology of many fruit species, and in view of its impact on fruit production it has been extensively studied by several research groups worldwide. Taking advantage of modern high-throughput technologies and multi-disciplinary approaches, recent studies provided interesting insights on many aspects related to this phenomenon, including the biochemical and cytological events underlying it, their genetic control, and the complex evolution of self-incompatibility genes in the Rosaceae. Hereby we discuss some of the most relevant results recently produced by the scientific community in this field, addressing theoretical and practical questions of fruit breeding and growing, and focusing on future research challenges
Use of semi-compatible crosses in breeding for apple scab resistance
No full textGametophytic self-incompatibility is generally considered a hurdle for breeding programs, as it reduces the number of possible cross combinations. The wide variety of S-haplotypes in apple (Malus × domestica) reduces the probability of fully incompatible crosses, while the occurrence of semi-compatible combinations is more frequent. The yield in such combinations does not vary much with respect to full compatibility, but noteworthy a single S-haplotype from the male parent (pollen donor) will be transmitted to the progeny. This aspect should be carefully taken into account in breeding programs when one or more genes of interest are placed in proximity to the S-locus, as the segregation of the paternal alleles in the progeny will skew from the expected 1:1 ratio, reducing the frequency of the allele linked to the rejected S-haplotype. Among the genes linked to the S-locus in the rosaceous fruit trees, one of the most important is the apple scab resistance gene Rvi5. This gene, introduced in Malus × domestica from M. micromalus and × M. atrosanguinea 804, was fine-mapped in two large segregating populations and proved to be placed in close proximity to the S-locus, on the bottom of chromosome 17. Therefore, knowledge of the S-genotype of parental cultivars can be exploited to plan semi-compatible crosses that dramatically increase the frequency of the resistance gene in the progeny, and to avoid those combinations that conversely would reduce it
Correlation between tree-ring series as a dendroprovenancing evaluation tool
Full text linkThe use of correlation between tree-ring series as a proximity indicator in dendroprovenance analyses is often questioned. High correlations may occur between series at a great distance, but conversely, low correlations may occur between series that are close to each other. This discrepancy has prompted the exploration of alternative dendroprovenancing methods, but many of them have proven to be unreliable or impractical. In this study, approximately 12,000 geolocalised tree-ring series from the three main Alpine conifers—spruce, larch, and fir—were analysed to investigate the extent to which correlation analysis can be used as a dendroprovenance tool. The results clearly indicate a significant increase of correlation at low distance and validate the proposed correlation approach. The large dataset also made it possible to develop a simplified quantile regression model that could be used to estimate distance in kilometres based on correlation values between the tree-ring series. Spruce exhibited the most promising results, which is attributed in part to the extensive dataset available, while there were challenges with fir in accurately determining distances between sites. Finally, the study also evaluated the impact of altitude on distance estimation and showed how this environmental factor influences variations in dendroprovenance analyse
La sterilità del ciliegio: gruppi di incompatibilità e varietà autofertili.
No full textIl ciliegio, come molte altre specie da frutto appartenenti alle Rosacee, possiede un meccanismo di auto-incompatibilità controllato dal locus S (“sterilità”). Questo meccanismo si è evoluto per promuovere la fecondazione incrociata impedendo l’auto-fecondazione; il fiore di una pianta non può quindi essere fecondato dal suo stesso polline o da polline prodotto da piante della stessa varietà. Una cultivar di ciliegio per essere produttiva richiede pertanto la consociazione con almeno un genotipo compatibile che ne assicuri un’efficiente impollinazione. In alternativa si può ricorrere a cultivar auto-compatibili, in cui una mutazione (spontanea o indotta) inattiva il sistema di riconoscimento polline-pistillo che porta all’incompatibilità, rendendo la varietà autofertile
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Biomarker selection in R: the BioMark package
Full text linkThe introduction of high-throughput measurement techniques has transformed modern biology, where the phrase “high-throughput” should be seen in the light of the number of variables measured rather than the number of samples: that is, we have many data about few objects. Finding differences between two groups of objects (patients and controls, different varieties of fruits, different food products, ...) has become a very important area of research. The classical statistical tests in most cases suffer from many false positives from multiple testing, and correcting for this often leads to low power. Moreover, it is unclear what threshold to choose: in many cases the level of alpha is being adjusted until the number of “significant” variables seems more or less right (for whatever reason: follow-up experiments typically are more time-consuming and one may be forced to settle for the best twenty or thirty variables).
The R package BioMark addresses both the problem of what threshold to choose, and how to select relevant variables by providing Higher Criticism thresholding (Donoho and Jin, 2008) and Stability Selection (Meinshausen and Buehlmann, 2010), respectively. The HC approach is a kind of second-level significance testing: it assesses the distribution of p values from a primary test and compares that to the expected uniform distribution. Assuming that real differences are rare and weak, the method then suggests an appropriate cutoff point, based on the data at hand. Stability selection works by repeatedly subsampling the data, and only considering those variables as putative biomarkers that consistently show up as important.
We have adapted both Higher Criticism and Stability Selection for use with omics data, and provide an easily accessible implementation in our BioMark package, available from CRAN (http://cran.r-project.org). The Higher Criticism approach is extended to also work with methods typically employed in metabolomics and proteomics, such as PLSDA, PCLDA and the VIP measure (Wehrens and Franceschi, 2012). Since no null distribution can be defined beforehand, it is derived using label permutations, and the results show excellent performance for experimental spike-in data (also included in the BioMark package). The same multivariate methods have been combined with stability selection (Wehrens et al., 2011) and again show very good results, testifying of the robustness of the stability selection paradigm.
References:
Donoho D, Jin J (2008). “Higher criticism thresholding: optimal feature selection when useful
features are rare and weak.” PNAS, 105(39), 14790–14795.
Meinshausen N, Buehlmann P (2010). “Stability selection.” J. R. Statist. Soc. B, 72, 417–473. With discussion.
Wehrens R, Franceschi P, Vrhovsek U, Mattivi F (2011). “Stability-based biomarker selection.” Anal. Chim. Acta, 705, 15–23.
Wehrens R, Franceschi P (2012). “Thresholding for Biomarker Selection in Multivariate Data using Higher Criticism”. Submitted for publication
Is the E/Z Iminium Ratio a Good Enantioselectivity Predictor in Iminium Catalysis?
Full text linkDeveloping new enantioselective reactions is an important part of chemical discovery but requires time and resources to test large arrays of potential reaction conditions. New techniques are required to analyse many different reactions quickly and efficiently. Mass spectrometry is a high-throughput method; when combined with ion-mobility spectrometry, this technique can monitor diastereomeric reaction intermediates and thus be a handle to study enantioselective reactions. Through this technique and others, it was noted before that in the organocatalytic 1,4-addition to α,β-unsaturated aldehydes, the abundance of initial diastereomeric intermediates correlates strongly to that of the final enantiomeric products. This work determines isomeric abundance for various catalysts and aldehydes and uses it to predict the enantiomeric excess of two control reactions. The prediction matches well for one reaction but does not predict the obtained results for the second. This finding confirms that the E/Z ratio of the iminium intermediates can be used as a predictor for some reactions, but the kinetics of the following steps can dramatically change the true enantioselectivit
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