Unbalanced historical phenotypic data from seed regeneration of a barley ex situ collection.
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ABSTRACT:
SUBMITTER: Gonzalez MY
PROVIDER: S-EPMC6278694 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Genebanks are valuable sources of genetic diversity, which can help to cope with future problems of global food security caused by a continuously growing population, stagnating yields and climate change. However, the scarcity of phenotypic and genotypic characterization of genebank accessions severely restricts their use in plant breeding. To warrant the seed integrity of individual accessions during periodical regeneration cycles in the field phenotypic characterizations are performed. This study provides non-orthogonal historical data of 12,754 spring and winter wheat accessions characterized for flowering time, plant height, and thousand grain weight during 70 years of seed regeneration at the German genebank. Supported by historical weather observations outliers were removed following a previously described quality assessment pipeline. In this way, ready-to-use processed phenotypic data across regeneration years were generated and further validated. We encourage international and national genebanks to increase their efforts to transform into bio-digital resource centers. A first important step could consist in unlocking their historical data treasures that allows an educated choice of accessions by scientists and breeders.
| S-EPMC6662709 | biostudies-literature
Project description:Genebanks are a rich source of genetic variation. Most of this variation is absent in breeding programs but may be useful for further crop plant improvement. However, the lack of phenotypic information forms a major obstacle for the educated choice of genebank accessions for research and breeding. A promising approach to fill this information gap is to exploit historical information gathered routinely during seed regeneration cycles. Still, this data is characterized by a high non-orthogonality hampering their analysis. By examining historical data records for flowering time, plant height, and thousand grain weight collected during 70 years of regeneration of 6,207 winter wheat (Triticum aestivum L.) accessions at the German Federal ex situ Genebank, we aimed to elaborate a strategy to analyze and validate non-orthogonal historical data in order to charge genebank information platforms with high quality ready-to-use phenotypic information. First, a three-step quality control assessment considering the plausibility of trait values and a standard as well as a weather parameter index based outlier detection was implemented, resulting in heritability estimates above 0.90 for all three traits. Then, the data was analyzed by estimating best linear unbiased estimations (BLUEs) applying a linear mixed-model approach. An in silico resampling study mimicking different missing data patterns revealed that accessions should be regenerated in a random fashion and not blocked by origin or acquisition date in order to minimize estimation biases in historical data sets. Validation data was obtained from multi-environmental orthogonal field trials considering a random subsample of 3,083 accessions. Correlations above 0.84 between BLUEs estimated for historical data and validation trials outperformed previous approaches and confirmed the robustness of our strategy as well as the high quality of the historical data. The results indicate that the IPK winter wheat collection reveals an extraordinary high phenotypic diversity compared to other collections. The quality checked ready-to-use phenotypic information resulting from this study is the first brick to extend traditional, conservation driven genebanks into bio-digital resource centers.
| S-EPMC5953327 | biostudies-literature
Project description:Plant geneticists have proposed that the dynamic conservation of crop plants in farm environments (in situ conservation) is complementary to static conservation in seed banks (ex situ conservation) because it may help to ensure adaptation to changing conditions. Here, we test whether collections of a traditional variety of Moroccan barley (Hordeum vulgare ssp. vulgare) conserved ex situ showed differences in qualitative and quantitative resistance to the endemic fungal pathogen, Blumeria graminis f.sp. hordei, compared to collections that were continuously cultivated in situ. In detached-leaf assays for qualitative resistance, there were some significant differences between in situ and ex situ conserved collections from the same localities. Some ex situ conserved collections showed lower resistance levels, while others showed higher resistance levels than their in situ conserved counterparts. In field trials for quantitative resistance, similar results were observed, with the highest resistance observed in situ. Overall, this study identifies some cases where the Red Queen appears to drive the evolution of increased resistance in situ. However, in situ conservation does not always result in improved adaptation to pathogen virulence, suggesting a more complex evolutionary scenario, consistent with several published examples of plant-pathogen co-evolution in wild systems.
| S-EPMC3353358 | biostudies-other
Project description:Background and aimsLike other clades, the Coffea genus is highly diversified on the island of Madagascar. The 66 endemic species have colonized various environments and consequently exhibit a wide diversity of morphological, functional and phenological features and reproductive strategies. The trends of interspecific trait variation, which stems from interactions between genetically defined species and their environment, still needed to be addressed for Malagasy coffee trees.MethodsData acquisition was done in the most comprehensive ex situ collection of Madagascan wild Coffea. The structure of endemic wild coffees maintained in an ex situ collection was explored in terms of morphological, phenological and functional traits. The environmental (natural habitat) effect was assessed on traits in species from distinct natural habitats. Phylogenetic signal (Pagel's λ, Blomberg's K) was used to quantify trait proximities among species according to their phylogenetic relatedness.Key resultsDespite the lack of environmental difference in the ex situ collection, widely diverging phenotypes were observed. Phylogenetic signal was found to vary greatly across and even within trait categories. The highest values were exhibited by the ratio of internode mass to leaf mass, the length of the maturation phase and leaf dry matter content (ratio of dry leaf mass to fresh leaf mass). By contrast, traits weakly linked to phylogeny were either constrained by the original natural environment (leaf size) or under selective pressures (phenological traits).ConclusionsThis study gives insight into complex patterns of trait variability found in an ex situ collection, and underlines the opportunities offered by living ex situ collections for research characterizing phenotypic variation.
| S-EPMC7539352 | biostudies-literature
Project description:Key messageGenomic prediction with special weight of major genes is a valuable tool to populate bio-digital resource centers. Phenotypic information of crop genetic resources is a prerequisite for an informed selection that aims to broaden the genetic base of the elite breeding pools. We investigated the potential of genomic prediction based on historical screening data of plant responses against the Barley yellow mosaic viruses for populating the bio-digital resource center of barley. Our study includes dense marker data for 3838 accessions of winter barley, and historical screening data of 1751 accessions for Barley yellow mosaic virus (BaYMV) and of 1771 accessions for Barley mild mosaic virus (BaMMV). Linear mixed models were fitted by considering combinations for the effects of genotypes, years, and locations. The best linear unbiased estimations displayed a broad spectrum of plant responses against BaYMV and BaMMV. Prediction abilities, computed as correlations between predictions and observed phenotypes of accessions, were low for the marker-assisted selection approach amounting to 0.42. In contrast, prediction abilities of genomic best linear unbiased predictions were high, with values of 0.62 for BaYMV and 0.64 for BaMMV. Prediction abilities of genomic prediction were improved by up to ~ 5% using W-BLUP, in which more weight is given to markers with significant major effects found by association mapping. Our results outline the utility of historical screening data and W-BLUP model to predict the performance of the non-phenotyped individuals in genebank collections. The presented strategy can be considered as part of the different approaches used in genebank genomics to valorize genetic resources for their usage in disease resistance breeding and research.
| S-EPMC8263548 | biostudies-literature
Project description:Genebanks aim to optimize their storage conditions in order to postpone seed ageing as long as possible. As most genebanks have a relatively short life history, empirical data about seed longevity during ex situ storage are almost absent. Based on seed characteristics, theoretical predictions indicate that cereal seeds can be stored without substantial loss of viability for time periods exceeding 100 years, even under temperatures of a few degrees above zero. Here we present the results of a germination study in wheat and barley, comparing genebank seed samples maintained at different temperatures for 23-33 years. Wheat and barley seed samples stored at -20°C showed a mean germination of 94% and 90%, respectively, indicating no loss of the initial viability determined for the accessions prior to introduction in the collection. Seed samples maintained at 4°C showed a mean germination of 62% for wheat and 75% for barley. In addition to the observed loss of viability, the 4°C samples also showed a loss in vigour as the time period to reach their final germination was about twice as long compared to the -20°C samples. A subset of the wheat accessions tested in 2011 were retested in 2017, showing further reduction in mean germination to 35% for the 4°C samples, while the -20°C samples remained stable at 95%. Several 4°C samples were even close to a complete loss of viability. Considering that wheat and barley are generally regarded as good maintainers, the rapid loss of seed viability observed in the present study indicates that the ex situ seed storage of genetic resources at 4°C should be treated with caution by genebanks, particularly when used for long-term conservation.
| S-EPMC6016650 | biostudies-literature
Project description:Background:Research projects often involve observation, registration, and data processing starting from information obtained in field experiments. In many cases, these tasks are carried out by several persons in different places, times, and ways, adding different levels of complexity and error in data collecting. Furthermore, data processing can be time consuming, and input errors may produce unwanted results. Results:We have developed a novel, open source software called Phenobook, an easy, flexible, and intuitive tool to organize, collect, and save experimental data for further analyses. Phenobook was conceived to collect phenotypic observations in a user-friendly, cost-effective way. It consists of a web-based software for experiment design, data input and visualization, and exportation, combined with a mobile application for remote data collecting. We provide in this article a detailed description of the developed tool. Conclusion:Phenobook is a software tool that can be easily implemented in collaborative research and development projects involving data collecting and forward analyses. Adopting Phenobook is expected to improve the involved processes by minimizing input errors, resulting in higher quality and reliability of the research outcomes.
| S-EPMC5530315 | biostudies-literature
Project description:Fluctuations in the growth rate of a bacterial culture during unbalanced growth are generally considered undesirable in quantitative studies of bacterial physiology. Under well-controlled experimental conditions, however, these fluctuations are not random but instead reflect the interplay between intra-cellular networks underlying bacterial growth and the growth environment. Therefore, these fluctuations could be considered quantitative phenotypes of the bacteria under a specific growth condition. Here, we present a method to identify "phenotypic signatures" by time-frequency analysis of unbalanced growth curves measured with high temporal resolution. The signatures are then applied to differentiate amongst different bacterial strains or the same strain under different growth conditions, and to identify the essential architecture of the gene network underlying the observed growth dynamics. Our method has implications for both basic understanding of bacterial physiology and for the classification of bacterial strains.
| S-EPMC4125075 | biostudies-literature
Project description:The goal of this study is the discovery of (a) meaningful phylogenomic relationships among members of this B. cereus/B. anthracis group, and (b) reliable gene-phenotype associations, e.g. recognition of links between genomic traits and the ability of certain strains to cause various forms of disease. We also tried to elucidate genome evolution aspects that may lead to the emergence of variants that are capable (or have the potential) of causing anthrax-like disease. This large-scale comparative genomics approach is unprecedented for this taxonomic group. Dr. A. Hoffmaster (CDC) provided the PFGRC with 73 B. cereus and B. anthracis isolates from the CDC culture collection. Of these, 27 were isolated from patients with severe or systemic disease; ten isolates of this group were obtained from patients (welding factory workers) with anthrax-like disease or from the environment near their workplace. Another set of 26 represented isolates from food-born illnesses. Of the 26 gastrointestinal disease isolates (GIDI), 10 were obtained from patients with diarrhea, whereas another set of 10 had been shown to harbor the emetic (vomit) toxin gene by PCR. The rest of the group consisted of 20 isolates with various phenotypes. All strains were screened for their genomic content using the B. cereus/B. anthracis species microarray.
2009-11-25 | GSE19125 | GEO
Project description: Not available
| S-BSST36 | biostudies-other