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PLOS Genetics: Polygenic Modeling with Bayesian Sparse Linear Mixed Models

PLOS Genetics: Polygenic Modeling with Bayesian Sparse Linear Mixed Models | Plant Breeding and Genomics News | Scoop.it

Both linear mixed models (LMMs) and sparse regression models are widely used in genetics applications, including, recently, polygenic modeling in genome-wide association studies. These two approaches make very different assumptions, so are expected to perform well in different situations. However, in practice, for a given dataset one typically does not know which assumptions will be more accurate. Motivated by this, we consider a hybrid of the two, which we refer to as a “Bayesian sparse linear mixed model” (BSLMM) that includes both these models as special cases. We address several key computational and statistical issues that arise when applying BSLMM, including appropriate prior specification for the hyper-parameters and a novel Markov chain Monte Carlo algorithm for posterior inference. We apply BSLMM and compare it with other methods for two polygenic modeling applications: estimating the proportion of variance in phenotypes explained (PVE) by available genotypes, and phenotype (or breeding value) prediction. For PVE estimation, we demonstrate that BSLMM combines the advantages of both standard LMMs and sparse regression modeling. For phenotype prediction it considerably outperforms either of the other two methods, as well as several other large-scale regression methods previously suggested for this problem. Software implementing our method is freely available from http://stephenslab.uchicago.edu/software.html.

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BMC Bioinformatics | Abstract | Prediction of a time-to-event trait using genome wide SNP data

Abstract (provisional)Background

A popular objective of many high-throughput genome projects is to discover various genomic markers associated with traits and develop statistical models to predict traits of future patients based on marker values.

Results

In this paper, we present a prediction method for time-to-event traits using genome-wide single-nucleotide polymorphisms (SNPs). We also propose a MaxTest associating between a time-to-event trait and a SNP accounting for its possible genetic models. The proposed MaxTest can help screen out nonprognostic SNPs and identify genetic models of prognostic SNPs. The performance of the proposed method is evaluated through simulations.

Conclusions

In conjunction with the MaxTest, the proposed method provides more parsimonious prediction models but includes more prognostic SNPs than some naive prediction methods. The proposed method is demonstrated with real GWAS data.

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Identification of QTLs for capsaicinoids, fruit quality, and plant architecture-related traits in an interspecific Capsicum RIL population - Genome

Identification of QTLs for capsaicinoids, fruit quality, and plant architecture-related traits in an interspecific Capsicum RIL population - Genome | Plant Breeding and Genomics News | Scoop.it

Quantitative trait loci (QTL) analyses in pepper are common for horticultural, disease resistance, and fruit quality traits; although none of the studies to date have used sequence-based markers associated with genes. In this study we measured plant architectural, phenological, and fruit quality traits in a pepper mapping population consisting of 92 recombinant inbred lines derived from a cross between Capsicum frutescens acc. 2814-6 and C. annuum var. NuMexRNAKY. Phenotypic measurements were correlated to loci in a high-density EST-based genetic map. In total, 96 QTL were identified for 38 traits, including 12 QTL associated with capsaicinoid levels. Twenty-one loci showed correlation among seemingly unrelated phenotypic categories, highlighting tight linkage or shared genetics between previously unassociated traits in pepper.

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BMC Bioinformatics | Abstract | A computational method for detecting copy number variations using scale-space filtering

Background: As next-generation sequencing technology made rapid and cost-effective sequencing available, theimportance of computational approaches in finding and analyzing copy number variations (CNVs)has been amplified. Furthermore, most genome projects need to accurately analyze sequences withfairly low-coverage read data. It is urgently needed to develop a method to detect the exact types andlocations of CNVs from low coverage read data. Results: Here, we propose a new CNV detection method, CNV_SS, which uses scale-space filtering. Thescale-space filtering is evaluated by applying to the read coverage data the Gaussian convolution forvarious scales according to a given scaling parameter. Next, by differentiating twice and finding zerocrossingpoints, inflection points of scale-space filtered read coverage data are calculated per scale.Then, the types and the exact locations of CNVs are obtained by analyzing the finger print map, thecontours of zero-crossing points for various scales. Conclusions: The performance of CNV_SS showed that FNR and FPR stay in the range of 1.27% to 2.43% and1.14% to 2.44%, respectively, even at a relatively low coverage(0.5x=C=2x). CNV_SS gave alsomuch more effective results than the conventional methods in the evaluation of FNR, at 3.82% at leastand 76.97% at most even when the coverage level of read data is low. CNV_SS source code is freelyavailable from http://dblab.hallym.ac.kr/CNV_SS/.

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PLOS ONE: Genetic Analysis of Grain Filling Rate Using Conditional QTL Mapping in Maize

PLOS ONE: Genetic Analysis of Grain Filling Rate Using Conditional QTL Mapping in Maize | Plant Breeding and Genomics News | Scoop.it
AbstractThe grain filling rate (GFR) is an important dynamic trait that determines the final grain yield and is controlled by a network of genes and environment factors. To determine the genetic basis of the GFR, a conditional quantitative trait locus (QTL) analysis method was conducted using time-related phenotypic values of the GFR collected from a set of 243 immortalized F2(IF2) population, which were evaluated at two locations over 2 years. The GFR gradually rose in the 0–15 days after pollination (DAP) and 16–22 DAP, reaching a maximum at 23–29 DAP, and then gradually decreasing. The variation of kernel weight (KW) was mainly decided by the GFR, and not by the grain filling duration (GFD). Thirty-three different unconditional QTLs were identified for the GFR at the six sampling stages over 2 years. Among them, QTLs qGFR7b,qGFR9 and qGFR6d were identified at the same stages at two locations over 2 years. In addition, 14 conditional QTLs for GFR were detected at five stages. The conditional QTLqGFR7c was identified at stage V|IV (37–43 DAP) at two locations over 2 years, and qGFR7bwas detected at the sixth stage (44–50 DAP) in all four environments, except at Anyang location in 2009. QTLs qQTL7b and qQTL6f were identified by unconditional and conditional QTL mapping at the same stages, and might represent major QTLs for regulating the GFR in maize in the IF2 population. Moreover, most of the QTLs identified were co-located with QTLs from previous studies that were associated with GFR, enzyme activities of starch synthesis, soluble carbohydrates, and grain filling related genes. These results indicated that the GFR is regulated by many genes, which are specifically expressed at different grain filling stages, and the specific expression of the genes between 16–35 DAP might be very important for deciding the final kernel weight.
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ERISdb: A Database of Plant Splice Sites and Splicing Signals

Splicing is one of the major contributors to observed spatiotemporal diversification of transcripts and proteins in metazoans. There are numerous factors that affect the process, but splice sites themselves along with the adjacent splicing signals are critical here. Unfortunately, there is still little known about splicing in plants and, consequently, further research in some fields of plant molecular biology will encounter difficulties. Keeping this in mind, we performed a large-scale analysis of splice sites in eight plant species, using novel algorithms and tools developed by us. The analyses included identification of orthologous splice sites, polypyrimidine tracts and branch sites. Additionally we identified putative intronic and exonic cis-regulatory motifs, U12 introns as well as splice sites in 45 microRNA genes in five plant species. We also provide experimental evidence for plant splice sites in the form of expressed sequence tag and RNA-Seq data. All the data are stored in a novel database called ERISdb and are freely available at http://lemur.amu.edu.pl/share/ERISdb/.

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Texas A&M cotton breeder recognized on multiple levels | AgriLife Today

Texas A&M cotton breeder recognized on multiple levels | AgriLife Today | Plant Breeding and Genomics News | Scoop.it
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BMC Plant Biology | Abstract | Genetic structure in cultivated grapevines is linked to geography and human selection

Abstract (provisional)Background

Grapevine (Vitis vinifera subsp. vinifera) is one of the most important and ancient horticultural plants in the world. Domesticated about 8--10,000 years ago in the Eurasian region, grapevine evolved from its wild relative (V. vinifera subsp. sylvestris) into very diverse and heterozygous cultivated forms. In this work we study grapevine genetic structure in a large sample of cultivated varieties, to interpret the wide diversity at morphological and molecular levels and link it to cultivars utilization, putative geographic origin and historical events.

Results

We analyzed the genetic structure of cultivated grapevine using a dataset of 2,096 multi-locus genotypes defined by 20 microsatellite markers. We used the Bayesian approach implemented in the STRUCTURE program and a hierarchical clustering procedure based on Ward's method to assign individuals to sub-groups. The analysis revealed three main genetic groups defined by human use and geographic origin: a) wine cultivars from western regions, b) wine cultivars from the Balkans and East Europe, and c) a group mainly composed of table grape cultivars from Eastern Mediterranean, Caucasus, Middle and Far East countries. A second structure level revealed two additional groups, a geographic group from the Iberian Peninsula and Maghreb, and a group comprising table grapes of recent origins from Italy and Central Europe. A large number of admixed genotypes were also identified. Structure clusters regrouped together a large proportion of family-related genotypes. In addition, Ward's method revealed a third level of structure, corresponding either to limited geographic areas, to particular grape use or to family groups created through artificial selection and breeding.

Conclusions

This study provides evidence that the cultivated compartment of Vitis vinifera L. is genetically structured. Genetic relatedness of cultivars has been shaped mostly by human uses, in combination with a geographical effect. The finding of a large portion of admixed genotypes may be the trace of both large human-mediated exchanges between grape-growing regions throughout history and recent breeding.

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Plant Methods | Abstract | Advances in plant gene-targeted and functional markers: a review

Public genomic databases have provided new directions for molecular marker development and initiated a shift in the types of PCR-based techniques commonly used in plant science. Alongside commonly used arbitrarily amplified DNA markers, other methods have been developed. Targeted fingerprinting marker techniques are based on the well-established practices of arbitrarily amplified DNA methods, but employ novel methodological innovations such as the incorporation of gene or promoter elements in the primers. These markers provide good reproducibility and increased resolution by the concurrent incidence of dominant and co-dominant bands. Despite their promising features, these semi-random markers suffer from possible problems of collision and non-homology analogous to those found with randomly generated fingerprints. Transposable elements, present in abundance in plant genomes, may also be used to generate fingerprints. These markers provide increased genomic coverage by utilizing specific targeted sites and produce bands that mostly seem to be homologous. The biggest drawback with most of these techniques is that prior genomic information about retrotransposons is needed for primer design, prohibiting universal applications. Another class of recently developed methods exploits length polymorphism present in arrays of multi-copy gene families such as cytochrome P450 and beta-tubulin genes to provide cross-species amplification and transferability. A specific class of marker makes use of common features of plant resistance genes to generate bands linked to a given phenotype, or to reveal genetic diversity. Conserved DNA-based strategies have limited genome coverage and may fail to reveal genetic diversity, while resistance genes may be under specific evolutionary selection. Markers may also be generated from functional and/or transcribed regions of the genome using different gene-targeting approaches coupled with the use of RNA information. Such techniques have the potential to generate phenotypically linked functional markers, especially when fingerprints are generated from the transcribed or expressed region of the genome. It is to be expected that these recently developed techniques will generate larger datasets, but their shortcomings should also be acknowledged and carefully investigated.

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Sucrose functions as a signal involved in the regulation of strawberry fruit development and ripening - Jia - 2013 - New Phytologist - Wiley Online Library

Sucrose functions as a signal involved in the regulation of strawberry fruit development and ripening - Jia - 2013 - New Phytologist - Wiley Online Library | Plant Breeding and Genomics News | Scoop.it
SummaryFleshy fruits are classically divided into climacteric and nonclimacteric types. It has long been thought that the ripening of climacteric and nonclimacteric fruits is regulated by ethylene and abscisic acid (ABA), respectively. Here, we report that sucrose functions as a signal in the ripening of strawberry (Fragaria × ananassa), a nonclimacteric fruit.Pharmacological experiments, as well as gain- and loss-of-function studies, were performed to demonstrate the critical role of sucrose in the regulation of fruit ripening.Fruit growth and development were closely correlated with a change in sucrose content. Exogenous sucrose and its nonmetabolizable analog, turanose, induced ABA accumulation in fruit and accelerated dramatically fruit ripening. A set of sucrose transporters, FaSUT1–7, was identified and characterized, among which FaSUT1 was found to be a major component responsible for sucrose accumulation during fruit development. RNA interference-induced silencing of FaSUT1 led to a decrease in both sucrose and ABA content, and arrested fruit ripening. By contrast, overexpression of FaSUT1 led to an increase in both sucrose and ABA content, and accelerated fruit ripening.In conclusion, this study demonstrates that sucrose is an important signal in the regulation of strawberry fruit ripening.
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Pop Chart Lab — The Various Varieties of Vegetables

Pop Chart Lab — The Various Varieties of Vegetables | Plant Breeding and Genomics News | Scoop.it
The Various Varieties of Vegetables: The most extensive mapping of vegetables ever! We have lovingly illustrated and charted over 400  crops, from Root Vegetables like Potatoes...
Plant Breeding and Genomics News's insight:

Cool vegetable poster!

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BMC Genomics | Abstract | Characterisation of the wheat (triticum aestivum L.) transcriptome by de novo assembly for the discovery of phosphate starvation-responsive genes: gene expression in Pi-st...

Phosphorus (P) is an essential macronutrient for plant growth and development. To modulate their P homeostasis, plants must balance P uptake, mobilisation, and partitioning to various organs.
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The compatibility of agricultural i... [Proc Natl Acad Sci U S A. 2013] - PubMed - NCBI

Integrating the conservation of biodiversity by smallholder farmers with agricultural intensification is increasingly recognized as a leading priority of sustainability and food security amid global environmental and socioeconomic change. An international research project investigated the smallholder agrobiodiversity of maize (corn) in a global hotspot (Bolivia) undergoing significant intensification. Peach-based intensification was pronounced (300-400%) and prolonged (2000-2010) in study areas. Intensification and maize agrobiodiversity were found to co-occur within smallholder landscapes. Interactions of these field systems did not trigger land-change tipping points leading to landrace extirpation. By 2010 maize landraces in the study areas still demonstrated high levels of taxonomic and ecological biodiversity and contributed significantly to this crop's agrobiodiversity at national (31%) and hemispheric (3%) scales. Social and ecological resilience and in situ conservation of the maize agrobiodiversity by Bolivian smallholders was enabled through robust linkages to off-farm migration; resource access and asset capabilities among both traditional and nontraditional growers; landrace agroecology and food uses; and innovative knowledge and skills. The smallholders' resilience resulting from these linkages was integral to the conditional success of the in situ conservation of maize agrobiodiversity. Environment-development interactions both enabled smallholders' agrobiodiversity resilience and influenced the limits and vulnerability of agrobiodiversity. Scientific policy recommendations regarding land-use planning and sustainability analysis are targeted to specific Río+20 priorities for agrobiodiversity.

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BMC Genetics | Abstract | Empirical Bayesian LASSO-logistic regression for multiple binary trait locus mapping

Background: Complex binary traits are influenced by many factors including the main effects of many quantitative trait loci (QTLs), the epistatic effects involving more than one QTLs, environmental effects and the effects of gene-environment interactions. Although a number of QTL mapping methods for binary traits have been developed, there still lacks an efficient and powerful method that can handle both main and epistatic effects of a relatively large number of possible QTLs. Results: In this paper, we use a Bayesian logistic regression model as the QTL model for binary traits that includes both main and epistatic effects. Our logistic regression model employs hierarchical priors for regression coefficients similar to the ones used in the Bayesian LASSO linear model for multiple QTL mapping for continuous traits. We develop efficient empirical Bayesian algorithms to infer the logistic regression model. Our simulation study shows that our algorithms can easily handle a QTL model with a large number of main and epistatic effects on a personal computer, and outperform five other methods examined including the LASSO, HyperLasso, BhGLM, RVM and the single-QTL mapping method based on logistic regression in terms of power of detection and false positive rate. The utility of our algorithms is also demonstrated through analysis of a real data set. A software package implementing the empirical Bayesian algorithms in this paper is freely available upon request. Conclusions: The EBLASSO logistic regression method can handle a large number of effects possibly including the main and epistatic QTL effects, environmental effects and the effects of gene-environment interactions. It will be a very useful tool for multiple QTLs mapping for complex binary traits.

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PLOS ONE: Linear Regression in Genetic Association Studies

PLOS ONE: Linear Regression in Genetic Association Studies | Plant Breeding and Genomics News | Scoop.it
AbstractIn genomic research phenotype transformations are commonly used as a straightforward way to reach normality of the model outcome. Many researchers still believe it to be necessary for proper inference. Using regression simulations, we show that phenotype transformations are typically not needed and, when used in phenotype with heteroscedasticity, result in inflated Type I error rates. We further explain that important is to address a combination of rare variant genotypes and heteroscedasticity. Incorrectly estimated parameter variability or incorrect choice of the distribution of the underlying test statistic provide spurious detection of associations. We conclude that it is a combination of heteroscedasticity, minor allele frequency, sample size, and to a much lesser extent the error distribution, that matter for proper statistical inference.
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Genomic valorization of the fine scale classification of small millet landraces in southern India - Genome

Genomic valorization of the fine scale classification of small millet landraces in southern India - Genome | Plant Breeding and Genomics News | Scoop.it
ABSTRACT

Our research seeks to investigate genomic diversity of landraces of millet, addressing a key uncertainty that will provide a framework for (i) a DNA barcode method that could be used for fast, sensitive, and accurate identification of millet landraces, and (ii) millet landrace conservation including biocultural diversity. We found considerable intraspecific variation among 15 landraces representing six species of small millets using nuclear regions (ITS, ITS1, and ITS2); there was no variation in plastid regions (rbcL, matK, and trnH-psbA). An efficacious ITS2 DNA barcode was used to make 100% accurate landrace assignments for 150 blind samples representing 15 landraces. Our research revealed that genomic variation is aligned with a fine-scale classification of landraces using traditional knowledge (TK) of local farmers. The landrace classification was highly correlated with traits (morphological, agricultural, and cultural utility) associated with considerable factors such as yield, drought tolerance, growing season, medicinal properties, and nutrition. This could provide a DNA-based model for conservation of genetic diversity and the associated bicultural diversity (TK) of millet landraces, which has sustained marginal farming communities in harsh environments for many generations.

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BMC Genomics | Abstract | High-density SNP-based genetic map development and linkage disequilibrium assessment in Brassica napus L

Abstract (provisional)Background

High density genetic maps built with SNP markers that are polymorphic in various genetic backgrounds are very useful for studying the genetics of agronomical traits as well as genome organization and evolution. Simultaneous dense SNP genotyping of segregating populations and variety collections was applied to oilseed rape (Brassica napus L.) to obtain a high density genetic map for this species and to study the linkage disequilibrium pattern.

Results

We developed an integrated genetic map for oilseed rape by high throughput SNP genotyping of four segregating doubled haploid populations. A very high level of collinearity was observed between the four individual maps and a large number of markers (>59%) was common to more than two maps. The precise integrated map comprises 5764 SNP and 1603 PCR markers. With a total genetic length of 2250 cM, the integrated map contains a density of 3.27 markers (2.56 SNP) per cM. Genotyping of these mapped SNP markers in oilseed rape collections allowed polymorphism level and linkage disequilibrium (LD) to be studied across the different collections (winter vs spring, different seed quality types) and along the linkage groups. Overall, polymorphism level was higher and LD decayed faster in spring than in "00" winter oilseed rape types but this was shown to vary greatly along the linkage groups.

Conclusions

Our study provides a valuable resource for further genetic studies using linkage or association mapping, for marker assisted breeding and for Brassica napus sequence assembly and genome organization analyses.

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PLOS Biology: Can You Sequence Ecology? Metagenomics of Adaptive Diversification

PLOS Biology: Can You Sequence Ecology? Metagenomics of Adaptive Diversification | Plant Breeding and Genomics News | Scoop.it

The capacity of current sequencing technologies has revolutionized fields such as microbial ecology and evolution. Research projects and entire careers have been invented. For example, it has now become respectable, indeed fashionable, to sequence poop. Mouse poop, human poop: it is officially a cottage industry. Why? The microbial flora that outnumber our cells 10-fold and have a total gene content 100-fold greater than our own genome are finally getting the credit (or blame) they deserve for the diverse ways in which they affect our health.

But how much can be gleaned from sequencing alone? The direct sequencing of mixed communities (i.e., metagenomics) and subsequent annotation generates fantastic hypotheses of the functions various members are engaged in. From the perspective of population biology, it is thrilling to know that somewhere in the petabytes of data are the mutations that underlie processes such as evolutionary adaptation or ecological interactions. But which ones? For example, which signals are present in time-course data that could distinguish typical adaptation of a microbe to a single niche from whether it had also diversified into multiple specialists occupying distinct niches? Given the tremendous layers of complexity in our gut community, the challenge is formidable.

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Home - Uniformed Viewer for Integrative Omics

Plant hormones play important roles as signaling molecules in the regulation of growth and development by controlling the expression of downstream genes. Since the hormone signaling system represents a complex network involving functional cross-talk through the mutual regulation of signaling and metabolism, a comprehensive and integrative analysis of plant hormone concentrations and gene expression is important for a deeper understanding of hormone actions. We have developed a database named Uniformed Viewer for Integrated Omics (UniVIO: http://univio.psc.riken.jp/), which displays hormone-metabolome (hormonome) and transcriptome data in a single formatted (uniformed) heat map. At the present time, hormonome and transcriptome data obtained from 14 organ parts of rice plants at the reproductive stage and seedling shoots of three gibberellin signaling mutants are included in the database. The hormone concentration and gene expression data can be searched by substance name, probe ID, gene locus ID or gene description. A correlation search function has been implemented to enable users to obtain information of correlated substance accumulation and gene expression. In the correlation search, calculation method, range of correlation coefficient and plant samples can be selected freely.

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PRIMe: Platform for RIKEN Metabolomics

PRIMe (http://prime.psc.riken.jp/), the Platform for RIKEN Metabolomics, is a website that was designed and implemented to support research and analyses ranging from metabolomics to transcriptomics. To achieve functional genomics and annotation of unknown metabolites, we established the following PRIMe contents: MS2T, a library comprising >1 million entries of untargeted tandem mass spectrometry (MS/MS) data of plant metabolites; AtMetExpress LC-MS, a database of transcriptomics and metabolomics approaches in Arabidopsis developmental stages (AtMetExpress Development LC-MS) and a data set of the composition of secondary metabolites among 20 Arabidopsis ecotypes (AtMetExpress 20 ecotypes LC-MS); and ReSpect, hybrid reference MS/MS data resources (acquisitions and literature). PRIMeLink is a new web application that allows access to the innovative data resources of PRIMe. The MS2T library was generated from a set of MS/MS spectra acquired using the automatic data acquisition function of mass spectrometry. To increase the understanding of mechanisms driving variations in metabolic profiles among plant tissues, we further provided the AtMetExpress Development LC-MS database in PRIMe, facilitating the investigation of relationships between gene expression and metabolite accumulation. This information platform therefore provides an integrative analysis resource by linking Arabidopsis transcriptome and metabolome data. Moreover, we developed the ReSpect database, a plant-specific MS/MS data resource, which allows users to identify candidate structures from the suite of complex phytochemical structures. Finally, we integrated the three databases into PRIMeLink and established a walk-through link between transcriptome and metabolome information. PRIMeLink offers a bi-directional searchable function, from the gene and the metabolite perspective, to search for targets seamlessly and effectively.

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Cambridge Journals Online - Abstract

Cambridge Journals Online - Abstract | Plant Breeding and Genomics News | Scoop.it

Abstract

Studies to quantify genetic variation in cassava germplasm, available within the national breeding programmes in Africa, have been limited. Here, we report on the nature and extent of genetic variation that exists within 1401 cassava varieties from seven countries: Tanzania (270 genotypes); Uganda (268); Kenya (234); Rwanda (184); Democratic Republic of Congo (DRC; 177); Madagascar (186); Mozambique (82). The vast majority of these genotypes do not exist within a formal germplasm conservation initiative and were derived from farmers' fields and National Agricultural Research Systems breeding programmes. Genotypes were assayed using 26 simple sequence repeat markers. Moderate genetic variation was observed with evidence of a genetic bottleneck in the region. Some differentiation was observed among countries in both cultivars and landraces. Euclidean distance revealed the pivotal position of Tanzanian landraces in the region, and STRUCTURE analysis revealed subtle and fairly complex relationships among cultivars and among landraces and cultivars analysed together. This is likely to reflect original germplasm introductions, gene flow including farmer exchanges, disease pandemics, past breeding programmes and the introduction of cultivars from the International Institute of Tropical Agriculture – Nigeria. Information generated from this study will be useful to justify and guide a regional cassava genetic resource conservation strategy, to identify gaps in cassava diversity in the region and to guide breeding strategies.

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Shedding some light on cold acclimation, cold adaptation, and phenotypic plasticity1 - Botany

Shedding some light on cold acclimation, cold adaptation, and phenotypic plasticity1 - Botany | Plant Breeding and Genomics News | Scoop.it
ABSTRACT

In the past, the role of light as an energy source was largely ignored in research focused on cold acclimation and freezing tolerance in plants. However, cold acclimation is an energy-requiring process. We summarize research illustrating that photoautrophs as diverse as cyanobacteria (Plectonema boryanum), green algae (Chlorella vulgaris, Dunaliella salina, Chlamydomonas raudensis), crop plants (Triticum aestivum L., Secale cereale L., Brassica napus L.), and conifers (Pinus banksiana) L.) tailor the structure and function of the photosynthetic apparatus to changes in temperature and irradiance to maintain cellular energy balance called photostasis. Modulation of either temperature or irradiance results in a similar imbalance in cellular energy that is sensed through changes in chloroplastic excitation pressure. Thus, concepts of photostasis and excitation pressure provide the context through which one can explain the congruence of phenotypic plasticity and photosynthetic performance associated with cold acclimation and photoacclimation. Photosynthetic organisms can sense changes in temperature and irradiance through modulation of the redox state of the photosynthetic electron transport chain, which, in turn, governs phenotype through the regulation of nuclear gene expression and chloroplast biogenesis. We suggest that elucidation of the molecular mechanism(s) by which excitation pressure regulates phenotypic plasticity and photosynthetic performance will be essential in addressing the challenge of maintaining or perhaps enhancing crop productivity under the suboptimal growth conditions predicted to occur as a consequence of climate change.

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BMC Plant Biology | Abstract | Selective defoliation affects plant growth, fruit transcriptional ripening program and flavonoid metabolism in grapevine

"Background

The selective removal of grapevine leaves around berry clusters can improve the quality of ripening fruits by influencing parameters such as the berry sugar and anthocyanin content at harvest. The outcome depends strongly on the timing of defoliation, which influences the source--sink balance and the modified microclimate surrounding the berries. We removed the basal leaves from Vitis vinifera L. cv Sangiovese berry clusters at the pre-bloom and veraison stages, and investigated responses such as shoot growth, fruit morphology and composition compared to untreated controls. Moreover, we performed a genome-wide expression analysis to explore the impact of these defoliation treatments on berry transcriptome.

Results

We found that pre-bloom defoliation improved berry quality traits such as sugar and anthocyanin content, whereas defoliation at veraison had a detrimental effect, e.g. less anthocyanin and higher incidence of sunburn damage. Genome-wide expression analysis during berry ripening revealed that defoliation at either stage resulted in major transcriptome reprogramming, which slightly delayed the onset of ripening. However, a closer investigation of individual gene expression profiles identified genes that were specifically modulated by defoliation at each stage, reflecting the uncoupling of metabolic processes such as flavonoid biosynthesis, cell wall and stress metabolism, from the general ripening program.

Conclusions

The specific transcriptional modifications we observed following defoliation at different time points allow the identification of the developmental or metabolic processes affected in berries thus deepening the knowledge of the mechanisms by which these agronomical practices impact the final berry ripening traits.

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Trends in Biotechnology - Plant genetic engineering and agricultural biotechnology 1983–2013

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Convergent gene loss following gene... [Proc Natl Acad Sci U S A. 2013] - PubMed - NCBI

The importance of gene gain through duplication has long been appreciated. In contrast, the importance of gene loss has only recently attracted attention. Indeed, studies in organisms ranging from plants to worms and humans suggest that duplication of some genes might be better tolerated than that of others. Here we have undertaken a large-scale study to investigate the existence of duplication-resistant genes in the sequenced genomes of 20 flowering plants. We demonstrate that there is a large set of genes that is convergently restored to single-copy status following multiple genome-wide and smaller scale duplication events. We rule out the possibility that such a pattern could be explained by random gene loss only and therefore propose that there is selection pressure to preserve such genes as singletons. This is further substantiated by the observation that angiosperm single-copy genes do not comprise a random fraction of the genome, but instead are often involved in essential housekeeping functions that are highly conserved across all eukaryotes. Furthermore, single-copy genes are generally expressed more highly and in more tissues than non-single-copy genes, and they exhibit higher sequence conservation. Finally, we propose different hypotheses to explain their resistance against duplication.

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