Biotecnology
154 views | +0 today
Follow
Your new post is loading...
Your new post is loading...
Scooped by Thiago Marconi
Scoop.it!

SNP genotyping allows an in-depth characterisation of the genome of sugarcane and other complex autopolyploids : Scientific Reports : Nature Publishing Group

SNP genotyping allows an in-depth characterisation of the genome of sugarcane and other complex autopolyploids : Scientific Reports : Nature Publishing Group | Biotecnology | Scoop.it
Many plant species of great economic value (e.g., potato, wheat, cotton, and sugarcane) are polyploids. Despite the essential roles of autopolyploid plants in human activities, our genetic understanding of these species is still poor.
more...
No comment yet.
Rescooped by Thiago Marconi from DNA and RNA research
Scoop.it!

Solar PCR: There’s an App for That

Solar PCR: There’s an App for That | Biotecnology | Scoop.it

Smartphones can forecast the weather, direct you to your next meeting, or entertain you during a long flight. But can they diagnose cancer?


Via Integrated DNA Technologies
more...
No comment yet.
Rescooped by Thiago Marconi from Plant Genetics, NGS and Bioinformatics
Scoop.it!

MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations

MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations | Biotecnology | Scoop.it

Abstract

We have optimized and extended the widely used annotation engine MAKER in order to better support plant genome annotation efforts. New features include better parallelization for large repeat-rich plant genomes, noncoding RNA annotation capabilities, and support for pseudogene identification. We have benchmarked the resulting software tool kit, MAKER-P, using the Arabidopsis (Arabidopsis thaliana) and maize (Zea mays) genomes. Here, we demonstrate the ability of the MAKER-P tool kit to automatically update, extend, and revise the Arabidopsis annotations in light of newly available data and to annotate pseudogenes and noncoding RNAs absent from The Arabidopsis Informatics Resource 10 build. Our results demonstrate that MAKER-P can be used to manage and improve the annotations of even Arabidopsis, perhaps the best-annotated plant genome. We have also installed and benchmarked MAKER-P on the Texas Advanced Computing Center. We show that this public resource can de novo annotate the entire Arabidopsis and maize genomes in less than 3 h and produce annotations of comparable quality to those of the current The Arabidopsis Information Resource 10 and maize V2 annotation builds.


Via Ali Taheri
more...
No comment yet.
Rescooped by Thiago Marconi from Next-generation sequencing (NGS)
Scoop.it!

San Diego-based White Labs is decoding beer DNA

San Diego-based White Labs is decoding beer DNA | Biotecnology | Scoop.it

At White Labs in San Diego, technicians work to reanimate cryogenically frozen single-celled organisms. Their quest: to unravel the genetics behind the more than 500 flavour and aroma compounds found in beers.


Via Integrated DNA Technologies
more...
No comment yet.
Rescooped by Thiago Marconi from Plant Breeding and Genomics News
Scoop.it!

The Influence of Climate Change on Global Crop Productivity

The Influence of Climate Change on Global Crop Productivity | Biotecnology | Scoop.it

Climate trends over the past few decades have been fairly rapid in many agricultural regions around the world, and increases in atmospheric carbon dioxide (CO2) and ozone (O3) levels have also been ubiquitous. The virtual certainty that climate and CO2 will continue to trend in the future raises many questions related to food security, one of which is whether the aggregate productivity of global agriculture will be affected. We outline the mechanisms by which these changes affect crop yields and present estimates of past and future impacts of climate and CO2 trends. The review focuses on global scale grain productivity, notwithstanding the many other scales and outcomes of interest to food security. Over the next few decades, CO2 trends will likely increase global yields by roughly 1.8% per decade. At the same time, warming trends are likely to reduce global yields by roughly 1.5% per decade without effective adaptation, with a plausible range from roughly 0% to 4%. The upper end of this range is half of the expected 8% rate of gain from technological and management improvements over the next few decades. Many global change factors that will likely challenge yields, including higher O3 and greater rainfall intensity, are not considered in most current assessments.


Via Plant Breeding and Genomics News
more...
No comment yet.
Rescooped by Thiago Marconi from Plant Breeding and Genomics News
Scoop.it!

Molecular Markers and Genotyping - eXtension Learning Lessons

Molecular Markers and Genotyping - eXtension Learning Lessons | Biotecnology | Scoop.it

These tutorials describe different types of molecular markers and how they are used to genotype and inform breeding selections.


Via Plant Breeding and Genomics News
more...
No comment yet.
Rescooped by Thiago Marconi from Plant Breeding and Genomics News
Scoop.it!

BMC Plant Biology | Abstract | Tissue culture-induced genetic and epigenetic alterations in rice pure-lines, F1 hybrids and polyploids

Background

Genetic and epigenetic alterations can be invoked by plant tissue culture, which may result in heritable changes in phenotypes, a phenomenon collectively termed somaclonal variation. Although extensive studies have been conducted on the molecular nature and spectrum of tissue culture-induced genomic alterations, the issue of whether and to what extent distinct plant genotypes, e.g., pure-lines, hybrids and polyploids, may respond differentially to the tissue culture condition remains poorly understood.

Results

We investigated tissue culture-induced genetic and epigenetic alterations in a set of rice genotypes including two pure-lines (different subspecies), a pair of reciprocal F1 hybrids parented by the two pure-lines, and a pair of reciprocal tetraploids resulted from the hybrids. Using two molecular markers, amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified polymorphism (MSAP), both genetic and DNA methylation alterations were detected in calli and regenerants from all six genotypes, but genetic alteration is more prominent than epigenetic alteration. While significant genotypic difference was observed in frequencies of both types of alterations, only genetic alteration showed distinctive features among the three types of genomes, with one hybrid (N/9) being exceptionally labile. Surprisingly, difference in genetic alteration frequencies between the pair of reciprocal F1 hybrids is much greater than that between the two pure-line subspecies. Difference also exists in the pair of reciprocal tetraploids, but is to a less extent than that between the hybrids. The steady-state transcript abundance of genes involved in DNA repair and DNA methylation was significantly altered in both calli and regenerants, and some of which were correlated with the genetic and/or epigenetic alterations.

Conclusions

Our results, based on molecular marker analysis of ca. 1,000 genomic loci, document that genetic alteration is the major cause of somaclonal variation in rice, which is concomitant with epigenetic alterations. Perturbed expression by tissue culture of a set of 41 genes encoding for enzymes involved in DNA repair and DNA methylation is associated with both genetic and epigenetic alterations. There exist fundamental differences among distinct genotypes, pure-lines, hybrids and tetraploids, in propensities of generating both genetic and epigenetic alterations under the tissue culture condition. Parent-of-origin has a conspicuous effect on the alteration frequencies.


Via Plant Breeding and Genomics News
more...
No comment yet.
Rescooped by Thiago Marconi from Plant Breeding and Genomics News
Scoop.it!

Database: Plant Resistance Gene Wiki (2013)

Database: Plant Resistance Gene Wiki (2013) | Biotecnology | Scoop.it

PRG-Wiki is an open and daily update space about plant resistance gene, in which all information about this family is stored, curated and discussed. The purpose of our work is creating a worldwide community working on plant resistance genes with a constant update on all aspects of this research field and to encourage scientists to be actors of the discussion and of the data exchange. PRG-Wiki actually stores more than 112 reference resistance gene and 104335 putative disease resistance gene. Through the wiki pages any contributor can suggest changes to the PRG database and directly update it with new data, new information and with corrections of wrong information.

 


Via Kamoun Lab @ TSL, Plant Breeding and Genomics News
more...
No comment yet.
Rescooped by Thiago Marconi from Plant Genetics, NGS and Bioinformatics
Scoop.it!

Brazil, Canada and South Africa bullish on agbiotech

Brazil, Canada and South Africa bullish on agbiotech | Biotecnology | Scoop.it

Transgenic crop plantings in developing countries surpassed those in industrial nations, with the former growing 52% of the world's transgenic varieties. Although the United States dominates overall, transgenic acreage in Brazil, Canada and South Africa continued double-digit growth. Elsewhere, Sudan and Cuba planted their first transgenic crops (Bt cotton and Bt maize, respectively). Europe continues to wind down its field trials; Germany and Sweden withdrew the low-starch Amflora transgenic potato from the market.


Via Ali Taheri
more...
No comment yet.
Rescooped by Thiago Marconi from Plant Breeding and Genomics News
Scoop.it!

3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture.

Abstract

Identification of genes that control root system architecture in crop plants requires innovations that enable high-throughput and accurate measurements of root system architecture through time. We demonstrate the ability of a semiautomated 3D in vivo imaging and digital phenotyping pipeline to interrogate the quantitative genetic basis of root system growth in a rice biparental mapping population, Bala × Azucena. We phenotyped >1,400 3D root models and >57,000 2D images for a suite of 25 traits that quantified the distribution, shape, extent of exploration, and the intrinsic size of root networks at days 12, 14, and 16 of growth in a gellan gum medium. From these data we identified 89 quantitative trait loci, some of which correspond to those found previously in soil-grown plants, and provide evidence for genetic tradeoffs in root growth allocations, such as between the extent and thoroughness of exploration. We also developed a multivariate method for generating and mapping central root architecture phenotypes and used it to identify five major quantitative trait loci (r2 = 24-37%), two of which were not identified by our univariate analysis. Our imaging and analytical platform provides a means to identify genes with high potential for improving root traits and agronomic qualities of crops.

 


Via Plant Breeding and Genomics News
more...
Rescooped by Thiago Marconi from Amazing Science
Scoop.it!

100M-Year-Old Non-Coding DNA Regions Identified in Four Plants

100M-Year-Old Non-Coding DNA Regions Identified in Four Plants | Biotecnology | Scoop.it

A computational analysis of the genomes of the papaya, poplar, grape, and a small flowering plant called Arabidopsis thaliana, has identified hundreds of 100-million-year-old non-coding DNA sequences shared between these plants.

 

These conserved non-coding sequences, discovered by an international group of biologists, are not genes, but are located in the promoters upstream of genes and are around 100 DNA base pairs in length. As the papaya, poplar, grape and Arabidopsis have evolved separately for around 100 million years, the fact that these DNA regions have been conserved suggests they play an important role in the plants’ development and functioning.

 

“We know that certain genes are conserved between species – but we also see that sequences outside of genes are conserved,” said senior author Dr. Sascha Ott of the University of Warwick’s Systems Biology Center. “The regions outside genes that we have discovered have been kept for millions and millions of years across four species. There must be a reason for this – if something has been around for so long it is probably useful in some way. We believe it may be because these regions have a very important role to play in how the plant develops and functions.”


Via Dr. Stefan Gruenwald
more...
No comment yet.
Rescooped by Thiago Marconi from Plant Genetics, NGS and Bioinformatics
Scoop.it!

Integrated Analysis Platform: An Open-Source Information System for High-Throughput Plant Phenotyping

Integrated Analysis Platform: An Open-Source Information System for High-Throughput Plant Phenotyping | Biotecnology | Scoop.it

High-throughput phenotyping is emerging as an important technology to dissect phenotypic components in plants. Efficient image processing and feature extraction are prerequisites to quantify plant growth and performance based on phenotypic traits. Issues include data management, image analysis, and result visualization of large-scale phenotypic data sets. Here, we present Integrated Analysis Platform (IAP), an open-source framework for high-throughput plant phenotyping. IAP provides user-friendly interfaces, and its core functions are highly adaptable. Our system supports image data transfer from different acquisition environments and large-scale image analysis for different plant species based on real-time imaging data obtained from different spectra. Due to the huge amount of data to manage, we utilized a common data structure for efficient storage and organization of data for both input data and result data. We implemented a block-based method for automated image processing to extract a representative list of plant phenotypic traits. We also provide tools for build-in data plotting and result export. For validation of IAP, we performed an example experiment that contains 33 maize (Zea mays ‘Fernandez’) plants, which were grown for 9 weeks in an automated greenhouse with nondestructive imaging. Subsequently, the image data were subjected to automated analysis with the maize pipeline implemented in our system. We found that the computed digital volume and number of leaves correlate with our manually measured data in high accuracy up to 0.98 and 0.95, respectively. In summary, IAP provides a multiple set of functionalities for import/export, management, and automated analysis of high-throughput plant phenotyping data, and its analysis results are highly reliable.


Via Ali Taheri
more...
No comment yet.
Rescooped by Thiago Marconi from Plant Genetics, NGS and Bioinformatics
Scoop.it!

Opportunities in plant synthetic biology

Opportunities in plant synthetic biology | Biotecnology | Scoop.it

Synthetic biology is an emerging field uniting scientists from all disciplines with the aim of designing or re-designing biological processes. Initially, synthetic biology breakthroughs came from microbiology, chemistry, physics, computer science, materials science, mathematics, and engineering disciplines. A transition to multicellular systems is the next logical step for synthetic biologists and plants will provide an ideal platform for this new phase of research. This meeting report highlights some of the exciting plant synthetic biology projects, and tools and resources, presented and discussed at the 2013 GARNet workshop on plant synthetic biology.


Via Ali Taheri
more...
No comment yet.
Rescooped by Thiago Marconi from Plant Genetics, NGS and Bioinformatics
Scoop.it!

So you want to be a computational biologist? : Nature Biotechnology : Nature Publishing Group

Two computational biologists give advice when starting out on computational projects.

Via Pedro Fernandes, Ali Taheri
more...
Pedro Fernandes's curator insight, November 10, 2013 2:21 PM

Well done @pathogenomenick and  @biomickwatson

Rescooped by Thiago Marconi from Plant Breeding and Genomics News
Scoop.it!

Upcoming Webinar: Selective Sequencing Through Combinatorial Pooling - eXtension

Upcoming Webinar: Selective Sequencing Through Combinatorial Pooling - eXtension | Biotecnology | Scoop.it

Wednesday 21 August 2013 at Noon EDT


Stefano Leonardi and Timothy Close will describe the use of combinatorial pooling to reconstruct gene sequences within BACs. Recent work in barley has shown that this level of sequence knowledge is sufficient to support critical end-point objectives such as map-based cloning and marker-assisted breeding.

 
Via Plant Breeding and Genomics News
more...
No comment yet.
Rescooped by Thiago Marconi from Plant Genetics, NGS and Bioinformatics
Scoop.it!

eQTL Mapping Using RNA-seq Data

eQTL Mapping Using RNA-seq Data | Biotecnology | Scoop.it

As RNA-seq is replacing gene expression microarrays to assess genome-wide transcription abundance, gene expression Quantitative Trait Locus (eQTL) studies using RNA-seq have emerged. RNA-seq delivers two novel features that are important for eQTL studies. First, it provides information on allele-specific expression (ASE), which is not available from gene expression microarrays. Second, it generates unprecedentedly rich data to study RNA-isoform expression. In this paper, we review current methods for eQTL mapping using ASE and discuss some future directions. We also review existing works that use RNA-seq data to study RNA-isoform expression and we discuss the gaps between these works and isoform-specific eQTL mapping.


Via Ali Taheri
more...
No comment yet.
Rescooped by Thiago Marconi from Plant Breeding and Genomics News
Scoop.it!

Different Beers with Different Hops. Relevant Compounds for Their Aroma Characteristics - Journal of Agricultural and Food Chemistry (ACS Publications)

Hop-derived aroma characteristics in beer are very important for the quality of beer. This study compared the differences of hop aroma characteristics and the compounds contained in beer by changing the variety of hops applying the idea of “food metabolomics” on the GC×GC/TOF-MS analysis data, to clarify which aroma compounds contribute to the differences of hop aroma profiles indicated by sensory descriptors. As a result, by focusing only on hop-derived compounds, 67 compounds were strongly correlated with one or more of the sensory descriptors. Furthermore, the odor descriptions of each key compound corresponded well to each sensory descriptor. Thus, these compounds are likely to be the key compounds explaining the differences of hop aroma characteristics in beer. This study led to the suggestion that understanding the relationship between the comprehensive nontarget analysis by GC×GC-TOF/MS and organoleptic evaluation using PCA is effective in estimating the key compounds.


Via Plant Breeding and Genomics News
more...
Rescooped by Thiago Marconi from Plant Breeding and Genomics News
Scoop.it!

BMC Plant Biology | Abstract | Genetic characterization of a core collection of flax (Linum usitatissimum L.) suitable for association mapping studies and evidence of divergent selection between fi...

Background

Flax is valued for its fiber, seed oil and nutraceuticals. Recently, the fiber industry has invested in the development of products made from linseed stems, making it a dual purpose crop. Simultaneous targeting of genomic regions controlling stem fiber and seed quality traits could enable the development of dual purpose cultivars. However, the genetic diversity, population structure and linkage disequilibrium (LD) patterns necessary for association mapping (AM) have not yet been assessed in flax because genomic resources have only recently been developed. We characterized 407 globally distributed flax accessions using 448 microsatellite markers. The data was analyzed to assess the suitability of this core collection for AM. Genomic scans to identify candidate genes selected during the divergent breeding process of fiber flax and linseed were conducted using the whole genome shotgun sequence of flax.

Results

Combined genetic structure analysis assigned all accessions to two major groups with six sub-groups. Population differentiation was weak between the major groups (FST = 0.094) and for most of the pairwise comparisons among sub-groups. The molecular coancestry analysis indicated weak relatedness (mean = 0.287) for most individual pairs. Abundant genetic diversity was observed in the total panel (5.32 alleles per locus), and some sub-groups showed a high proportion of private alleles. The average genome-wide LD (r2) was 0.036, with a relatively fast decay of 1.5 cM. Genomic scans between fiber flax and linseed identified candidate genes involved in cell-wall biogenesis/modification, xylem identity and fatty acid biosynthesis congruent with genes previously identified in flax and other plant species.

Conclusions

Based on the abundant genetic diversity, weak population structure and relatedness and relatively fast LD decay, we concluded that this core collection is suitable for AM studies targeting multiple agronomic and quality traits aiming at the improvement of flax as a true dual purpose crop. Our genomic scans provide the first insights into candidate regions affected by divergent selection in flax. In combination with AM, genomic scans have the ability to increase the power to detect loci influencing complex traits.


Via Plant Breeding and Genomics News
more...
No comment yet.
Rescooped by Thiago Marconi from Amazing Science
Scoop.it!

Merely a Sip of Beer Can Trigger a Rush of Chemical Pleasure in the Brain

Merely a Sip of Beer Can Trigger a Rush of Chemical Pleasure in the Brain | Biotecnology | Scoop.it

New research shows just a sip can cause the potent neurotransmitter dopamine to flood the brain.

 

If you take just a sip of beer, and moments later—before you’ve had close to enough alcohol to get intoxicated, perhaps even before the beer has hit your stomach—feel a distinctly pleasurable sensation, it might not be strictly due to subtle aromas that result from the beverage’s blend of malt, hops and yeast. The cause of your pleasure might be due to tangible changes in your brain chemistry—specifically, a surge in levels of the neurotransmitter dopamine.

 

Scientists have long known that part of the reason alcohol induces pleasure is that intoxication leads to the release of dopamine, which is associated with the use of other drugs (as well as sleep and sex) and acts as a reward for the brain. But new research suggests that, for some people, intoxication isn’t necessary: Simply the taste of beer alone can provoke a release of the neurotransmitter within minutes.

 

A group of researchers led by David Kareken of Indiana University came to the finding, published today in the journal Neuropsychopharmacology, by giving tiny amounts of beer to 49 adult men and tracking changes in their brain chemistry with a positron emission tomography (PET) scanner, which measures levels of various molecules in the brain. They chose participants with varying levels of typical alcohol consumption—from heavy drinkers to near-teetotalers—and even tested them with the beer they reported that they drank most frequently. Because they used an automated system to spray just 15 milliliters (about half an ounce) of beer on each participant’s tongue over the course of 15 minutes, they could be sure that any changes in brain chemistry wouldn’t be due to intoxication.

 

The effect was significant. When the men tasted the beer, their brains released much higher levels of dopamine within minutes, compared to when the same test was conducted on the subjects at other times with both water and Gatorade. They were also asked to rate how much they “craved” a beer at several points during the experiment, and perhaps less surprisingly, their cravings were generally much higher after tasting beer than Gatorade or water.

 

Interestingly, the amount of dopamine release per person wasn’t random. People who had a family history of alcoholism (as reported on a survey) showed notably higher dopamine levels after tasting beer as compared to others. But participants who were heavy drinkers but didn’t have the family history had merely average dopamine levels.

 

The researchers believe this could be a clue as to why some people are predisposed towards alcoholism—and why it’s more difficult for them stay on the wagon if they’re trying to quit. The immediate release of dopamine from just a taste of beer would likely serve as a powerful mechanism that drives their cravings, and a tendency towards experiencing this burst of pleasure might be genetically inheritable. This could be part of the reason that people with a family history of alcoholism are twice as likely to experience alcoholism themselves.

 

Previous work has shown that in people with alcoholic tendencies, stimuli that are merely associated with drinking (such as the smell and sight of a alcoholic drinks or a bar) can trigger dopamine release in the brain. This work shows that for an unlucky group predisposed to suffering from alcoholism, bursts of dopamine can occur even if they’re not heavy drinkers—and it only takes a sip for the pattern to start.


Via Dr. Stefan Gruenwald
more...
No comment yet.
Rescooped by Thiago Marconi from Plant Genetics, NGS and Bioinformatics
Scoop.it!

List of Bioinformatics Workshops and Training Resources

List of Bioinformatics Workshops and Training Resources | Biotecnology | Scoop.it

Via Ali Taheri
more...
No comment yet.
Rescooped by Thiago Marconi from BIG data, Data Mining, Predictive Modeling, Visualization
Scoop.it!

Beach bacteria: DNA tests offer quick results on water health - Mother Nature Network

Beach bacteria: DNA tests offer quick results on water health - Mother Nature Network | Biotecnology | Scoop.it

Mother Nature Network Beach bacteria: DNA tests offer quick results on water health Mother Nature Network Predictive modeling, however, isn't used in many ocean communities, where larger waves and less summer rainfall make it much less useful than...


Via AnalyticsInnovations
more...
No comment yet.