Plant Gene Seeker -PGS
8.4K views | +2 today
 
Scooped by Andres Zurita
onto Plant Gene Seeker -PGS
Scoop.it!

Closing gaps: linking elements that control stomatal movement

Closing gaps: linking elements that control stomatal movement | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Stomata are an attractive experimental system in plant biology, because the responses of guard cells to environmental signals can be directly linked to changes in the aperture of stomatal pores. In this review, the mechanics of stomatal movement are discussed in relation to ion transport in guard cells. Emphasis is placed on the ion pumps, transporters, and channels in the plasma membrane, as well as in the vacuolar membrane. The biophysical properties of transport proteins for H+, K+, Ca2+, and anions are discussed and related to their function in guard cells during stomatal movements. Guard cell signaling pathways for ABA, CO2, ozone, microbe-associated molecular patterns (MAMPs) and blue light are presented. Special attention is given to the regulation of the slow anion channel (SLAC) and SLAC homolog (SLAH)-type anion channels by the ABA signalosome. Over the last decade, several knowledge gaps in the regulation of ion transport in guard cells have been closed. The current state of knowledge is an excellent starting point for tackling important open questions concerning stress tolerance in plants.

more...
No comment yet.
Plant Gene Seeker -PGS
Absolutely Fascinated for plant & genomes
Curated by Andres Zurita
Your new post is loading...
Your new post is loading...
Scooped by Andres Zurita
Scoop.it!

Nitrogen nutrition in plants: rapid progress and new challenges

Nitrogen nutrition in plants: rapid progress and new challenges | Plant Gene Seeker -PGS | Scoop.it
As a main feature of plant autotrophy, assimilation of inorganic nitrogen is not only of fundamental scientific interest, but also a crucial factor in crop productivity. In its broad sense – from root uptake of various forms of N in the soil to allocation of N assimilates to different organs – it involves a wide range of physiological processes whose mechanisms are far from being fully understood. The aim of this special issue is to provide a wide overview of recent progress in this field, and to draw an interdisciplinary picture of the prospects for future research.
more...
No comment yet.
Scooped by Andres Zurita
Scoop.it!

Developmental transitions: integrating environmental cues with hormonal signaling in the chromatin landscape in plants

Developmental transitions: integrating environmental cues with hormonal signaling in the chromatin landscape in plants | Plant Gene Seeker -PGS | Scoop.it
Plant development is predominantly postembryonic and tuned in to respond to environmental cues. All living plant cells can be triggered to de-differentiate, assume different cell identities, or form a new organism. This developmental plasticity is thought to be an adaptation to the sessile lifestyle of plants. Recent discoveries have advanced our understanding of the orchestration of plant developmental switches by transcriptional master regulators, chromatin state changes, and hormone response pathways. Here, we review these recent advances with emphasis on the earliest stages of plant development and on the switch from pluripotency to differentiation in different plant organ systems.
more...
No comment yet.
Scooped by Andres Zurita
Scoop.it!

The common transcriptional subnetworks of the grape berry skin in the late stages of ripening

The common transcriptional subnetworks of the grape berry skin in the late stages of ripening | Plant Gene Seeker -PGS | Scoop.it
Wine grapes are important economically in many countries around the world. Defining the optimum time for grape harvest is a major challenge to the grower and winemaker. Berry skins are an important source of flavor, color and other quality traits in the ripening stage. Senescent-like processes such as chloroplast disorganization and cell death characterize the late ripening stage. To better understand the molecular and physiological processes involved in the late stages of berry ripening, RNA-seq analysis of the skins of seven wine grape cultivars (Cabernet Franc, Cabernet Sauvignon, Merlot, Pinot Noir, Chardonnay, Sauvignon Blanc and Semillon) was performed. RNA-seq analysis identified approximately 2000 common differentially expressed genes for all seven cultivars across four different berry sugar levels (20 to 26 °Brix). Network analyses, both a posteriori (standard) and a priori (gene co-expression network analysis), were used to elucidate transcriptional subnetworks and hub genes associated with traits in the berry skins of the late stages of berry ripening. These independent approaches revealed genes involved in photosynthesis, catabolism, and nucleotide metabolism. The transcript abundance of most photosynthetic genes declined with increasing sugar levels in the berries. The transcript abundance of other processes increased such as nucleic acid metabolism, chromosome organization and lipid catabolism. Weighted gene co-expression network analysis (WGCNA) identified 64 gene modules that were organized into 12 subnetworks of three modules or more and six higher order gene subnetworks. Some gene subnetworks were highly correlated with sugar levels and some subnetworks were highly enriched in the chloroplast and nucleus. The petal R package was utilized independently to construct a true small-world and scale-free complex gene co-expression network model. A subnetwork of 216 genes with the highest connectivity was elucidated, consistent with the module results from WGCNA. Hub genes in these subnetworks were identified including numerous members of the core circadian clock, RNA splicing, proteolysis and chromosome organization. An integrated model was constructed linking light sensing with alternative splicing, chromosome remodeling and the circadian clock. A common set of differentially expressed genes and gene subnetworks from seven different cultivars were examined in the skin of the late stages of grapevine berry ripening. A densely connected gene subnetwork was elucidated involving a complex interaction of berry senescent processes (autophagy), catabolism, the circadian clock, RNA splicing, proteolysis and epigenetic regulation. Hypotheses were induced from these data sets involving sugar accumulation, light, autophagy, epigenetic regulation, and fruit development. This work provides a better understanding of berry development and the transcriptional processes involved in the late stages of ripening.
more...
No comment yet.
Scooped by Andres Zurita
Scoop.it!

Frontiers | Abiotic Stress Tolerance in Plants: Myriad Roles of Ascorbate Peroxidase | Plant Science

Frontiers | Abiotic Stress Tolerance in Plants: Myriad Roles of Ascorbate Peroxidase | Plant Science | Plant Gene Seeker -PGS | Scoop.it
One of the most significant manifestations of environmental stress in plants is the increased production of Reactive Oxygen Species (ROS). These ROS, if allowed to accumulate unchecked, can lead to cellular toxicity. A battery of antioxidant molecules is present in plants for keeping ROS levels under check and to maintain the cellular homeostasis under stress. Ascorbate peroxidase (APX) is a key antioxidant enzyme of such scavenging systems. It catalyses the conversion of H2O2 into H2O, employing ascorbate as an electron donor. The expression of APX is differentially regulated in response to environmental stresses and during normal plant growth and development as well. Different isoforms of APX show differential response to environmental stresses, depending upon their sub-cellular localization and the presence of specific regulatory elements in the upstream regions of the respective genes. The present review delineates role of APX isoforms with respect to different types of abiotic stresses and its importance as a key antioxidant enzyme in maintaining cellular homeostasis.
more...
No comment yet.
Scooped by Andres Zurita
Scoop.it!

Improvements in Genomic Technologies: Application to Crop Genomics

Improvements in Genomic Technologies: Application to Crop Genomics | Plant Gene Seeker -PGS | Scoop.it
Second-generation sequencing (SGS) has advanced the study of crop genomes and has provided insights into diversity and evolution. However, repetitive DNA sequences in crops often lead to incomplete or erroneous assemblies because SGS reads are too short to fully resolve these repeats. To overcome some of these challenges, long-read sequencing and optical mapping have been developed to produce high-quality assemblies for complex genomes. Previously, high error rates, low throughput, and high costs have limited the adoption of long-read sequencing and optical mapping. However, with recent improvements and the development of novel algorithms, the application of these technologies is increasing. We review the development of long-read sequencing and optical mapping, and assess their application in crop genomics for breeding improved crops.
more...
No comment yet.
Scooped by Andres Zurita
Scoop.it!

Plant, Cell & Environment - Special Issue on Water Transport 

Plant, Cell & Environment - Special Issue on Water Transport  | Plant Gene Seeker -PGS | Scoop.it
Outstanding articles on water transport and regulation, plus effects on Carbon dioxide, stomatal responses, drought.
more...
No comment yet.
Scooped by Andres Zurita
Scoop.it!

Technology: The Future of Agriculture : Nature 

Technology: The Future of Agriculture : Nature  | Plant Gene Seeker -PGS | Scoop.it
A technological revolution in farming led by advances in robotics and sensing technologies looks set to disrupt modern practice.
more...
No comment yet.
Scooped by Andres Zurita
Scoop.it!

Malate-dependent Fe accumulation is a critical checkpoint in the root developmental response to low phosphate

Malate-dependent Fe accumulation is a critical checkpoint in the root developmental response to low phosphate | Plant Gene Seeker -PGS | Scoop.it

Low phosphate (Pi) availability constrains plant development and seed production in both natural and agricultural ecosystems. When Pi is scarce, modifications of root system architecture (RSA) enhance the soil exploration ability of the plant and lead to an increase in Pi uptake. In Arabidopsis, an iron-dependent mechanism reprograms primary root growth in response to low Pi availability. This program is activated upon contact of the root tip with low-Pi media and induces premature cell differentiation and the arrest of mitotic activity in the root apical meristem, resulting in a short-root phenotype. However, the mechanisms that regulate the primary root response to Pi-limiting conditions remain largely unknown. Here we report on the isolation and characterization of two low-Pi insensitive mutants (lpi5 and lpi6), which have a long-root phenotype when grown in low-Pi media. Cellular, genomic, and transcriptomic analysis of low-Pi insensitive mutants revealed that the genes previously shown to underlie Arabidopsis Al tolerance via root malate exudation, known as SENSITIVE TO PROTON RHIZOTOXICITY (STOP1) and ALUMINUM ACTIVATED MALATE TRANSPORTER 1 (ALMT1), represent a critical checkpoint in the root developmental response to Pi starvation in Arabidopsis thaliana. Our results also show that exogenous malate can rescue the long-root phenotype of lpi5 and lpi6. Malate exudation is required for the accumulation of Fe in the apoplast of meristematic cells, triggering the differentiation of meristematic cells in response to Pi deprivation.

more...
No comment yet.
Scooped by Andres Zurita
Scoop.it!

Prospect on Ionomic Signatures for the Classification of Grapevine Berries According to Their Geographical Origin | Plant Science

Prospect on Ionomic Signatures for the Classification of Grapevine Berries According to Their Geographical Origin | Plant Science | Plant Gene Seeker -PGS | Scoop.it
The determination of food geographical origin has been an important subject of study over the past decade, with an increasing number of analytical techniques being developed to determine the provenance of agricultural products. Agricultural soils can differ for the composition and the relative quantities of mineral nutrients and trace elements whose bioavailability depends on soil properties. Therefore, the ionome of fruits, vegetables and derived products can reflect the mineral composition of the growth substrate. Multi-elemental analysis has been successfully applied to trace the provenance of wines from different countries or different wine-producing regions. However, winemaking process and environmental and cultural conditions may affect a geographical fingerprint. In this article, we discuss the possibility of applying ionomics in wines classification on a local scale and also by exploiting grape berry analyses. In this regard, we present the ionomic profile of grapevine berries grown within an area of approximately 300 km2 and the subsequent application of chemometric methods for the assignment of their geographical origin. The best discrimination was obtained by using a dataset composed only of rare earth elements (REEs). Considering the experiences reported in the literature and our results, we concluded that sample representativeness and the application of a preliminary Principal Component Analysis, as pattern recognition techniques, might represent two necessary starting points for the geographical determination of the geographical origin of grape berries; therefore, on the basis of these observations we also include some recommendations to be considered for future application of these techniques for grape and wines classification.
more...
No comment yet.
Scooped by Andres Zurita
Scoop.it!

Genome Editing of Plants

Genome Editing of Plants | Plant Gene Seeker -PGS | Scoop.it
Genome editing in organisms via random mutagenesis is a naturally occurring phenomenon. As a technology, genome editing has evolved from the use of chemical and physical mutagenic agents capable of altering DNA sequences to biological tools such as designed sequence-specific nucleases (SSN) to produce knock-out (KO) or knock-in (KI) edits and Oligonucleotide Directed Mutagenesis (ODM) where specific nucleotide changes are made in a directed manner resulting in custom single nucleotide polymorphisms (SNPs). Cibus' SU Canola™, which the US Department of Agriculture (USDA) views as non-genetically modified (non-GM), is Cibus' first commercial product arising from plant genome editing and had its test launch in 2014. Regulatory aspects of the various genome editing tools will be discussed.
more...
No comment yet.
Scooped by Andres Zurita
Scoop.it!

The Accumulation of miRNAs Differentially Modulated by Drought Stress Is Affected by Grafting in Grapevine

The Accumulation of miRNAs Differentially Modulated by Drought Stress Is Affected by Grafting in Grapevine | Plant Gene Seeker -PGS | Scoop.it
Grapevine (Vitis vinifera) is routinely grafted, and rootstocks inducing drought tolerance represent a source for adapting vineyards to climate change in temperate areas. Our goal was to investigate drought stress effects on microRNA (miRNA) abundance in a drought-resistant grapevine rootstock, M4 (Vitis vinifera × Vitis berlandieri), compared with a commercial cultivar, Cabernet Sauvignon, using their autografts and reciprocal grafts. RNA extracted from roots and leaves of droughted and irrigated plants of different graft combinations was used to prepare cDNA libraries for small RNA sequencing and to analyze miRNAs by quantitative real-time polymerase chain reaction (RT-qPCR). Measurements of leaf water potential, leaf gas exchange, and root hydraulic conductance attested that, under irrigation, M4 reduced water loss in comparison with cultivar Cabernet Sauvignon mostly through nonhydraulic, root-specific mechanisms. Under drought, stomatal conductance decreased at similar levels in the two genotypes. Small RNA sequencing allowed the identification of 70 conserved miRNAs and the prediction of 28 novel miRNAs. Different accumulation trends of miRNAs, observed upon drought and in different genotypes and organs, were confirmed by RT-qPCR. Corresponding target transcripts, predicted in silico and validated by RT-qPCR, often showed opposite expression profiles than the related miRNAs. Drought effects on miRNA abundance differed between the two genotypes. Furthermore, the concentration of drought-responsive miRNAs in each genotype was affected by reciprocal grafting, suggesting either the movement of signals inducing miRNA expression in the graft partner or, possibly, miRNA transport between scion and rootstock. These results open new perspectives in the selection of rootstocks for improving grapevine adaptation to drought.
more...
No comment yet.
Scooped by Andres Zurita
Scoop.it!

Factors influencing stomatal conductance in response to water availability in grapevine: a meta‐analysis

The main factors regulating grapevine response to decreasing water availability were assessed under statistical support using published data related to leaf water relations in an extensive range of scion and rootstock genotypes. Matching leaf water potential (Ψleaf) and stomatal conductance (gs) data were collected from peer-reviewed literature with associated information. The resulting database contained 718 data points from 26 different Vitis vinifera varieties investigated as scions, 15 non-V. vinifera rootstock genotypes and 11 own-rooted V. vinifera varieties. Linearised data were analysed using the univariate general linear model (GLM) with factorial design including biological (scion and rootstock genotypes), methodological and environmental (soil) fixed factors. The first GLM performed on the whole database explained 82.4% of the variability in data distribution having the rootstock genotype the greatest contribution to variability (19.1%) followed by the scion genotype (16.2%). A classification of scions and rootstocks according to their mean predicted gs in response to moderate water stress was generated. This model also revealed that gs data obtained using a porometer were in average 2.1 times higher than using an infra-red gas analyser. The effect of soil water-holding properties was evaluated in a second analysis on a restricted database and showed a scion-dependant effect, which was dominant over rootstock effect, in predicting gs values. Overall the results suggest that a continuum exists in the range of stomatal sensitivities to water stress in V. vinifera, rather than an isohydric–anisohydric dichotomy, that is further enriched by the diversity of scion-rootstock combinations and their interaction with different soils.
more...
No comment yet.
Scooped by Andres Zurita
Scoop.it!

Frontiers | Transcriptional Responses of Chilean Quinoa (Chenopodium quinoa Willd.) Under Water Deficit Conditions Uncovers ABA-Independent Expression Patterns | Crop Science and Horticulture

Frontiers | Transcriptional Responses of Chilean Quinoa (Chenopodium quinoa Willd.) Under Water Deficit Conditions Uncovers ABA-Independent Expression Patterns | Crop Science and Horticulture | Plant Gene Seeker -PGS | Scoop.it
Global freshwater shortage is one of the biggest challenges of our time, often associated to misuse, increased consumption demands and the effects of climate change, paralleled with the desertification of vast areas. Chenopodium quinoa (Willd.) represents a very promising species, due to both nutritional content and cultivation under water constraint. We characterized drought tolerance of three Chilean genotypes and selected Genotype R49 (Salares ecotype) based upon Relative Water Content (RWC), Electrolyte Leakage (EL) and maximum efficiency of photosystem II (Fv/Fm) after drought treatment, when compared to another two genotypes. Exploratory RNA-Seq of R49 was generated by Illumina paired-ends method comparing drought and control irrigation conditions. We obtained 104.8 million reads, with 54 million reads for control condition and 51 million reads for drought condition. Reads were assembled in 150,952 contigs, were 31,523 contigs have a reading frame of at least 300 nucleotides (100 aminoacids). BLAST2GO annotation showed a 15% of genes without homology to NCBI proteins, but increased to 19% (306 contigs) when focused into drought-induced genes. Expression pattern for canonical drought responses such as ABA biosynthesis and other genes induced were assessed by qPCR, suggesting novelty of R49 drought responses.
more...
No comment yet.
Scooped by Andres Zurita
Scoop.it!

Identification of Putative Transmembrane Proteins Involved in Salinity Tolerance in Chenopodium quinoa by Integrating Physiological Data, RNAseq, and SNP Analyses | Plant Science

Identification of Putative Transmembrane Proteins Involved in Salinity Tolerance in Chenopodium quinoa by Integrating Physiological Data, RNAseq, and SNP Analyses | Plant Science | Plant Gene Seeker -PGS | Scoop.it
Chenopodium quinoa (quinoa) is an emerging crop that produces nutritious grains with the potential to contribute to global food security. Quinoa can also grow on marginal lands, such as soils affected by high salinity. To identify candidate salt tolerance genes in the recently sequenced quinoa genome, we used a multifaceted approach integrating RNAseq analyses with comparative genomics and topology prediction. We identified 219 candidate genes by selecting those that were differentially expressed in response to salinity, were specific to or overrepresented in quinoa relative to other Amaranthaceae species, and had more than one predicted transmembrane domain. To determine whether these genes might underlie variation in salinity tolerance in quinoa and its close relatives, we compared the response to salinity stress in a panel of 21 Chenopodium accessions (14 C. quinoa, 5 C. berlandieri and 2 C. hircinum). We found large variation in salinity tolerance, with one C. hircinum displaying the highest salinity tolerance. Using genome re-sequencing data from these accessions, we investigated single nucleotide polymorphisms and copy number variation in the 219 candidate genes in accessions of contrasting salinity tolerance, and identified 15 genes that could contribute to the differences in salinity tolerance of these Chenopodium accessions.
more...
No comment yet.
Scooped by Andres Zurita
Scoop.it!

Polymorphisms and minihaplotypes in the VvNAC26 gene associate with berry size variation in grapevine

Polymorphisms and minihaplotypes in the VvNAC26 gene associate with berry size variation in grapevine | Plant Gene Seeker -PGS | Scoop.it
Domestication and selection of Vitis vinifera L. for table and wine grapes has led to a large level of berry size diversity in current grapevine cultivars. Identifying the genetic basis for this natural variation is paramount both for breeding programs and for elucidating which genes contributed to crop evolution during domestication and selection processes. The gene VvNAC26, which encodes a NAC domain-containing transcription factor, has been related to the early development of grapevine flowers and berries. It was selected as candidate gene for an association study to elucidate its possible participation in the natural variation of reproductive traits in cultivated grapevine.

Methods
A grapevine collection of 114 varieties was characterized during three consecutive seasons for different berry and bunch traits. The promoter and coding regions of VvNAC26 gene (VIT_01s0026g02710) were sequenced in all the varieties of the collection, and the existing polymorphisms (SNP and INDEL) were detected. The corresponding haplotypes were inferred and used for a phylogenetic analysis. The possible associations between genotypic and phenotypic data were analyzed independently for each season data, using different models and significance thresholds.

Results
A total of 30 non-rare polymorphisms were detected in the VvNAC26 sequence, and 26 different haplotypes were inferred. Phylogenetic analysis revealed their clustering in two major haplogroups with marked phenotypic differences in berry size between varieties harboring haplogroup-specific alleles. After correcting the statistical models for the effect of the population genetic stratification, we found a set of polymorphisms associated with berry size explaining between 8.4 and 21.7 % (R2) of trait variance, including those generating the differentiation between both haplogroups. Haplotypes built from only three polymorphisms (minihaplotypes) were also associated with this trait (R2: 17.5 – 26.6 %), supporting the involvement of this gene in the natural variation for berry size.

Conclusions
Our results suggest the participation of VvNAC26 in the determination of the grape berry final size. Different VvNAC26 polymorphisms and their combination showed to be associated with different features of the fruit. The phylogenetic relationships between the VvNAC26 haplotypes and the association results indicate that this nucleotide variation may have contributed to the differentiation between table and wine grapes.
more...
No comment yet.
Scooped by Andres Zurita
Scoop.it!

Introduction to a Virtual Issue on root traits

Introduction to a Virtual Issue on root traits | Plant Gene Seeker -PGS | Scoop.it

Plant traits – ‘morphological, anatomical, physiological, biochemical and phenological characteristics of plants and their organs’ (Kattge et al., 2011) – are increasingly being harnessed by empiricists and modelers as a framework to understand patterns in the structure and function of species across the globe. Trait-based ecology, which emphasizes functional traits over the taxonomical relationships among organisms (Laliberté, 2017), promises to improve generality, synthesis, and predictive ability across ecological scales (Shipley et al., 2016).

more...
No comment yet.
Rescooped by Andres Zurita from Plant and Seed Biology
Scoop.it!

State of the World's Plants | Royal Botanic Gardens, Kew

State of the World's Plants | Royal Botanic Gardens, Kew | Plant Gene Seeker -PGS | Scoop.it
Annual cutting-edge horizon scan of global plant status. Produced by Royal Botanic Gardens Kew - Science.

Via Loïc Lepiniec
more...
No comment yet.
Scooped by Andres Zurita
Scoop.it!

The Tea Tree Genome Provides Insights into Tea Flavor and Independent Evolution of Caffeine Biosynthesis

The Tea Tree Genome Provides Insights into Tea Flavor and Independent Evolution of Caffeine Biosynthesis | Plant Gene Seeker -PGS | Scoop.it
Tea is the world's oldest and most popular caffeine-containing beverage with immense economic, medicinal, and cultural importance. Here, we present the first high-quality nucleotide sequence of the repeat-rich (80.9%), 3.02-Gb genome of the cultivated tea tree Camellia sinensis. We show that an extraordinarily large genome size of tea tree is resulted from the slow, steady, and long-term amplification of a few LTR retrotransposon families. In addition to a recent whole-genome duplication event, lineage-specific expansions of genes associated with flavonoid metabolic biosynthesis were discovered, which enhance catechin production, terpene enzyme activation, and stress tolerance, important features for tea flavor and adaptation. We demonstrate an independent and rapid evolution of the tea caffeine synthesis pathway relative to cacao and coffee. A comparative study among 25 Camellia species revealed that higher expression levels of most flavonoid- and caffeine- but not theanine-related genes contribute to the increased production of catechins and caffeine and thus enhance tea-processing suitability and tea quality. These novel findings pave the way for further metabolomic and functional genomic refinement of characteristic biosynthesis pathways and will help develop a more diversified set of tea flavors that would eventually satisfy and attract more tea drinkers worldwide.
more...
No comment yet.
Scooped by Andres Zurita
Scoop.it!

Nutrition: A world of insecurity: Nature Research

Nutrition: A world of insecurity: Nature Research | Plant Gene Seeker -PGS | Scoop.it
Malnutrition is a global problem. With population and consumption set to rise over the coming decades, achieving food security will require action on many fronts.
more...
No comment yet.
Scooped by Andres Zurita
Scoop.it!

Unique Physiological and Transcriptional Shifts under Combinations of Salinity, Drought, and Heat

Unique Physiological and Transcriptional Shifts under Combinations of Salinity, Drought, and Heat | Plant Gene Seeker -PGS | Scoop.it
Climate-change-driven stresses such as extreme temperatures, water deficit, and ion imbalance are projected to exacerbate and jeopardize global food security. Under field conditions, these stresses usually occur simultaneously and cause damages that exceed single stresses. Here, we investigated the transcriptional patterns and morpho-physiological acclimations of Brachypodium dystachion to single salinity, drought, and heat stresses, as well as their double and triple stress combinations. Hierarchical clustering analysis of morpho-physiological acclimations showed that several traits exhibited a gradually aggravating effect as plants were exposed to combined stresses. On the other hand, other morphological traits were dominated by salinity, while some physiological traits were shaped by heat stress. Response patterns of differentially expressed genes, under single and combined stresses (i.e. common stress genes), were maintained only among 37% of the genes, indicating a limited expression consistency among partially overlapping stresses. A comparison between common stress genes and genes that were uniquely expressed only under combined stresses (i.e. combination unique genes) revealed a significant shift from increased intensity to antagonistic responses, respectively. The different transcriptional signatures imply an alteration in the mode of action under combined stresses and limited ability to predict plant responses as different stresses are combined. Coexpression analysis coupled with enrichment analysis revealed that each gene subset was enriched with different biological processes. Common stress genes were enriched with known stress response pathways, while combination unique-genes were enriched with unique processes and genes with unknown functions that hold the potential to improve stress tolerance and enhance cereal productivity under suboptimal field conditions.
more...
No comment yet.
Scooped by Andres Zurita
Scoop.it!

An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations

An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations | Plant Gene Seeker -PGS | Scoop.it

Advances in genome sequencing and assembly technologies are generating many high-quality genome sequences, but assemblies of large, repeat-rich polyploid genomes, such as that of bread wheat, remain fragmented and incomplete. We have generated a new wheat whole-genome shotgun sequence assembly using a combination of optimized data types and an assembly algorithm designed to deal with large and complex genomes. The new assembly represents >78% of the genome with a scaffold N50 of 88.8 kb that has a high fidelity to the input data. Our new annotation combines strand-specific Illumina RNA-seq and Pacific Biosciences (PacBio) full-length cDNAs to identify 104,091 high-confidence protein-coding genes and 10,156 noncoding RNA genes. We confirmed three known and identified one novel genome rearrangements. Our approach enables the rapid and scalable assembly of wheat genomes, the identification of structural variants, and the definition of complete gene models, all powerful resources for trait analysis and breeding of this key global crop.

more...
No comment yet.
Scooped by Andres Zurita
Scoop.it!

The interaction of human population, food production, and biodiversity protection

Research suggests that the scale of human population and the current pace of its growth contribute substantially to the loss of biological diversity. Although technological change and unequal consumption inextricably mingle with demographic impacts on the environment, the needs of all human beings—especially for food—imply that projected population growth will undermine protection of the natural world. Numerous solutions have been proposed to boost food production while protecting biodiversity, but alone these proposals are unlikely to staunch biodiversity loss. An important approach to sustaining biodiversity and human well-being is through actions that can slow and eventually reverse population growth: investing in universal access to reproductive health services and contraceptive technologies, advancing women’s education, and achieving gender equality.
more...
No comment yet.
Scooped by Andres Zurita
Scoop.it!

Genomic history of the origin and domestication of common bean unveils its closest sister species

Genomic history of the origin and domestication of common bean unveils its closest sister species | Plant Gene Seeker -PGS | Scoop.it
Background
Modern civilization depends on only a few plant species for its nourishment. These crops were derived via several thousands of years of human selection that transformed wild ancestors into high-yielding domesticated descendants. Among cultivated plants, common bean (Phaseolus vulgaris L.) is the most important grain legume. Yet, our understanding of the origins and concurrent shaping of the genome of this crop plant is limited.

Results
We sequenced the genomes of 29 accessions representing 12 Phaseolus species. Single nucleotide polymorphism-based phylogenomic analyses, using both the nuclear and chloroplast genomes, allowed us to detect a speciation event, a finding further supported by metabolite profiling. In addition, we identified ~1200 protein coding genes (PCGs) and ~100 long non-coding RNAs with domestication-associated haplotypes. Finally, we describe asymmetric introgression events occurring among common bean subpopulations in Mesoamerica and across hemispheres.

Conclusions
We uncover an unpredicted speciation event in the tropical Andes that gave rise to a sibling species, formerly considered the “wild ancestor” of P. vulgaris, which diverged before the split of the Mesoamerican and Andean P. vulgaris gene pools. Further, we identify haplotypes strongly associated with genes underlying the emergence of domestication traits. Our findings also reveal the capacity of a predominantly autogamous plant to outcross and fix loci from different populations, even from distant species, which led to the acquisition by domesticated beans of adaptive traits from wild relatives. The occurrence of such adaptive introgressions should be exploited to accelerate breeding programs in the near future.
more...
No comment yet.
Scooped by Andres Zurita
Scoop.it!

Shoot-to-root mobile polypeptides involved in systemic regulation of nitrogen acquisition

Shoot-to-root mobile polypeptides involved in systemic regulation of nitrogen acquisition | Plant Gene Seeker -PGS | Scoop.it

Plants uptake nitrogen (N) from the soil mainly in the form of nitrate. However, nitrate is often distributed heterogeneously in natural soil. Plants, therefore, have a systemic long-distance signalling mechanism by which N starvation on one side of the root leads to a compensatory N uptake on the other N-rich side1,2. This systemic N acquisition response is triggered by a root-to-shoot mobile peptide hormone, C-TERMINALLY ENCODED PEPTIDE (CEP), originating from the N-starved roots3,4, but the molecular nature of the descending shoot-to-root signal remains elusive. Here, we show that phloem-specific polypeptides that are induced in leaves upon perception of root-derived CEP act as descending long-distance mobile signals translocated to each root. These shoot-derived polypeptides, which we named CEP DOWNSTREAM 1 (CEPD1) and CEPD2, upregulate the expression of the nitrate transporter gene NRT2.1 in roots specifically when nitrate is present in the rhizosphere. Arabidopsis plants deficient in this pathway show impaired systemic N acquisition response accompanied with N-deficiency symptoms. These fundamental mechanistic insights should provide a conceptual framework for understanding systemic nutrient acquisition responses in plants.

more...
No comment yet.
Scooped by Andres Zurita
Scoop.it!

Push–pull strategy in the regulation of postembryonic root development

Push–pull strategy in the regulation of postembryonic root development | Plant Gene Seeker -PGS | Scoop.it
Highlights 
• Multiple local regulators maintain the integrity of root stem cell niche. 
• Mobile signals from the stem cell niche affect transit-amplifying cells and beyond. 
• Top-down signals through vascular system regulate the meristem activity. 
• Bottom-up and top-down signals coordinate the postembryonic root growth. 

Unlike animals, plants continue to grow throughout their lives. The stem cell niche, protected in meristems of shoots and roots, enables this process. In the root, stem cells produce precursors for highly organized cell types via asymmetric cell divisions. These precursors, which are “transit-amplifying cells,” actively divide for several rounds before entering into differentiation programs. In this review, we highlight positive feedback regulation between shoot- and root-ward signals during the postembryonic root growth, which is reminiscent of a “push–pull strategy” in business parlance. This property of molecular networks underlies the regulation of stem cells and their organizer, the “quiescent center,” as well as of the signaling between stem cell niche, transit-amplifying cells, and beyond.
more...
No comment yet.