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Biofortification of Cassava for Africa

Biofortification of Cassava for Africa | Plant Breeding and Genomics News | Scoop.it

Presentation by Dr. Richard Sayer is now available for viewing. Dr. Richard Sayre is the Director of the Biofuels project at the New Mexico Consortium working in conjunction with Los Alamos National Laboratory. Dr. Sayre received his Ph.D. from the University of Iowa and did post-doctoral work at Harvard University. Dr. Sayre is a former member of the Donald Danforth Plant Science Center where he served as the Director of the Enterprise Rent-A-Car Institute for Renewable Fuels. From 2005-2010, he was Director of the BioCassava Plus Program funded by the Bill and Melinda Gates Foundation; and from 2009-2011, was the Director of the Center for Advanced Biofuel Systems a DOE Energy Frontier Research Center. In relation to biofortification, his group currently focuses on increasing bio-available levels of iron in cassava, reducing cyanogen toxicity, increasing root protein content, reducing root post-harvest physiological deterioration, and developing root-specific promoters for transgene expression in cassava. Additional research programs focus on starch metabolism and biofuel production from cassava.

Plant Breeding and Genomics News's insight:

Recorded broadcast from the December 12, 2012 Michigan State University Plant Breeding, Genetics and Biotechnology Graduate Programs's Crop Improvement for Human Nutrition Symposium

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BMC Plant Biology | Abstract | OPTIMAS-DW: A comprehensive transcriptomics, metabolomics, ionomics, proteomics and phenomics data resource for maize

Background: Maize is a major crop plant, grown for human and animal nutrition, as well as a renewable resource forbioenergy. When looking at the problems of limited fossil fuels, the growth of the world's population or theworld's climate change, it is important to find ways to increase the yield and biomass of maize and to studyhow it reacts to specific abiotic and biotic stress situations. Within the OPTIMAS systems biology projectmaize plants were grown under a large set of controlled stress conditions, phenotypically characterised andplant material was harvested to analyse the effect of specific environmental conditions or developmentalstages. Transcriptomic, metabolomic, ionomic and proteomic parameters were measured from the same plantmaterial allowing the comparison of results across different omics domains. A data warehouse wasDescriptionThe OPTIMAS Data Warehouse (OPTIMAS-DW) is a comprehensive data collection for maize and integratesdata from different data domains such as transcriptomics, metabolomics, ionomics, proteomics andphenomics. Within the OPTIMAS project, a 44K oligo chip was designed and annotated to describe thefunctions of the selected unigenes. Several treatment- and plant growth stage experiments were performed andmeasured data were filled into data templates and imported into the data warehouse by a Java based importtool. A web interface allows users to browse through all stored experiment data in OPTIMAS-DW includingall data domains. Furthermore, the user can filter the data to extract information of particular interest. All datacan be exported into different file formats for further data analysis and visualisation. The data analysisintegrates data from different data domains and enables the user to find answers to different systems biologyquestions. Finally, maize specific pathway information is provided. Conclusions: With OPTIMAS-DW a data warehouse for maize was established, which is able to handle different datadomains, comprises several analysis results that will support researchers within their work and supportssystems biological research in particular. The system is available athttp://www.optimas-bioenergy.org/optimas_dw.

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Foodies Shouldn’t Waste Time Worrying About Food Labels. They Should Follow the Money.

Foodies Shouldn’t Waste Time Worrying About Food Labels. They Should Follow the Money. | Plant Breeding and Genomics News | Scoop.it
If the food movement really wants to improve the food supply, it needs to follow the money instead of wasting its time on labels. 
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Metabolic Engineering of Tomato Fruit Organic Acid Content Guided by Biochemical Analysis of an Introgression Line

Organic acid content is regarded as one of the most important quality traits of fresh tomato (Solanum lycopersicum). However, the complexity of carboxylic acid metabolism and storage means that it is difficult to predict the best way to engineer altered carboxylic acid levels. Here, we used a biochemical analysis of a tomato introgression line with increased levels of fruit citrate and malate at breaker stage to identify a metabolic engineering target that was subsequently tested in transgenic plants. Increased carboxylic acid levels in introgression line 2-5 were not accompanied by changes in the pattern of carbohydrate oxidation by pericarp discs or the catalytic capacity of tricarboxylic acid cycle enzymes measured in isolated mitochondria. However, there was a significant decrease in the maximum catalytic activity of aconitase in total tissue extracts, suggesting that a cytosolic isoform of aconitase was affected. To test the role of cytosolic aconitase in controlling fruit citrate levels, we analyzed fruit of transgenic lines expressing an antisense construct against SlAco3b, one of the two tomato genes encoding aconitase. A green fluorescent protein fusion of SlAco3b was dual targeted to cytosol and mitochondria, while the other aconitase, SlAco3a, was exclusively mitochondrial when transiently expressed in tobacco (Nicotiana tabacum) leaves. Both aconitase transcripts were decreased in fruit from transgenic lines, and aconitase activity was reduced by about 30% in the transgenic lines. Other measured enzymes of carboxylic acid metabolism were not significantly altered. Both citrate and malate levels were increased in ripe fruit of the transgenic plants, and as a consequence, total carboxylic acid content was increased by 50% at maturity.

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Genome-Wide Characterization of Nonreference Transposons Reveals Evolutionary Propensities of Transposons in Soybean

Preferential accumulation of transposable elements (TEs), particularly long terminal repeat retrotransposons (LTR-RTs), in recombination-suppressed pericentromeric regions seems to be a general pattern of TE distribution in flowering plants. However, whether such a pattern was formed primarily by preferential TE insertions into pericentromeric regions or by selection against TEinsertions into euchromatin remains obscure. We recently investigated TEinsertions in 31 resequenced wild and cultivated soybean (Glycine max) genomes and detected 34,154 unique nonreference TE insertions mappable to the reference genome. Our data revealed consistent distribution patterns of the nonreferenceLTR-RT insertions and those present in the reference genome, whereas the distribution patterns of the nonreference DNA TE insertions and the accumulated ones were significantly different. The densities of the nonreference LTR-RTinsertions were found to negatively correlate with the rates of local genetic recombination, but no significant correlation between the densities of nonreference DNA TE insertions and the rates of local genetic recombination was detected. These observations suggest that distinct insertional preferences were primary factors that resulted in different levels of effectiveness of purifying selection, perhaps as an effect of local genomic features, such as recombination rates and gene densities that reshaped the distribution patterns of LTR-RTs and DNA TEs in soybean.

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ScienceDirect.com - Plant Science - A rice stress-responsive NAC gene enhances tolerance of transgenic wheat to drought and salt stresses

ScienceDirect.com - Plant Science - A rice stress-responsive NAC gene enhances tolerance of transgenic wheat to drought and salt stresses | Plant Breeding and Genomics News | Scoop.it

Drought and salinity are the primary factors limiting wheat production worldwide. It has been shown that a rice stress-responsive transcription factor encoded by the rice NAC1 gene (SNAC1) plays an important role in drought stress tolerance. Therefore, we introduced the SNAC1 gene under the control of a maize ubiquitin promoter into an elite Chinese wheat variety Yangmai12. Plants expressing SNAC1 displayed significantly enhanced tolerance to drought and salinity in multiple generations, and contained higher levels of water and chlorophyll in their leaves, as compared to wild type. In addition, the fresh and dry weights of the roots of these plants were also increased, and the plants had increased sensitivities to abscisic acid (ABA), which inhibited root and shoot growth. Furthermore, quantitative real-time polymerase chain reactions revealed that the expressions of genes involved in abiotic stress/ABA signaling, such as wheat 1-phosphatidylinositol-3-phosphate-5-kinase, sucrose phosphate synthase, type 2C protein phosphatases and regulatory components of ABA receptor, were effectively regulated by the alien SNAC1 gene. These results indicated high and functional expression of the rice SNAC1 gene in wheat. And our study provided a promising approach to improve the tolerances of wheat cultivars to drought and salinity through genetic engineering.

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Metabolomic Analysis of the Effect of Shade Treatment on the Nutritional and Sensory Qualities of Green Tea - Journal of Agricultural and Food Chemistry (ACS Publications)

We analyzed metabolites from a 50% aqueous methanol extract of green teas treated with different shade periods (0, 15, 18, and 20 days) to investigate the effect of low light on their nutritional and sensory qualities. The shaded groups could be clearly distinguished from the control (0 day), and the 20 day group was separated from the 15 and 18 day groups. The shade treatment increased quercetin-galactosylrutinoside, kaempferol-glucosylrutinoside, epicatechin gallate, epigallocatechin gallate, tryptophan, phenylalanine, theanine, glutamine, glutamate, and caffeine levels but decreased quercetin-glucosylrutinoside, kaempferol-glucoside, gallocatechin, and epigallocatechin levels. Further studies on the nutritional benefits of these metabolites are needed. However, this result, along with the sensory evaluation and color measurement data, suggests that shade treatment improves the nutritional and sensory quality of green tea. Thus, we proposed a metabolomic pathway related to the effect of low light, which could elucidate the relationship between low light and tea quality.

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PLOS Genetics: Genetic Adaptation Associated with Genome-Doubling in Autotetraploid Arabidopsis arenosa

PLOS Genetics: Genetic Adaptation Associated with Genome-Doubling in Autotetraploid Arabidopsis arenosa | Plant Breeding and Genomics News | Scoop.it

Genome duplication, which results in polyploidy, is disruptive to fundamental biological processes. Genome duplications occur spontaneously in a range of taxa and problems such as sterility, aneuploidy, and gene expression aberrations are common in newly formed polyploids. In mammals, genome duplication is associated with cancer and spontaneous abortion of embryos. Nevertheless, stable polyploid species occur in both plants and animals. Understanding how natural selection enabled these species to overcome early challenges can provide important insights into the mechanisms by which core cellular functions can adapt to perturbations of the genomic environment. Arabidopsis arenosa includes stable tetraploid populations and is related to well-characterized diploids A. lyrata and A. thaliana. It thus provides a rare opportunity to leverage genomic tools to investigate the genetic basis of polyploid stabilization. We sequenced the genomes of twelve A. arenosa individuals and found signatures suggestive of recent and ongoing selective sweeps throughout the genome. Many of these are at genes implicated in genome maintenance functions, including chromosome cohesion and segregation, DNA repair, homologous recombination, transcriptional regulation, and chromatin structure. Numerous encoded proteins are predicted to interact with one another. For a critical meiosis gene, ASYNAPSIS1, we identified a non-synonymous mutation that is highly differentiated by cytotype, but present as a rare variant in diploid A. arenosa, indicating selection may have acted on standing variation already present in the diploid. Several genes we identified that are implicated in sister chromatid cohesion and segregation are homologous to genes identified in a yeast mutant screen as necessary for survival of polyploid cells, and also implicated in genome instability in human diseases including cancer. This points to commonalities across kingdoms and supports the hypothesis that selection has acted on genes controlling genome integrity in A. arenosa as an adaptive response to genome doubling.

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Can observations of a hardy weed help feed the world?

Can observations of a hardy weed help feed the world? | Plant Breeding and Genomics News | Scoop.it
Scientists have explored how the responses to environmental stresses by one small, genetically diverse plant species might illuminate possible approaches to addressing growing human demand for crop products amid decreasing resources.
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PLOS Computational Biology: Chapter 10: Mining Genome-Wide Genetic Markers

PLOS Computational Biology: Chapter 10: Mining Genome-Wide Genetic Markers | Plant Breeding and Genomics News | Scoop.it

Genome-wide association study (GWAS) aims to discover genetic factors underlying phenotypic traits. The large number of genetic factors poses both computational and statistical challenges. Various computational approaches have been developed for large scale GWAS. In this chapter, we will discuss several widely used computational approaches in GWAS. The following topics will be covered: (1) An introduction to the background of GWAS. (2) The existing computational approaches that are widely used in GWAS. This will cover single-locus, epistasis detection, and machine learning methods that have been recently developed in biology, statistic, and computer science communities. This part will be the main focus of this chapter. (3) The limitations of current approaches and future directions.

 
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PLOS Computational Biology: Chapter 8: Biological Knowledge Assembly and Interpretation

PLOS Computational Biology: Chapter 8: Biological Knowledge Assembly and Interpretation | Plant Breeding and Genomics News | Scoop.it

Most methods for large-scale gene expression microarray and RNA-Seq data analysis are designed to determine the lists of genes or gene products that show distinct patterns and/or significant differences. The most challenging and rate-liming step, however, is to determine what the resulting lists of genes and/or transcripts biologically mean. Biomedical ontology and pathway-based functional enrichment analysis is widely used to interpret the functional role of tightly correlated or differentially expressed genes. The groups of genes are assigned to the associated biological annotations using Gene Ontology terms or biological pathways and then tested if they are significantly enriched with the corresponding annotations. Unlike previous approaches, Gene Set Enrichment Analysis takes quite the reverse approach by using pre-defined gene sets. Differential co-expression analysis determines the degree of co-expression difference of paired gene sets across different conditions. Outcomes in DNA microarray and RNA-Seq data can be transformed into the graphical structure that represents biological semantics. A number of biomedical annotation and external repositories including clinical resources can be systematically integrated by biological semantics within the framework of concept lattice analysis. This array of methods for biological knowledge assembly and interpretation has been developed during the past decade and clearly improved our biological understanding of large-scale genomic data from the high-throughput technologies.

 
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Differential selection pressures exerted by host resistance quantitative trait loci on a pathogen population: a case study in an apple × Venturia inaequalis pathosystem - Van - 2012 - New Phytologi...

Differential selection pressures exerted by host resistance quantitative trait loci on a pathogen population: a case study in an apple × Venturia inaequalis pathosystem - Van - 2012 - New Phytologi... | Plant Breeding and Genomics News | Scoop.it

Understanding how pathogens evolve according to pressures exerted by their plant hosts is essential for the derivation of strategies aimed at the durable management of resistant cultivars. The spectrum of action of the resistance factors in the partially resistant cultivars is thought to be an important determinant of resistance durability. However, it has not yet been demonstrated whether the pressures exerted by quantitative resistance are different according to their spectrum of action.To investigate selection pressures exerted by apple genotypes harbouring various resistance quantitative trait loci (QTLs) on a mixed inoculum of the scab disease agent, Venturia inaequalis, we monitoredV. inaequalis isolate proportions on diseased apple leaves of an F1 progeny using quantitative pyrosequencing technology and QTL mapping.Broad-spectrum resistances did not exert any differential selection pressures on the mixed inoculum, whereas narrow-spectrum resistances decreased the frequencies of some isolates in the mixture relative to the susceptible host genotypes.Our results suggest that the management of resistant cultivars should be different according to the spectrum of action of their resistance factors. The pyramiding of broad-spectrum factors or the use of a mixture of apple genotypes that carry narrow-spectrum resistance factors are two possible strategies for the minimization of resistance erosion.
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Trends in Plant Science - Gateway vectors for transformation of cereals

Until now, the availability of vectors for transgenic research in cereal crops has been rather limited. We present a novel collection of Agrobacterium tumefaciens binary T-DNA vectors compatible with Gateway recombinational cloning that facilitate the modular assembly of genes of interest together with new regulatory sequences, such as strong constitutive or endosperm-specific Brachypodium distachyon promoters. This resource aims at streamlining the creation of vectors and transgenes designed to explore gene functions in vital monocotyledonous crops.

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Jewels in the Genome Update and Upcoming PAG Workshop

Jewels in the Genome Update and Upcoming PAG Workshop | Plant Breeding and Genomics News | Scoop.it

RosBreed presents seven new Jewels in the Genome articles highlighting genomic regions important to the Rosacea. Jewels in the Genome is our short review series. Each Jewel highlights genomic regions that can be used for marker-assisted selection. The Jewels in the Genome series is written to describe marker-assisted breeding advances to an audience that includes producers, students, and professional plant breeders.

 
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In Fields and Markets, Guatemalans Feel Squeeze of Biofuel Demand

In Fields and Markets, Guatemalans Feel Squeeze of Biofuel Demand | Plant Breeding and Genomics News | Scoop.it
Biofuel expansion has contributed to spikes in food prices and a shortage of farmland; both are felt keenly in Guatemala, with its corn-based diet and land owned by a handful of families.
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Genome-Wide Analysis of Stowaway-Like MITEs in Wheat Reveals High Sequence Conservation, Gene Association, and Genomic Diversification

The diversity and evolution of wheat (Triticum-Aegilops group) genomes is determined, in part, by the activity of transposable elements that constitute a large fraction of the genome (up to 90%). In this study, we retrieved sequences from publicly available wheat databases, including a 454-pyrosequencing database, and analyzed 18,217 insertions of 18 Stowaway-like miniature inverted-repeat transposable element (MITE) families previously characterized in wheat that together account for approximately 1.3 Mb of sequence. All 18 families showed high conservation in length, sequence, and target site preference. Furthermore, approximately 55% of the elements were inserted in transcribed regions, into or near known wheat genes. Notably, we observed significant correlation between the mean length of the MITEs and their copy number. In addition, the genomic composition of nine MITE families was studied by real-time quantitative polymerase chain reaction analysis in 40 accessions of Triticum spp. and Aegilops spp., including diploids, tetraploids, and hexaploids. The quantitative polymerase chain reaction data showed massive and significant intraspecific and interspecific variation as well as genome-specific proliferation and nonadditive quantities in the polyploids. We also observed significant differences in the methylation status of the insertion sites among MITE families. Our data thus suggest a possible role for MITEs in generating genome diversification and in the establishment of nascent polyploid species in wheat.

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Loose Plant Architecture1, an INDETERMINATE DOMAIN Protein Involved in Shoot Gravitropism, Regulates Plant Architecture in Rice

Tiller angle and leaf angle are two important components of rice (Oryza sativa) plant architecture that play a crucial role in determining grain yield. Here, we report the cloning and characterization of the Loose Plant Architecture1 (LPA1) gene in rice, the functional ortholog of the AtIDD15/SHOOT GRAVITROPISM5 (SGR5) gene in Arabidopsis (Arabidopsis thaliana). LPA1 regulates tiller angle and leaf angle by controlling the adaxial growth of tiller node and lamina joint. LPA1 was also found to affect shoot gravitropism. Expression pattern analysis suggested that LPA1 influences plant architecture by affecting the gravitropism of leaf sheath pulvinus and lamina joint. However, LPA1 only influences gravity perception or signal transduction in coleoptile gravitropism by regulating the sedimentation rate of amyloplasts, distinct from the actions of LAZY1. LPA1encodes a plant-specific INDETERMINATE DOMAIN protein and defines a novel subfamily of 28 INDETERMINATE DOMAIN proteins with several unique conserved features. LPA1 is localized in the nucleus and functions as an active transcriptional repressor, an activity mainly conferred by a conserved ethylene response factor-associated amphiphilic repression-like motif. Further analysis suggests that LPA1 participates in a complicated transcriptional and protein interaction network and has evolved novel functions distinct from SGR5. This study not only facilitates the understanding of gravitropism mechanisms but also generates a useful genetic material for rice breeding.

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In Planta Somatic Homologous Recombination Assay Revisited: A Successful and Versatile, but Delicate Tool

Marker-transgene–dependent lines of Arabidopsis thaliana measuring somatic homologous recombination (SHR) have been available for almost two decades. Here we discuss mechanisms of marker-gene restoration, comment on results obtained using the reporter lines, and stress how caution must be applied to avoid experimental problems or false interpretation in the use of SHR reporter lines. Although theoretically possible, we conclude that explanations other than SHR are unlikely to account for restoration of marker gene expression in the SHR lines when used with appropriate controls. We provide an overview of some of the most important achievements obtained with the SHR lines, give our view of the limitations of the system, and supply the reader with suggestions on the proper handling of the SHR lines. We are convinced that SHR lines are and will remain in the near future a valuable tool to explore the mechanism and influence of external and internal factors on genome stability and DNA repair in plants.

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Characterization of Normal and Waxy Corn Starch for Bioethanol Production - Journal of Agricultural and Food Chemistry (ACS Publications)

Objectives of this study were to compare ethanol production between normal and waxy corn using a cold fermentation process and to understand effects of starch structures and properties on ethanol production. Ethanol yields positively correlated (p < 0.01) with starch contents of kernels of the normal and waxy corn. The average starch–ethanol conversion efficiency of waxy corn (93.0%) was substantially greater than that of normal corn (88.2%). Waxy corn starch consisted of very little amylose and mostly amylopectin that had a shorter average branch chain length than normal corn amylopectin. Regression analyses showed that average amylopectin branch chain lengths and percentage of long branch chains (DP > 37) of waxy corn starch negatively correlated with the starch hydrolysis rate and the ethanol yield. These results indicated that starch structures and properties of the normal and waxy corn had significant effects on the ethanol yield using a cold fermentation process.

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Functional characterization of proanthocyanidi... [Plant Physiol. 2013] - PubMed - NCBI

Tea (Camellia sinensis) is rich in specialized metabolites, especially polyphenolic proanthocyanidins (PAs) and their precursors. To better understand the PA pathway in tea, we generated a cDNA library from leaf tissue of the blister blight-resistant tea cultivar TRI2043, and functionally characterized key enzymes responsible for the biosynthesis of PA precursors. Structural genes encoding enzymes involved in the general phenylpropanoid/flavonoid pathway and the PA-specific branch pathway were well represented in the library. Recombinant tea leucoanthocyanidin reductase (CsLAR) expressed in E. coli was active with leucocyanidin as substrate to produce the 2R,3S-trans-flavan-ol (+)-catechin in vitro. Two genes encoding anthocyanidin reductase, CsANR1 and CsANR2, were also expressed in E. coli, and the recombinant proteins exhibited similar kinetic properties. Both converted cyanidin to a mixture of (+)-epicatechin and (-)-catechin, although in different proportions, indicating that both enzymes possess epimerase activity. These epimers were unexpected based on the belief that tea PAs are made from (-)-epicatechin and (+)-catechin. Ectopic expression of CsANR2 or CsLAR led to accumulation of low levels of PA precursors and their conjugates in Medicago truncatula hairy roots and anthocyanin over-producing tobacco, but levels of oligomeric PAs were very low. Surprisingly, expression of CsLAR in tobacco over-producing anthocyanin led to accumulation of higher levels of epicatechin and its glucoside than of catechin, again highlighting the potential importance of epimerization in flavan-3-ol biosynthesis. The present data provide a resource for understanding tea PA biosynthesis, and tools for the bioengineering of flavanols..

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BMC Genomics | Abstract | Genomic basis of broad host range and environmental adaptability of Rhizobium tropici CIAT 899 and Rhizobium sp. PRF 81 which are used in inoculants for common bean (Phase...

"Background

Rhizobium tropici CIAT 899 and Rhizobium sp. PRF 81 are alpha-Proteobacteria that establish nitrogen-fixing symbioses with a range of legume hosts. These strains are broadly used in commercial inoculants for application to common bean (Phaseolus vulgaris) in South America and Africa. Both strains display intrinsic resistance to several abiotic stressful conditions such as low soil pH and high temperatures, which are common in tropical environments, and to several antimicrobials, including pesticides. The genetic determinants of these interesting characteristics remain largely unknown.

Results

Genome sequencing revealed that CIAT 899 and PRF 81 share a highly-conserved symbiotic plasmid (pSym) that is present also in Rhizobium leucaenae CFN 299, a rhizobium displaying a similar host range. This pSym seems to have arisen by a co-integration event between two replicons. Remarkably, three distinct nodA genes were found in the pSym, a characteristic that may contribute to the broad host range of these rhizobia. Genes for biosynthesis and modulation of plant-hormone levels were also identified in the pSym. Analysis of genes involved in stress response showed that CIAT 899 and PRF 81 are well equipped to cope with low pH, high temperatures and also with oxidative and osmotic stresses. Interestingly, the genomes of CIAT 899 and PRF 81 had large numbers of genes encoding drug-efflux systems, which may explain their high resistance to antimicrobials. Genome analysis also revealed a wide array of traits that may allow these strains to be successful rhizosphere colonizers, including surface polysaccharides, uptake transporters and catabolic enzymes for nutrients, diverse iron-acquisition systems, cell wall-degrading enzymes, type I and IV pili, and novel T1SS and T5SS secreted adhesins.

Conclusions

Availability of the complete genome sequences of CIAT 899 and PRF 81 may be exploited in further efforts to understand the interaction of tropical rhizobia with common bean and other legume hosts.

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Population genomic and genome-wide association studies of agroclimatic traits in sorghum

Accelerating crop improvement in sorghum, a staple food for people
in semiarid regions across the developing world, is key to ensuring
global food security in the context of climate change. To facilitate
gene discovery and molecular breeding in sorghum, we have characterized ∼265,000 single nucleotide polymorphisms (SNPs) in 971
worldwide accessions that have adapted to diverse agroclimatic
conditions. Using this genome-wide SNP map, we have characterized
population structure with respect to geographic origin and morphological type and identified patterns of ancient crop diffusion to
diverse agroclimatic regions across Africa and Asia. To better understand the genomic patterns of diversification in sorghum, we quantified variation in nucleotide diversity, linkage disequilibrium, and
recombination rates across the genome. Analyzing nucleotide diversity in landraces, we find evidence of selective sweeps around starch
metabolism genes, whereas in landrace-derived introgression lines,
we find introgressions around known height and maturity loci. To
identify additional loci underlying variation in major agroclimatic
traits, we performed genome-wide association studies (GWAS) on
plant height components and inflorescence architecture. GWAS maps
several classical loci for plant height, candidate genes for inflorescence architecture. Finally, we trace the independent spread of multiple haplotypes carrying alleles for short stature or long inflorescence
branches. This genome-wide map of SNP variation in sorghum provides a basis for crop impr

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PLOS Computational Biology: Chapter 11: Genome-Wide Association Studies

PLOS Computational Biology: Chapter 11: Genome-Wide Association Studies | Plant Breeding and Genomics News | Scoop.it

Genome-wide association studies (GWAS) have evolved over the last ten years into a powerful tool for investigating the genetic architecture of human disease. In this work, we review the key concepts underlying GWAS, including the architecture of common diseases, the structure of common human genetic variation, technologies for capturing genetic information, study designs, and the statistical methods used for data analysis. We also look forward to the future beyond GWAS.

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BMC Plant Biology | Abstract | Analysis of ripening-related gene expression in papaya using an Arabidopsis-based microarray

Background

Papaya (Carica papaya L.) is a commercially important crop that produces climacteric fruits with a soft and sweet pulp that contain a wide range of health promoting phytochemicals. Despite its importance, little is known about transcriptional modifications during papaya fruit ripening and their control. In this study we report the analysis of ripe papaya transcriptome by using a cross-species (XSpecies) microarray technique based on the phylogenetic proximity between papaya and Arabidopsis thaliana.

Results

Papaya transcriptome analyses resulted in the identification of 414 ripening-related genes with some having their expression validated by qPCR. The transcription profile was compared with that from ripening tomato and grape. There were many similarities between papaya and tomato especially with respect to the expression of genes encoding proteins involved in primary metabolism, regulation of transcription, biotic and abiotic stress and cell wall metabolism. XSpecies microarray data indicated that transcription factors (TFs) of the MADS-box, NAC and AP2/ERF gene families were involved in the control of papaya ripening and revealed that cell wall-related gene expression in papaya had similarities to the expression profiles seen in Arabidopsis during hypocotyl development.

Conclusion

The cross-species array experiment identified a ripening-related set of genes in papaya allowing the comparison of transcription control between papaya and other fruit bearing taxa during the ripening process.

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Prevalence of gene expression additivity in genetically stable wheat allohexaploids - Chelaifa - 2012 - New Phytologist - Wiley Online Library

Prevalence of gene expression additivity in genetically stable wheat allohexaploids - Chelaifa - 2012 - New Phytologist - Wiley Online Library | Plant Breeding and Genomics News | Scoop.it
The reprogramming of gene expression appears as the major trend in synthetic and natural allopolyploids where expression of an important proportion of genes was shown to deviate from that of the parents or the average of the parents.In this study, we analyzed gene expression changes in previously reported, highly stable synthetic wheat allohexaploids that combine the D genome of Aegilops tauschii and the AB genome extracted from the natural hexaploid wheat Triticum aestivum. A comprehensive genome-wide analysis of transcriptional changes using the Affymetrix GeneChip Wheat Genome Array was conducted.Prevalence of gene expression additivity was observed where expression does not deviate from the average of the parents for 99.3% of 34 820 expressed transcripts. Moreover, nearly similar expression was observed (for 99.5% of genes) when comparing these synthetic and natural wheat allohexaploids. Such near-complete additivity has never been reported for other allopolyploids and, more interestingly, for other synthetic wheat allohexaploids that differ from the ones studied here by having the natural tetraploidTriticum turgidum as the AB genome progenitor.Our study gave insights into the dynamics of additive gene expression in the highly stable wheat allohexaploids.
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