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How Microbes Can Help Feed the World, August 2013

How Microbes Can Help Feed the World, August 2013 | Plant Breeding and Genomics News | Scoop.it

A greater focus on the role of microbiology in agriculture combined with new technologies can help mitigate potential food shortages associated with world population increases according to a new report from the American Academy of Microbiology.

“Microbes are essential partners in all aspects of plant physiology, but human efforts to improve plant productivity have focused mostly on the plant,” says Ian Sanders of University of Lausanne, chair of the colloquium that produced the report. “Optimizing the microbial communities that live in, on and around plants, can substantially reduce the need for chemical fertilizers, pesticides and herbicides.”

The report, "How Microbes can Help Feed the World," is based on the deliberation of a group of scientific experts who gathered for two days in Washington DC in December 2012 to consider a series of questions regarding how plant-microbe interactions could be employed to boost agricultural productivity in an environmentally and economically responsible way.

It starts with a startling statistic: In order to feed the estimated global population of 9 billion in the year 2050, agricultural yields will have to increase by 70-100%.

Improved understanding of plant-microbe interactions has the potential to increase crop productivity by 20% while reducing fertilizer and pesticide requirements by 20%, within 20 years, according to the report. These estimates rest on the recognition that all plants rely on microbial partners to secure nutrients, deter pathogens and resist environmental stress.

The report looks in depth at the intimate relationship between microbes and agriculture including why plants need microbes, what types of microbes they need, how they interact and the scientific challenges posed by the current state of knowledge. It then makes a series of recommendations, including greater investment in research, the taking on of one or more grand challenges such as characterization of the complete microbiome of one important crop plant, and the establishment of a formal process for moving scientific discoveries from the lab to the field.

“New technologies are making plant-microbe ecosystems easier to study and investment in this area of research could have dramatic benefits,” says Marilynn Roossinck, Pennsylvania State University, who helped organize the colloquium.

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BMC Plant Biology | Abstract | Tall fescue endophyte effects on tolerance to water-deficit stress

Background: The endophytic fungus, Neotyphodium coenophialum, can enhance drought tolerance of its host grass, tall fescue. To investigate endophyte effects on plant responses to acute water deficit stress, we did comprehensive profiling of plant metabolite levels in both shoot and root tissues of genetically identical clone pairs of tall fescue with endophyte (E+) and without endophyte (E-) in response to direct water deficit stress. The E- clones were generated by treating E+ plants with fungicide and selectively propagating single tillers. In time course studies on the E+ and E- clones, water was withheld from 0 to 5 days, during which levels of free sugars, sugar alcohols, and amino acids were determined, as were levels of some major fungal metabolites. Results: After 2--3 days of withholding water, survival and tillering of re-watered plants was significantly greater for E+ than E- clones. Within two to three days of withholding water, significant endophyte effects on metabolites manifested as higher levels of free glucose, fructose, trehalose, sugar alcohols, proline and glutamic acid in shoots and roots. The fungal metabolites, mannitol and loline alkaloids, also significantly increased with water deficit. Conclusions: Our results suggest that symbiotic N. coenophialum aids in survival and recovery of tall fescue plants from water deficit, and acts in part by inducing rapid accumulation of these compatible solutes soon after imposition of stress.

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Trends in Plant Science - New insights into the regulation of anthocyanin biosynthesis in fruits

HighlightsAnthocyanin pigments make a major contribution to fruit quality.R2R3-MYB genes control anthocyanin biosynthesis as characterized for many fruit species.Novel interactions between regulators of anthocyanin accumulation exist.Summary

Anthocyanins are important health-promoting pigments that make a major contribution to the quality of fruits. The biosynthetic pathway leading to anthocyanins is well known and the key regulatory genes controlling the pathway have been isolated in many species. Recently, a considerable amount of new information has been gathered on the developmental and environmental regulation of anthocyanin biosynthesis in fruits, specifically the impact of regulation through light. New discoveries have begun to reveal links between the developmental regulatory network and the specific regulators of anthocyanin biosynthesis during fruit ripening. In this opinion article, a simplified model for the different regulatory networks involved with anthocyanin production in fruit is proposed.

  
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Plant Methods | Abstract | Analysing complex Triticeae genomes - concepts and strategies

The genomic sequences of many important Triticeae crop species are hard to assemble and analyse due to their large genome sizes, (in part) polyploid genomes and high repeat content. Recently, the draft genomes of barley and bread wheat were reported thanks to cost-efficient and fast NGS technologies. The genome of barley is estimated to be 5 Gb in size whereas the genome of bread wheat accounts for 17 Gb and harbours an allo-hexaploid genome. Direct assembly of the sequence reads and access to the gene content is hampered by the repeat content. As a consequence, novel strategies and data analysis concepts had to be developed to provide much-needed whole genome sequence surveys and access to the gene repertoires. Here we describe some analytical strategies that now enable structuring of massive NGS data generated and pave the way towards structured and ordered sequence data and gene order. Specifically we report on the genomeZipper, a synteny driven approach to order and structure NGS survey sequences of grass genomes that lack a physical map. In addition, to access and analyse the gene repertoire of allo-hexaploid bread wheat from the raw sequence reads, a reference-guided approach was developed utilizing representative genes from rice, Brachypodium distachyon, sorghum and barley. Stringent sub-assembly on the reference genes prevented collapsing of homeologous wheat genes and allowed to estimate gene retention rate and determine gene family sizes. Genomic sequences from the wheat sub-genome progenitors enabled to discriminate a large number of sub-assemblies between the wheat A, B or D sub-genome using machine learning algorithms. Many of the concepts outlined here can readily be applied to other complex plant and non-plant genomes.

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Agricultural landscape simplification does not consistently drive insecticide use

The increase in agricultural production over the past 40 y has greatly altered land-use patterns, often resulting in simplified landscapes composed of large swaths of monocultures separated by small fragments of natural lands. These simplified landscapes may be more susceptible to insect pest pressure because of the loss of natural enemies and the increased size and connectivity of crop resources, and a recent analysis from a single year (2007) suggests this increased susceptibility results in increased insecticide use. I broaden the temporal analysis of this connection between landscape simplification and insecticide use by examining cross-sectional and panel data models from multiple decades (US Department of Agriculture Census of Agriculture years 2007, 2002, 1997, 1992, 1987) for seven Midwestern states composed of over 560 counties. I find that although the proportion of county in cropland-my metric for landscape simplification-was positively correlated with insecticide use in 2007, this relationship is absent or reversed in prior census years and when all years are analyzed together. This broader temporal perspective suggests that landscape simplification has inconsistent effects on insecticide use and that multiyear studies will be key to unlocking the true drivers of variation in insecticide application.

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gmopundit's curator insight, September 7, 2013 4:22 PM

Provides evidence that needs to be considered as part of a factual approach to decisions

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PLOS Computational Biology: Genome-Wide Signatures of Transcription Factor Activity: Connecting Transcription Factors, Disease, and Small Molecules

PLOS Computational Biology: Genome-Wide Signatures of Transcription Factor Activity: Connecting Transcription Factors, Disease, and Small Molecules | Plant Breeding and Genomics News | Scoop.it

Identifying transcription factors (TF) involved in producing a genome-wide transcriptional profile is an essential step in building mechanistic model that can explain observed gene expression data. We developed a statistical framework for constructing genome-wide signatures of TF activity, and for using such signatures in the analysis of gene expression data produced by complex transcriptional regulatory programs. Our framework integrates ChIP-seq data and appropriately matched gene expression profiles to identify True REGulatory (TREG) TF-gene interactions. It provides genome-wide quantification of the likelihood of regulatory TF-gene interaction that can be used to either identify regulated genes, or as genome-wide signature of TF activity. To effectively use ChIP-seq data, we introduce a novel statistical model that integrates information from all binding “peaks” within 2 Mb window around a gene's transcription start site (TSS), and provides gene-level binding scores and probabilities of regulatory interaction. In the second step we integrate these binding scores and regulatory probabilities with gene expression data to assess the likelihood of True REGulatory (TREG) TF-gene interactions. We demonstrate the advantages of TREG framework in identifying genes regulated by two TFs with widely different distribution of functional binding events (ERα and E2f1). We also show that TREG signatures of TF activity vastly improve our ability to detect involvement of ERα in producing complex diseases-related transcriptional profiles. Through a large study of disease-related transcriptional signatures and transcriptional signatures of drug activity, we demonstrate that increase in statistical power associated with the use of TREG signatures makes the crucial difference in identifying key targets for treatment, and drugs to use for treatment. All methods are implemented in an open-source R package treg. The package also contains all data used in the analysis including 494 TREG binding profiles based on ENCODE ChIP-seq data. The treg package can be downloaded at http://GenomicsPortals.org.

 
PLOS Computational Biology is an open-access
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PLOS ONE: RNA-Seq Reveals Infection-Related Gene Expression Changes in Phytophthora capsici

PLOS ONE: RNA-Seq Reveals Infection-Related Gene Expression Changes in Phytophthora capsici | Plant Breeding and Genomics News | Scoop.it

Phytophthora capsici is a soilborne plant pathogen capable of infecting a wide range of plants, including many solanaceous crops. However, genetic resistance and fungicides often fail to manage P. capsici due to limited knowledge on the molecular biology and basis of P. capsici pathogenicity. To begin to rectify this situation, Illumina RNA-Seq was used to perform massively parallel sequencing of three cDNA samples derived from P. capsici mycelia (MY), zoospores (ZO) and germinating cysts with germ tubes (GC). Over 11 million reads were generated for each cDNA library analyzed. After read mapping to the gene models of P. capsici reference genome, 13,901, 14,633 and 14,695 putative genes were identified from the reads of the MY, ZO and GC libraries, respectively. Comparative analysis between two of samples showed major differences between the expressed gene content of MY, ZO and GC stages. A large number of genes associated with specific stages and pathogenicity were identified, including 98 predicted effector genes. The transcriptional levels of 19 effector genes during the developmental and host infection stages of P. capsici were validated by RT-PCR. Ectopic expression in Nicotiana benthamiana showed that P. capsici RXLR and Crinkler effectors can suppress host cell death triggered by diverse elicitors including P. capsici elicitin and NLP effectors. This study provides a first look at the transcriptome and effector arsenal of P. capsici during the important pre-infection stages.

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Steve Marek's curator insight, September 5, 2013 11:43 AM

Anti-death effectors expressed early during infection.  Sounds analogous to hemibiotroph Colletotrichum.

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Monitoring African Food and Agricultural Policies

Monitoring African Food and Agricultural Policies | Plant Breeding and Genomics News | Scoop.it
MAFAP in a nutshell

FAO is working with national partners to set up a sustainable system for monitoring the impact of food and agricultural policies for the first time in Africa.
Through MAFAP, FAO has developed common indicators for monitoring key commodities and public expenditure in agriculture. This helps policy makers and donors understand if policies are having a positive impact and compare results across countries and over time.
 

Plant Breeding and Genomics News's insight:

Links to recent reports and policy recommendations

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A BAC physical map of aus rice cultivar ‘Kasalath’ and the map-based genomic sequence of ‘Kasalath’ chromosome 1 - Kanamori - The Plant Journal - Wiley Online Library

A BAC physical map of aus rice cultivar ‘Kasalath’ and the map-based genomic sequence of ‘Kasalath’ chromosome 1 - Kanamori - The Plant Journal - Wiley Online Library | Plant Breeding and Genomics News | Scoop.it

Comparative analysis using available genomic resources within closely related species is an effective way to investigate genomic sequence and structural diversity. Rice (Oryza sativa L.) has undergone significant physiological and morphological changes during its domestication and local adaptation. We present a complete bacterial artificial chromosome (BAC) physical map for the aus rice cultivar 'Kasalath', which covers 90% of the sequence of temperate japonica rice cultivar 'Nipponbare'. Examination of physical distances between the computational and experimental measurements of 'Kasalath' BAC insert size revealed the presence of more than 500 genomic regions that appear to have significant chromosome structural changes between the two cultivars. In particular, a genomic region on the long arm of 'Kasalath' chromosome 11 carrying a disease-resistance gene cluster was greatly expanded relative to the 'Nipponbare' genome. We also decoded 41.37 Mb of high-quality genomic sequence from 'Kasalath' chromosome 1. Extensive comparisons of chromosome 1 between 'Kasalath' and 'Nipponbare' led to the discovery of 317,843 single-nucleotide polymorphisms (SNPs) and 66,331 insertion/deletion (indel) sites. Nearly two-thirds of the expressed genes on rice chromosome 1 carried natural variations involving SNPs and/or indels that resulted in substitutions, insertions, or deletions of amino acids in one cultivar relative to the other. We also observed gain and loss of genes caused by large indels. This study provides an important framework, and an invaluable dataset, for our further understanding of the molecular mechanisms underlying the evolution and functions of the rice genome. This article is protected by copyright. All rights reserved.

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Crop pests and pathogens move polewards in a warming world

Global food security is threatened by the emergence and spread of crop pests and pathogens. Spread is facilitated primarily by human transportation, but there is increasing concern that climate change allows establishment in hitherto unsuitable regions. However, interactions between climate change, crops and pests are complex, and the extent to which crop pests and pathogens have altered their latitudinal ranges in response to global warming is largely unknown. Here, we demonstrate an average poleward shift of 2.7±0.8 km yr−1 since 1960, in observations of hundreds of pests and pathogens, but with significant variation in trends among taxonomic groups. Observational bias, where developed countries at high latitudes detect pests earlier than developing countries at low latitudes, would result in an apparent shift towards the Equator. The observed positive latitudinal trends in many taxa support the hypothesis of global warming-driven pest movement.

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PLOS ONE: Plastid Genome Sequence of a Wild Woody Oil Species, Prinsepia utilis, Provides Insights into Evolutionary and Mutational Patterns of Rosaceae Chloroplast Genomes

PLOS ONE: Plastid Genome Sequence of a Wild Woody Oil Species, Prinsepia utilis, Provides Insights into Evolutionary and Mutational Patterns of Rosaceae Chloroplast Genomes | Plant Breeding and Genomics News | Scoop.it

Prinsepia utilis Royle is a wild woody oil species of Rosaceae that yields edible oil which has been proved to possess particular benefits for human health and medical therapy. However, the lack of bred varieties has largely impeded exploiting immense potentials for high quality of its seed oil. It is urgently needed to enlarge the knowledge of genetic basis of the species and develop genetic markers to enhance modern breeding programs. Results

Here we reported the complete chloroplast (cp) genome of 156,328 bp. Comparative cp sequence analyses of P. utilis along with other four Rosaceae species resulted in similar genome structures, gene orders, and gene contents. Contraction/expansion of inverted repeat regions (IRs) explained part of the length variation in the Rosaceae cp genomes. Genome sequence alignments revealed that nucleotide diversity was associated with AT content, and large single copy regions (LSC) and small single copy regions (SSC) harbored higher sequence variations in both coding and non-coding regions than IRs. Simple sequence repeats (SSRs) were detected in the P. utilis and compared with those of the other fourRosaceae cp genomes. Almost all the SSR loci were composed of A or T, therefore it might contribute to the A-T richness of cp genomes and be associated with AT biased sequence variation. Among all the protein-coding genes, ycf1 showed the highest sequence divergence, indicating that it could accomplish the discrimination of species within Rosaceae as well as within angiosperms better than other genes. Conclusions

With the addition of this new sequenced cp genome, high nucleotide substitution rate and abundant deletions/insertions were observed, suggesting a greater genomic dynamics than previously explored inRosaceae. The availability of the complete cp genome of P. utilis will provide chloroplast markers and genetic information to better enhance the conservation and utilization of this woody oil plant.

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Scientific American Special Edition: Food

Scientific American Special Edition: Food | Plant Breeding and Genomics News | Scoop.it
Plant Breeding and Genomics News's insight:

An interesting popular press collection of food realted science, albeit not very balanced scientiifcally on the issue of GMO food.

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gmopundit's curator insight, September 7, 2013 4:28 PM

Good quality science writing helps people make better choices in their lives.

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Bringing policy relevance and scientific discipline to environmental risk assessment for genetically modified crops

Although public opinion is important in deciding what is valued by society, governments have determined that scientific expertise is required to evaluate potential environmental effects of genetically modified (GM) crops. We suggest how to evaluate rigorously the environmental effects of GM crops in the context of a scientific investigation. Following a disciplined scientific approach to environmental risk assessment (ERA) for GM crops should help resolve controversy in identifying and addressing risk.

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Buddhist Economics and A GMO rethink | Food Matters, Scientific American Blog Network

Buddhist Economics and A GMO rethink | Food Matters, Scientific American Blog Network | Plant Breeding and Genomics News | Scoop.it
Wisdom demands a new orientation of science and technology towards the organic, the gentle, the non-violent, the elegant and beautiful.
E. F. Schumacher, Small Is Beautiful, 1973


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Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ) - Mascher - The Plant Journal - Wiley Online Library

Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ) - Mascher - The Plant Journal - Wiley Online Library | Plant Breeding and Genomics News | Scoop.it

Next-generation, whole genome shotgun (WGS) assemblies of complex genomes are highly enabling, but fail to link nearby sequence contigs with each other or provide a linear order of contigs along individual chromosomes. Here, we introduce a strategy based on sequencing progeny of a segregating population that allows the de novo production of a genetically anchored, linear assembly of the gene space of an organism. We demonstrate the power of the approach by reconstructing the chromosomal organization of the gene space of barley, a large, complex and highly repetitive 5.1-Gb genome. We evaluate the robustness of the new assembly by comparison to a recently released physical and genetic framework of the barley genome, and to different genetically ordered sequence-based genotypic datasets. The method is independent of the need for any prior sequence resources and will enable the rapid and cost efficient establishment of powerful genomic information for many species. This article is protected by copyright. All rights reserved.

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The impact of strain diversity and mixed infections on the evolution of resistance to Bacillus thuringiensis

Pesticide mixtures can reduce the rate at which insects evolve pesticide resistance. However, with live biopesticides such as the naturally abundant pathogen Bacillus thuringiensis (Bt), a range of additional biological considerations might affect the evolution of resistance. These can include ecological interactions in mixed infections, the different rates of transmission post-application and the impact of the native biodiversity on the frequency of mixed infections. Using multi-generation selection experiments, we tested how applications of single and mixed strains of Bt from diverse sources (natural isolates and biopesticides) affected the evolution of resistance in the diamondback moth, Plutella xylostella, to a focal strain. There was no significant difference in the rate of evolution of resistance between single and mixed-strain applications although the latter did result in lower insect populations. The relative survivorship of Bt-resistant genotypes was higher in the mixed-strain treatment, in part owing to elevated mortality of susceptible larvae in mixtures. Resistance evolved more quickly with treatments that contained natural isolates, and biological differences in transmission rate may have contributed to this. Our data indicate that the use of mixtures can have unexpected consequences on the fitness of resistant and susceptible insects.

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Priming of jasmonate-mediated antiherbivore defense responses in rice by silicon

Although the function of silicon (Si) in plant physiology has long been debated, its beneficial effects on plant resistance against abiotic and biotic stresses, including insect herbivory, have been well documented. In addition, the jasmonate (JA) signaling pathway plays a crucial role in mediating antiherbivore defense responses in plants. However, potential interactions between JA and Si in response to insect attack have not been examined directly. To explore the role JA may play in Si-enhanced resistance, we silenced the expression of allene oxide synthase (OsAOS; active in JA biosynthesis) and CORONATINE INSENSITIVE1 (OsCOI1; active in JA perception) genes in transgenic rice plants via RNAi and examined resulting changes in Si accumulation and defense responses against caterpillar Cnaphalocrocis medinalis (rice leaffolder, LF) infestation. Si pretreatment increased rice resistance against LF larvae in wild-type plants but not in OsAOS and OsCOI1 RNAi lines. Upon LF attack, wild-type plants subjected to Si pretreatment exhibited enhanced defense responses relative to untreated controls, including higher levels of JA accumulation; increased levels of transcripts encoding defense marker genes; and elevated activities of peroxidase, polyphenol oxidase, and trypsin protease inhibitor. Additionally, reduced Si deposition and Si cell expansion were observed in leaves of OsAOS and OsCOI1 RNAi plants in comparison with wild-type plants, and reduced steady-state transcript levels of the Si transporters OsLsi1, OsLsi2, and OsLsi6 were observed in Si-pretreated plants after LF attack. These results suggest a strong interaction between Si and JA in defense against insect herbivores involving priming of JA-mediated defense responses by Si and the promotion of Si accumulation by JA.

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BMC Genetics | Abstract | Nitrogen-metabolism related genes in barley - haplotype diversity, linkage mapping and associations with malting and kernel quality parameters

Background: Several studies report about intra-specific trait variation of nitrogen-metabolism related traits, such as N(itrogen)-use efficiency, protein content, N-storage and remobilization in barley and related grass species. The goal of this study was to assess the intra-specific genetic diversity present in primary N-metabolism genes of barley and to investigate the associations of the detected haplotype diversity with malting and kernel quality related traits. Results: Partial sequences of five genes related to N-metabolism in barley (Hordeum vulgare L.) were obtained, i.e. nitrate reductase 1, glutamine synthetase 2, ferredoxin-dependent glutamate synthase, aspartate aminotransferase and asparaginase. Two to five haplotypes in each gene were discovered in a set of 190 various varieties. The development of 33 SNP markers allowed the genotyping of all these barley varieties consisting of spring and winter types. Furthermore, these markers could be mapped in several doubled haploid populations. Cluster analysis based on haplotypes revealed a more uniform pattern of the spring barleys as compared to the winter barleys. Based on linear model approaches associations to several malting and kernel quality traits including soluble N and protein were identified. Conclusions: A study was conducted to investigate the presence of sequence variation of several genes related to the primary N-metabolism in barley. The detected diversity could be related to particular phenotypic traits. Specific differences between spring and winter barleys most likely reflect different breeding aims. The developed markers can be used as tool for further genetic studies and marker-assisted selection during breeding of barley.

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Biome | The power of plant genomics

Biome | The power of plant genomics | Plant Breeding and Genomics News | Scoop.it

Following on from Genome Biology’s special issue on plant genomics, five leaders in the field of plant research discuss why they think plant genomics is flourishing in a special edition podcast. The speakers include Dale Sanders (The John Innes Centre, UK), Catherine Feuillet (Bayer CropScience, USA*), Mario Pezzotti (Verona University, Italy), David Kuhn (USDA-ARS stationed in Florida, USA) and Guest Editor of the Genome Biology special issue, Mario Caccamo (The Genome Analysis Centre, UK).§

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Nothing Is More Important Than Food- Nigerian Agriculture Minister

Nothing Is More Important Than Food- Nigerian Agriculture Minister | Plant Breeding and Genomics News | Scoop.it

The Minister of Agriculture and Rural Development, Dr. Akinwunmi Adeshina on Tuesday vehemently and unequivocally stated that “nothing is more important than food”.


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Estimating and interpreting FST: The impact of rare variants

In a pair of seminal papers, Sewall Wright and Gustave Malécot introduced FST as a measure of structure in natural populations. In the decades that followed, a number of papers provided differing definitions, estimation methods, and interpretations beyond Wright's. While this diversity in methods has enabled many studies in genetics, it has also introduced confusion regarding how to estimate FST from available data. Considering this confusion, wide variation in published estimates of FST for pairs of HapMap populations is a cause for concern. These estimates changed—in some cases more than twofold—when comparing estimates from genotyping arrays to those from sequence data. Indeed, changes in FST from sequencing data might be expected due to population genetic factors affecting rare variants. While rare variants do influence the result, we show that this is largely through differences in estimation methods. Correcting for this yields estimates of FST that are much more concordant between sequence and genotype data. These differences relate to three specific issues: (1) estimating FST for a single SNP, (2) combining estimates ofFST across multiple SNPs, and (3) selecting the set of SNPs used in the computation. Changes in each of these aspects of estimation may result in FST estimates that are highly divergent from one another. Here, we clarify these issues and propose solutions.

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Uncertainty in simulating wheat yields under climate change

Projections of climate change impacts on crop yields are inherently uncertain1. Uncertainty is often quantified when projecting future greenhouse gas emissions and their influence on climate2. However, multi-model uncertainty analysis of crop responses to climate change is rare because systematic and objective comparisons among process-based crop simulation models1, 3 are difficult4. Here we present the largest standardized model intercomparison for climate change impacts so far. We found that individual crop models are able to simulate measured wheat grain yields accurately under a range of environments, particularly if the input information is sufficient. However, simulated climate change impacts vary across models owing to differences in model structures and parameter values. A greater proportion of the uncertainty in climate change impact projections was due to variations among crop models than to variations among downscaled general circulation models. Uncertainties in simulated impacts increased with CO2 concentrations and associated warming. These impact uncertainties can be reduced by improving temperature and CO2 relationships in models and better quantified through use of multi-model ensembles. Less uncertainty in describing how climate change may affect agricultural productivity will aid adaptation strategy development andpolicymaking.

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PLOS ONE: Phenotypic Variation in the Plant Pathogenic Bacterium Acidovorax citrulli

PLOS ONE: Phenotypic Variation in the Plant Pathogenic Bacterium Acidovorax citrulli | Plant Breeding and Genomics News | Scoop.it

Acidovorax citrulli causes bacterial fruit blotch (BFB) of cucurbits, a disease that threatens the cucurbit industry worldwide. Despite the economic importance of BFB, little is known about pathogenicity and fitness strategies of the bacterium. We have observed the phenomenon of phenotypic variation in A. citrulli. Here we report the characterization of phenotypic variants (PVs) of two strains, M6 and 7a1, isolated from melon and watermelon, respectively. Phenotypic variation was observed following growth in rich medium, as well as upon isolation of bacteria from inoculated plants or exposure to several stresses, including heat, salt and acidic conditions. When grown on nutrient agar, all PV colonies possessed a translucent appearance, in contrast to parental strain colonies that were opaque. After 72 h, PV colonies were bigger than parental colonies, and had a fuzzy appearance relative to parental strain colonies that are relatively smooth. A. citrulli colonies are generally surrounded by haloes detectable by the naked eye. These haloes are formed by type IV pilus (T4P)-mediated twitching motility that occurs at the edge of the colony. No twitching haloes could be detected around colonies of both M6 and 7a1 PVs, and microscopy observations confirmed that indeed the PVs did not perform twitching motility. In agreement with these results, transmission electron microscopy revealed that M6 and 7a1 PVs do not produce T4P under tested conditions. PVs also differed from their parental strain in swimming motility and biofilm formation, and interestingly, all assessed variants were less virulent than their corresponding parental strains in seed transmission assays. Slight alterations could be detected in some DNA fingerprinting profiles of 7a1 variants relative to the parental strain, while no differences at all could be seen among M6 variants and parental strain, suggesting that, at least in the latter, phenotypic variation is mediated by slight genetic and/or epigenetic alterations.

  
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Comparative analysis of genetic diversity in Canadian barley assessed by SSR, DarT, and pedigree data

The aim of this study was to measure genetic diversity and population structure among 92 Canadian barley cultivars using two types of molecular markers (SSRs and DArTs) and pedigree data. A total of 368 alleles were identified at 50 SSR loci. The number of alleles per locus ranged between 2 and 13. A third distance matrix was computed based on the kinship coefficient. Clustering of genotypes was performed based on the genetic distance matrix and the three dendrograms obtained showed the genetic relationships among barley cultivars. The topological similarity of the three dendrograms was estimated using a congruence index and showed the three dendrograms to be in very good agreement. Statistical analysis also showed a highly significant correlation between the SSR and DArT matrices (r = 0.80, p < 0.002) compared with lower yet significant correlations of the pedigree data with both marker types (r = 0.46, p < 0.002; r = 0.52, p < 0.002). Finally, we assessed linkage disequilibrium in this germplasm and found it to be quite extensive, as the mean distance between marker pairs with significant (p < 0.001) r2 values >0.5 was 3.8 cM. Information obtained from comparing results of different genetic diversity estimation methods should be useful for the improvement and conservation of barley genetic resources.

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