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Genetic diversity within a dominant plant outweighs plant species diversity in structuring an arthropod community

Genetic diversity within a dominant plant outweighs plant species diversity in structuring an arthropod community | Plant Breeding and Genomics News | Scoop.it
"Plant biodiversity is being lost at a rapid rate. This has spurred much interest in elucidating the consequences of this loss for higher trophic levels. Experimental tests have shown that both plant species diversity and genetic diversity within a plant species can influence arthropod community structure. However, the majority of these studies have been conducted in separate systems, so their relative importance is currently unresolved. Furthermore, potential interactions between the two levels of diversity, which likely occur in natural systems, have not been investigated. To clarify these issues, we conducted three experiments in a freshwater sand dune ecosystem. We 1) independently manipulated plant species diversity, 2) independently manipulated genetic diversity within the dominant plant species, Ammophila breviligulata, and 3) jointly manipulated genetic diversity within the dominant plant and species diversity. We found that genetic diversity within the dominant plant species, Ammophila breviligulata, more strongly influenced arthropod communities than plant species diversity, but this effect was dependent on the presence of other species. In species mixtures, A. breviligulata genetic diversity altered overall arthropod community composition, and arthropod richness and abundance peaked at the highest level of genetic diversity. Positive non-additive effects of diversity were detected, suggesting that arthropods respond to emergent properties of diverse plant communities. However, in the independent manipulations where A. breviligulata was alone, effects of genetic diversity were weaker, with only arthropod richness responding. In contrast, plant species diversity only influenced arthropods when A. breviligulata was absent, and then only influenced herbivore abundance. In addition to showing that genetic diversity within a dominant plant species can have large effects on arthropod community composition, these results suggest that understanding how species diversity and genetic diversity interact to influence community structure may be critically important for predicting the consequences of biodiversity loss.
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Effects of High-Temperature Stress on Soybean Isoflavone Concentration and Expression of Key Genes Involved in Isoflavone Synthesis - Journal of Agricultural and Food Chemistry (ACS Publications)

"Isoflavones have been reported to have putative health-beneficial properties, which has led to increased interest and demand for soybeans and soy-based products. This study was conducted to determine the effects of high-temperature stress on isoflavone concentration and expression of four key genes involved in isoflavone synthesis (i.e., CHS7, CHS8, IFS1, andIFS2) in both soybean pods and seeds during their late reproductive stage (i.e., R5–R8). Isoflavone concentrations were quantified using high-performance liquid chromatography (HPLC), and gene expression was studied using quantitative real-time (qRT)-PCR. High-temperature stress [33/25 °C (day/night temperatures)] imposed at the late reproductive stage (R5–R8) reduced total isoflavone concentration by 46–86 and 20–73% in seeds and pods, respectively, the reduction depending on the stage of maturity. At stage R5, the reduction in total isoflavone concentration was greater in seeds than in pods, whereas at subsequent stages, the reverse was observed. High-temperature stress had a large impact on the expression of CHS7, CHS8, IFS1, and IFS2 in both seeds and pods. In seeds, temperature stress reduced the expression of one gene at the R5 stage (CHS8), two genes at the R6 stage (CHS7 and IFS1), and all four genes at the R7 stage, the reduction ranging between 35 and 97%. In pods, high-temperature stress affected the expression of two genes at the R6 stage (CHS7 and IFS2) and all four genes at the R7 stage. Unlike in seeds, at the R6 stage, high temperature increased the expression of CHS7 and IFS2 by 72 and 736%, respectively, whereas at R7 stage the expression of all genes was reduced by an average of 97%. The present study reveals that high-temperature stress initiated at the R5 stage and maintained until maturation (i.e., R8 stage) has a rapid and sustained negative effect on isoflavone concentration in both seeds and pods. High temperature also affects gene expression; however, there was no clear correlation between isoflavone concentration and gene expression."
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BMC Bioinformatics | Abstract | Improving stability and understandability of genotype-phenotype mapping in Saccharomyces using regularized variable selection in L-PLS regression

"Applying the proposed methodology to yeast Saccharomyces cerevisiae data, we found the relationship between genotype-phenotype to have improved understandability. Phenotypic variations were explained by the variations of relatively stable genes and stable background variations. The suggested procedure provides an automatic way for genotype-phenotype mapping. The selected phenotype influencing genes were evolving 29% faster than non-influential genes, and the current results are supported by a recently conducted study. Further power analysis on simulated data verified that the proposed methodology selects relevant variables."
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An Heuristic Framework for Identifying Multiple Ways of Supporting the Conservation and Use of Traditional Crop Varieties within the Agricultural Production System

An Heuristic Framework for Identifying Multiple Ways of Supporting the Conservation and Use of Traditional Crop Varieties within the Agricultural Production System | Plant Breeding and Genomics News | Scoop.it
"This paper reviews and discusses how studies on (i) on-farm diversity assessment, (ii) access to diversity and information, (iii) extent of use of available materials and information, and (iv) benefits obtained by the farmer or farming community from their use of local crop diversity, are necessary to identify the different ways of supporting farmers and farming communities in the maintenance of traditional varieties and crop genetic diversity within their production systems. Throughout this paper two key themes are emphasized. First, any description or analysis within the four main areas (assessment, access, use and benefit) can, and most probably will, lead to a number of different actions. Second, the decision to implement a particular action, and therefore its success, will depend on farmers and the farming community having the knowledge and leadership capacity to evaluate the benefits that this action will have for them. This in turn emphasizes the importance of activities (whether by local, national and international organizations and agencies) of strengthening local institutions so as to enable farmers to take a greater role in the management of their resources."
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Maximizing genetic differentiation in core collections by PCA-based clustering of molecular marker data - Springer

"Developing genetically diverse core sets is key to the effective management and use of crop genetic resources. Core selection increasingly uses molecular marker-based dissimilarity and clustering methods, under the implicit assumption that markers and genes of interest are genetically correlated. In practice, low marker densities mean that genome-wide correlations are mainly caused by genetic differentiation, rather than by physical linkage. Although of central concern, genetic differentiation per se is not specifically targeted by most commonly employed dissimilarity and clustering methods. Principal component analysis (PCA) on genotypic data is known to effectively describe the inter-locus correlations caused by differentiation, but to date there has been no evaluation of its application to core selection. Here, we explore PCA-based clustering of marker data as a basis for core selection, with the aim of demonstrating its use in capturing genetic differentiation in the data. Using simulated datasets, we show that replacing full-rank genotypic data by the subset of genetically significant PCs leads to better description of differentiation and improves assignment of genotypes to their population of origin. We test the effectiveness of differentiation as a criterion for the formation of core sets by applying a simple new PCA-based core selection method to simulated and actual data and comparing its performance to one of the best existing selection algorithms. We find that although gains in genetic diversity are generally modest, PCA-based core selection is equally effective at maximizing diversity at non-marker loci, while providing better representation of genetically differentiated groups."

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Genetic and phenotypic diversity in a germplasm working collection of cultivated tropical yams (Dioscorea spp.) - Springer

Genetic and phenotypic diversity in a germplasm working collection of cultivated tropical yams (Dioscorea spp.) - Springer | Plant Breeding and Genomics News | Scoop.it

"A working collection of yam (Dioscorea spp.) comprising 53 landraces and seven improved cultivars of four species (D. alata L., D. cayenensis Lam., D. dumetorum (Kunth) and D. rotundata Poir.) was evaluated for phenotypic and genetic diversity. The evaluation involved field assessment of 24 morphological traits and DNA analysis with 32 Simple sequence repeat (SSR) polymorphic markers. Diversity was greater between species than within species; highest in D. rotundata and lowest in D. alata and D. cayenensis. Analysis based on combined phenotypic and SSR marker data sets revealed a close relationship between D. rotundata and D. cayenensis, but D. alata and D. dumetorum remained as distinct species. D. alata was related genetically to D. rotundata and D. cayenensis, but phenotypically to D. dumetorum. The study showed that cultivars obtained from different farmers may bear the same name but be genetically different. Polymorphic SSR markers were identified that may be used for genetic analysis across yam species. The working collection assessed in this study represents a good gene pool for intra- and inter-specific hybridization in yam genetic improvement."

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PLOS ONE: QTL Analysis of Na+ and K+ Concentrations in Roots and Shoots under Different Levels of NaCl Stress in Rice (Oryza sativa L.)

PLOS ONE: QTL Analysis of Na+ and K+ Concentrations in Roots and Shoots under Different Levels of NaCl Stress in Rice (Oryza sativa L.) | Plant Breeding and Genomics News | Scoop.it

"The key to plant survival under NaCl salt stress is maintaining a low Na+ level or Na+/K+ ratio in the cells. A population of recombinant inbred lines (RILs, F2∶9) derived from a cross between the salt-tolerant japonica rice variety Jiucaiqing and the salt-sensitive indica variety IR26, was used to determine Na+ and K+ concentrations in the roots and shoots under three different NaCl stress conditions (0, 100 and 120 mM NaCl). A total of nine additive QTLs were identified by QTL Cartographer program using single-environment phenotypic values, whereas eight additive QTLs were identified by QTL IciMapping program. Among these additive QTLs, five were identified by both programs. Epistatic QTLs and QTL-by-environment interactions were detected by QTLNetwork program in the joint analyses of multi-environment phenotypic values, and one additive QTL and nine epistatic QTLs were identified. There were three epistatic QTLs identified for Na+ in roots (RNC), three additive QTLs and two epistatic QTLs identified for Na+ in shoots (SNC), four additive QTLs identified for K+ in roots (RKC), four additive QTLs and three epistatic QTLs identified for K+ in shoots (SKC) and one additive QTL and one epistatic QTL for salt tolerance rating (STR). The phenotypic variation explained by each additive, epistatic QTL and QTL×environment interaction ranged from 8.5 to 18.9%, 0.5 to 5.3% and 0.7 to 7.5%, respectively. By comparing the chromosomal positions of these additive QTLs with those previously identified, five additive QTLs, qSNC9, qSKC1, qSKC9, qRKC4 and qSTR7, might represent novel salt tolerance loci. The identification of salt tolerance in selected RILs showed that a major QTL qSNC11 played a significant role in rice salt tolerance, and could be used to improve salt tolerance of commercial rice varieties with marker-assisted selection (MAS) approach."

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Reference Genes for High-Throughput Quantitative Reverse Transcription–PCR Analysis of Gene Expression in Organs and Tissues of Eucalyptus Grown in Various Environmental Conditions

"Interest in the genomics of Eucalyptus has skyrocketed thanks to the recent sequencing of the genome of Eucalyptus grandis and to a growing number of large-scale transcriptomic studies. Quantitative reverse transcription–PCR (RT–PCR) is the method of choice for gene expression analysis and can now also be used as a high-throughput method. The selection of appropriate internal controls is becoming of utmost importance to ensure accurate expression results in Eucalyptus. To this end, we selected 21 candidate reference genes and used high-throughput microfluidic dynamic arrays to assess their expression among a large panel of developmental and environmental conditions with a special focus on wood-forming tissues. We analyzed the expression stability of these genes by using three distinct statistical algorithms (geNorm, NormFinder and ΔCt), and used principal component analysis to compare methods and rankings. We showed that the most stable genes identified depended not only on the panel of biological samples considered but also on the statistical method used. We then developed a comprehensive integration of the rankings generated by the three methods and identified the optimal reference genes for 17 distinct experimental sets covering 13 organs and tissues, as well as various developmental and environmental conditions. The expression patterns of Eucalyptus master genes EgMYB1 and EgMYB2 experimentally validated our selection. Our findings provide an important resource for the selection of appropriate reference genes for accurate and reliable normalization of gene expression data in the organs and tissues of Eucalyptus trees grown in a range of conditions including abiotic stresses."

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An assessment of wheat yield sensitivity and breeding gains in hot environments

"These results imply that targeted breeding efforts help us to ensure progress in building heat tolerance, and that intensified (and possibly new) approaches are needed to improve the yield potential of wheat in hot environments in order to maintain global food security in a warmer climate."

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Physiological Traits for Improving Heat Tolerance in Wheat

"Wheat (Triticum aestivum) represents about 30% of the world’s cereal area, with over 220 million ha cultivated worldwide, often under abiotic stress. Wheat growth can be impaired by heat stress (HS) at any developmental stage, and modeling scenarios predict even warmer temperatures in the future (Easterling and Apps, 2005). The worst impacts of rising temperatures will occur at low latitudes (where approximately 100 million ha of wheat are cultivated, producing approximately 280 million tons of grain), while some benefits at high latitudes are expected. In terms of breeding targets, 12 different wheat mega-environments have been defined worldwide based on cropping system (e.g. rain fed versus irrigated, spring versus winter type) together with biotic and abiotic constraints (Braun et al., 2010). While mega-environment 5 encompasses 7 million ha under continuous HS (e.g. in Sudan and south and central India), over one-half of the total wheat area is prone to periods of HS already, and climate models suggest further increases in average temperatures (Fig. 1; Supplemental Table S1) as well as extreme temperature anomalies, which are already detectable (Hansen et al., 2012). Yield penalties are associated with both chronically high temperatures (mean temperature of the growth cycle being 18°C–25°C, and maximum day temperatures up to 32°C during grain filling) as well as heat shocks, where temperatures greater than 32°C occur during mid or late reproductive wheat stages, including grain filling (Wardlaw and Wrigley, 1994). A recent analysis of extensive international nursery data suggests that spring wheat breeding targeted for abiotic stress delivers better genetic gains in warmer environments (S.M. Gourdji, K.L. Mathews, M.P. Reynolds, J. Crossa, and D.B. Lobell, unpublished data). This Update considers the physiological processes and traits for which there is evidence that genetic improvement could improve wheat adaptation to HS. The issue of biotic threats to wheat is beyond the scope of this review, and readers are referred to other sources (Legreve and Duveiller, 2010)."

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The Influence of Climate Change on Global Crop Productivity

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

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Genic and nongenic contributions to natural variation of quantitative traits in maize

"Our findings suggest that efficient, cost-effective genome-wide association studies (GWAS) in species with complex genomes can focus on genic and promoter regions."

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Plant Cell: In Silico Plant Biology Comes of Age

"In this issue, four invited reviews describe how systems biology approaches are being used by plant researchers to generate mechanistic insights that span from genomic to cellular scales."

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Morphological evaluation of common bean diversity on the Island of Madeira.

"The variability of fifty populations of common bean (Phaseolus vulgaris L.), representing a wide range of ecological conditions on the Island of Madeira, was evaluated based on morphological and reproductive traits. Individual data of 58 traits related to earliness, plant and tassel structure and the shape of the ear and grain were analysed using multivariate analysis. The populations belonging to two major common varieties were clustered into fifteen groups by their degree of dissimilarity, based on discriminant analysis. The dissimilarity of these groups was confirmed by one way ANOVA. The racial rank of these groups was proposed and a brief description of the common bean landraces was presented. This work represents the first morphological characterization and analysis of diversity of bean germplasm from the Archipelago of Madeira, where the traditional agricultural practices are still keeping this Portuguese region free from improved bean varieties. The description of the Madeiran bean landraces allows the preservation of the existing bean biodiversity and could be used for their registration as conservation landraces, or for conservation and breeding purposes worldwide."
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Crop Improvement for Human Nutrition Symposium at Michigan State University

Crop Improvement for Human Nutrition Symposium at Michigan State University | Plant Breeding and Genomics News | Scoop.it
Register now to take part in Friday's two-part webinar live from Michigan State University.
Plant Breeding and Genomics News's insight:

Date: Friday, December 14, 2012

 

Register for afternoon session 1:30-3:30 pm ET now at:
https://www1.gotomeeting.com/register/167134233

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BMC Genomics | Abstract | Transcriptome analysis at four developmental stages of grape berry (Vitis vinifera cv. Shiraz) provides insights into regulated and coordinated gene expression

"In this study we report the global transcriptional profile of Shiraz grapes at key stages of development. We have undertaken a comprehensive analysis of gene families contributing to commercially important berry characteristics and present examples of co-regulation and differential gene expression. The data reported here will provide an invaluable resource for the on-going molecular investigation of wine grapes."
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State of the World’s Science: In-Depth Reports

State of the World’s Science: In-Depth Reports | Plant Breeding and Genomics News | Scoop.it

"The pursuit of knowledge is now a global enterprise. Scientific American and Nature have teamed up on this special report on how this trend is changing the way science is done, and how it informs the world"

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Fortifying plants with the essential amino acids lysine and methionine to improve nutritional quality - Galili - 2012 - Plant Biotechnology Journal - Wiley Online Library

Fortifying plants with the essential amino acids lysine and methionine to improve nutritional quality - Galili - 2012 - Plant Biotechnology Journal - Wiley Online Library | Plant Breeding and Genomics News | Scoop.it

"Humans, as well as farm animals, cannot synthesize a number of essential amino acids, which are critical for their survival. Hence, these organisms must obtain these essential amino acids from their diets. Cereal and legume crops, which represent the major food and feed sources for humans and livestock worldwide, possess limiting levels of some of these essential amino acids, particularly Lys and Met. Extensive efforts were made to fortify crop plants with these essential amino acids using traditional breeding and mutagenesis. However, aside from some results obtained with maize, none of these approaches was successful. Therefore, additional efforts using genetic engineering approaches concentrated on increasing the synthesis and reducing the catabolism of these essential amino acids and also on the expression of recombinant proteins enriched in them. In the present review, we discuss the basic biological aspects associated with the synthesis and accumulation of these amino acids in plants and also describe recent developments associated with the fortification of crop plants with essential amino acids by genetic engineering approaches."

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Open Variety Rights: Rethinking the Commodification of Plants - Deibel - 2012 - Journal of Agrarian Change - Wiley Online Library

Open Variety Rights: Rethinking the Commodification of Plants - Deibel - 2012 - Journal of Agrarian Change - Wiley Online Library | Plant Breeding and Genomics News | Scoop.it

Again, ironic "open access" article in a subscription journal

 

"Open Variety Rights refer to the removal of the conditions attached to the usage of plants in agriculture, and to an analogy with open licensing in informatics that is notably different from the one that is taking shape at the intersection of the life sciences and informatics. This paper argues for the open licensing of plants as part of a response to the commodification of DNA; rather than a singular focus on farming or source code, this implies an analogy that aims at the removal of restrictions, whether as seeds, biodiversity, genetic sequences or DNA in informatics formats. First, the commodification of plants will be conceptualized. Second, the proposal for open licensing for varieties of crops will be discussed. Third, examples of the introduction of open licensing in the life sciences will be examined in relation to the potential to reformulate the definition of ‘openness’ to support those who wish to live and work with plants on their own terms."

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Overexpression of a Wheat Aquaporin Gene, TaAQP8, Enhances Salt Stress Tolerance in Transgenic Tobacco

"Aquaporin (AQP) proteins have been shown to transport water and other small molecules through biological membranes, which is crucial for plants to combat salt stress. However, the precise role of AQP genes in salt stress response is not completely understood in plants. In this study, a PIP1 subgroup AQP gene, designated TaAQP8, was cloned and characterized from wheat. Transient expression of TaAQP8–green fluorescent protein (GFP) fusion protein revealed its localization in the plasma membrane. TaAQP8 exhibited water channel activity in Xenopus laevis oocytes. TaAQP8 transcript was induced by NaCl, ethylene and H2O2. Further investigation showed that up-regulation of TaAQP8 under salt stress involves ethylene and H2O2 signaling, with ethylene causing a positive effect and H2O2 acting as a negative factor. Overexpression of TaAQP8 in tobacco increased root elongation compared with controls under salt stress. The roots of transgenic plants also retained a high K+/Na+ ratio and Ca2+ content, but reduced H2O2 accumulation by an enhancement of superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD) activities under salt stress. Further investigation showed that whole seedlings from transgenic lines displayed higher SOD, CAT and POD activities, increased NtSOD and NtCAT transcript levels, and decreased H2O2 accumulation and membrane injury under salt stress. Taken together, our results demonstrate that TaAQP8 confers salt stress tolerance not only by retaining high a K+/Na+ ratio and Ca2+ content, but also by reducing H2O2 accumulation and membrane damage by enhancing the antioxidant system."

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BMC Genomics | Abstract | Asymmetric purine-pyrimidine distribution in cellular small RNA population of papaya

"We have identified 60 miRNAs in papaya. Our study revealed the asymmetric purine-pyrimidine distribution in cellular sRNA population. The 21nt species of sRNAs have higher expression levels than 24nt sRNA. The miRNA* of some miRNAs shows higher accumulation in PRSV infected tissues, suggesting that these strands are not totally functionally redundant. The findings open a new avenue for further investigation of the sRNA silencing pathway in plants."

 

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Editor’s Choice: Crop Genome Plasticity and Its Relevance to Food and Feed Safety of Genetically Engineered Breeding Stacks

"Genetically engineered (GE) stacks, combinations of two or more single transgenic events (i.e. single-locus insertions) that have been produced by crossing sexually compatible parents, are an important and growing sector of the crop seed market. Stacked traits covered 26% of the global transgenic crop area in 2011 and were the fastest growing trait group, with a 31% increase in the area planted compared with 2010 (James, 2011). Stacked traits already dominate the market in some regions. For example, 95% of the cotton (Gossypium spp.) grown in Australia during 2011 had both herbicide tolerance and insect resistance traits (James, 2011). Worldwide, at least 12 countries are now growing stacked varieties, of which nine are developing countries (James, 2011). The rapid adoption of GE stacks has focused attention on whether the safety of such products differs from that of the individual events."

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Waterproofing Crops: Effective Flooding Survival Strategies

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

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BMC Genomics | Abstract | Comparative transcriptomic analysis of roots of contrasting gossypium herbaceum genotypes revealing adaptation to drought

"Root length and its architecture govern the adaptability of plants to various stress conditions, including drought stress. Genetic variations in root growth, length, and architecture are genotypes dependent. In this study, we compared the drought-induced transcriptome of four genotypes of Gossypium herbaceum that differed in their drought tolerance adaptability. Three different methodologies, namely, microarray, pyrosequencing, and qRT--PCR, were used for transcriptome analysis and validation."

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Cornell receives $25.2M funding for cassava breeding

Cornell receives $25.2M funding for cassava breeding | Plant Breeding and Genomics News | Scoop.it

"Cassava, a rough and ready root crop that has long been the foundation of food security in Africa is finally getting the respect it deserves. The Bill & Melinda Gates Foundation and the Department for International Development of the United Kingdom (DFID) are investing $25.2 million to improve the staple crop’s productivity and build human and technical capacity for plant breeding in sub-Saharan Africa."

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