Cassava Brown Streak Virus Infection Genome

Cassava Brown Streak Virus Infection Genome Genome-wide prediction and association analysis for sensitivity to cassava brown streak virus infection in Cassava Siraj Ismail Kayondo, Dunia Pino Del Carpio, Roberto Lozano, Alfred Ozimati, Marnin Wolfe, Yona Baguma, Vernon Gracen, Offei Samuel,  Robert Kawuki  and Jean-Luc Jannink ABSTRACT Cassava (manihot esculenta Crantz), a key carbohydrate source faces unprecedented challenge of viral diseases importantly, cassava brown streak disease (CBSD) and cassava mosaic disease (CMD). The economic parts of the crop are rendered unmarketable by these viral diseases resulting into mega fiscal setbacks. The remarkable completion of the cassava genome sequence equips cassava breeders with more precise selection strategies to offer superior varieties with both farmer and industry preferred traits. This article reports genomic segments associated to foliar and root CBSV sensitivity measured at different growth stages and environmental conditions. We identified significant single nucleotide polymorphisms (SNPs) associated to CBSV sensitivity in cassava on chromosome 4 and 11. The significantly associated regions on chromosome 4 co-localises with a Manihot glaziovii introgression from the wild progenitors. While significant SNPs markers on chromosome 11 are in linkage disequilibrium (LD) with a cluster of nucleotide-binding site leucine-rich repeat (NBS-LRR) proteins encoded by disease resistance genes in plants. Genotype by environmental interactions were significant since SNP marker effects differed across environments and years. Key words: Genome-wide association studies (GWAS), virus sensitivity, augmented designs, de-regressed best linear unbiased Predictions (dr-BLUPs), NBS-LRR proteins, QTLs    INTRODUCTION Cassava (Manihot esculenta crantz), is a major source of income and dietary calories for over a billion lives across the globe especially in Sub Saharan Africa (SSA). Edge cutting technologies are rapidly turning cassava into an industrial crop especially tapping into its unique starch qualities hence opening new income opportunities for the poor (Pà ©rez et al., 2011). Cassava brown streak virus disease (CBSD), a leading viral constraint limiting production across SSA is responsible for mega fiscal setbacks estimated at 100 US million dollars per annum at physiological maturity (ASARECA:, 2013; Ndunguru et al., 2015). As a consequence of CBSVs, cassava yields were recorded to be eight times lower than the expected yield potential in Uganda(). Two major strains; Cassava brown streak virus (CBSV) and Uganda Cassava brown streak virus (UCBSV), have successfully colonized both the lowland and highland altitudes across East Africa though newer strains are being reported (Winter et al., 2010; Ndunguru et al., 2015; Alicai et al., 2016a). In addition to uncontrolled exchange of infected cassava steaks among cassava farmers across porous borders, the African whitefly (Besimia tobaci) stands out as the famous semi-persistent virus transmitter under field conditions (Legg et al., 2014; McQuaid et al., 2015). Upon entry, the virus exploits the plants transport system to traverse the susceptible cassava plant resulting into yellow chlorotic vein clearing patterns along minor veins of the leaves. Prominent brown elongated lesions are formed on the stem commonly referred to as brown streaks. While the brown necrotic hard-corky layers are randomly formed in the root cortex of most susceptible cassava clones. In view of the rapid but steadily virus evolution rates and the insufficiency of dependable virus diagnostic tools (Alicai et al., 2016b), breeding for durable CBSD resistance emerges as a timely and economically viable option. Earlier CBSD resistance breeding initiatives have highlighted its polygenic but recessive nature of inheritance in both intraspecific and interspecific cassava hybrids (Nichols, 1947; Hillocks and Jennings, 2003; Munga, 2008; Kulembeka, 2010). The rate of progress to genetic improvement in a traditional cassava breeding pipeline has been slower due to several biology-related opportunities like; shy flowering, length of breeding cycle, limited genetic diversity and slow rate of multiplication of planting materials. Most of the available elite cassava lines have exhibited some level of sensitivity to CBSVs ranging from mild sensitivity total susceptibility. Therefore, a concise but then targeted exploration for potential sources of resistance using the available biotechnology tools could be a promising strategy. The remarkable completion of the cassava genome sequence equips cassava breeders with more precise selection strategies to offer superior varieties with both farmer and industry preferred traits. A study by Bredeson et al., (2016) reports the presence of introgressions segments from the wild progenitors into the elite breeding lines developed by the Amani breeding program in Tanzania. Hence, resistance sources to CBSD exist but may have been reshuffled over generations of recurrent selection thus not fully fixed and need to be exploited. Moving forward, a genome wide survey for existing natural variations as explained by the observed phenotypes for a given series of agronomic traits could facilitate identification of causal loci associated with the inheritance of a trait of interest. This tool, commonly referred to as genome-wide association study (GWAS) exploits the power of statistical analyses to identify such historical recombination events that have occurred over time (Jannink and Walsh, 2002; Hamblin, Buckler and Jannink, 2011). Hence, GWA-studies will complement bi-parental mapping efforts that have been widely applied in cassava breeding in the previous decade (Ferguson et al., 2012; Ceballos et al., 2015). GWA-studies have been widely undertaken by animal, human and plant geneticists to identify quantitative trait loci (QTLs) in close association to several important traits. However, GWAS has been thinly applied in cassava breeding especially in the definition of the genetic architecture of cassava mosaic di sease (Wolfe et al., 2016) and beta carotene (unpublished). In this study, we exploited the reduced genotyping costs using genotyping by sequencing (GBS) to genotype data for our association mapping panel. The goal of this study was to identify genomic regions closely associated with sensitivity to CBSV infection in a diverse regional cassava breeding panel. Fine mapping around the identified regions would guide in marker discovery as well as identification of franking genes for CBSV sensitivity for marker assisted breeding. MATERIALS AND METHODS Plant material The data set comprised of field disease evaluations undertaken across five locations; Namulonge, Kamuli, Serere, Ngetta and Kasese in Uganda. Two different but closely related GWAS panels were evaluated across environments. Between 2012 and 2013, GWAS panel 1 consisted of between 308 to 429 entries that were replicated twice across three locations. Each trial was designed as a randomized complete block (RCB) with two-row plots of five plants each at a spacing of 1 meter by 1 meter. In 2015, GWAS panel 2 consisting of entries ranging from 715 to 872 clones was evaluated in three locations but contrasting sites for CBSD pressure. These entries were evaluated as single entries per site being connected by six common checks in an augmented completely randomized block design with 38 blocks per site (Federer, Nguyen and others, 2002; Federer and Crossa, 2012). The two GWAS panels had one location in common; Namulonge that is regarded as the CBSD hot spot with the highest CBSD pressure. The data was generated from 1281 cassava clones developed through three cycles of genetic recombination with local elite lines by the National root crops breeding program at NaCRRI. These cassava clones had a diverse genetic background whose pedigree could be traced back to introductions from international institute for tropical agriculture (IITA), International center for tropical Agriculture (CIAT) and Tanzania[KI1] breeding program (sup.fig1). Phenotyping protocol for CBSV sensitivity   Ã‚   The key traits were CBSD severity and incidence scored at 3, 6, and 9 months after planting (MAP) for foliar and 12 MAP for root symptoms respectively. CBSD severity was measured based on a 5 point scale with a score of 1 implying asymptomatic conditions and a score 5 implying over 50% leaf vain clearing under foliar symptoms. However, at 12 MAP a score of 5 implies over 50% of root-core being covered by a necrotic corky layer. (fig.1) Clones were classified with a score of 5 if pronounced vein clearing at major leaf veins were jointly displayed with brown streaks on the stems and shoot die-back that appeared as a candle-stick. Clones with 31 40% leaf vein clearing together with brown steaks at the stems were classified under score 4. A Score of 3 was assigned to clones with 21 30% leaf vein clearing with emerging brown streaks on the stems. While a score of 2 was assigned to clones that only displayed 1 20% leaf vein clearing without any visible brown streak symptoms on the stems. Plants classified with a score of 1 showed no visible sign of leaf necrosis and brown streaks on the stems. On the other hand, root symptoms were also classified into 5 different categories based on a 5 point standard scale. Two-stage genomic analyses For the panel 1 which was designed as a randomized complete block (RCB) we fit the model: , using the lmer function from the lme4 R package (Bates et al., 2015).In this model, ÃŽÂ ² included a fixed effect for the population mean and location. The incidence matrix Zclone and the vector c represent a random effect for clone and I represent the identity matrix. The range variable, which is the row or column along which plots are arrayed, is nested in location-rep and is represented by the incidence matrix Zrange(loc.) and random effects vector .Block effects were nested in ranges and incorporated as random with incidence matrix Zblock(range) and effects vector . Residuals were fit as random, with . For panel 2, which followed an augmented design, we fit the model Where y was the vector of raw phenotypes, ÃŽÂ ² included a fixed effect for the population mean and location with checks included as a covariate, The incidence matrix Zclone and the vector c are the same as above and the blocks were also modeled with incidence matrix and b represents the random effect for block. The best linear predictors (BLUPs) of the clone effect (Ć°) were extracted as de-regressed BLUPS following the formula: Broad sense heritability was calculated using variance components extracted from the two step lmer output. SNP-based heritability was calculated by extracting the variance components from the output obtained by fitting the SNPs as a kinship covariate calculated using the A.mat function from the rrBLUP R package and included in a one step model using the emmreml function from the EMMREML R package (Akdemir and Okeke, 2015). DNA preparation and Genotyping by sequencing (GBS) All cassava clones included in the phenotypic data set had their total genomic DNA extracted from young tender leaves according to standard procedures using the DNAeasy plant mini extraction kit (Qiagen, 2012). Genotyping-by-sequencing (GBS) (Elshire et al., 2011) libraries were constructed using the ApeKI restriction enzyme as used before (Hamblin Rabbi, 2014). Marker genotypes were called using TASSEL GBS pipeline V4 (Glaubitz et al., 2014) after aligning the reads to the Cassava v6 reference genome (Phytozome 10.3; http://phytozome.jgi.doe.gov) (International Cassava Genetic Map Consortium, 2014; Prochnik et al., 2012). Variant Calling Format (VCF) files were generated for each chromosome. Markers with more than 60% missing calls were removed. Genotypes with less than 5 reads were masked before imputation. Additionally, only biallelic SNP markers were considered for further steps. The marker dataset consisted of a total of 173,647 SNP bi-allelic markers called for 986 individuals. This initial dataset was imputed using Beagle 4.1 (Browning and Browning, 2016). After the imputation 63,016 SNPs had an AR2 (Estimated Allelic r-squared) higher than 0.3 and were kept for analysis; from these, 41,530 had a minor allele frequency (MAF) higher than 0.01 in our population. Dosage files for this final dataset were generated and used for both GWAS and GS. Structure and Genetic stratification analysis The extent of phylogenetic relationship and degree of family relatedness within the cassava lines was assessed using principal component analysis (PCA) implemented in R. Genome-wide association analysis for CBSV sensitivity The input binary PED files were prepared from the genotype dosage files using PLINK version 1.07 (Renterà ­a, Cortes and Medland, 2013; Purcell et al., 2007). Mixed linear modal association analysis (MLMA) implemented by GCTA version 1.26.0 was used to generated GWAS results (Yang et al., 2011). MLMA was implemented such that in every cycle of analysis, the chromosome on which the candidate SNPs existed got excluded from the GRM calculation using the modal in equation 3. Where y is the phenotype, a is being the mean term, b being the fixed additive effects of the candidate SNP being tested for association, x being the SNP genotype indicator variable and g is the accumulated effect of all SNPs excluding those where the candidate SNP is located making our analysis model more powerful. We estimated variance components using restricted maximum likelihood (REML). Sub population stratification was corrected for by taking GRM as a random effect term in the model during analysis. A more conservative Bonferroni correction method was used to fix genome-wide significance threshold at Pà ¢Ã¢â‚¬ °Ã‚ ¤10-7 as a way of correcting for experimental-wise error. Manhattan and Quantile Quantile plots for all the traits were constructed using R package qqman package implemented in R (Turner, 2014). Genomic prediction models GBLUP. In this prediction model the GEBVs are obtained by assuming , where is the additive genetic variance, and K is the symmetric genomic realized relation matrix based on GBS SNP marker dosages. The genomic relationship matrix used was constructed using the function A.mat in the R package rrBLUP(Endelman, 2011) and follows the formula of VanRaden (2008), method two. GBLUP predictions were made with the function emmreml in the R package EMMREML (Akdemir and Okeke, 2015). RKHS. Unlike GBLUP for RKHS we use a Gaussian kernel function: , where Kij is the measured relationship between two individuals, dij is their euclidean genetic distance based on marker dosages and ÃŽÂ ¸ is a tuning (bandwidth) parameter that determines the rate of decay of correlation among individuals. This function is nonlinear therefore the kernels used for RKHS can capture non-additive as well as additive genetic variation. To fit a multiple-kernel model with six covariance matrices we used the emmremlMultiKernel function in the EMMREML package, with the following bandwidth parameters: 0.0000005, 0.00005, 0.0005, 0.005, 0.01, 0.05 (Multi-kernel RKHS) and allowed REML to find optimal weights for each kernel.For the optimal kernel RKHS we used the kernel weights assigned by emmremlMultiKernel in the first step to construct a single kernel that is the weighted average of the original six. We then used this optimal kernel in single-kernel predictions. Bayesian maker regressions.We tested four Bayesian prediction models: BayesCpi (Habier et al., 2011), the Bayesian LASSO (BL; Park and Casella, 2008), BayesA, and BayesB (Meuwissen, Hayes and Goddard, 2001). The Bayesian models we tested allow for alternative genetic architectures by differential shrinkage of marker effects. We performed Bayesian predictions with the R package BGLR (Pà ©rez and De Los Campos, 2014) Random Forest. Random forest (RF) is a machine learning method used for regression and classification (Strobl et al. 2009, Breiman 2001). Random forest regression with marker data has been shown to capture epistatic effects and has been successfully used for prediction (Sakar et al 2015, Heslot et al 2012, Charmet et al 2014, Spindel et al 2015, Breiman, et al 2001, Michaelson et al 2010, Motsinger-Reif et al 2008). We implemented RF using the randomForest package in R (Liaw and Wiener 2002) with the parameter, ntree set to 500 and the number of variables sampled at each split (mtry) equal to 300. Multikernel GBLUP We followed a multikernel approach by fitting three kernels constructed with SNPs with MAF> 0.01 from chromosomes 4,11 and the SNPs from the other chromosomes. We selected chromosomes 4 and 11 because they contained QTLs for foliar severity 3 and 6 MAP. Multikernel GBLUP predictions were made with the function emmremlMultiKernel in the R package EMMREML (Akdemir and Okeke, 2015) Introgression Segment Detection To identify the genome segments in our germplasm, we followed the approach of Bredeson et al. (2015). We used the M. glaziovii diagnostic markers identified Supplementary Dataset 2 of Bredeson et al. (2015). These ancestry diagnostic (AI) SNPs were identified as being fixed for different alleles in a sample of two pure M. esculenta (Albert and CM33064) and two pure M. glaziovii (GLA XXX-8 and M. glaziovii(S)). Out of 173,647 SNP in our imputed dataset, 12,502 matched published AI SNPs. For these AI SNPs, we divided each chromosome into non-overlapping windows of 20 SNP. Within each window, for each individual, we calculated the proportion of genotypes that were homozygous (G/G) or heterozygous (G/E) for M. glaziovii allele and the proportion that were homozygous for the M. esculenta allele (E/E). We assigned G/G, G/E or E/E ancestry to each window, for each individual only when the proportion of the most common genotype in that window was at least twice the proportion of the second most common genotype. We assigned windows a No Call status otherwise. We also used this approach on six whole-genome sequenced samples from the cassava HapMap II (Punna et al. under Review). These included the two pure cassava and M. glaziovii(S) from Bredeson et al. (2015), plus an additional M. glaziovii, and two samples labeled Namikonga. Because these samples came from a different source from the majority of our samples, we were able to find only 11,686 SNPs that matched both the sites in the rest of our study sample and the list of ancestry informative sites for analysis. Linkage disequilibrium plots LD scores were calculated for every SNP in chromosome 4 with a window of 1Mb using the GCTA Software (Yang et al., 2011). Briefly, LD score for a given marker is the sum of R2 adjusted between the index marker and all markers within a specified window. The adjusted R2 is an unbiased measure of LD: where n is the population size and R2 is the usual estimator of the squared Pearsons correlation (Bulik-Sullivan et al 2015). We calculated the LD between that marker and other markers in a window of 2Mb (1Mb upstream and 1Mb downstream) For the top significant SNP hit in chromosome 11 for the 6MAP GWAS result from panel 1 and panel 2. The LD was evaluated using squared Pearsons correlation coefficient (r2) as calculated with the à ¢Ã‹â€ Ã¢â‚¬â„¢r2 -ld-snp commands in the software PLINK version 1.9. Candidate gene identification To identify candidate genes for CBSD severity in leaves and CBSD root necrosis we used the GCTA mlma GWAS output obtained for each trait. We filtered the SNP markers based on -log10 (P-value)> Bonf, being these values higher than the Bonferroni threshold (~ 5.9). The resulting SNP markers were assigned onto genes using the SNP location and gene description from the Mesculenta_305_v6.1.gene.gff3 available in Phytozome 11 (ref) for Manihot esculenta v6.1 using the intersect function from bedtools (ref). RESULTS Phenotypic assessment of cassava for sensitivity to cassava brown streak virus infection Most clones showed varied responses to CBSV infection spanning from super susceptibility that represented candle-like die-back of the shoot to tolerance (Fig.). Foliar phenotyping clumped these plant responses into five major classes based on a 1 to 5 scale. The broad sense heritability of the studied traits ranged 0.17 to 0.72 for both GWAS panels (Table 1). Analysis of the phenotypic data showed very significant GxE interactions (P Genetic correlations and heritability estimates We found moderate heritability estimates for CBSV sensitivity for foliar phenotypes at 3, 6 and 9 MAP as well as root phenotypes under five environments (fig..) . Genetic correlation on the traits assayed were performed and revealed that ranged from moderate to high positive correlations among traits studied. Assessment of linkage disequilibrium Genome-wide association mapping often explores the benefit of existence of several historic recombination events over time to associate observed phenotypic variation with genome. Detection of candidate QTLs for CBSV sensitivity in cassava To efficiently a run GWAS, we used SNP data to examine the extent of genetic interrelatedness and sub-population structure of the cassava clones. A principal component analysis (PCA) to account for structure showed no distinct clusters implying that the selected clones were not highly structured (Fig.1). Therefore, we did not include PCs in our GWAS linear modal analysis. The Bonferroni suggestive threshold (ÃŽÂ ± = 0.05) was used to identify loci associated to CBSV sensitivity on both chromosome 4 and 11 that had clear peak signals at the different stages of phenotyping (Fig. 2). The observed P-values initially aligned well with the expected P-values but later differed substantially due the large introgression block on chromosome 4 presumably from the wild progenitors of cassava traceable from the AMANI breeding program (Jennings, 1959). The significant signals on chromosome 11 contained loci with strong association with CBSV sensitivity in a 2 Mb region that annotated well with several candidate genes. Genome-wide prediction for CBSV sensitivity in cassava We did genome wide prediction for CBSV sensitivity based on the identified SNPs with the highest effects found on both chromosome 4 and 11 in order to capture most of the genetic variation. We explored several genomic prediction model methods; GBLUP, RR-BLUP, B-LASSO, random forest, BayesA, BayesB, and BayesC. References Akdemir, D. and Okeke, U. G. (2015) EMMREML: Fitting Mixed Models with Known Covariance Structures,. Alicai, T., Ndunguru, J., Sseruwagi, P., Tairo, F., Okao-Okuja, G., Nanvubya, R., Kiiza, L., Kubatko, L., Kehoe, M. A. and Boykin, L. M. (2016a) Characterization by Next Generation Sequencing Reveals the Molecular Mechanisms Driving the Faster Evolutionary rate of Cassava brown streak virus Compared with Ugandan cassava brown streak virus, bioRxiv, Cold Spring Harbor Labs Journals, [online] Available at: http://biorxiv.org/lookup/doi/10.1101/053546 (Accessed 27 June 2016). Alicai, T., Ndunguru, J., Sseruwagi, P., Tairo, F., Okao-Okuja, G., Nanvubya, R., Kiiza, L., Kubatko, L., Kehoe, M. A. and Boykin, L. M. (2016b) Characterization by Next Generation Sequencing Reveals the Molecular Mechanisms Driving the Faster Evolutionary rate of Cassava brown streak virus Compared with Ugandan cassava brown streak virus, [online] Available at: http://biorxiv.org/lookup/doi/10.1101/053546 (Accessed 10 June 2016). ASARECA: (2013) ASARECA Annual Report 2012: Transforming Agriculture for Economic Growth in Eastern and Central Africa, Entebbe, Uganda. Bredeson, J. V, Lyons, J. B., Prochnik, S. E., Wu, G. A., Ha, C. M., Edsinger-Gonzales, E., Grimwood, J., Schmutz, J., Rabbi, I. Y., Egesi, C., Nauluvula, P., Lebot, V., Ndunguru, J., Mkamilo, G., Bart, R. S., Setter, T. L., Gleadow, R. M., Kulakow, P., Ferguson, M. E., Rounsley, S. and Rokhsar, D. S. (2016) Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity., Nature biotechnology, 34(5), pp. 562-570, [online] Available at: http://dx.doi.org/10.1038/nbt.3535. Browning, B. L. and Browning, S. R. (2016) Genotype Imputation with Millions of Reference Samples, The American Journal of Human Genetics, 98(1), pp. 116-126. Ceballos, H., Kawuki, R. S., Gracen, V. E., Yencho, G. C. and Hershey, C. H. (2015) Conventional breeding, marker-assisted selection, genomic selection and inbreeding in clonally propagated crops: a case study for cassava, Theoretical and Applied Genetics, [online] Available at: http://link.springer.com/10.1007/s00122-015-2555-4 (Accessed 25 June 2015). Endelman, J. B. (2011) Ridge Regression and Other Kernels for Genomic Selection with R Package rrBLUP, The Plant Genome Journal, 4(3), pp. 250-255. Federer, W. T. and Crossa, J. (2012) Screening Experimental Designs for Quantitative Trait Loci, Association Mapping, Genotype-by Environment Interaction, and Other Investigations, Frontiers in Physiology, 3, [online] Available at: http://www.frontiersin.org/Journal/10.3389/fphys.2012.00156/full (Accessed 2 September 2014). Federer, W. T., Nguyen, N.-K. and others (2002) Constructing Augmented Experiment Designs with Gendex, [online] Available at: https://dspace.library.cornell.edu/handle/1813/32208 (Accessed 2 September 2014). Ferguson, M., Rabbi, I., Kim, D.-J., Gedil, M., Lopez-Lavalle, L. A. B. and Okogbenin, E. (2012) Molecular Markers and Their Application to Cassava Breeding: Past, Present and Future, Tropical Plant Biology, 5(1), pp. 95-109, [online] Available at: http://link.springer.com/10.1007/s12042-011-9087-0 (Accessed 5 August 2014). Habier, D., Fernando, R. L., Kizilkaya, K. and Garrick, D. J. (2011) Extension of the bayesian alphabet for genomic selection., BMC bioinformatics, BioMed Central Ltd, 12(1), p. 186. Hamblin, M. T., Buckler, E. S. and Jannink, J.-L. (2011) Population genetics of genomics-based crop improvement methods, Trends in Genetics, 27(3), pp. 98-106, [online] Available at: http://www.sciencedirect.com/science/article/pii/S0168952510002301 (Accessed 18 April 2014). Hillocks, R. J. and Jennings, D. L. (2003) Cassava brown streak disease: a review of present knowledge and research needs, International Journal of Pest Management, 49(3), pp. 225-234, [online] Available at: http://www.tandfonline.com/doi/abs/10.1080/0967087031000101061 (Accessed 5 February 2014). Jannink, J.-L. and Walsh, B. (2002) Association mapping in plant populations, Quantitative genetics, genomics and plant breeding, pp. 59-68, [online] Available at: http://books.google.com/books?hl=enlr=id=hMBY_MvS39ACoi=fndpg=PA59dq=%22of+meioses+that+have+occurred+and+(in+the+case+of+advanced+intercross+lines)%22+%22discussion+of+rigorous+methods+to+test+for+marker+association+with+a+quantitative%22+ots=wo7fd. Jennings, D. L. (1959) Manihot melanobasis Mà ¼ll. Arg.-a useful parent for cassava breeding, Euphytica, 8(2), pp. 157-162, [online] Available at: http://link.springer.com/article/10.1007/BF00022435 (Accessed 8 October 2014). Kulembeka, H. P. (2010) Genetic linkage mapping of Field Resistance to cassava brown streak Disease in cassava landraces from Tanzania, Doctoral thesis, University of the Free State. Legg, J. P., Sseruwagi, P., Boniface, S., Okao-Okuja, G., Shirima, R., Bigirimana, S., Gashaka, G., Herrmann, H. W., Jeremiah, S., Obiero, H., Ndyetabula, I., Tata-Hangy, W., Masembe, C. and Brown, J. K. (2014) Spatio-temporal patterns of genetic change amongst populations of cassava Bemisia tabaci whiteflies driving virus pandemics in East and Central Africa, Virus Research, Elsevier B.V., 186, pp. 61-75, [online] Available at: http://dx.doi.org/10.1016/j.virusres.2013.11.018. McQuaid, C. F., Sseruwagi, P., Pariyo, A. and van den Bosch, F. (2015) Cassava brown streak disease and the sustainability of a clean seed system, Plant Pathology, p. n/a-n/a, [online] Available at: http://doi.wiley.com/10.1111/ppa.12453 (Accessed 17 September 2015). Meuwissen, T. H., Hayes, B. J. and Goddard, M. E. (2001) Prediction of total genetic value using genome-wide dense marker maps., Genetics, 157(4), pp. 1819-29. Munga, T. L. (2008) Breeding for Cassava Brown Streak Resistance in Coastal Kenya, Doctoral thesis, University of KwaZulu-Natal Republic of South Africa. Ndunguru, J., Sseruwagi, P., Tairo, F., Stomeo, F., Maina, S., Djinkeng, A., Kehoe, M. and Boykin, L. M. (2015) Analyses of Twelve New Whole Genome Sequences of Cassava Brown Streak Viruses and Ugandan Cassava Brown Streak Viruses from East Africa: Diversity, Supercomputing and Evidence for Further Speciation, PloS one, 10(10), p. e0139321, [online] Available at: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0139321 (Accessed 18 March 2016). Nichols, R. F. W. (1947) Breeding cassava for virus resistance., East African Agricultural Journal, 12, pp. 184-94, [online] Available at: http://www.cabdirect.org/abstracts/19471600996.html (Accessed 5 February 2014). Park, T. and Casella, G. (2008) The Bayesian Lasso, Journal of the American Statistical Association, 103(482), pp. 681-686. Pà ©rez, J. C., Lenis, J. I., Calle, F., Morante, N., Sà ¡nchez, T., Debouck, D. and Ceballos, H. (2011) Genetic variability of root peel thickness and its influence in extractable starch from cassava (Manihot esculenta Crantz) roots, Plant Breeding, 130(6), pp. 688-693. Pà ©rez, P. and De Los Campos, G. (2014)

Time Warner Essay -- essays research papers

Time Warner In 1989, the largest Media Corporation was formed. The integration of Time Inc. and Warner communications produced Time Warner, which in 1996 with the acquisition of Turner broadcasting, regained it's status from Disney as the largest media corporation in the world. The company right now, with over 200 subsidiaries world- wide, is becoming fully global with it's profits from the USA falling, and it's profits throughout the world rising. Globalisation is proving to be Time Warner's major asset in beating other competition to the World market. Currently, Time Warner has interests in many different business fields. Music accounts for a large proportion of its income, while not far behind are its cable systems, entertainment, films, video and television holdings. But, the company has also centred its resources and invested in the global media, producing programmes and channels for countries around the world, which in turn has proven to be a very lucrative area of growth. Time Warner in general has become a 'major force in virtually every medium and on every continent'; So then, why should a company like Time Warner be a threat to the public, and something which all of us citizens around the World should be aware of ? Isn't Time Warner just a success of capitalism ? A successful company, which employs thousands of people and makes massive turnovers, while at the same time advancing the cause of the global market and promoting commercialism doesn't seem like a thing of public concern. In the World village today, why should we need thousand's upon thousand's of small independent company's and tv stations and newspaper's, when we could have ten large conglomerates who would control everything from production to sales to distribution ? The way in which thing's have developed over the past ten years, that scenario or fiction might even become fact or reality. So why should it bother the people of the World ? To begin answering that question, we need to go back a hundred years or so and look at the work of Karl Marx and his interpretations of 'socio-economic order produced by industrial capitalism'; . Marx believed that the unequal distribution of wealth and the way in which the capitalist class controlled this wealth through the possession of raw materials, means of distribution and labour, enabled them to make... ...in maintaining its role as a public broadcaster, and given more financial aid from the government. Advertising could be controlled more vigorously and regulated, particularly during children's programming (As in Sweden). A more drastic approach would be the breaking up of the vertically integrated oligopolies, and establishing more competitive markets. In general, any change must strive to serve all of societies needs and interests, which includes audiences and broadcasters, and not only advertisers and media moguls. So, in the end are oligopolies, vertical integration and concentration matters of public concern ? Of course they are. Matters of ownership of the media and the means of production, distribution and sales are too important to be ignored. In the interests of holding on to a healthy democracy, diversity has to be achieved and maintained. As I have tried to show oligopolies and vertically integrated media industries are just as dangerous as state run ministries that have a monopoly over information. 'Concentrated media power is political and social power';. Thankfully, the World hasn't yet become like the latest offering from James Bond 'Goldeneye';.

Leaders: born or made

There has always been a difference opinion on whether leaders are made or born. At numerous times people have been heard to exclaim about someone that he or she is a person that is born to lead. People have tendency to believe that good and effective leaders are people who are naturally bestowed with excellent communication skills, persuasive ability, and born with knack to integrate them in any team structure. Further, there are also firm opinions that it is not possible for every one to naturally acquire the skills of seamlessly inspiring a group of people, set sufficient challenges, and make every one of the group to accept those challenges and strive together to achieve them.However, years of academic research among leaders from social, business and corporate world and political domain have brought out results that stand contrary to popular perception of leaders and their ‘innate qualities and abilities’ of leading people and show that effective leadership is an art that can be very much learned and practiced to perfection by anyone who devotes sufficient time and attention to it.   This paper takes the point of view that leadership is a quality that can be learned by anyone with ordinary levels of intelligence and smartness and looks into the range of skills, requirements and capabilities needed by a person to develop leadership qualities.Leadership: DefinitionLeadership is the attribute of inspiring people to channel their efforts towards achieving common goals and objectives (Rosenbach and Taylor, 1998, 1). Leadership is the recognition that attainment of the group objectives and goals can be accomplished through empowering individuals and encouraging them to overcome their rank and position in order to associate themselves and their colleagues with specific works, duties and responsibilities by setting directions, building commitment and taking challenges (Day and Halpin, 2004, 3). An important attribute of a leader is his ability to comm and implicit faith, confidence, and respect of his followers, irrespective of his position and power in the organization.. A leader motivates the employees by setting personal examples, and takes decisions that are quite unconventional, innovative and on the spot to resolve a deadlock. However, the most important quality of a leader is that he/she encourages leadership qualities their followers and help to create a multi-tier leader structure within the organization/group.Organizational leadership: Roles and necessitiesAs the corporate world becomes increasingly competitive and diversified, organizational focus has shifted on developing leadership talents among the employees to maintain their competitive edge.   Transnational companies, with their multi-level reporting structure, multiple communication networks, numerous levels of responsibilities and faced with significant differences in time, language and organizational culture are faced with the responsibility of leadership dev elopment among their employees to meet customers’ demands within the limited time and resources (Collins, 2001).  Organizations are managed by several forms of leadership based on the exertion of authority within the organization. Two main, but interconnected types of leadership in organizations are the transformational leadership and the transactional leadership, both having strong philosophical and ethical foundations. Transformational leadership gives followers the opportunity to assess the leader’s view, to seek explanations and provide solutions, while transactional leadership is more based on imposition, where followers are driven by the praise, promise or reward of the leader. In the transactional leadership, the followers are confronted by reproof, threats and disciplinary actions.Transformational leadership has become more popular in the last three decades primarily due to the changing global economy. Transformational leadership promotes equality, justice an d human rights through loyalty and fairness. Recent findings suggest that team performance and communication are improved under transformational leadership. Authentic transformational leaders are sometimes transactional too. The leader may present his opinion, plans and exhort agreement on them, which however may be in the mutual interest of all involved. I consider myself as a typical transformational leader open to criticism and discussion, unafraid of my decisions being questioned. After all only collective thinking and cooperation can bring results.Today the business world realizes that leadership is neither hierarchal nor stratified nor leadership is management. Instead leadership is about inspiring people to pool themselves together towards achieving common goals and objectives (Rosenbach and Taylor, 1998, 1. Leadership is about building commitment and taking challenges by timely distribution of specific works, duties and responsibilities and through setting directions (Day an d Halpin, 2004, 3). Its not surprising then that companies are ready to invest hugely in leadership development program, as a guaranteed way to emerge ahead than their competitors.Developing Leadership QualitiesThere are abundant examples from almost every quarter of business and public domains to show that with well help   designed training programs and experience even otherwise ordinary individuals can emerge as successful leaders in their own spheres. Leadership development process works on two levels. It is suggested coaching and mentoring involves practical and goal focused methods of individual and group learning and behavioral change. For obtaining most effective results and developing specific leadership skills coaching allows individuals to collaborate in methodologically assessing, understanding and solving the issue before them. It leads them to challenge the existing solution models and explore further possibilities through joint effort and accountability. Mentoring is an essential part of educational program, involves commitment and long term relationship between a senior employee and a junior employee where the latter helps in professional and personal development of the former.The second level of leadership development is action learning that requires participants to tackle   real life and real time organizational problems (ibid). Through a careful selection of objectives and problems, participants are trained on delivering organizational results, communication learning and management and develop general leadership qualities. It benefits participants greatly as it provides them crucial exposure and considerable experience within a short time. Along with these, modern organizations have also adopted the technique of job rotation, so that individuals have widest possible exposure and experience of company’s functional and organizational processes.It is vital to remember that the focus should not be on teaching leadership, instead gettin g participants to learn leadership. Every person has a potential to emerge in a leader by gaining   knowledge, purpose and experience and apply themselves more   effectively in their personal and professional domains Leadership is not a characteristic that can unfold in isolation. By its definition, it implies establishing coordination, cooperation, collaboration and orientation among the followers to achieve the designated objectives and goals. However, it is only possible when leaders can inspire their followers with respect, admiration, discipline, sense of emulation and confidence in the abilities of the leader while being helped to envision themselves as empowered individuals (Brown and Lord, 2004, 2).  Most relevant qualities of a leaderWithin every social, institutional or organizational structure, a leader is always looked upon the person with abilities to broach reconciliation and resolution in situation of conflict. A good leader exercises his control over most compl ex, demanding and otherwise impossible condition by exhibiting personal integrity, ethical and moral traits and values that other can relate to and get inspired to include them in their personal conduct (Laurie, 2000, 53). Another very crucial characteristics of leadership is that it produces new leaders from among the followers and hence, through a multiplier effect, results in empowerment of individuals and communities.Leadership helps the followers to discover and grow their internal abilities and encourage them to become an integral part of the process, not a mere tool. This causes a reinstating of self pride and confidence among followers and it earns leaders willing obedience of people who realize the integrity of the leader in creating a just, legitimate and encouraging environment where they see themselves as valued members and in turn lend their unconditional support to the joint cause under the leadership (Messick, 2005, 81)Arguably, there are no definite copybook rules to construct a leader. The difficulties, complexities, and challenges associated with a situation give impetus to leadership qualities in otherwise ordinary people who believe in themselves that they are capable of rising up to the difficulties as well as helping others out of it. Therefore although it might be difficult to ‘teach’ a person quality of good leader, yet one can expect to inculcate leadership qualities by observing styles and principles of successful leaders. It is said that a leader is a dealer in hope. Leadership is then about inspiration, motivation, encouragement and direction that pulls people to accomplishments that they would not had managed if left alone. However, effective leadership is a very challenging domain as it requires some impeccable personal and organizational traits that can be developed and realized through considerable experience, knowledge and self- discipline.  Quite often the leadership is situational and the leader is required to act purely through intuition and circumstantial requirements. However there are certain essential skills and characteristics that are rather mandatory for effective leadership are1 Trustworthiness: Trustworthiness is about integrity in action. Effective leadership is about achieving coordination in words and actions and following the age old principles of truth, honesty and personal integrity.2. Fairness: Leaders can’t afford to be biased or prejudiced or it would jeopardize the confidence of the followers in their secular character.3. Communication and listening skill. Leadership requires excellent communication and listening skill through which the leaders can articulate their views unambiguously and also hear the views of others to give them sense of participation and involvement.4. Initiative: Leadership is about taking initiative and orienting other people towards it. Taking initiative pulls the organization rapidly ahead.5. Good judgment: Leaders must have the ability t o process all information in the backdrop of their knowledge to make correct decisions6. Motivational capacity: Leadership is ineffective if it cant motivate people to the dream and vision of the leader. It is the most desirous quality of a leader and one that is hallmark of leadership.Motivation has a large role to play in developing leadership. According to Isaac, Pitt and Zerbe (2001) individuals aspiring for leadership are greatly assisted a motivational model, called as expectancy theory, that suggests that self interest prompts individuals to charter a course where they tend to maximize the chances of success and growth. Thus self interest acts as a motivation that spurs people to take upon leadership roles and aspire to meet needs of followers along with requirements of the organization (ibid). Also, when leaders meet with followers, it generally results in entire work atmosphere getting highly motivated and people are spirited with aspiration to transcend their present roles and step in the role of leaders (ibid).Leadership is influenced by both extrinsic motivation and intrinsic motivation. In the former, motivational behavior is seen as product of external rewards and remunerations while the latter treat motivational behavior as result of internal drives such as enjoyment of work and inner sense of competence (Isaac, Pitt and Zerbe). In either case, individuals are motivated to assume leadership to maximize their self-interest.Leadership: Personal AttributesA good leader should be honest, loyal and committed to the goals of the organization he intends to lead. A good leader should not have a desire for wrongful gains or hidden agendas. This is why perhaps people emphasize on transparency in all dealings of any organization. Some leaders have a self plan and pursue them rather than acting in the interests of the organization. Committed to the cause of the organization or group and being live to the sacrifices and pains of your colleagues is a basic qu ality of a good leader. National leaders and particularly the freedom fighters of several nations had steadfast qualities and determination in them, which helped them carry on and ultimately succeed. A good leader is perhaps a good follower.There is never a stage in which one can have mastered everything and this applies even to leadership. Each day brings learning and experience of various types. A good leader is one who applies these learning and experience by identifying the most appropriate situation of their application.   perhaps the rights and wrongs of your own acts too. . A leader is accountable for his actions and should voluntarily open up to any questions or suspicions in his dealings. Similarly a good leader should also emphasize such qualities among his followers and make them accountable too. Simplicity is a mark of identity for any leader and projecting himself as a role model. A leader’s thoughts, actions and words should be a reflection of him, inspiring a ll who follow. A leader indeed should have uncommon qualities to successfully lead his organization.ConclusionLeadership is a quality that comes through effective utilization of experience, education, self-evaluation eagerness to learn and grow. None of these qualities require a transcendental genius or divine abilities to master. They are human attributes that are present among every one of us and given time, training and motivation to master them. The truth about leadership is that any person who has wholly ingrained the necessary leadership qualities as an integral part of their character would appear as one who is born with them.referenceCollins DB, 2001, ‘Organizational Performance: The Future Focus of Leadership Development Programs’, Journal of Leadership Studies. Volume: 7. Issue: 4.Day DV and Halpin SM, 2004, Leader Development for Transforming Organizations: Growing Leaders for Tomorrow,   (edit) David V. Day, Stanley M. Halpin, Stephen J. Zaccaro, Lawrence Erlbaum Associates,   Mahwah, NJ.Rosenbach WE and Taylor RL, 1998, Contemporary Issues in Leadership, (edit) William E. Rosenbach, Robert L. Taylor, Westview Press,Boulder, CO.Brown DJ, Lord, RG,   2004, Leadership Processes and Follower Self-Identity,   Lawrence Erlbaum Mahwah, NJChampy J, Nohria N, 1999, The Arc of Ambition: Defining the Leadership Journey, Perseus Books (Current Publisher: Perseus PublishingCambridge, MA.Rosenbach WE and Taylor RL, 1998, Contemporary Issues in Leadership, (edit) William E. Rosenbach, Robert L. Taylor, Westview Press,Boulder, CO.

Purpose of Social Studies in Schools - 1771 Words

What is social studies? * Social studies is the integrated study of social sciences and humanities to promote civic competence. Social studies provides coordinated, systematic study drawn upon such disciplines as anthropology, archaeology, economics, geography, history, law, philosophy, political science, psychology, religion and sociology as well as a appropriate content from the humanities and natural sciences. The goals of social studies 1. Fostering attitudes and identifying values Values are ends or ideas which are held by a person. They are the standards or codes which direct our actions. Attitudes are directly derived from values. Our values determine how we behave, each person or society have different values. The†¦show more content†¦Knowledge, values, attitudes and skills are necessary for active participation in civic affairs. These skills provide the link between knowledge and values and attitudes which make participatory action possible. Justify the place of social studies in the primary school curriculum. Personally I think social studies are out on the back burner too often; more emphasis should be place on this subject area. Social studies help children to develop their identity. The study of individual development and identity will help students to describe factors important to the development of personal identity. They will explore the influence of peoples, places, and environments on personal development. Students will hone personal skills such as demonstrating self-direction when working towards and accomplishing personal goals, and making an effort to understand others and their beliefs, feelings, and convictions. I believe social studies should be part of the curriculum for the purpose of helping students understand human interactions that occurred in the past, and occurring now, and that are likely to occur in the future. 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