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A sobering study of the troubled African nation, both pre- and post-genocide, and its uncertain future The brutal civil war between Hutu and Tutsi factions in Rwanda ended in 1994 when the Rwandan Patriotic Front came to power and embarked on an ambitious social, political, and economic project to remake the devastated central-east African nation. Susan Thomson, who witnessed the hostilities firsthand, has written a provocative modern history of the country, its rulers, and its people, covering the years prior to, during, and following the genocidal conflict. Thomson's hard-hitting analysis explores the key political events that led to the ascendance of the Rwandan Patriotic Front and its leader, President Paul Kagame. This important and controversial study examines the country's transition from war to reconciliation from the perspective of ordinary Rwandan citizens, Tutsi and Hutu alike, and raises serious questions about the stability of the current peace, the methods and motivations of the ruling regime and its troubling ties to the past, and the likelihood of a genocide-free future.

For 100 days in 1994, genocide engulfed Rwanda. Since then, many in the international community have praised the country's postgenocide government for its efforts to foster national unity and reconciliation by downplaying ethnic differences and promoting \"one Rwanda for all Rwandans.\" Examining how ordinary rural Rwandans experience and view these policies, Whispering Truth to Power challenges the conventional wisdom on postgenocide Rwanda. Susan Thomson finds that many of Rwanda's poorest citizens distrust the local officials charged with implementing the state program and believe that it ignores the deepest problems of the countryside: lack of land, jobs, and a voice in policies that affect lives and livelihoods. Based on interviews with dozens of Rwandan peasants and government officials, this book reveals how the nation's disenfranchised poor have been engaging in everyday resistance, cautiously and carefully—\"whispering\" their truth to the powers that be. This quiet opposition, Thomson argues, suggests that some of the nation's most celebrated postgenocide policies have failed to garner the grassroots support needed to sustain peace. “Reveals the lengths [to which] the current government has gone to restructure all spaces of Rwandan society, and how Rwandans continue to resist this state interference in their everyday lives.”— Ethnic and Racial Studies “Thomson’s elegant research is praiseworthy and her arguments are forthright. . . . This important publication will be of great value to scholars of Rwanda and genocide as well as students of reconciliation politics and transitional justice.”— Human Rights Quarterly “Sobering and disturbing. . . . The peasant peoples’ resistance to official policies of national unity and reconciliation emerged because these national schemes do not reflect the peasants’ own lived realities and experiences of state power, genocide, and day-to-day living within their communities. Instead, these official policies disrupt everyday life and endanger existing networks of mutual support and dependence.”— Canadian Journal of Development Studies Outstanding Academic Title, Choice Magazine

Zebra chip disease of potato is caused by a bacterial pathogen, ‘ Candidatus Liberibacter solanacearum’, vectored by the tomato potato psyllid ( Bactericera cockerelli Sulc.). The plant response to the disease was explored using a combined transcriptomic and metabolomic approach. The effects of the disease were greater in tuber than in leaf or stem tissues, and represent a massive reprogramming of the tuber metabolism, with expression changes observed for many genes. In the tuber, starch synthesis was severely disrupted, with reduced expression of most starch synthesis genes, but increased expression of the gene encoding vacuolar invertase. This was consistent with increased glucose and fructose and reduced starch in the tuber, which are the hallmarks of the disease and the causes of the symptoms problematic to the potato industry. The phenylpropanoid pathway was more active in diseased tubers, as shown by increased transcript accumulation for phenylalanine ammonia lyase, cinnamate-4-hydroxylase, 4-coumarate:CoA ligase and cinnamyl alcohol dehydrogenase, and increased quantities of hydroxycinnamic acid amides, phenolic acids and coumarins. The expression of several genes encoding patatin storage proteins in the tuber was also decreased. In addition to the carbohydrate changes which cause undesirable visual symptoms associated with frying, the diseased tubers showed detrimental changes in nutritional value, such as increased toxic glycoalkaloids and decreased ascorbic acid.

Nanopore sequencing enables detection of DNA methylation at the same time as identification of canonical sequence. A recent study validated low-pass nanopore sequencing to accurately estimate global methylation levels in vertebrates with sequencing coverage as low as 0.01x. We investigated the applicability of this approach to plants by testing three plant species and analysed the effect of technical and biological parameters on estimate precision and accuracy. Our results indicate that higher coverage (0.1x) is required to achieve accuracy in assessing plant global methylation comparable to that in vertebrates. Shorter read length and a closer sequence match between sample and reference genome improved measurement accuracy. Application of this method in Vitis vinifera showed consistent global methylation levels across different leaf sizes, and different sample preservation and DNA extraction methods, whereas different varieties and tissue types did exhibit methylation differences. Similarly, distinct methylation patterns were observed in different genomic features. Our findings suggest the suitability of this method as a low-cost screening tool for validation of experimental parameters, developmental time courses, and to assess methylation status for different modification types and sequence contexts at the level of whole genome or for abundant genomic features such as transposable elements.

Background Genomic methods for identifying causative variants for trait loci applicable to a wide range of germplasm are required for plant biologists and breeders to understand the genetic control of trait variation. Results We implemented Cas9-targeted sequencing for fine-mapping in apple, a method combining CRISPR-Cas9 targeted cleavage of a region of interest, followed by enrichment and long-read sequencing using the Oxford Nanopore Technology (ONT). We demonstrated the capability of this methodology to specifically cleave and enrich a plant genomic locus spanning 8 kb. The repeated mini-satellite motif located upstream of the Malus  ×  domestica (apple) MYB10 transcription factor gene, causing red fruit colouration when present in a heterozygous state, was our exemplar to demonstrate the efficiency of this method: it contains a genomic region with a long structural variant normally ignored by short-read sequencing technologies Cleavage specificity of the guide RNAs was demonstrated using polymerase chain reaction products, before using them to specify cleavage of high molecular weight apple DNA. An enriched library was subsequently prepared and sequenced using an ONT MinION flow cell (R.9.4.1). Of the 7,056 ONT reads base-called using both Albacore2 (v2.3.4) and Guppy (v3.2.4), with a median length of 9.78 and 9.89 kb, respectively, 85.35 and 91.38%, aligned to the reference apple genome. Of the aligned reads, 2.98 and 3.04% were on-target with read depths of 180 × and 196 × for Albacore2 and Guppy, respectively, and only five genomic loci were off-target with read depth greater than 25 × , which demonstrated the efficiency of the enrichment method and specificity of the CRISPR-Cas9 cleavage. Conclusions We demonstrated that this method can isolate and resolve single-nucleotide and structural variants at the haplotype level in plant genomic regions. The combination of CRISPR-Cas9 target enrichment and ONT sequencing provides a more efficient technology for fine-mapping loci than genome-walking approaches .

Background: The genetic regulation of flower color has been widely studied, notably as a character used by Mendel and his predecessors in the study of inheritance in pea. Methodology/Principal Findings: We used the genome sequence of model legumes, together with their known synteny to the pea genome to identify candidate genes for the A and A2 loci in pea. We then used a combination of genetic mapping, fast neutron mutant analysis, allelic diversity, transcript quantification and transient expression complementation studies to confirm the identity of the candidates. Conclusions/Significance: We have identified the pea genes A and A2. A is the factor determining anthocyanin pigmentation in pea that was used by Gregor Mendel 150 years ago in his study of inheritance. The A gene encodes a bHLH transcription factor. The white flowered mutant allele most likely used by Mendel is a simple G to A transition in a splice donor site that leads to a mis-spliced mRNA with a premature stop codon, and we have identified a second rare mutant allele. The A2 gene encodes a WD40 protein that is part of an evolutionarily conserved regulatory complex.

Key messageGenome-wide targets of Actinidia chinensis SVP2 confirm roles in ABA- and dehydration-mediated growth repression and reveal a conservation in mechanism of action between SVP genes of taxonomically distant Arabidopsis and a woody perennial kiwifruit.The molecular mechanisms underlying growth and dormancy in woody perennials are largely unknown. In Arabidopsis, the MADS-box transcription factor SHORT VEGETATIVE PHASE (SVP) plays a key role in the progression from vegetative to floral development, and in woody perennials SVP-like genes are also proposed to be involved in controlling dormancy. During kiwifruit development SVP2 has a role in growth inhibition, with high-chill kiwifruit Actinidia deliciosa transgenic lines overexpressing SVP2 showing suppressed bud outgrowth. Transcriptomic analyses of these plants suggests that SVP2 mimics the well-documented abscisic acid (ABA) effect on the plant dehydration response. To corroborate the growth inhibition role of SVP2 in kiwifruit development at the molecular level, we analysed the genome-wide direct targets of SVP2 using chromatin immunoprecipitation followed by high-throughput sequencing in kiwifruit A. chinensis. SVP2 was found to bind to at least 297 target sites in the kiwifruit genome, and potentially modulates 252 genes that function in a range of biological processes, especially those involved in repressing meristem activity and ABA-mediated dehydration pathways. In addition, our ChIP-seq analysis reveals remarkable conservation in mechanism of action between SVP genes of taxonomically distant plant species.

Background Tuber bruising in tetraploid potatoes ( Solanum tuberosum ) is a trait of economic importance, as it affects tubers’ fitness for sale. Understanding the genetic components affecting tuber bruising is a key step in developing potato lines with increased resistance to bruising. As the tetraploid setting renders genetic analyses more complex, there is still much to learn about this complex phenotype. Here, we used capture sequencing data on a panel of half-sibling populations from a breeding programme to perform a genome-wide association analysis (GWAS) for tuber bruising. In addition, we collected transcriptomic data to enrich the GWAS results. However, there is currently no satisfactory method to represent both GWAS and transcriptomics analysis results in a single visualisation and to compare them with existing knowledge about the biological system under study. Results When investigating population structure, we found that the STRUCTURE algorithm yielded greater insights than discriminant analysis of principal components (DAPC). Importantly, we found that markers with the highest (though non-significant) association scores were consistent with previous findings on tuber bruising. In addition, new genomic regions were found to be associated with tuber bruising. The GWAS results were backed by the transcriptomics differential expression analysis. The differential expression notably highlighted for the first time the role of two genes involved in cellular strength and mechanical force sensing in tuber resistance to bruising. We proposed a new visualisation, the HIDECAN plot, to integrate the results from the genomics and transcriptomics analyses, along with previous knowledge about genomic regions and candidate genes associated with the trait. Conclusion This study offers a unique genome-wide exploration of the genetic components of tuber bruising. The role of genetic components affecting cellular strength and resistance to physical force, as well as mechanosensing mechanisms, was highlighted for the first time in the context of tuber bruising. We showcase the usefulness of genomic data from breeding programmes in identifying genomic regions whose association with the trait of interest merit further investigation. We demonstrate how confidence in these discoveries and their biological relevance can be increased by integrating results from transcriptomics analyses. The newly proposed visualisation provides a clear framework to summarise of both genomics and transcriptomics analyses, and places them in the context of previous knowledge on the trait of interest.

Genomic selection (GS) is a breeding tool, which is rapidly gaining popularity for plant breeding, particularly for traits that are difficult to measure. One such trait is ascochyta blight resistance in pea ( L.), which is difficult to assay because it is strongly influenced by the environment and depends on the natural occurrence of multiple pathogens. Here we report a study of the efficacy of GS for predicting ascochyta blight resistance in pea, as represented by ascochyta blight disease score (ASC), and using nucleotide polymorphism data acquired through genotyping-by-sequencing. The effects on prediction accuracy of different GS models and different thresholds for missing genotypic data (which modified the number of single nucleotide polymorphisms used in the analysis) were compared using cross-validation. Additionally, the inclusion of marker × environment interactions in a genomic best linear unbiased prediction (GBLUP) model was evaluated. Finally, different ways of combining trait data from two field trials using bivariate, spatial, and single-stage analyses were compared to results obtained using a mean value. The best prediction accuracy achieved for ASC was 0.56, obtained using GBLUP analysis with a mean value for ASC and data quality threshold of 70% (i.e., missing SNP data in <30% of lines). GBLUP and Bayesian Reproducing kernel Hilbert spaces regression (RKHS) performed slightly better than the other models trialed, whereas different missing data thresholds made minimal differences to prediction accuracy. The prediction accuracies of individual, randomly selected, testing/training partitions were highly variable, highlighting the effect that the choice of training population has on prediction accuracy. The inclusion of marker × environment interactions did not increase the prediction accuracy for lines which had not been phenotyped, but did improve the results of prediction across environments. GS is potentially useful for pea breeding programs pursuing ascochyta blight resistance, both for predicting breeding values for lines that have not been phenotyped, and for providing enhanced estimated breeding values for lines for which trait data is available.