Transcriptome-wide identification and expression analysis of the NAC gene family in lowland bamboo [Oxytenanthera abyssinica (A.Rich) Munro] under abiotic stresses

NAC (NAM, no apical meristem, ATAF and CUC) is one of the largest gene families of the plant-specific transcription factors (TF). NAC TFs have immense involvement in plant growth and developmental processes and have particular importance in enhancing plant resistance to multiple abiotic stresses. NAC members have unique structural makeup and a range of biological activities. Despite their enormous roles in plants, comprehensive study on identification, characterization and expression profiling of NACs under abiotic stress is lacking in Lowland bamboo [Oxytenanthera abyssinica (A.Rich) Munro]. Thus, this study aimed to identify NAC members, characterize their protein properties, construct their phylogenetic relationships and more importantly, establish their expression profiling under abiotic stress. From this abiotic stress-induced transcriptome, 220 lowland bamboo TFs with intact and complete NAC DNA binding domains (PF01849) were identified. Following their identification, analysis of functional annotation, protein characterization, phylogenetic relationships and expression profiling were conducted. The analysis presented up-regulation of 142 unigenes in response to abiotic stress, the association of 26 unigenes directly to stress response and the involvement of 92 unigenes in genetic information processing and 29 in environmental information processing according to KEGG analysis. These results suggest the most likely involvement of NACs in lowland bamboo stress response and adaptation. As a species best survived in a moisture-stressed environment, this study has provided valuable information that could shed light on further functional analysis research efforts aiming to exploit NACs in developing stress-resilient bamboo and related plants

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Assessment on the Current State of On-Farm Diversity and Genetic Erosion in Barley (Hordeum vulgare L.) Landraces from Bale Highlands, Southeast Ethiopia

Barley landraces is among the major cereal crops grown in Ethiopian highlands including Bale highlands. However, in recent days, the crop is highly declining to the extents of total loss. This study was, therefore, aimed at assessing the extents of its on-farm diversity and genetic erosion from Bale highlands, Ethiopia. Data were generated from twelve administrative districts and analyzed considering important ecological and genetic erosion models. A total of 25 distinct (at least in naming) barley landraces with varying distribution patterns have been identified in the areas. Landrace richness (R) revealed higher magnitude among all the study districts, the smallest being 2.02 (DMg) and 1.41 (DMn) and considerable range of variations (DMg=2.02 to 5.02, DMn=1.41 to 3.17). Among the study districts, Dinsho consisted the highest on-farm diversity estimate (DMg=5.02, DMn=3.17) followed by Goba and Sinana (DMg=4.50 and 3.97; DMn=2.87 and 2.57 in that order). Estimate of the landrace evenness (E) also showed the highest magnitude (>0.95) except in Agarfa district (0.77). The result suggests potentiality of the areas and wide cultivation of majority of the landraces in the villages. However, nowadays, only 14 landraces are under cultivation and the remaining 11 are totally eroded from the district(s) constituting the highest (56.0%) combined genetic erosion suggesting loss of important agronomic traits and, thus, a major bottleneck for further improvement and conservation plans. Thus, attention should be payed to conserving the landraces for better further use

Genetic diversity and population structure analyses of Plectranthus edulis (Vatke) Agnew collections from diverse agro-ecologies in Ethiopia using newly developed EST-SSRs marker system

Abstract Background Plectranthus edulis (Vatke) Agnew (locally known as Ethiopian dinich or Ethiopian potato) is one of the most economically important edible tuber crops indigenous to Ethiopia. Evaluating the extent of genetic diversity within and among populations is one of the first and most important steps in breeding and conservation measures. Hence, this study was aimed at evaluating the genetic diversity and population structure of this crop using collections from diverse agro-ecologies in Ethiopia. Results Twenty polymorphic expressed sequence tag based simple sequence repeat (EST-SSRs) markers were developed for P. edulis based on EST sequences of P. barbatus deposited in the GenBank. These markers were used for genetic diversity analyses of 287 individual plants representing 12 populations, and a total of 128 alleles were identified across the entire loci and populations. Different parameters were used to estimate the genetic diversity within populations; and gene diversity index (GD) ranged from 0.31 to 0.39 with overall mean of 0.35. Hierarchical analysis of molecular variance (AMOVA) showed significant but low population differentiation with only 3% of the total variation accounted for variation among populations. Likewise, cluster and STRUCTURE analyses did not group the populations into sharply distinct clusters, which could be attributed to historical and contemporary gene flow and the reproductive biology of the crop. Conclusions These newly developed EST-SSR markers are highly polymorphic within P. edulis and hence are valuable genetic tools that can be used to evaluate the extent of genetic diversity and population structure of not only P. edulis but also various other species within the Lamiaceae family. Among the 12 populations studied, populations collected from Wenbera, Awi and Wolaita showed a higher genetic diversity as compared to other populations, and hence these areas can be considered as hot spots for in-situ conservation as well as for identification of genotypes that can be used in breeding programs