Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1126719 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29541168_1.fastq.gz | Fastqsanger.gz | |||
| SRR29541168_2.fastq.gz | Fastqsanger.gz | |||
| SRR29541169_1.fastq.gz | Fastqsanger.gz | |||
| SRR29541169_2.fastq.gz | Fastqsanger.gz | |||
| SRR29541170_1.fastq.gz | Fastqsanger.gz |
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Project description:Background: Sorghum bicolor is a remarkably drought tolerant cereal crop. Its natural biodiversity that enables this tolerance has developed in sub-Saharan Africa. The sequencing of the sorghum genome in 2009 has expedited research of this crop which has also been proposed as a model C4 cereal crop for genomics. In this study, the genetic response mechanisms involved in sorghums’ tolerance to progressive water deficit and moderate re-watering were investigated in three previously uncharacterized South African landraces (designated: LR5, LR6 and LR35) using cDNA microarrays comprising 35 899 transcript probes. Results: Across the three landraces, significant differential expression of 1 797 genes, including 264 genes with currently unknown functions, were altered in response to progressive water stress and re-watering. The modulated sorghum genes had homology to proteins involved in growth, regulation, and protection. Gene ontology analysis identified significant enrichment of 26 genes involved in the ‘response to abiotic stimulus’ GO category in LR6 during severe stress. The expression of USP responded to progressive water stress and moderate re-watering in LR6 and LR35. Moreover, our results indicate a putative role for β-alanine betaine biosynthesis in drought tolerance of sorghum. Conclusions: This study identified the drought responsive gene complement of three previously uncharacterized South African sorghum landraces. Each landrace is a distinct genotype and similar responses to water deficit and re-watering were not expected. Functional characterizations of some of the differentially expressed genes found in this study may be used as possible targets for marker-assisted breeding or transgenic initiatives for sorghum and, other closely related crop species.
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Project description:The emergence and fast global spread of COVID-19 has presented one of the greatest public health challenges in modern times with no proven cure or vaccine. Africa is still early in this epidemic, therefore the extent of disease severity is not yet clear. We used a mathematical model to fit to the observed cases of COVID-19 in South Africa to estimate the basic reproductive number and critical vaccination coverage to control the disease for different hypothetical vaccine efficacy scenarios. We also estimated the percentage reduction in effective contacts due to the social distancing measures implemented. Early model estimates show that COVID-19 outbreak in South Africa had a basic reproductive number of 2.95 (95% credible interval [CrI] 2.83–3.33). A vaccine with 70% efficacy had the capacity to contain COVID-19 outbreak but at very higher vaccination coverage 94.44% (95% Crl 92.44–99.92%) with a vaccine of 100% efficacy requiring 66.10% (95% Crl 64.72–69.95%) coverage. Social distancing measures put in place have so far reduced the number of social contacts by 80.31% (95% Crl 79.76–80.85%). These findings suggest that a highly efficacious vaccine would have been required to contain COVID-19 in South Africa. Therefore, the current social distancing measures to reduce contacts will remain key in controlling the infection in the absence of vaccines and other therapeutics.
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