The Journey to R4D: An institutional history of an Australian Initiative on Food Security in Africa

Internal Revie

Invited review: Genomic selection for small ruminants in developed countries: how applicable for the rest of the world?

Improved management and use of estimated breeding values in breeding programmes, have resulted in rapid genetic progress for small ruminants (SR) in Europe and other developed countries. The development of single nucleotide polymorphisms chips opened opportunities for genomic selection (GS) in SR in these countries. Initially focused on production traits (growth and milk), GS has been extended to functional traits (reproductive performance, disease resistance and meat quality). The GS systems have been characterized by smaller reference populations compared with those of dairy cattle and consisting mostly of cross- or multi-breed populations. Molecular information has resulted in gains in accuracy of between 0.05 and 0.27 and proved useful in parentage verification and the identification of QTLs for economically important traits. Except for a few established breeds with some degree of infrastructure, the basic building blocks to support conventional breeding programmes in small holder systems are lacking in most developing countries. In these systems, molecular data could offer quick wins in undertaking parentage verification and genetic evaluations using G matrix, and determination of breed composition. The development of next-generation molecular tools has prompted investigations on genome-wide signatures of selection for mainly adaptive and reproduction traits in SR in developing countries. Here, the relevance of the developments and application of GS and other molecular tools in developed countries to developing countries context is examined. Worth noting is that in the latter, the application of GS in SR will not be a ‘one-size fits all’ scenario. For breeds with some degree of conventional genetic improvement, classical GS may be feasible. In small holder systems, where production is key, community-based breeding programmes can provide the framework to implement GS. However, in fragile growth systems, for example those found in marginal environments, innovative GS to maximize adaptive diversity will be required. A cost-benefit analysis should accompany any strategy of implementing GS in these systems

Viral metagenomics of aphids present in bean and maize plots on mixed-use farms in Kenya reveals the presence of three dicistroviruses including a novel Big Sioux River virus-like dicistrovirus

Background: Aphids are major vectors of plant viruses. Common bean (Phaseolus vulgaris L.) and maize (Zea mays L.) are important crops that are vulnerable to aphid herbivory and aphid-transmitted viruses. In East and Central Africa, common bean is frequently intercropped by smallholder farmers to provide fixed nitrogen for cultivation of starch crops such as maize. We used a PCR-based technique to identify aphids prevalent in smallholder bean farms and next generation sequencing shotgun metagenomics to examine the diversity of viruses present in aphids and in maize leaf samples. Samples were collected from farms in Kenya in a range of agro-ecological zones. Results: Cytochrome oxidase 1 (CO1) gene sequencing showed that Aphis fabae was the sole aphid species present in bean plots in the farms visited. Sequencing of total RNA from aphids using the Illumina platform detected three dicistroviruses. Maize leaf RNA was also analysed. Identification of Aphid lethal paralysis virus (ALPV), Rhopalosiphum padi virus (RhPV), and a novel Big Sioux River virus (BSRV)-like dicistrovirus in aphid and maize samples was confirmed using reverse transcription-polymerase chain reactions and sequencing of amplified DNA products. Phylogenetic, nucleotide and protein sequence analyses of eight ALPV genomes revealed evidence of intra-species recombination, with the data suggesting there may be two ALPV lineages. Analysis of BSRV-like virus genomic RNA sequences revealed features that are consistent with other dicistroviruses and that it is phylogenetically closely related to dicistroviruses of the genus Cripavirus.Work was funded by a grant from the Sustainable Crop Production Research for International Development programme funded by the UK Biotechnology and Biological Sciences Research Council (BBSRC) with co-funding from the UK Department for International Development, the Bill & Melinda Gates Foundation, the Department of Biotechnology of India’s Ministry of Science and Technology, and the Indian Council of Agricultural Research (BB/J011762/1) and a Global Challenges Research Fund Foundation Award (BB/P023223/1). LAB was funded by a Cambridge BBSRC doctoral training programme studentship

Identification of Schistosoma mansoni microRNAs

Background: MicroRNAs (miRNAs) constitute a class of single-stranded RNAs which play a crucial role in regulating development and controlling gene expression by targeting mRNAs and triggering either translation repression or messenger RNA (mRNA) degradation. miRNAs are widespread in eukaryotes and to date over 14,000 miRNAs have been identified by computational and experimental approaches. Several miRNAs are highly conserved across species. In Schistosoma, the full set of miRNAs and their expression patterns during development remain poorly understood. Here we report on the development and implementation of a homology-based detection strategy to search for miRNA genes in Schistosoma mansoni. In addition, we report results on the experimental detection of miRNAs by means of cDNA cloning and sequencing of size-fractionated RNA samples. Results: Homology search using the high-throughput pipeline was performed with all known miRNAs in miRBase. A total of 6,211 mature miRNAs were used as reference sequences and 110 unique S. mansoni sequences were returned by BLASTn analysis. The existing mature miRNAs that produced these hits are reported, as well as the locations of the homologous sequences in the S. mansoni genome. All BLAST hits aligned with at least 95% of the miRNA sequence, resulting in alignment lengths of 19-24 nt. Following several filtering steps, 15 potential miRNA candidates were identified using this approach. By sequencing small RNA cDNA libraries from adult worm pairs, we identified 211 novel miRNA candidates in the S. mansoni genome. Northern blot analysis was used to detect the expression of the 30 most frequent sequenced miRNAs and to compare the expression level of these miRNAs between the lung stage schistosomula and adult worm stages. Expression of 11 novel miRNAs was confirmed by northern blot analysis and some presented a stage-regulated expression pattern. Three miRNAs previously identified from S. japonicum were also present in S. mansoni. Conclusion: Evidence for the presence of miRNAs in S. mansoni is presented. The number of miRNAs detected by homology-based computational methods in S. mansoni is limited due to the lack of close relatives in the miRNA repository. In spite of this, the computational approach described here can likely be applied to the identification of pre-miRNA hairpins in other organisms. Construction and analysis of a small RNA library led to the experimental identification of 14 novel miRNAs from S. mansoni through a combination of molecular cloning, DNA sequencing and expression studies. Our results significantly expand the set of known miRNAs in multicellular parasites and provide a basis for understanding the structural and functional evolution of miRNAs in these metazoan parasites

Contribution of Genome Analysis to Understanding of the Biology of, and Diseases Caused by, African Trypanosomes

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Human Immunodeficiency Virus and Hepatitis C Virus Co-infection in Cameroon: Investigation of the Genetic Diversity and Virulent Circulating Strains

Background: RNA virus infections represent a significant cause of illness and death in vertebrates. Specifically in humans, RNA viruses are responsible for a wide range of acute, chronic, emerging and re-emerging infections. HIV and HCV rank as some of the most severe RNA viruse infections facing Africa. Methods: To determine genotypes and subtypes of HIV and HCV among co-infected patients in Cameroon, viral RNA was isolated from HIV/HCV co-infected individuals, in Douala, Cameroon. A total of 36 HIV/HCV co-infected isolates (22 from volunteer blood donors and 14 from people living with HIV/AIDS not yet on antiretroviral treatment) were analyzed using molecular biology techniques that involved RT-PCR, gene/TOPO cloning, DNA sequencing, and bioinformatics tools for sequence management and analysis. Epidemiological data were examined as well.Results: Results show that HIV strains isolated belong to the circulating recombinant forms CRF02_AG, whereas HCV isolates from Cameroon belong to genotypes 1, 2, and 4. The corresponding HCV subtypes investigated were 1a, 1b, 1c, 2a, 2c, 2k, and 4a. Subtypes 1a and 1b, most frequently found in developed countries, also circulate in Cameroon. Epidemiologic data show that HIV/HCV co-infected patients are older than HIVmono-infected patients.Conclusions: These results indicate that HIV/HCV co-infection represent a significant threat in Cameroon. There is evidence of genetic diversity of HIV and HCV; virulent hepatitis C virus subtypes 1a and 1b circulate in Cameroon. An epidemiological and molecular database on HIV and HCV is necessary for the development of further intervention in Cameroon as an imperative for monitoring disease progression.Key words: HIV; HCV; Co-infection ; Genotypes ; Virulent

Genetic diversity and population structure of the endangered Tanzanian Mpwapwa cattle breed

Mpwapwa cattle is a synthetic dual-purpose breed developed at the Mpwapwa Cattle Research Station, Tanzania, in the 1920s. The development and maintenance of Mpwapwa cattle have faced many challenges, and this breed has never been characterized at the genomic level. Our objectives were to assess the current genetic diversity and population structure of Mpwapwa cattle owing to its highly admixed origin and decline in active genetic management in recent years. Hair samples were collected from 251 cattle from different agro-ecological zones in Tanzania and were genotyped with the Bovine 100K SNP chip (Neogen Geneseek®). After quality control (using PLINK 1.9), we assessed heterozygosity (PLINK 1.9), inbreeding (detectRUNS package in R), and admixture (LEA package in R). We found the observed heterozygosity (0.32) was higher than the expected based on observed allele frequencies (0.29). Furthermore, more than 75% of studied animals had a runs-of-homozygosity-based inbreeding higher than 20%. Admixture analyses have indicated separation of the sampled animals by agro-ecological zones. Our results provide information for developing conservation and improvement strategies for this endangered Tanzania cattle breed

Genetic diversity and population structure of the endangered Tanzanian Mpwapwa cattle breed

Mpwapwa cattle is a synthetic dual-purpose breed developed at the Mpwapwa Cattle Research Station, Tanzania, in the 1920s. The development and maintenance of Mpwapwa cattle have faced many challenges, and this breed has never been characterized at the genomic level. Our objectives were to assess the current genetic diversity and population structure of Mpwapwa cattle owing to its highly admixed origin and decline in active genetic management in recent years. Hair samples were collected from 251 cattle from different agro-ecological zones in Tanzania and were genotyped with the Bovine 100K SNP chip (Neogen Geneseek®). After quality control (using PLINK 1.9), we assessed heterozygosity (PLINK 1.9), inbreeding (detectRUNS package in R), and admixture (LEA package in R). We found the observed heterozygosity (0.32) was higher than the expected based on observed allele frequencies (0.29). Furthermore, more than 75% of studied animals had a runs-of-homozygosity-based inbreeding higher than 20%. Admixture analyses have indicated separation of the sampled animals by agro-ecological zones. Our results provide information for developing conservation and improvement strategies for this endangered Tanzania cattle breed

Mitochondrial phylogeography and population structure of the cattle tick Rhipicephalus appendiculatus in the African Great Lakes region

Abstract Background The ixodid tick Rhipicephalus appendiculatus is the main vector of Theileria parva, wich causes the highly fatal cattle disease East Coast fever (ECF) in sub-Saharan Africa. Rhipicephalus appendiculatus populations differ in their ecology, diapause behaviour and vector competence. Thus, their expansion in new areas may change the genetic structure and consequently affect the vector-pathogen system and disease outcomes. In this study we investigated the genetic distribution of R. appendiculatus across agro-ecological zones (AEZs) in the African Great Lakes region to better understand the epidemiology of ECF and elucidate R. appendiculatus evolutionary history and biogeographical colonization in Africa. Methods Sequencing was performed on two mitochondrial genes (cox1 and 12S rRNA) of 218 ticks collected from cattle across six AEZs along an altitudinal gradient in the Democratic Republic of Congo, Rwanda, Burundi and Tanzania. Phylogenetic relationships between tick populations were determined and evolutionary population dynamics models were assessed by mismach distribution. Results Population genetic analysis yielded 22 cox1 and 9 12S haplotypes in a total of 209 and 126 nucleotide sequences, respectively. Phylogenetic algorithms grouped these haplotypes for both genes into two major clades (lineages A and B). We observed significant genetic variation segregating the two lineages and low structure among populations with high degree of migration. The observed high gene flow indicates population admixture between AEZs. However, reduced number of migrants was observed between lowlands and highlands. Mismatch analysis detected a signature of rapid demographic and range expansion of lineage A. The star-like pattern of isolated and published haplotypes indicates that the two lineages evolve independently and have been subjected to expansion across Africa. Conclusions Two sympatric R. appendiculatus lineages occur in the Great Lakes region. Lineage A, the most diverse and ubiquitous, has experienced rapid population growth and range expansion in all AEZs probably through cattle movement, whereas lineage B, the less abundant, has probably established a founder population from recent colonization events and its occurrence decreases with altitude. These two lineages are sympatric in central and eastern Africa and allopatric in southern Africa. The observed colonization pattern may strongly affect the transmission system and may explain ECF endemic instability in the tick distribution fringes