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

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

Internal Revie

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

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

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

Climate-Smart \u3cem\u3eBrachiaria\u3c/em\u3e Grasses for Improving Livestock Production in East Africa

Climate change is a global phenomenon with negative impacts severely felt by poor people in developing countries (Morton 2007). Across many parts of Africa, rural poor communities rely greatly for their survival on agriculture and livestock that are amongst the most climate-sensitive economic sectors. Climate-smart agriculture helps farmers to increase food production, become more resilient to climate change and reduce greenhouse gas (GHG) emissions. The main anthro-pogenic GHGs are carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O); they are critically important for regulating the Earth’s surface temperature. Inadequate quantity and quality of feed is a major constraint to livestock production, particularly during the dry seasons across Africa. The overall objective of this inter-institutional program is to increase feed availability in action areas of the target countries in East Africa (e.g. Kenya, Rwanda) by use of climate-smart Brachiaria forage grasses (Rao et al. 2011) for increased animal productivity and for generation of extra income to smallholder famers. An innovative programmatic approach will be used to reintroduce high quality, persistent and productive Brachiaria genotypes that were selected and improved in Latin America (Miles et al. 2004) back to Africa. These forage grasses will contribute to alleviate feed shortages, increase income to resource poor farmers, improve soil fertility, adapt to and mitigate climate change, increase milk and beef production, and as a result improve livelihoods and protect the environment

Climate-Smart \u3cem\u3eBrachiaria\u3c/em\u3e for Improving Livestock Production in East Africa: Emerging Opportunities

Brachiaria grass is an important tropical forage of African origin with desirable attributes of agricultural and environmental significance. Brachiaria has been extensively cultivated as a pasture across the tropics except in its endemic provenance of Africa. In 2013, a collaborative research program was initiated in Kenya and Rwanda with the aim of improving the availability of quality livestock feeds adapted to drought and low fertility soils using Brachiaria. The outcomes sought were increased livestock productivity leading to improved farmer income and the development of seed production opportunities. The program has identified five preferred cultivars, and four of them are currently being evaluated on-farm by over 2000 small-holder farmers in Kenya and Rwanda for livestock productivity. Preliminary milk production data has shown a 15 to 40% increase in milk production in Kenya and an average increase of 36% in Rwanda. The substitution of Napier grass by Brachiaria in the feed has increased average daily body weight gain of cattle by 205g during a 12 week period. Kenyan farmers reported increased on-farm forage availability by three months after Brachiaria introduction. The program has also worked to determine the role of endophytes and plant associated microbes for the improvement of biomass production and adaptation of Brachiaria to biotic and abiotic stresses. A diverse group of fungi and bacteria were isolated, identified and characterized, and the role of these microbes on plant growth and plant pathogen suppression is being investigated. This paper discusses the rationale for selecting Brachiaria as potential forage for eastern Africa and highlights current achievements, and identifies areas for future research

Genetic diversity and population structure of Urochloa grass accessions from Tanzania using simple sequence repeat (SSR) markers

Urochloa (syn.—Brachiaria s.s.) is one of the most important tropical forages that transformed livestock industries in Australia and South America. Farmers in Africa are increasingly interested in growing Urochloa to support the burgeoning livestock business, but the lack of cultivars adapted to African environments has been a major challenge. Therefore, this study examines genetic diversity of Tanzanian Urochloa accessions to provide essential information for establishing a Urochloa breeding program in Africa. A total of 36 historical Urochloa accessions initially collected from Tanzania in 1985 were analyzed for genetic variation using 24 SSR markers along with six South American commercial cultivars. These markers detected 407 alleles in the 36 Tanzania accessions and 6 commercial cultivars. Markers were highly informative with an average polymorphic information content of 0.79. The analysis of molecular variance revealed high genetic variation within individual accessions in a species (92%), fixation index of 0.05 and gene flow estimate of 4.77 showed a low genetic differentiation and a high level of gene flow among populations. An unweighted neighbor-joining tree grouped the 36 accessions and six commercial cultivars into three main clusters. The clustering of test accessions did not follow geographical origin. Similarly, population structure analysis grouped the 42 tested genotypes into three major gene pools. The results showed the Urochloa brizantha (A. Rich.) Stapf population has the highest genetic diversity (I = 0.94) with high utility in the Urochloa breeding and conservation program. As the Urochloa accessions analyzed in this study represented only 3 of 31 regions of Tanzania, further collection and characterization of materials from wider geographical areas are necessary to comprehend the whole Urochloa diversity in Tanzania