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 structure of domestic cavy (Cavia porcellus) populations from smallholder farms in southern Cameroon

Although domestic cavies are widely used in sub-Saharan Africa as a source of meat and income, there are only a few studies of their population structure and genetic relatedness. This seminal study was designed with the main objective to assess the genetic diversity and determine the population structure of cavy populations from Cameroon to guide the development of a cavy improvement program. Sixteen microsatellite markers were used to genotype 109 individuals from five cavy populations (Wouri, Moungo and Nkongsamba in the Littoral region, and Mémé and Fako in the Southwest region of Cameroon). Twelve markers worked in the five populations with a total of 17 alleles identified, with a range of 2.9 to 4.0 alleles per locus. Observed heterozygosity (from 0.022 to 0.277) among populations was lower than expected heterozygosity (from 0.42 to 0.54). Inbreeding rates between individuals of the populations and between individuals in each population were 59.3% and 57.2%, respectively, against a moderate differentiation rate of 4.9%. All the tested loci deviated from Hardy-Weinberg equilibrium, except for locus 3. Genetic distances between populations were small (from 0.008 to 0.277), with a high rate of variability among individuals within each population (54.4%). Three distinct genetic groups were structured. This study has shown that microsatellites are useful for the genetic characterization of cavy populations in Cameroon and that the populations investigated have sufficient genetic diversity that can be used to be deployed as a basis for weight, prolificacy and disease resistance improvement. The genetic of diversity in Southern Cameroon is wide and constitute an opportunity for cavy breeding program

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

A mini-atlas of gene expression for the domestic goat (Capra hircus)

Goats (Capra hircus) are an economically important livestock species providing meat and milk across the globe. They are of particular importance in tropical agri-systems contributing to sustainable agriculture, alleviation of poverty, social cohesion, and utilisation of marginal grazing. There are excellent genetic and genomic resources available for goats, including a highly contiguous reference genome (ARS1). However, gene expression information is limited in comparison to other ruminants. To support functional annotation of the genome and comparative transcriptomics, we created a mini-atlas of gene expression for the domestic goat. RNA-Seq analysis of 17 transcriptionally rich tissues and 3 cell-types detected the majority (90%) of predicted protein-coding transcripts and assigned informative gene names to more than 1000 previously unannotated protein-coding genes in the current reference genome for goat (ARS1). Using network-based cluster analysis, we grouped genes according to their expression patterns and assigned those groups of coexpressed genes to specific cell populations or pathways. We describe clusters of genes expressed in the gastro-intestinal tract and provide the expression profiles across tissues of a subset of genes associated with functional traits. Comparative analysis of the goat atlas with the larger sheep gene expression atlas dataset revealed transcriptional similarities between macrophage associated signatures in the sheep and goats sampled in this study. The goat transcriptomic resource complements the large gene expression dataset we have generated for sheep and contributes to the available genomic resources for interpretation of the relationship between genotype and phenotype in small ruminants

Jersey cattle in Africa: From the Breed's Documented Past to a Profit Index-Linked Future

The aim of this paper was to review the documented reports of the Jersey breed in Africa; and the suitability of the breed for a dairy profit index relevant for the future of Rwanda's dairy development programmes. We extended our review of available reports on the Jersey breed to various African countries to deliver on our main objective of providing relevant knowledge to support long term genetic improvement plans that could be customised to any targeted countries based on the productions systems, constraints, national policies and the local socioeconomic development targets. Through extensive research the authors have confirmed a presence for the Jersey breed across the majority of the continent of Africa, whether current or historic, as a pure breed or used in cross breeding programmes