Performance Evaluation of Highly Admixed Tanzanian Smallholder Dairy Cattle Using SNP Derived Kinship Matrix

Abstract

The main purpose of this study was to understand the type of dairy cattle that can be optimally used by smallholder farmers in various production environments such that they will maximize their yields without increasing the level of inputs. Anecdotal evidence and previous research suggests that the optimal level of taurine inheritance in crossbred animals lies between 50 and 75% when considering total productivity in tropical management clusters. We set out to assess the relationship between breed composition and productivity for various smallholder production systems in Tanzania. We surveyed 654 smallholder dairy households over a 1-year period and grouped them into production clusters. Based on supplementary feeding, milk productivity and sale as well as household wealth status four clusters were described: low-feed–low-output subsistence, medium-feed–low-output subsistence, maize germ intensive semi-commercial and feed intensive commercial management clusters. About 839 crossbred cows were genotyped at approximately 150,000 single nucleotide polymorphism (SNP) loci and their breed composition determined. Percentage dairyness (proportion of genes from international dairy breeds) was estimated through admixture analysis with Holstein, Friesian, Norwegian Red, Jersey, Guernsey, N’Dama, Gir, and Zebu as references. Four breed types were defined as RED–GUE (Norwegian Red/Friesian–Guernsey; Norwegian Red/Friesian–Jersey), RED–HOL (Norwegian Red/Friesian–Holstein), RED–Zebu (Norwegian Red/Friesian–Zebu), Zebu–RED (Zebu–Norwegian Red/Friesian) based on the combination of breeds that make up the top 76% breed composition. A fixed regression model using a genomic kinship matrix was used to analyze milk yield records. The fitted model accounted for year-month-test-date, parity, age, breed type and the production clusters as fixed effects in the model in addition to random effects of animal and permanent environment effect. Results suggested that RED–Zebu breed type with dairyness between 75 and 85% is the most appropriate for a majority of smallholder management clusters. Additionally, for farmers in the feed intensive management group, animals with a Holstein genetic background with at least 75% dairy composition were the best performing. These results indicate that matching breed type to production management group is central to maximizing productivity in smallholder systems. The findings from this study can serve as a basis to inform the development of the dairy sector in Tanzania and beyond.

Prediction of Milk Production of Holstein Cattle Using Principal Component Analysis

“…Also, Chi-square = 9094.8 and significant (P≤0.001) of factor analysis application on the data in (Table, 3). The same model reported by many authors (Tolenkhomba et al, 2013;Shah et al, 2018;Romero et al, 2018 andMujibi et al, 2019) studying different productive traits in cattle. Principal Components Analysis (PCA) converts a group of large variables into a relatively small (PC) without losing information.…”

Multi-level Association Rule Mining for the Discovery of Strong Underrepresented Patterns

“…Most farmers in high-and medium-producing clusters have 3 preferred breeds: Friesian, Ayrshire, and Jersey. Low milk producers did not have preferred breed types, raising questions about their dairy orientation and breeding selections [29]. The use of improved crossbreeding types is preferred to increase milk production compared to pure exotic breeds that have low production due to the production environments that are highly resource deprived.…”

“…The use of improved crossbreeding types is preferred to increase milk production compared to pure exotic breeds that have low production due to the production environments that are highly resource deprived. Improved breeds that are well suited for the environment of Tanzania, such as Friesian, Ayrshire, and Jersey, have been proven to be among the top 10 effective in dairy production [29]. Farmers in high and low clusters preferred the use of bull breeding while farmers in the medium cluster preferred artificial insemination, which is an efficient and effective tool to increase milk production by breeding many cows with semen from good breeds in different geographic locations.…”

Smallholders Livestock Keepers Breeding Choice and Its Implication on Poverty Reduction in Tanzania

“…Few studies have been carried out in the area of smallholder livestock keepers' breeding choice with largely never discuss anything about these smallholder decisions on choices of the type of cattle to be reared and its implication in poverty reduction, this increases demands for knowledge on the discipline and methodological attributes. However, the available few studies have paid attention to livestock and poverty (Engida et al 2015; Grace et al 2016 andKonga, 2014) while others have focused on livestock and food security (IFAD, 2016) while few have discussed breeding preferences (Mutenje et al, 2020 andMartin-Collado, 2018) However, Mujibi et al (2019) highlight that nearly 40% of the entire agricultural contribution to GDP in African countries is due to livestock activities which are highly dominated by the smallholder keepers. The contribution is higher in individual countries as it ranges between 30-80%.…”