Genomic analysis of 10 years of artificial selection in community-based breeding programs in two Ethiopian indigenous sheep breeds.

In recent times, community-based breeding programs (CBBPs) have been advocated as the best strategy for genetic improvement of local breeds in smallholder farms in developing countries. Since 2009, CBBPs have been implemented for Ethiopian Bonga and Menz sheep to improve growth rates resulting in significant genetic gains in 6-month weights. With the hypothesis that selection could be impacting their genomes, we systematically screened for possible genome changes in the two breeds by analyzing 600K BeadChip genotype data of 151 individuals (with the highest breeding values for 6-month weights) from CBBP flocks against 98 individuals from non-CBBP flocks. We observed no differences in genetic diversity and demographic dynamics between CBBP and non-CBBP flocks. Selection signature analysis employing ROH, logistic regression genome-wide association study , FST , XP-EHH and iHS revealed 5 (Bonga) and 11 (Menz) overlapping regions under selection, that co-localized with QTLs for production (body size/weight, growth, milk yield), meat/milk quality, and health/parasite resistance, suggesting that the decade-long selection has likely started to impact their genomes. However, genome-wide genetic differentiation between the CBBP and non-CBBP flocks is not yet clearly evident.

Three easy fixes for sire use can enhance genetic progress in community-based breeding programmes.

We analysed options to optimize the use of sires in sheep and goat community-based breeding programmes (CBBP) for three scenarios occurring under field conditions: premature sale of selection candidates, fixed service periods of selected sires and incomplete sire pedigrees. The first scenario was studied by looking at the outcome of combinations of selection pressures in successive selection stages. A compromise of early sale of sire candidates and genetic progress can be obtained by selecting in two stages, such that selection pressure in the first stage is chosen in terms of achieving an acceptable selection potential after the second stage. Simulations showed the dependency of this compromise on selection accuracies and correlation between selection criteria. For a typical sheep CBBP, only 20% of the top three months weighting male lambs need to be retained to achieve 80% of the potential selection differential on six months weight. For the second scenario, two alternatives to fixed service periods were analysed. When across-age BLUP EBVs are not available, individual sires can be programmed to stay in service according to their initial ranking. In typical sheep, CBBPs genetic progress can be increased by about 9% over response to selection with optimum fixed sire service periods. When BLUP EBVs are available, a simulated retrospective analyses of across-age selection of sires in two current sheep CBBPs increased more than twofold the average breeding values actually observed. Thirdly, we studied the benefit of considering possible sires and their mating probabilities when estimating BLUP breeding values instead of setting such sires as unknown. In a current goat CBBP with up to three possible sires included in the pedigree, the accuracy of breeding values nears the accuracy when sires are known and are higher than accuracies when sires are unknown or when possible sires are ignored.

Estimates of genetic parameters and trends for reproduction traits in Bonga sheep, Ethiopia.

Investigation was carried out to assess the effects of environmental factors and to estimate genetic parameters and trends for reproductive traits in Bonga sheep, Ethiopia. Animals used in this study were managed by two communities involved in a community-based breeding programs (CBBPs) from 2009 to 2018. The database consisted of 15,595 individual phenotypic information from about 1500 ewes with variable number of records for each trait. The traits analyzed were age at first lambing (AFL), lambing interval (LI), and litter size (LS). Fixed effect analysis was done using the general linear model procedures of SAS. The Average Information Restricted Maximum Likelihood method of WOMBAT, fitting univariate animalmodel, was used to estimate heritabilities, repeatabilities and breeding values. Results showed that Bonga sheep had overall mean AFL, LI, and LS of 453 ± 109 days, 254 ± 51 days, and 1.43 ± 0.008, respectively. All traits were influenced (p < 0.01) by lambing year, lambing season, breeder communities, and parity of ewes. Estimates of heritability for AFL, LI, and LS were 0.015 ± 0.143, 0.009 ± 0.070, and 0.085 ± 0.110, respectively. The low heritabilities for the traits are expected and indicate low possibility of achieving rapid genetic progress through phenotypic selection. The repeatability estimates for LI and LS were low (0.109 and 0.196, respectively) indicating that non-genetic factors had significant influence to the variation in these traits among parities; therefore, selection decision on ewes should consider repeated records. The genetic trend for AFL, LI, and LS over the years was significant (p < 0.01). Positive values for LS and negative for AFL and LI were recorded, implying that the well-structured CBBPs have resulted in measurable genetic gains for the reproductive traits.

How to succeed in implementing community-based breeding programs: Lessons from the field in Eastern and Southern Africa.

Breeding programs involving either centralized nucleus schemes and/or importation of exotic germplasm for crossbreeding were not successful and sustainable in most Africa countries. Community-based breeding programs (CBBPs) are now suggested as alternatives that aim to improve local breeds and concurrently conserve them. Community-based breeding program is unique in that it involves the different actors from the initial phase of design up until implementation of the programs, gives farmers the knowledge, skills and support they need to continue making improvements long into the future and is suitable for low input systems. In Ethiopia, we piloted CBBPs in sheep and goats, and the results show that they are technically feasible to implement, generate genetic gains in breeding goal traits and result in socio-economic impact. In Malawi, CBBPs were piloted in local goats, and results showed substantial gain in production traits of growth and carcass yields. CBBPs are currently being integrated into goat pass-on programs in few NGOs and is out-scaled to local pig production. Impressive results have also been generated from pilot CBBPs in Tanzania. From experiential monitoring and learning, their success depends on the following: 1) identification of the right beneficiaries; 2) clear framework for dissemination of improved genetics and an up/out scaling strategy; 3) institutional arrangements including establishment of breeders' cooperatives to support functionality and sustainability; 4) capacity development of the different actors on animal husbandry, breeding practices, breeding value estimation and sound financial management; 5) easy to use mobile applications for data collection and management; 6) long-term technical support mainly in data management, analysis and feedback of estimated breeding values from committed and accessible technical staff; 7) complementary services including disease prevention and control, proper feeding, and market linkages for improved genotypes and non-selected counterparts; 8) a system for certification of breeding rams/bucks to ensure quality control; 9) periodic program evaluation and impact assessment; and 10) flexibility in the implementation of the programs. Lessons relating to technical, institutional, community dynamics and the innovative approaches followed are discussed.

Point-of-care testing can achieve same-day diagnosis for infants and rapid ART initiation: results from government programmes across six African countries.

INTRODUCTION: Point-of-care (POC) early infant diagnosis (EID) testing has been shown to dramatically decrease turnaround times from sample collection to caregiver result receipt and time to ART initiation for HIV-positive infants compared to centralized laboratory testing. As governments in sub-Saharan Africa implement POC EID technologies, we report on the feasibility and effectiveness of POC EID testing and the impact of same-day result delivery on rapid ART initiation within national programmes across six countries. METHODS: This pre-/post-evaluation compared centralized laboratory-based (pre) with POC (post) EID testing in 52 facilities across Cameroon, Democratic Republic of Congo, Ethiopia, Kenya, Senegal and Zimbabwe between April 2017 and October 2019 (country-dependent). Data were collected retrospectively from routine records at health facilities for all infants tested under two years of age. Hazard ratios and 95% confidence intervals were calculated to compare time-to-event outcomes, visualized with Kaplan-Meier curves, and the Somers' D test was used to compare continuous outcomes. RESULTS: Data were collected for 2892 EID tests conducted on centralized laboratory-based platforms and 4610 EID tests on POC devices with 127 (4%) and 192 (4%) HIV-positive infants identified, respectively. POC EID significantly reduced the time from sample collection to caregiver result receipt (POC median: 0 days, IQR: 0 to 0 vs. centralized: 35 days, IQR: 26 to 56) and time from sample collection to ART initiation for HIV-positive infants (POC median: 1 day, IQR: 0 to 7 vs. centralized: 39 days, IQR: 26 to 57). With POC testing, 72% of infants received results on the same day as sample collection; HIV-positive infants with a same-day diagnosis had six times the rate of ART initiation compared to those diagnosed one or more days after sample collection (HR: 6.39; 95% CI: 3.44 to 11.85). CONCLUSIONS: Same-day diagnosis and treatment initiation for infants is possible with POC EID within routine government-led and -supported public sector healthcare facilities in resource-limited settings. Given that POC EID allows for rapid ART initiation, aligning to the World Health Organization's recommendation of ART initiation within seven days, its use in public sector programmes has the potential to reduce overall mortality for infants with HIV through early treatment initiation.

Increased number of large non-atretic follicles and co-dominance effects account for high litter sizes in Bonga sheep.

To understand the ovarian basis for prolificacy of Bonga sheep, a total of 31 ewes were selected based on litter size (LS) records and divided into two groups: High Prolificacy (HP) (n = 20) with LS ≥ 2 and Low Prolificacy (LP) (n = 11) with LS = 1. At a synchronized estrus, follicular dynamics were determined using transrectal ultrasonography. Plasma estradiol concentrations were also monitored. In total 27 ewes were observed in estrus being 9/11 LP (82%) and 18/20 HP (90%). On the day of estrus (day 0), the mean number of large follicles was higher (p < .05) in HP (1.78 ± 0.19) than in LP (1.0 ± 0.28) ewes. Prior to estrus, more (p < .05) medium follicles were visible for HP compared to LP ewes. Plasma estradiol concentrations were higher in HP compared to LP ewes (18.91 ± 0.41 vs. 14.51 ± 0.65 pg/ml; p < .05) and similarly was ovulation number (2.3 ± 0.15 vs. 1.28 ± 0. 14; p < .05). Higher ovulation rates and litter size in Bonga sheep are evidenced by the previous presence of more large follicles and the existence of co-dominance effects as most likely medium follicles are selected to ovulate.