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The African livestock sector plays a key role in improving the livelihoods of people through the supply of food, improved nutrition and consequently health. However, its impact on the economy of the people and contribution to national GDP is highly variable and generally below its potential. This study was conducted to assess the current state of livestock phenomics and genetic evaluation methods being used across the continent, the main challenges, and to demonstrate the effects of various genetic models on the accuracy and rate of genetic gain that could be achieved. An online survey of livestock experts, academics, scientists, national focal points for animal genetic resources, policymakers, extension agents and animal breeding industry was conducted in 38 African countries. The results revealed 1) limited national livestock identification and data recording systems, 2) limited data on livestock production and health traits and genomic information, 3) mass selection was the common method used for genetic improvement with very limited application of genetic and genomic-based selection and evaluation, 4) limited human capacity, infrastructure, and funding for livestock genetic improvement programmes, as well as enabling animal breeding policies. A joint genetic evaluation of Holstein-Friesian using pooled data from Kenya and South Africa was piloted. The pilot analysis yielded higher accuracy of prediction of breeding values, pointing to possibility of higher genetic gains that could be achieved and demonstrating the potential power of multi-country evaluations: Kenya benefited on the 305-days milk yield and the age at first calving and South Africa on the age at first calving and the first calving interval. The findings from this study will help in developing harmonized protocols for animal identification, livestock data recording, and genetic evaluations (both national and across-countries) as well as in designing subsequent capacity building and training programmes for animal breeders and livestock farmers in Africa. National governments need to put in place enabling policies, the necessary infrastructure and funding for national and across country collaborations for a joint genetic evaluation which will revolutionize the livestock genetic improvement in Africa.

This study examines genetic and genomic approaches for sustainability in the dairy systems of developing countries of sub-Saharan Africa, where farms are predominately managed by smallholders, with 80% of land holdings being smaller than ten hectares. Sustainability in these systems involves addressing the global challenges of climate change while ensuring food security. Feed intake is a major trait with huge impact on both the efficiency of small holder systems and on methane emission. Improvement in feed efficiency will both mitigate the effects of climate change and reduce the cost of milk production. Body weight provides an indirect means of improving feed efficiency for body maintenance. Using daily milk yield and body weight records for 2716 cows, genomic predictions were undertaken, and a selection index for improving milk yield while restricting changes in body weight was implemented in Tanzania. However, defining broader breeding goals continue to be a challenge due to the lack of data but collection of milk components and somatic cell counts is being piloted in Tanzania and Ethiopia. Breeding for heat tolerance has been based on the rate of decline in milk yield due to changes in the temperature and humidity index (THI). An analysis of 14,367 daily milk records of 3511 dairy cows and weather records in Tanzania indicated that heat stress significantly affected daily milk production and reduced milk yield by 4.16% to 14.42% across THI groups. Reaction norms for sire EBVs along the trajectory of THI indicates that genetic variations exist which can be used to select animals that perform optimally in different environments. Also, other indicators of resilience including log-transformed variance and skewness of deviation, based on fluctuations in animals’ milk yield have been examined. Cows with less than 50% of exotic dairy genes showed significant levels higher degree of resilience.

On station small ruminant researches in Ethiopia were ineffective due to various factors. As alternative, community based breeding program (CBBP) has emerged. In the current CBBPs, sires’ side selection only (SN1) was practiced. The objective of the present work was to compare SN1 by simulating alternative breeding scenarios for Abergelle (AB), Centeral Highland (CH) and Woyto-Guji (WG) goat breeds in Ethiopia. Three scenarios including selection on dam’s side (SN2) in addition to SN1, application of genomic selection (SN3) on SN1 and use of sires from SN1 for mating in additional flocks (SN4) were simulated and compared with SN1 based on the predicted annual genetic gain (PAGG) and discounted profits. The breeding objective traits or selection criteria were six month weight (6mw, kg) for all breeds, average daily milk yield (ADM, kg) and survival to six month of age (SURV) for AB, litter size at birth (LSB) for CH and WG, litter size at weaning (LSW) for CH and kidding interval (KI, days) for WG. ZPLAN + software was used for the simulation. The PAGG for 6mw ranged from 0.086 kg (SN4) to 0.249 kg (SN3) for AB where it ranged from 0.471 kg (SN4) to 0.970 kg (SN3) for ADM for same breed. PAGG ranging from 0.130 kg (SN4) to 0.467 kg (SN3) and from 0.204 kg (SN4) to 0.311 kg (SN3) for CH Gonder and Ambo sites, respectively were simulated whereas this parameter ranged from 0.103 kg (SN4) to 0.271 kg (SN3) for WG. The alternative breeding scenarios to SN1 resulted in better PAGGs, especially for 6mw in three of the goat breeds and for ADM in AB. Based on the PAGGs and profitability we recommend SN2 over SN1. However, SN4 could also be applied, compared to SN1, in view of better profitability and suitability of addressing emerging demands.

Additional file 1: Figure S1. Nucleotide diversity for G. g. spadiceus and chicken populations (grouped by samling locations and breeds). Figure S2. Demographic histories for G. g. spadiceus and diverse chicken groups by PSMC. A total of 18 chicken populations were included in this analysis. Figure S3. Four tested demographic models for dadi analysis. Nanc, ancestral population size before the split; T, timepoints; m, migrations; Napop, ancestral population size after split. Ncpop, current population size. Arrows depict migration directions. Figure S4. Comparing observed data and model allele frequency spectrum for the best model (Model 3). Figure S5. Provean-scores for nonsynonymous mutations (for all mutations, left; and for mutations with Provean-scores ≤ –2.5, right) in microchromosomes, macrochromosomes, and intermediate chromosomes. Figure S6. Pipeline for constructing the mouse model with a mutation at the mouse TSHR locus (p. Gly559Arg; c.1675G>A). Figure S7. Photograph showing TSHR-559Arg knock-in homozygous (HO) and wild-type mice at 10 months old. Figure S8. Gly558Arg knock-in mice consumed less food than wild-type. *, P

In most smallholder dairy programmes, farmers are not fully benefitting from the genetic potential of their dairy cows. This is in part due to the mismatch between the available genotypes and the environment, including management, in which the animals perform. With sparse performance and pedigree records in smallholder dairy farms, the true degree of baseline genetic variability and breed composition is not known and hence rendering any genetic improvement initiative difficult to implement. Using the Girinka programme of Rwanda as an exemplar, the current study was aimed at better understanding the genetic diversity and population structure of dairy cattle in the smallholder dairy farm set up. Further, the association between farmer self-reported cow genotypes and genetically determined genotypes was investigated. The average heterozygosity estimates were highest (0.38 ± 0.13) for Rwandan dairy cattle and lowest for Gir and N'Dama (0.18 ± 0.19 and 0.25 ± 0.20, respectively). Systematic characterization of the genetic variation and diversity available may inform the formulation of sustainable improvement strategies such as targeting and matching the genotype of cows to productivity goals and farmer profile and hence reducing the negative impact of genotype by environment interaction.

Accurate information on the genetic and phenotypic characteristics and diversity of the indigenous Farm Animal Genetic Resources (FAnGR) is the basis on which their present and future sustainable utilization and conservation should be made. The paper describes the objectives, structure, functionality, content, utility and future prospects of the Country- Domestic Animal Genetic Resources Information System (DAGRIS) of ILRI. This electronic database is designed to cater for the needs of researchers, policy makers, development practitioners, teachers, students and farmers in developing countries for efficient access to available published and grey literature from past and present research results on the origin, distribution, diversity, present use and status of selected Farm Animal Genetic Resources (FAnGR) of the countries. Development of the country-modules of c-DAGRIS in English and French for Anglophone and Francophone countries is finalized and ready to be used.

Economic values for production traits (milk yield, MY, g; 12-month live weight, yLW, kg; consumable meat percentage, CM, %) and functional traits (mature doe live weight, DoLW, kg; mature buck live weight, LWb, kg; kidding frequency, KF; pre-weaning survival rate, PrSR, %; post-weaning survival rate, PoSR,%; doe survival rate, DoSR, %; and residual feed intake, RFI, kg) were estimated using profit functions for the Small East African goat. The scenario evaluated was a fixed flock size, and the resultant economic values (Kes per doe per year) were 34.46 (MY), 62.35 (yLW), 40.69 (CM), 0.15 (DoLW), 2.84 (LWb), 8.69 (KF), 17.38 (PrSR), 16.60 (PoSR), 16.69 (DoSR) and -3.00 (RFI). Similarly, the economic values decreased by -14.7 % (MY), -2.7 % (yLW), -23.9 % (CM), -6.6 % (DoLW), -98 % (LWb), -8.6 % (KF), -8.2 % (PrSR), -8.9 % (PoSR), -8.1 % (DoSR) and 0 % (RFI) when they were risk rated. The economic values for production and functional traits, except RFI, were positive, which implies that genetic improvement of these traits would have a positive effect on the profitability in the pastoral production systems. The application of an Arrow-Pratt coefficient of absolute risk aversion (λ) at the level of 0.02 resulted in a decrease on the estimated economic values, implying that livestock keepers who were risk averse were willing to accept lower expected returns. The results indicate that there would be improvement in traits of economic importance, and, therefore, easy-to-manage genetic improvement programmes should be established.

Se propone una utilizacion sostenible de los recursos zoogeneticos para la agricultura y la alimentacion como mejor estrategia para el mantenimiento de su diversidad. Alcanzar el uso sostenible contribuira a la mejora de la calidad de vida y minimizara el riesgo a largo plazo de la supervivencia de las poblaciones animales. El concepto de utilizacion sostenible conlleva dimensiones economicas, ambientales y socioculturales. La utilizacion sostenible de los recursos zoogeneticos tambien contribuye a la seguridad alimentaria, el desarrollo rural, el aumento de oportunidades de empleo y la mejora de los estandares de vida de los ganaderos. Apoyar la cria de razas a traves de una mejor infraestructura, servicios, cuidados sanitarios de los animales, oportunidades de mercado y otras intervenciones contribuiria de forma significativa a la utilizacion sostenible de los recursos zoogeneticos. La utilizacion sostenible comporta el uso y mejora de las razas que poseen altos niveles de adaptacion de su forma fisica a los principales ambientes. Tambien conlleva el despliegue de principios geneticos adecuados para el desarrollo sostenible de las razas y la intensificacion sostenible de los sistemas de produccion en si mismos. La utilizacion sostenible y la mejora genetica se basan en el acceso a un amplia gama de recursos geneticos. Los programas de mejora genetica necesitan ser considerados en terminos de agricultura nacional y desarrollo de objetivos ganaderos, asi como compatibilidad con las condiciones locales y seguridad de sustento y sostenibilidad ambientales. La mejora genetica puede implicar la eleccion de las razas mas apropiadas, la raza mas pura adecuada o un sistema de cruce de razas y la aplicacion de mejora genetica dentro de la raza. La eleccion de la raza adecuada y de los sistemas de cruces de razas en los paises en via de desarrollo ha sido uno de los factores que mas ha influido en el incremento de la productividad, y se ha beneficiado ampliamente del hecho que en los paises desarrollados los recursos zoogeneticos estan bien caracterizados y gozan de un intercambio relativamente libre. Donde se han seguido los pasos adecuados con evaluaciones correctas sobre la demanda, ejecucion, consigna, impacto y analisis de costo-beneficio, el exito de la mejora dentro de la raza ha sido alcanzado con poblaciones indigenas en paises en via de desarrollo. Los objetivos de mejora y los programas para la subsistencia y sistemas pastorales seran mayormente distintos de los programas convencionales. Los cruces de razas han tenido mayor exito donde se ha seguido un programa de seleccion riguroso que implique la participacion de ganaderos y parte substancial del sector publico en forma de inversion y soporte tecnico. En todo programa de mejora genetica es necesario controlar y monitorear la consanguinidad. La mejora genetica dentro de la raza es una practica normal en el mundo desarrollado y se ha convertido una empresa altamente tecnica que cubre los campos de reproduccion, control, computo y tecnologias de genoma. Las nuevas tecnologias de genoma prometen la capacidad para identificar mejor y la utilizacion y mejora de los recursos zoogeneticos del mundo en via de desarrollo en un futuro proximo. Los sistemas utiles pueden sin embargo ser establecidos sin la necesidad de aplicar procedimientos o tecnologias de vanguardia.

The study investigated the population structure, diversity and differentiation of almost all of the ecotypes representing the African Ankole Longhorn cattle breed on the basis of morphometric (shape and size), genotypic and spatial distance data. Twentyone morphometric measurements were used to describe the morphology of 439 individuals from 11 sub-populations located in five countries around the Great Lakes region of central and eastern Africa. Additionally, 472 individuals were genotyped using 15 DNA microsatellites. Femoral length, horn length, horn circumference, rump height, body length and fore-limb circumference showed the largest differences between regions. An overall F ST index indicated that 2.7% of the total genetic variation was present among sub-populations. The least differentiation was observed between the two sub-populations of Mbarara south and Luwero in Uganda, while the highest level of differentiation was observed between the Mugamba in Burundi and Malagarasi in Tanzania. An estimated membership of four for the inferred clusters from a model-based Bayesian approach was obtained. Both analyses on distance-based and model-based methods consistently isolated the Mugamba sub-population in Burundi from the others.