Community-based breeding programs can realize sustainable genetic gain and economic benefits in tropical dairy cattle systems.

Implementing an appropriate breeding program is crucial to control fluctuation in performance, enhance adaptation, and further improve the crossbred population of dairy cattle. Five alternative breeding programs (BPs) were modeled considering available breeding units in the study area, the existing crossbreeding practices, and the future prospects of dairy research and development in Ethiopia. The study targeted 143,576 crossbred cows of 54,822 smallholder households in the Arsi, West Shewa, and North Shewa zones of the Oromia Region, as well as the North Shewa zone of the Amhara Region. The alternative BPs include conventional on-station progeny testing (SPT), conventional on-farm progeny testing (FPT), conventional on-station and on-farm progeny testing (SFPT), genomic selection (GS), and genomic progeny testing (GPT). Input parameters for modeling the BPs were taken from the analysis of long-term data obtained from the Holetta Agricultural Research Center and a survey conducted in the study area. ZPLAN+ software was used to predict estimates of genetic gain (GG) and discounted profit for goal traits. The predicted genetic gains (GGs) for milk yield (MY) per year were 34.52 kg, 49.63 kg, 29.35 kg, 76.16 kg, and 77.51 kg for SPT, FPT, SFPT, GS, and GPT, respectively. The GGs of the other goal traits range from 0.69 to 1.19 days per year for age at first calving, from 1.20 to 2.35 days per year for calving interval, and from 0.06 to 0.12 days per year for herd life. Compared to conventional BPs, genomic systems (GPT and GS) enhanced the GG of MY by 53%-164%, reduced generation interval by up to 21%, and improved the accuracy of test bull selection from 0.33 to 0.43. The discounted profit of the BPs varied from 249.58 Ethiopian Birr (ETB, 1 USD = 39.55696 ETB) per year in SPT to 689.79 ETB per year in GS. Genomic selection outperforms SPT, SFPT, and FPT by 266, 227%, and 138% of discounted profit, respectively. Community-based crossbreeding accompanied by GS and gradual support with progeny testing (GPT) is recommended as the main way forward to attain better genetic progress in dairy farms in Ethiopia and similar scenarios in other tropical countries.

Using the community-based breeding program (CBBP) model as a collaborative platform to develop the African Goat Improvement Network-Image collection protocol (AGIN-ICP) with mobile technology for data collection and management of livestock phenotypes.

Introduction: The African Goat Improvement Network Image Collection Protocol (AGIN-ICP) is an accessible, easy to use, low-cost procedure to collect phenotypic data via digital images. The AGIN-ICP collects images to extract several phenotype measures including health status indicators (anemia status, age, and weight), body measurements, shapes, and coat color and pattern, from digital images taken with standard digital cameras or mobile devices. This strategy is to quickly survey, record, assess, analyze, and store these data for use in a wide variety of production and sampling conditions. Methods: The work was accomplished as part of the multinational African Goat Improvement Network (AGIN) collaborative and is presented here as a case study in the AGIN collaboration model and working directly with community-based breeding programs (CBBP). It was iteratively developed and tested over 3 years, in 12 countries with over 12,000 images taken. Results and discussion: The AGIN-ICP development is described, and field implementation and the quality of the resulting images for use in image analysis and phenotypic data extraction are iteratively assessed. Digital body measures were validated using the PreciseEdge Image Segmentation Algorithm (PE-ISA) and software showing strong manual to digital body measure Pearson correlation coefficients of height, length, and girth measures (0.931, 0.943, 0.893) respectively. It is critical to note that while none of the very detailed tasks in the AGIN-ICP described here is difficult, every single one of them is even easier to accidentally omit, and the impact of such a mistake could render a sample image, a sampling day's images, or even an entire sampling trip's images difficult or unusable for extracting digital phenotypes. Coupled with tissue sampling and genomic testing, it may be useful in the effort to identify and conserve important animal genetic resources and in CBBP genetic improvement programs by providing reliably measured phenotypes with modest cost. Potential users include farmers, animal husbandry officials, veterinarians, regional government or other public health officials, researchers, and others. Based on these results, a final AGIN-ICP is presented, optimizing the costs, ease, and speed of field implementation of the collection method without compromising the quality of the image data collection.

The African Goat Improvement Network: a scientific group empowering smallholder farmers.

The African Goat Improvement Network (AGIN) is a collaborative group of scientists focused on genetic improvement of goats in small holder communities across the African continent. The group emerged from a series of workshops focused on enhancing goat productivity and sustainability. Discussions began in 2011 at the inaugural workshop held in Nairobi, Kenya. The goals of this diverse group were to: improve indigenous goat production in Africa; characterize existing goat populations and to facilitate germplasm preservation where appropriate; and to genomic approaches to better understand adaptation. The long-term goal was to develop cost-effective strategies to apply genomics to improve productivity of small holder farmers without sacrificing adaptation. Genome-wide information on genetic variation enabled genetic diversity studies, facilitated improved germplasm preservation decisions, and provided information necessary to initiate large scale genetic improvement programs. These improvements were partially implemented through a series of community-based breeding programs that engaged and empowered local small farmers, especially women, to promote sustainability of the production system. As with many international collaborative efforts, the AGIN work serves as a platform for human capacity development. This paper chronicles the evolution of the collaborative approach leading to the current AGIN organization and describes how it builds capacity for sustained research and development long after the initial program funds are gone. It is unique in its effectiveness for simultaneous, multi-level capacity building for researchers, students, farmers and communities, and local and regional government officials. The positive impact of AGIN capacity building has been felt by participants from developing, as well as developed country partners.

Evaluation of reciprocal F1 crosses of Fayoumi with two exotic chicken breeds 2: additive and non-additive effects on egg quality traits.

The current study evaluates additive and non-additive genetic variances for egg quality traits in six genotypes generated through pure mating and reciprocal crossing of Fayoumi (FM) with Koekoek (KK) and White Leghorn (WL). For each genotype, measurements were taken on 30 eggs randomly sampled at 32, 36, and 40 weeks of age to evaluate both external and internal egg quality parameters. The results revealed significant differences (P < 0.001) among the genotypes in all external quality traits and most internal quality traits, including yolk weight (YW), albumen weight (AW), and yolk height (YH). The results also showed that variations due to purebred effect (PE), general combining ability (GCA), maternal effect (ME), and specific combining ability (SCA) were significant in most traits, which reflects that both additive and non-additive variances are important for the inheritances of the parameters investigated. In most of the traits, the ME and PE were higher in KK and WL, while GCA was higher in KK and FM. The FM x WL had higher SCA than FM x KK. The results suggest the likelihood of genetic improvement in these genotypes through selection and crossbreeding strategies and/or a combination of the two.

Evaluation of reciprocal F1 crosses of Fayoumi with two exotic chicken breeds 1: additive and non-additive effects on egg production traits.

The present study estimates additive and non-additive effects on egg production traits in genotypes generated through pure mating and reciprocal crossing of Fayoumi (FM) with Koekoek (KK) and White Leghorn (WL). Age at first egg (AFE) and body weight at first egg (BWAFE) were determined when the first bird in the pen laid its first egg, and egg weight at first egg (EWAFE) was the average weight of eggs laid consecutively during the first 10 days. Egg number (EN) and egg weight (EW) were recorded daily from AFE to 40 weeks of age. Egg mass (EM) was the product of EN and EW. EN of hens initially housed and hens alive during the experiment were used to calculate hen-housed egg production (HHEP) and hen-day egg production (HDEP), respectively. All the traits showed statistically significant differences among the genotypes. The results revealed the importance of additive and non-additive effects, where purebred effect (PE), general combining ability (GCA), maternal effect (ME), specific combining ability (SCA), and residual reciprocal effect (RRE) significantly affected most of the traits. The KK and WL had a higher PE, and GCA was highest in KK, with FM and WL showing a higher ME. The FM x WL had higher SCA and RRE. The KK x FM and FM x WL outperformed their main and reciprocal crosses, respectively, and purebred contemporaries. Therefore, a synthetic breeding program involving KK as a sire and FM, WL, FM x WL, and KK x FM as a dam would be feasible.

Genetic diversity and within-breed variation in three indigenous Ethiopian sheep based on whole-genome analysis.

The objective of this work was to study genetic diversity by comparing whole genome sequence data of Rutana, Gumuz and Washera sheep found in Amhara and Benishanguel gumuz regional states of Ethiopia. We employed variant calling format tools version 0.1.15 to calculate some genetic diversity indices such as observed heterozygosity, expected heterozygosity, inbreeding coefficient, and nucleotide diversity. The results revealed that, observed heterozygosity ranged from 0.33 in Gumuz to 0.34 in Rutana and Washera sheep. Expected heterozygosity ranged from 0.37 in Rutana to 0.38 in Gumuz and Washera sheep. Expected heterozygosity was found to be higher than observed heterozygosity. Higher inbreeding coefficient (0.12) was recorded for Gumuz sheep compared to 0.09 of Rutana and Washera sheep. Mean nucleotide diversity values were 0.0029, 0.0030 and 0.0028 for Gumuz, Rutana and Washera sheep, respectively. Higher values of nucleotide diversity were recorded. Population structure analysis using principal component analysis revealed no clear separation between Gumuz, Rutana and Washera sheep populations with possibility of gene flow attributed to geographical location proximity. The smaller population size, closed breeding system, genetic drift and uncontrolled (non-random) mating might lead to higher rate of inbreeding in Gumuz, Rutana and Washera sheep, requiring timely intervention. This intervention helps to prevent inbreeding depression and extinction of these valuable breeds of sheep, which helps in sustaining the livelihood of sheep keepers in lowlands and highlands. Nevertheless, the whole-genome analysis revealed high within-breed variation. Uncovered areas of studies like mapping quantitative trait loci, identifying genes underpinning productivity traits such as carcass quantity and meat quality could be carried out on diversified sheep resources identified by the current study. Identifying the genomic regions and biological pathways that contribute to explaining variability in these traits is of great importance for selection purposes. Designing conservation-based within-breed sheep selective breeding programs are recommended considering economically important traits into account.

Defining smallholders' breeding objectives for common Tigray highland sheep in Northern Ethiopia.

A sound breeding objective is a basis for genetic improvement in the overall economic merit of farm animals. This study aimed to define smallholders' sheep breeding objectives using a conjoint-based choice experiment and bio-economic model. Multinomial logistic regression analysis showed differences (p < 0.001) among the derived weights allocated by farmers to body size, twining rate, mothering ability, libido, tail type, colour and lambing interval which formed the high priority traits. The likelihood values of farmer's top three preferred traits for ram were body size (0.659 ± 0.009), tail type (0.325 ± 0.016) and libido (0.247 ± 0.016) while body size (0.459 ± 0.010), twining rate (0.313 ± 0.010) and mothering ability (0.261 ± 0.010) were more preferred traits for selection of breeding ewes. Conjoint-based choice experiment and bio-economic model indicated that live body weight at 6 months of age, twining rate (litter size) and mothering ability (preweaning lamb survival) were the most economically important traits of the breeding ewes. A genetic improvement by one genetic standard deviation (σa ) in these traits resulted in a profit of Ethiopian Birr 36.03-60.47/ewe/year. A fair correlation (r = 0.63) was observed between farmers' traits preference (conjoint-based choice card experiment) and the estimated economic value of traits indicating a good relationship between farmers' preferences for traits and economic values of the traits. This would indicate that weighting traits in selection indexes with farmers' trait selection using a conjoint-based choice experiment would direct genetic improvement towards desired profitability. Moreover, the fair correspondence between the two methods suggests that bio-economic modelling, if designed properly considering farmers' concerns, could be used to reflect farmers' breeding objectives. Therefore, for reasonable genetic progress and sheep flock profitability, more attention should be given to litter size, preweaning lamb survival and body weight at 6 months of age as they are preferred by farmers and their economic weights. Further, research on the modalities for complementary use of the two methods to define breeding objectives under smallholder conditions is warranted.

Hatchability and growth performances of normal feathered local, Sasso-RIR and their F1-cross chickens managed under on-station condition in southern Ethiopia.

The Normal feathered local chicken (LL), Sasso-RIR (SRSR) and their F1-cross (LSR) chickens were hatched to evaluate for egg hatchability, body weight, feed efficiency, and survival rate. After 14 days of brooding, 150 chicks of each genotype were randomly selected and further replicated into five pens in a deep litter grower house consisting of 30 chicks each in a completely randomized design, and evaluated for a period of 16 weeks. Hatchability of fertile eggs was highest for LL (80.0%), intermediate for LSR (68.6%), and lowest for SRSR (55.9%) chickens. The body weight (BW) of chicks at 2 weeks of age was 80.0, 76.3, and 61.5 g/bird for SRSR, LSR, and LL, respectively, the latter being the lowest (p < 0.05). The respective BW at 8 weeks of age was 732, 587, and 451 g while at 18 weeks it was 1877, 1379, and 1070 g/bird and different from each other (p < 0.05). During 3- to 8-week and 9- to 18-week growth periods, the LL chickens were inferior (p < 0.05) in feed intake (29.7 and 66.9 g/d/bird) whereas the SRSR chickens were superior (p < 0.05) in body weight gain (15.5 and 16.3 g/d/bird) and feed conversion ratio (2.67 and 5.35 g feed/ g gain), respectively. The mortality rate of chicken was not affected by genotypes. It can be concluded that Sasso-RIR chicken genotype had played a significant role in upgrading the growth rate and market weight of the local normal feathered chicken without adverse effect on hatchability, feed efficiency, and survival rate.

On-farm evaluation of growth and reproductive performances of Washera and Gumuz sheep in northwestern Ethiopia: Basics for setting up breeding objectives/goals.

Growth and reproductive performance traits are traits of economic importance for sheep selection and productivity improvement interventions. This study aimed at comparative evaluation of growth and reproductive performance traits of sheep in the highland and lowland agro-ecologies of northwestern Ethiopia. Data on growth performance traits were collected from 144 Washera (78 males and 66 females) lambs and 72 Gumuz (37 males and 35 females) lambs. Data on reproductive performance traits were collected from 260 Washera (130 rams and 130 ewes) sheep and 150 Gumuz (75 rams and 75 ewes) sheep. General linear model univariate procedure was employed to analyze the collected data. Breed, the interaction effect between breed and season of birth as well as the interaction effect between breed and type of birth all exerted very high significant effect (P<0.001) on live weight at all age groups. Breed type affected pre-weaning average daily weight gain significantly (P<0.01). Pre-weaning average daily weight gain of Washera (70 g/day) was found much better performance than 60 g/day of Gumuz. Breed type exerts significant (P<0.05) effect on age at first lambing, lambing interval, annual reproductive rate and number of lambs born per ewe life time. Average age at first lambing and lambing interval of Washera sheep were 11.69 months and 9.27 months, respectively. The corresponding values for Gumuz sheep were 12.51 months and 10.43 months, respectively. Production and reproduction performance values of traits varied across the two breeds and sexes as well. These values can be used to set up breeding objectives or goals for selective breeding of sheep giving special emphasis to growth traits believed to have medium heritability values.

Correction to: Genetic diversity and matrilineal genetic origin of fat-rumped sheep in Ethiopia.

The article Genetic diversity and matrilineal genetic origin of fat-rumped sheep in Ethiopia, written by Nigussie H., Mwacharo J.M., Osama S., Agaba M., Mekasha Y., Kebede K., Abegaz S., Pal S.K., was originally published Online First without Open Access.

A Chicken Production Intervention and Additional Nutrition Behavior Change Component Increased Child Growth in Ethiopia: A Cluster-Randomized Trial.

BACKGROUND: Chicken production in the context of nutrition-sensitive agriculture may benefit child nutrition in low-income settings. OBJECTIVES: This study evaluated effects of 1) a chicken production intervention [African Chicken Genetic Gains (ACGG)], and 2) the ACGG intervention with nutrition-sensitive behavior change communication (BCC) [ACGG + Agriculture to Nutrition (ATONU)], on child nutrition and health outcomes and hypothesized intermediaries. METHODS: Forty ACGG villages received 25 genetically improved chickens and basic husbandry guidance; of these, 20 ACGG + ATONU villages in addition received a nutrition-sensitive behavior change and homegardening intervention; 20 control clusters received no intervention. We assessed effects of the interventions on height-for-age z scores (HAZ), weight-for-age z scores (WAZ), and weight-for-height z scores (WHZ) at 9 (midline) and 18 mo (endline) through unadjusted and adjusted ordinary least squares (OLS) regressions. We examined the interventions' effects on hypothesized intermediaries including egg production and consumption, dietary diversity, women's empowerment, income, child morbidities, anemia, and chicken management practices through OLS and log binomial models. RESULTS: Data included 829 children aged 0-36 mo at baseline. ACGG + ATONU children had higher midline HAZ [mean difference (MD): 0.28; 95% CI: 0.02, 0.54] than controls. The ACGG group had higher HAZ (MD: 0.28; 95% CI: 0.05, 0.50) and higher WAZ (MD: 0.18; 95% CI: 0.01, 0.36) at endline than controls; after adjusting for potential baseline imbalance, effects were similar but not statistically significant. At endline, differences in ACGG + ATONU children's HAZ and WAZ compared with controls were similar in magnitude to those of ACGG, but not statistically significant. There were no differences in anthropometry between the intervention groups. ACGG + ATONU children had higher dietary diversity and egg consumption than ACGG children at endline. Both interventions showed improvements in chicken management practices. The interventions did not increase anemia, diarrhea, fever, or vomiting, and the ACGG + ATONU group at midline showed reduced risk of fever. CONCLUSIONS: A chicken production intervention with or without nutrition-sensitive BCC may have benefited child nutrition and did not increase morbidity.This trial was registered at clinicaltrials.gov as NCT03152227.

Genetic diversity and matrilineal genetic origin of fat-rumped sheep in Ethiopia.

Ethiopia is home to a diverse gene pool of indigenous sheep populations. Therefore, a better understanding of genetic variation holds the key to future utilization through conservation. Three of these breeds, Afar, Blackhead Somali, and Hararghe Highland, are found in eastern Ethiopia where they contribute significantly to the livelihood of most pastoralist, agro-pastoralist, and smallholder farmers. These indigenous sheep are recognized on the basis of morphotype and their genetic distinction remains unknown. Here, to assess genetic variation, and matrilineal genetic origin and relationship of fat-rumed sheep found in eastern Ethiopia, 300 individuals from the three breeds were genotyped for 22 microsatellite markers and sequenced for the mitochondrial DNA displacement loop (mtDNA d-loop) region. The overall HO and HE were 0.57 and 0.75, respectively. Differentiation statistics revealed that a high proportion (97%) of the total genetic variation was explained by differences between individuals within populations. Genotype assignment independent of the population of origin showed K = 2 to be the optimum number of genetic backgrounds present in the dataset. This result was further confirmed by mtDNA D-loop sequences comparison in which the matrilineal genetic origin of eastern Ethiopia sheep is from two haplotype groups (types A and B) among the five haplotypes globally observed. Taken together, our findings suggest that the sheep populations from three breeds originated from two ancestral genetic backgrounds that may have diverged prior to their introduction to Ethiopia. However, to obtain a complete picture of the evolutionary dynamics of Ethiopian indigenous sheep, more samples and populations from within and outside of the country will need to be analyzed.