Whole-genome resequencing reveals genomic variation and dynamics in Ethiopian indigenous goats.

Ethiopia has about 52 million indigenous goats with marked phenotypic variability, which is the outcome of natural and artificial selection. Here, we obtained whole-genome sequence data of three Ethiopian indigenous goat populations (Arab, Fellata, and Oromo) from northwestern Ethiopia and analyzed their genome-wide genetic diversity, population structure, and signatures of selection. We included genotype data from four other Ethiopian goat populations (Abergelle, Keffa, Gumuz, and Woyto-Guji) and goats from Asia; Europe; and eastern, southern, western, and northern Africa to investigate the genetic predisposition of the three Ethiopian populations and performed comparative genomic analysis. Genetic diversity analysis showed that Fellata goats exhibited the lowest heterozygosity values (Ho = 0.288 ± 0.005 and He = 0.334 ± 0.0001). The highest values were observed in Arab goats (Ho = 0.310 ± 0.010 and He = 0.347 ± 4.35e-05). A higher inbreeding coefficient (FROH = 0.137 ± 0.016) was recorded for Fellata goats than the 0.105 ± 0.030 recorded for Arab and the 0.112 ± 0.034 recorded for Oromo goats. This indicates that the Fellata goat population should be prioritized in future conservation activities. The three goat populations showed the majority (∼63%) of runs of homozygosity in the shorter (100-150 Kb) length category, illustrating ancient inbreeding and/or small founder effects. Population relationship and structure analysis separated the Ethiopian indigenous goats into two distinct genetic clusters lacking phylogeographic structure. Arab, Fellata, Oromo, Abergelle, and Keffa represented one genetic cluster. Gumuz and Woyto-Guji formed a separate cluster and shared a common genetic background with the Kenyan Boran goat. Genome-wide selection signature analysis identified nine strongest regions spanning 163 genes influencing adaptation to arid and semi-arid environments (HOXC12, HOXC13, HOXC4, HOXC6, and HOXC9, MAPK8IP2), immune response (IL18, TYK2, ICAM3, ADGRG1, and ADGRG3), and production and reproduction (RARG and DNMT1). Our results provide insights into a thorough understanding of genetic architecture underlying selection signatures in Ethiopian indigenous goats in a semi-arid tropical environment and deliver valuable information for goat genetic improvement, conservation strategy, genome-wide association study, and marker-assisted breeding.

Growth curve analysis in different generations of Boer x Central Highland goats using alternative estimation models.

Growth curve analysis can help to optimize the management, determine nutritional requirements, predict the weight of animals at a specific age, and to select highly productive animals. Therefore, this study aimed to find the best-fitted nonlinear functions to provide a specific shape of the growth curve from birth to yearling age in different generations of Boer x Central Highland goats. Gompertz, Logistic, Brody, Von Bertalanffy, Monomolecular, Negative exponential, and Richards models were evaluated to quantify their ability to describe the biological growth curve. Root mean square error (RMSE), Bayesian information criterion (BIC), adjusted coefficient of determination (AdjR2), and Akaike's information criterion (AIC) were used to evaluate the goodness of fit and flexibility of the models. Data were analyzed using the nonlinear regression procedure of SAS. High AdjR2 and lower AIC, BIC, and RMSE values are indicators of best-fitted model. The best-fitting model for the first filial generation (F1), second filial generation (F2), and male goats' growth data was Brody function, whereas the Richards model, followed by Brody, best described the growth of third filial generation (F3) and female goats. The values of parameter A (asymptotic weight) for F1, F2, F3, female, and male goats based on the Brody model were 30.5±1.32, 28.2±1.38, 24.4±1.04, 27.8±0.94, and 29.8±1.32 kg for F1, F2, F3, female, and male goats, respectively. As per the best-fitted growth function, the asymptotic weight tended to reduce when the filial generation increased. The asymptotic weight for male goats was higher than for female goats. F1 had a slightly small value of parameter K, followed by F2 and F3. Both males and females had similar maturity rates. Based on the Brody function, the correlation between maturation rate and mature weight was high (-0.98, P<0.001). The correlation estimates for A-B and B-K were 0.27 and -0.15, respectively. Brody was best fitted for most goat categories, although Richards, followed by Brody, was best fitted for female and F3 goats. Besides, Brody could be better than Richards due to the ease of interpretation, convergence, and applicability for a small sample size. Therefore, the Brody function can predict the mature body weight, maturation rate, and growth rate of Boer x Central Highland goats and be used to formulate breeding and management strategies for profitable goat farming.

Estimation of crossbreeding and genetic parameters for reproductive traits of Boer x Central Highland goats in Ethiopia.

Additive genetic and non-additive parameters for reproductive traits of Boer x Central Highland goats were estimated. Pedigree and performance records comprised of Central Highland and their crosses with Boer goats were collected from 2009 to 2018 in the Sirinka Agricultural Research Center sheep and goat breeding station. Least-squares means for genotypes were obtained using a general linear model procedure in SAS. To estimate crossbreeding parameters, breed additive, heterotic, and recombination effects were fitted as fixed covariates instead of genotypes. Variance, heritability, and repeatability estimates were estimated through the AI-REML algorithm using WOMBAT software. Genotype did not significantly (P>0.05) influence most of the reproductive traits studied except for gestation length. The additive effect for litter size at birth (LSB), total litter birth weight (LBW), total litter weaning weight (LWW), litter size at weaning (LSW), and gestation length (GL) was estimated to be -0.004 kid, 0.08 kg, -3.18 kg, -0.54 kid, and 3.69 days, respectively. The contribution of heterosis to LSB, LWW, and GL of crossbred goats was negative, while the estimates for LBW and LSW were positive. However, Boer goats' heterosis effect and direct additive contribution to reproductive traits were insignificant (P>0.05) except for LSW. The recombination effect was negligible and not significant (P>0.05) for all traits examined. The direct heritability estimate for LSB, LWB, LWW, LSW, and GL were 0.050, 0.098, 0.086, 0.018, and 0.00, respectively. The repeatability estimates for LSB, LWB, LWW, LSW, and GL were 0.149, 0.116, 0.099, 0.086, and 0.061, respectively. The result indicates that improvement in reproductive traits would not be expected by crossing Boer with Central Highland goats. In addition, heritability estimates indicate that the improvement of reproductive traits through selection will be small, and the repeatability estimates indicate that multiple records have to be used to make a decision of culling or selection.

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.

Evaluation of growth and efficiency-related traits of different levels of Boer x Central Highland crossbred goats.

The growth and efficiency-related traits of the Boer x Central Highland goats raised semi-intensively were evaluated. Besides, genetic and non-genetic factors affecting growth and efficiency-related traits were identified. Data were collected over a period of nine years in a flock of Boer crossbred goats and analyzed using general linear model procedure of SAS. The overall least-squares mean live weight at birth, 3-, 6-, 9- and 12 months of age were 2.52 ± 0.01, 9.81 ± 0.13, 13.8 ± 0.15, 17.8 ± 0.19, and 20.5 ± 0.29 kg, respectively. The average weight gains from birth to 3 months, 3 to 6, 6 to 9 and 9-12 months of age were 80.3, 37.5, 41.9, and 31.2 g day-1, respectively. Boer blood level, birth type, season and year of kidding had a significant effect on growth traits. The overall least-squares mean of Kleiber ratio from birth to 3 months, 3-6 months, 6-9 months, and 9 month to yearling age were 13.99 ± 0.11, 5.23 ± 0.14, 4.66 ± 0.16, and 2.95 ± 0.18, respectively. Parity, birth type, Boer blood level, season and year of birth had a significant influence on the expression of efficiency-related traits (Kleiber ratios) in different growth phases. In terms of growth performance and efficiency-related traits, F2 and F3 crossbred goats did not show any benefit over F1 crossbred goats. Increasing Boer blood level above 50% would be worthless under the existing minimal input production system. Therefore, besides to improving the management of goats, producing the first filial generation would be suitable for medium to high input production systems.

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.

Phenotypic ranking experiments in identifying breeding objective traits of smallholder farmers in northwestern Ethiopia.

We executed two live animal ranking experiments, own-flock and group-animal ranking, to identify the breeding objectives of Arab and Oromo goat keepers in northwestern Ethiopia as a preliminary step towards designing sustainable breeding programs for two goat populations. In the own-flock ranking experiment, a total of 147 households, out of which 46 were Arab and 101 were Oromo goat keepers that live in semi-arid and sub-humid agroecologies respectively, were visited at their homesteads and were asked to choose their first best, second best, third best and the most inferior does from their own flock. The reasons of ranking and life history of the does (age, previous production and reproduction information) were inquired and recorded; live body weight and some linear body measurements were taken. In the group-animal ranking experiment, 12 breeding does and 12 breeding bucks from Arab goats and the same number of animals from Oromo goats were randomly selected. Life history of selected does and bucks (age, birth type, libido and temperament) were inquired from the owners. The selected animals were randomly grouped into four in Arab goats (three animals per group) and the same was applied in Oromo goats. Twelve farmers for Arab goats and the same number of farmers for Oromo goats who have not known the experimental animals were invited to do the ranking. Each person ranked the three animals in each group as 1st, 2nd and 3rd, giving reasons of ranking. After a first round of ranking, s/he was then provided with the history of each individual animal and asked whether s/he would consider re-ranking them. This procedure was continued eight times until a person covered all groups of does and bucks. It was found out that in own-flock ranking experiment, keepers focus on productive, reproductive and behavioral traits (such as body size, mothering ability, twinning rate, kidding interval and temperament) while in group-animal ranking experiment, there was a general tendency to focus on observable physical traits like coat color, body size and body conformation. Simultaneous use of both own-flock and group-animal ranking experiments is advisable to identify breeding objective traits in production systems where record keeping is absent.

Estimation of genetic parameters for growth traits and Kleiber ratios in Boer x Central Highland goat.

Accurate performance evaluation and genetic parameters estimation are the prerequisites for any successful genetic improvement program. This study was conducted to estimate genetic parameters for growth and Kleiber ratio traits in Boer x Central Highland goats. On-station data collected from 2009 to 2018 were utilized for the study. A general linear model procedure of the Statistical Analysis System (SAS, version 9.0) was used to analyze fixed effects, and genetic parameters were estimated using the WOMBAT software fitted animal model. The log-likelihood ratio test was used for selecting the best fitted model. Based on best fitted models, the total heritability (h2t) estimate for birth weight (BWT), weaning weight (WWT), six-month weight (SMWT), nine-month weight (NMWT), and yearling weight (YWT) were 0.38, 0.12, 0.05, 0.30, and 0.28, respectively. The total heritability (h2t) estimates for weight gain from birth to weaning (ADG1), 3 to 6 months (ADG2), 6 to 9 months (ADG3), and 9 to 12 months of age (ADG4) were 0.09, 0.08, 0.16, and 0.14, respectively. The heritability estimates for Kleiber ratios in different growth phases were found to be low (0.09 to 0.18) based on the selected models. Even with this figure, including the Kleiber ratio in the selection criteria would be imperative to improve the feed efficiency of crossbred goats. The direct genetic correlation estimates among growth traits range from 0.60 ± 0.14 to 0.97 ± 0.12. Except for NMWT, ADG4, and Kleiber ratio from 9 months to yearling age, the maternal effect had a significant influence on all considered traits. However, the contribution of the maternal genetic effect was more important for early growth traits. Thus, considering both the direct additive genetic effect and the maternal genetic effect is imperative for accurate genetic evaluation and for high selection response. The moderate heritability estimates for most of the growth traits implies the possibility of selection in conjunction with crossbreeding for a better genetic response. The positive and high genetic correlation estimates among growth traits confirm the possibility of a selection of goats at an early age.

Breeding practices and trait preferences of smallholder farmers for indigenous sheep in the northwest highlands of Ethiopia: Inputs to design a breeding program.

The aim of this study was to identify breeding practices and trait preferences for indigenous sheep in three districts (Estie, Farta and Lay Gayient) located in the northwest highlands of Ethiopia. Questionnaire survey and choice experiment methods were used to collect data from 370 smallholder farmers. Respondents were selected randomly among smallholder farmers who own sheep in the aforementioned districts. A generalized multinomial logit model was employed to examine preferences for sheep attributes, while descriptive statistics and index values were computed to describe sheep breeding practices. Having the highest index value of 0.36, income generation was ranked as the primary reason for keeping sheep, followed by meat and manure sources. The average flock size per smallholder farmer was 10.21 sheep. The majority of the smallholder farmers (91%) have the experience of selecting breeding rams and ewes within their own flock using diverse criteria. Given the highest index value of 0.34, body size was ranked as a primary ram and ewe selection criteria, followed by coat color. Furthermore, choice modeling results revealed that tail type, body size, coat color, growth rate, horn and ear size have shown significant influences on smallholder farmers' preference for breeding rams (P<0.01). The part-worth utility coefficients were positive for all ram attributes except ear size. For breeding ewes, mothering ability, coat color, body size, lambing interval, growth rate, tail type and litter size have shown significant effects on choice preferences of smallholder farmers (P<0.05). Moreover, significant scale heterogeneity was observed among respondents for ewe attributes (P<0.001). Overall, the results implied that sheep breeding objectives suitable for the northwest highlands of the country can be derived from traits such as linear body measurement, weight and survival at different ages, and lambing intervals. However, selection decisions at the smallholder level should not only be based on estimated breeding values of traits included in the breeding objective but instead, incorporate ways to address farmers' preference for qualitative traits.

Reproductive performance and milk production of Central Highland and Boer x Central Highland goats.

This study was conducted to evaluate the reproductive performance and milk production potential of Central Highland and Boer x Central Highland goats under semi-intensive management. Data were collected from 2009 till 2018 in the Sirinka goat breeding station. A general linear model procedure of the Statistical Analysis System (SAS) was used to analyze the data. The overall least-squares mean litter size at birth (LSB), litter size at weaning (LSW), total litter weight at birth, total litter weight at weaning and gestation length (GL) were 1.6 ± 0.02 kids, 1.4 ± 0.02 kids, 3.9 ± 0.05 kg, 13.6 ± 0.35 kg and 148.0 ± 0.33 days, respectively. The LSB, LSW and GL did not differ between Central Highland and their F1 and F2 crossbred dams. However, F2 dams produce the lightest kid at birth and weaning. Besides, birth type, season, year and parity were important sources of variation for most of the reproductive traits. The least-squares mean for daily milk yield (DMY), lactation milk yield (LMY) and lactation length (LL) were 0.34 ± 0.02 kg, 39.16 ± 3.00 kg and 104.2 ± 4.45 days, respectively. The DMY and LMY of Boer x Central Highland goats were higher than pure Central Highland goats by 46.4% and 27.2%, respectively. However, the LL for both genotypes was found to be similar (P > 0.05). Dams kidding during the short rainy season produce more milk than kidding during dry and main rainy seasons. Boer x Central Highland goats produce more milk than pure Central Highland goats. However, using Boer crossbred dams did not reveal any advantage over the base Central Highland dams in terms of reproductive performance. Therefore, using Central Highland goat as a dam line, improving the management and integration of crossbreeding with selection could be an ideal option to improve the overall productivity of goats.

Production systems and breeding practices of Arab and Oromo goat keepers in northwestern Ethiopia: implications for community-based breeding programs.

We conducted a household survey in the semi-arid and sub-humid parts of Benishangul Gumuz region in northwestern Ethiopia to better understand and describe production systems and breeding practices of Arab and Oromo goat keepers. Multistage random sampling was employed to select peasant associations, while probability proportional to size sampling was used to select households. Data were collected from 249 households, out of which 86 were Arab and 163 were Oromo goat keepers that live in semi-arid and sub-humid agroecologies, respectively. Personal observations, focus group discussions, and structured questionnaires were used to collect data. Data were analyzed using SPSS and results were presented using descriptive statistics and indices. Ninety-two percent of Arab and 86% of Oromo goat keepers indicated crop and livestock production as their main occupation. Goats were kept for a variety of purposes. Income generation, meat, and savings were the highest priorities. The average flock size owned by Arab goat keepers (12.5 ± 4.0) was significantly (p < 0.01) higher than that of Oromo goat keepers (9.9 ± 3.8). Breeding does constituted the largest average flock size followed by kids, young does, and young bucks. Body size, twining ability, coat color, and kid growth were considered important in selecting breeding does, while body size, growth rate, coat color, and libido were the most preferred traits for buck selection. Mating was predominantly uncontrolled mainly due to communal grazing lands. Castration of bucks was significantly (p < 0.01) more frequent in Arab goat keepers than in Oromo goat keepers. Arab goats have better reproductive performance than Oromo goats. On average, female goats in the study areas gave first births at the age of 1.2 years, kidded every 7.5 months, stayed on reproduction for about 7.6 years, and produced 10.7 kids per lifetime. Compared with Arab goats, Oromo goats had significantly (p < 0.01) higher average age at first mating, age at first kidding, kidding interval, and reproductive lifetime but produced lower average number of kids per lifetime. Nucleus breeding schemes are recommended to optimize the limited available resources in the study areas. A single nucleus could serve both Arab and Oromo goat keepers. In conclusion, breeding programs implemented in the study areas should consider the production systems and breeding practices of Arab and Oromo goat keepers appropriately.