Expression analysis of TLR signaling pathway genes under lipopolysaccharide-induced and E. coli F17-infected sheep intestinal epithelial cells.

Escherichia coli (E. coli) F17 is one of the main pathogens causing diarrhea in young livestock. The specific F17 fimbriae and lipopolysaccharide (LPS) in the surface components of E. coli F17 induces immune activation via interacting with the intestinal epithelial cells (IECs)-expressed innate immune toll-like receptors (TLRs) signaling pathway. In this study, the expression patterns of eight canonical genes from the TLR signaling pathway (IL-6, IL-8, IL-1ß, TLR4, MyD88, CD14, TNF-α and TRAF6) were analyzed in LPS-induced IECs, E. coli F17-infected IECs and ileum tissue of E. coli F17-infected lambs. The results showed that increased expression levels of all the studied genes were observed following post-LPS-induced and E. coli F17-infected treatment, with TLR4 having the highest up-regulated expression multiple (compared to NC, fold change = 17.94 and 20.11, respectively), and CD14 having the lowest up-regulated expression multiple (fold change = 2.68 and 1.59, respectively), and higher expression levels of all the studied TLR signaling pathway genes were observed in ileum tissue of E. coli F17 antagonistic (AN) lambs than in E. coli F17 sensitive (SE) lambs. Furthermore, when compared to LPS-induced IECs, E. coli F17-infected IECs showed a more pronounced increase in the expression of IL6, TLR4 and TNF-α, indicating the different roles of these genes in the IECs resistance to E. coli F17 infection. Our results demonstrate that the TLR signaling pathway likely promotes immune activation and provide the first evidence that TLRs have a significant potential to protect against E. coli F17 infections.

Whole-genome resequencing of Dorper and Hu sheep to reveal selection signatures associated with important traits.

Dorper and Hu sheep exhibit different characteristics in terms of reproduction, growth, and meat quality. Comparison of the genomes of two breeds help to reveal important genomic information. In this study, whole genome resequencing of 30 individuals (Dorper, DB and Hu sheep, HY) identified 15,108,125 single nucleotide polymorphisms (SNPs). Population differentiation (Fst) and cross population extended haplotype homozygosity (XP-EHH) were performed for selective signal analysis. In total, 106 and 515 overlapped genes were present in both the Fst results and XP-EHH results in HY vs DB and in DB vs HY, respectively. In HY vs DB, 106 genes were enriched in 12 GO terms and 83 KEGG pathways, such as ATP binding (GO:0005524) and PI3K-Akt signaling pathway (oas04151). In DB vs HY, 515 genes were enriched in 109 GO terms and 215 KEGG pathways, such as skeletal muscle cell differentiation (GO:0035914) and MAPK signaling pathway (oas04010). According to the annotation results, we identified a series of candidate genes associated with reproduction (UNC5C, BMPR1B, and GLIS1), meat quality (MECOM, MEF2C, and MYF6), and immunity (GMDS, GALK1, and ITGB4). Our investigation has uncovered genomic information for important traits in sheep and provided a basis for subsequent studies of related traits.

Effects of YAP1 on proliferation and differentiation of Hu sheep skeletal muscle satellite cells in vitro.

This study aimed to understand the expression level of YAP1 in the skeletal muscle of Hu sheep and to reveal the regulatory mechanism of YAP1 on Hu sheep skeletal muscle satellite cells (SMSCs). Previous research by our group has found that YAP1 may affect the growth and development of Hu sheep skeletal muscle. In the present study, we found the expression of YAP1 in the skeletal muscle is higher than in other tissues of Hu sheep. Then, we detected the effect of YAP1 on proliferation and differentiation in Hu sheep SMSCs. According to the results of qPCR, CCK-8, EDU, and Western blot, compared to the group of negative control, overexpression of YAP1 promoted the proliferation and inhibited the differentiation of SMSCs according to the results of qPCR, CCK-8, EDU, Western blot, while the interference of YAP1 was on the contrary. Overall, our study suggests that YAP1 is an important functional molecule in the growth and development of skeletal muscle by regulating the proliferation and differentiation of SMSCs. These findings are of great use for understanding the roles of YAP1 in the skeletal muscle of Hu sheep.

The identification and validation of target genes of IGFBP3 protein in sheep skeletal muscle cells.

This study aimed to identify the target genes of IGFBP3（insulin growth factor binding protein）protein and to investigate its target genes effects on the proliferation and differentiation of Hu sheep skeletal muscle cells. IGFBP3 was an RNA-binding protein that regulates mRNA stability. Previous studies have reported that IGFBP3 promotes the proliferation of Hu sheep skeletal muscle cells and inhibits differentiation, but the downstream genes that bind to it have not been reported yet. We predicted the target genes of IGFBP3 through RNAct and sequencing data, and verified by qPCR and RIP（RNA Immunoprecipitation）experiments, and demonstrated GNAI2（G protein subunit alpha i2）as one of the target gene of IGFBP3. After interference with siRNA, we carried out qPCR, CCK8, EdU, and immunofluorescence experiments, and found that GNAI2 can promote the proliferation and inhibit differentiation of Hu sheep skeletal muscle cells. This study revealed the effects of GNAI2 and provided one of the regulatory mechanisms of IGFBP3 protein underlying sheep muscle development.

Marker-assisted introgression of fecundity mutation into Barbarine sheep breed under low input production system.

Fecundity gene introgression has become an economical method to improve sheep prolificacy in developing countries. The FecXBar and FecGH mutations are variants of the BMP15 and GDF9 sheep genes, respectively, identified in Tunisian Barbarine sheep prolific line "W-INRAT," created through a prolificacy-based selection program. The first mutation caused increased prolificacy in heterozygous state and sterility in homozygous ewes. The aim of this work was to increase the number of effective carriers by the introgression of fecundity mutation into non-carrier conventional flocks based on a marker-assisted breeding program. The genotyping was carried out to follow up on the segregation of prolificacy mutation. The conventional ewes, raised in state farms of Tunisia and inseminated by "W-INRAT" rams, yielded 100% carriers females at heterozygous state. These females were selected to be inseminated with conventional rams and produced carriers' lambs with 66.7% males and 33.3% females. The prolific males will be kept in breeding centers to disseminate the fecundity mutation in commercial flocks. This approach facilitates the dissemination of fecundity genes and contributes to livelihood improvement in communities raising Barbarine sheep.

Genome variation in tick infestation and cryptic divergence in Tunisian indigenous sheep.

BACKGROUND: Ticks are obligate haematophagous ectoparasites considered second to mosquitos as vectors and reservoirs of multiple pathogens of global concern. Individual variation in tick infestation has been reported in indigenous sheep, but its genetic control remains unknown. RESULTS: Here, we report 397 genome-wide signatures of selection overlapping 991 genes from the analysis, using ROH, LR-GWAS, XP-EHH, and FST, of 600 K SNP genotype data from 165 Tunisian sheep showing high and low levels of tick infestations and piroplasm infections. We consider 45 signatures that are detected by consensus results of at least two methods as high-confidence selection regions. These spanned 104 genes which included immune system function genes, solute carriers and chemokine receptor. One region spanned STX5, that has been associated with tick resistance in cattle, implicating it as a prime candidate in sheep. We also observed RAB6B and TF in a high confidence candidate region that has been associated with growth traits suggesting natural selection is enhancing growth and developmental stability under tick challenge. The analysis also revealed fine-scale genome structure indicative of cryptic divergence in Tunisian sheep. CONCLUSIONS: Our findings provide a genomic reference that can enhance the understanding of the genetic architecture of tick resistance and cryptic divergence in indigenous African sheep.

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.

Preliminary study of melatonin in the proliferation and apoptosis of Hu sheep dermal papilla cells in vitro.

Previous studies have shown that melatonin has a certain regulatory effect on the growth of sheep wool. However, the mechanism of melatonin action remains unknown. In the present study, we aimed to understand the role of exogenous melatonin in the dermal papilla cells of Hu sheep. To confirm the optimal melatonin treatment regimen for Hu sheep dermal papilla cells, we detected the cell viability by exposing them to different concentrations of melatonin and different treatment times. The results showed that cell viability was best when dermal papilla cells were treated with 1000 pg/ml of melatonin for 48 h. According to the results of qPCR, CCK-8, EDU, Western blot, and Flow cytometry analysis, we found that 1000 pg/ml melatonin promoted the proliferation and inhibited the apoptosis of dermal papilla cells compared with the exogenous melatonin blank group (control group). Furthermore, we also found that 1000 pg/ml of melatonin promoted the cell cycle progress of dermal papilla cells according to the results of qPCR and Flow cytometry analysis. Overall, our findings showed that melatonin plays an important role in the dermal papilla cells of Hu sheep.

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.

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.

Coat color alterations over the years and their association with growth performances in the Menz sheep central nucleus and community-based breeding programs.

In the traditional Menz sheep breeding, communities select against black coat color and therefore its frequency is declining over time. We hypothesize that this exercise is causing the loss of an important gene pool. Data collected from on-station Menz sheep nucleus (n = 1992) and community-based breeding program (CBBP) (n = 5578) were analyzed to (1) assess color proportion dynamics over years and (2) associate phenotypic performances and estimated breeding values (EBVs) for growth traits with coat color of the animals. The on-station nucleus considered growth trait as selection criteria, while CBBP focused on a combination of growth and morphological characters. The results showed that the proportion of black coat color increased across years in the on-station nucleus flock (2.1% per year). However, in the CBBP, flocks' proportion of black coat color declined over time (1.03-1.05% per year). Birth and growth traits of black-colored sheep were consistently superior (P < 0.05) to white-colored sheep. Mean yearling weight and EBV of black rams used in the on-station flock was 24.3 kg and 3.7 kg, respectively, while the values for white-colored sheep were 19.7 kg and 1.6 kg, respectively. This variation in growth performances of Menz sheep among different colors may be due to the linkage between color and growth performance genes. Thus, selection against black coat color in the CBBPs seems to have an adverse effect on the genetic progress of growth traits in the Menz sheep. Understanding the core reasons behind the prevailing selection against black coat color and devising measures to address them should be considered. Developing a black line targeting specific markets might also be worthy to maximize production as well as maintain qualities associated with black color.

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.

Genome-wide scans identify known and novel regions associated with prolificacy and reproduction traits in a sub-Saharan African indigenous sheep (Ovis aries).

Maximizing the number of offspring born per female is a key functionality trait in commercial- and/or subsistence-oriented livestock enterprises. Although the number of offspring born is closely associated with female fertility and reproductive success, the genetic control of these traits remains poorly understood in sub-Saharan Africa livestock. Using selection signature analysis performed on Ovine HD BeadChip data from the prolific Bonga sheep in Ethiopia, 41 candidate regions under selection were identified. The analysis revealed one strong selection signature on a candidate region on chromosome X spanning BMP15, suggesting this to be the primary candidate prolificacy gene in the breed. The analysis also identified several candidate regions spanning genes not reported before in prolific sheep but underlying fertility and reproduction in other species. The genes associated with female reproduction traits included SPOCK1 (age at first oestrus), GPR173 (mediator of ovarian cyclicity), HB-EGF (signalling early pregnancy success) and SMARCAL1 and HMGN3a (regulate gene expression during embryogenesis). The genes involved in male reproduction were FOXJ1 (sperm function and successful fertilization) and NME5 (spermatogenesis). We also observed genes such as PKD2L2, MAGED1 and KDM3B, which have been associated with diverse fertility traits in both sexes of other species. The results confirm the complexity of the genetic mechanisms underlying reproduction while suggesting that prolificacy in the Bonga sheep, and possibly African indigenous sheep is partly under the control of BMP15 while other genes that enhance male and female fertility are essential for reproductive fitness.

Community-based breeding programmes are a viable solution for Ethiopian small ruminant genetic improvement but require public and private investments.

Ethiopia has a large and diverse population of small ruminants, which contribute substantially to the livelihood and income of the rural poor and the country at large. However, the sector faces a number of challenges. Productivity per animal and flock offtake are both very low. Reasons attributed for the apparent low productivity are as follows: absence of appropriate breeding programmes, lack of technical capacity, inadequate and poor-quality feeds, diseases leading to high lamb mortality, and underdeveloped markets in terms of infrastructure and information. Historically, sheep and goats have received little policy or investment attention. Genetic improvement of small ruminants could contribute to bridging the productivity gap. In the past, the government of Ethiopia has placed much emphasis on importing exotic genetics and cross-breeding with local stock as a strategy for genetic improvement. However, this has not led to a significant productivity improvement and the programmes have generally been unsustainable. Currently, there is a change in approach and a recognition of the need to focus genetic improvement efforts on the local genetic resources that are well adapted to the diverse agro-ecologies and production environments in the country. Community-based breeding programmes (CBBPs), which focus on indigenous stock and consider farmers' needs, views, decisions and active participation, from inception through to implementation, have been identified as programmes of choice. The Ethiopian government and the private sector need to invest in strategic areas around CBBPs to make the programme work for the poor and be sustainable in low-input systems.

Serial translocation by means of circular intermediates underlies colour sidedness in cattle.

Colour sidedness is a dominantly inherited phenotype of cattle characterized by the polarization of pigmented sectors on the flanks, snout and ear tips. It is also referred to as 'lineback' or 'witrik' (which means white back), as colour-sided animals typically display a white band along their spine. Colour sidedness is documented at least since the Middle Ages and is presently segregating in several cattle breeds around the globe, including in Belgian blue and brown Swiss. Here we report that colour sidedness is determined by a first allele on chromosome 29 (Cs(29)), which results from the translocation of a 492-kilobase chromosome 6 segment encompassing KIT to chromosome 29, and a second allele on chromosome 6 (Cs(6)), derived from the first by repatriation of fused 575-kilobase chromosome 6 and 29 sequences to the KIT locus. We provide evidence that both translocation events involved circular intermediates. This is the first example, to our knowledge, of a phenotype determined by homologous yet non-syntenic alleles that result from a novel copy-number-variant-generating mechanism.

Phenotypic characteristics and trypanosome prevalence of Mursi cattle breed in the Bodi and Mursi districts of South Omo Zone, southwest Ethiopia.

The study was conducted to characterize the morphological features of Mursi cattle breed and to identify the species of trypanosome infecting the cattle and its prevalence in these traditionally managed cattle in the Bodi and Mursi pastoral communities. Cattle body description and measurements were made on 201 matured animals. Blood samples were collected from 409 animals into heparin-treated capillary tubes and were centrifuged to 12,000 rpm for 5 min to identify trypanosome species from the wet smeared buffy coat and to estimate the degree of anemia (PCV). Tsetse flies were collected using phenol-treated biconical trap and the caught flies identified to species level. The breed possesses variable coat color pattern, coat color type, and have small to medium hump size on the thoracic vertebrae. Body measurement of Mursi cattle in the two locations did not show significant differences except chest girth, rump width, and horn length. Trypanosome prevalence in the Mursi cattle breed was 6.1%. The highest trypanosome infection was caused by Trypanosoma congolense (56%) followed by Trypanosoma vivax (40%) and Trypanosoma brucei (4%). Trypanosome prevalence significantly varies between dry (2.0%) and late rainy (10.1%) seasons (P < 0.001) and between lean (11.9%) and medium (2.4%) body condition score (P < 0.01). The PCV value was 22.1 ± 0.5%, which is significantly varied with season (P < 0.01) and parasitism (P < 0.001). Parasitaemic cattle show the lowest PCV value (20.4 ± 1%) than aparasitaemic (23.7 ± 0.3%) cattle and cattle with lean BCS showed the lowest (P < 0.0001) PCV value (20.4 ± 0.6%). Tsetse fly species identified in the study area were Glossina pallidipes, Glossina morsitans submorsitans, and Glossina fuscipes. The number of flies captured in late rainy season was higher than in dry season (P < 0.01). Despite the existence of trypanosome and high tsetse fly infestation in the areas, large proportion of the Mursi cattle shows medium BCS, low trypanosome prevalence, and higher PCV value.

Relative resistance of Menz and Washera sheep breeds to artificial infection with Haemonchus contortus in the highlands of Ethiopia.

The aim of this study was to evaluate the relative resistance of Menz and Washera sheep breeds to artificial infection with Haemonchus contortus. The challenge trial was conducted at the Debre Berhan Agricultural Research Center in Ethiopia. A total of 39 (Menz = 21, Washera = 18) lambs of about 6 months old were used for the trial. All lambs were initially treated against internal parasite using albendazole and Fasinex to free them from internal parasites and kept indoors. H. contortus third-stage larvae (L3) were prepared according to standard procedure from adult female parasite collected from abattoirs and recovered using the Baerman technique. Approximately 5000 infective larvae were inoculated to the experimental lambs at about 5 weeks after deworming. Fecal egg count (FEC), packed cell volume (PCV), FAffa MAlan CHArt (FAMACHA) score, lamb body weight, and survival of lambs were recorded at 28, 35, and 42 days after challenge. Breed effect was not significant (P > 0.05), whereas time of measurement and the interaction of breed and time had significant (P < 0.05) effects on FEC and PCV. At 28 days after challenge, Menz sheep had lower FEC than Washera sheep, whereas at days 35 and 42, the Washera sheep had lower FEC than Menz lambs. The PCV decreased significantly throughout the post-challenge period. Despite their parasite burden, Menz sheep were able to maintain live weight during the 42 days of challenge. Chi-square tests for breed differences in lamb survival were not significant at any time (28, 35, and 42 days after challenge). Lower FEC at 28 days and delayed rise in FEC after infection in Menz lamb would allow in delaying anthelmintic treatment. In addition to maintain body weights during the infection period, sheep of both breeds exhibited substantial variability in PCV and FEC, suggesting opportunity to consider parasite resistance in selection program.

Feasibility of pedigree recording and genetic selection in village sheep flocks of smallholder farmers.

Pedigree recording and genetic selection in village flocks of smallholder farmers have been deemed infeasible by researchers and development workers. This is mainly due to the difficulty of sire identification under uncontrolled village breeding practices. A cooperative village sheep-breeding scheme was designed to achieve controlled breeding and implemented for Menz sheep of Ethiopia in 2009. In this paper, we evaluated the reliability of pedigree recording in village flocks by comparing genetic parameters estimated from data sets collected in the cooperative village and in a nucleus flock maintained under controlled breeding. Effectiveness of selection in the cooperative village was evaluated based on trends in breeding values over generations. Heritability estimates for 6-month weight recorded in the village and the nucleus flock were very similar. There was an increasing trend over generations in average estimated breeding values for 6-month weight in the village flocks. These results have a number of implications: the pedigree recorded in the village flocks was reliable; genetic parameters, which have so far been estimated based on nucleus data sets, can be estimated based on village recording; and appreciable genetic improvement could be achieved in village sheep selection programs under low-input smallholder farming systems.

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.

Optimization of selection for growth in Menz sheep while minimizing inbreeding depression in fitness traits.

The genetic trends in fitness (inbreeding, fertility and survival) of a closed nucleus flock of Menz sheep under selection during ten years for increased body weight were investigated to evaluate the consequences of selection for body weight on fitness. A mate selection tool was used to optimize in retrospect the actual selection and matings conducted over the project period to assess if the observed genetic gains in body weight could have been achieved with a reduced level of inbreeding. In the actual selection, the genetic trends for yearling weight, fertility of ewes and survival of lambs were 0.81 kg, -0.00026% and 0.016% per generation. The average inbreeding coefficient remained zero for the first few generations and then tended to increase over generations. The genetic gains achieved with the optimized retrospective selection and matings were highly comparable with the observed values, the correlation between the average breeding values of lambs born from the actual and optimized matings over the years being 0.99. However, the level of inbreeding with the optimized mate selections remained zero until late in the years of selection. Our results suggest that an optimal selection strategy that considers both genetic merits and coancestry of mates should be adopted to sustain the Menz sheep breeding program.