Natural products for Gut-X axis: pharmacology, toxicology and microbiology in mycotoxin-caused diseases.

Introduction: The gastrointestinal tract is integral to defending against external contaminants, featuring a complex array of immunological, physical, chemical, and microbial barriers. Mycotoxins, which are toxic metabolites from fungi, are pervasive in both animal feed and human food, presenting substantial health risks. Methods: This review examines the pharmacological, toxicological, and microbiological impacts of natural products on mycotoxicosis, with a particular focus on the gut-x axis. The analysis synthesizes current understanding and explores the role of natural products rich in polysaccharides, polyphenols, flavonoids, and saponins. Results: The review highlights that mycotoxins can disrupt intestinal integrity, alter inflammatory responses, damage the mucus layer, and disturb the bacterial balance. The toxins' effects are extensive, potentially harming the immune system, liver, kidneys, and skin, and are associated with serious conditions such as cancer, hormonal changes, genetic mutations, bleeding, birth defects, and neurological issues. Natural products have shown potential anticancer, anti-tumor, antioxidant, immunomodulatory, and antitoxic properties. Discussion: The review underscores the emerging therapeutic strategy of targeting gut microbial modulation. It identifies knowledge gaps and suggests future research directions to deepen our understanding of natural products' role in gut-x axis health and to mitigate the global health impact of mycotoxin-induced diseases.

Anthropogenic events and responses to environmental stress are shaping the genomes of Ethiopian indigenous goats.

Anthropological and biophysical processes have shaped livestock genomes over Millenia and can explain their current geographic distribution and genetic divergence. We analyzed 57 Ethiopian indigenous domestic goat genomes alongside 67 equivalents of east, west, and north-west African, European, South Asian, Middle East, and wild Bezoar goats. Cluster, ADMIXTURE (K = 4) and phylogenetic analysis revealed four genetic groups comprising African, European, South Asian, and wild Bezoar goats. The Middle Eastern goats had an admixed genome of these four genetic groups. At K = 5, the West African Dwarf and Moroccan goats were separated from East African goats demonstrating a likely historical legacy of goat arrival and dispersal into Africa via the coastal Mediterranean Sea and the Horn of Africa. FST, XP-EHH, and Hp analysis revealed signatures of selection in Ethiopian goats overlaying genes for thermo-sensitivity, oxidative stress response, high-altitude hypoxic adaptation, reproductive fitness, pathogen defence, immunity, pigmentation, DNA repair, modulation of renal function and integrated fluid and electrolyte homeostasis. Notable examples include TRPV1 (a nociception gene); PTPMT1 (a critical hypoxia survival gene); RETREG (a regulator of reticulophagy during starvation), and WNK4 (a molecular switch for osmoregulation). These results suggest that human-mediated translocations and adaptation to contrasting environments are shaping indigenous African goat genomes.

Phenotypic and genomic characterisation of performance of tropically adapted chickens raised in smallholder farm conditions in Ethiopia.

Background: In sub-Saharan Africa, 80% of poultry production is on smallholder village farms, where chickens are typically reared outdoors in free-ranging conditions. There is limited knowledge on chickens' phenotypic characteristics and genetics under these conditions. Objective: The present is a large-scale study set out to phenotypically characterise the performance of tropically adapted commercial chickens in typical smallholder farm conditions, and to examine the genetic profile of chicken phenotypes associated with growth, meat production, immunity, and survival. Methods: A total of 2,573 T451A dual-purpose Sasso chickens kept outdoors in emulated free-ranging conditions at the poultry facility of the International Livestock Research Institute in Addis Ababa, Ethiopia, were included in the study. The chickens were raised in five equally sized batches and were individually monitored and phenotyped from the age of 56 days for 8 weeks. Individual chicken data collected included weekly body weight, growth rate, body and breast meat weight at slaughter, Newcastle Disease Virus (NDV) titres and intestinal Immunoglobulin A (IgA) levels recorded at the beginning and the end of the period of study, and survival rate during the same period. Genotyping by sequencing was performed on all chickens using a low-coverage and imputation approach. Chicken phenotypes and genotypes were combined in genomic association analyses. Results: We discovered that the chickens were phenotypically diverse, with extensive variance levels observed in all traits. Batch number and sex of the chicken significantly affected the studied phenotypes. Following quality assurance, genotypes consisted of 2.9 million Single Nucleotide Polymorphism markers that were used in the genomic analyses. Results revealed a largely polygenic mode of genetic control of all phenotypic traits. Nevertheless, 15 distinct markers were identified that were significantly associated with growth, carcass traits, NDV titres, IgA levels, and chicken survival. These markers were located in regions harbouring relevant annotated genes. Conclusion: Results suggest that performance of chickens raised under smallholder farm conditions is amenable to genetic improvement and may inform selective breeding programmes for enhanced chicken productivity in sub-Saharan Africa.

Landscape genomics reveals regions associated with adaptive phenotypic and genetic variation in Ethiopian indigenous chickens.

Climate change is a threat to sustainable livestock production and livelihoods in the tropics. It has adverse impacts on feed and water availability, disease prevalence, production, environmental temperature, and biodiversity. Unravelling the drivers of local adaptation and understanding the underlying genetic variation in random mating indigenous livestock populations informs the design of genetic improvement programmes that aim to increase productivity and resilience. In the present study, we combined environmental, genomic, and phenotypic information of Ethiopian indigenous chickens to investigate their environmental adaptability. Through a hybrid sampling strategy, we captured wide biological and ecological variabilities across the country. Our environmental dataset comprised mean values of 34 climatic, vegetation and soil variables collected over a thirty-year period for 260 geolocations. Our biological dataset included whole genome sequences and quantitative measurements (on eight traits) from 513 individuals, representing 26 chicken populations spread along 4 elevational gradients (6-7 populations per gradient). We performed signatures of selection analyses ([Formula: see text] and XP-EHH) to detect footprints of natural selection, and redundancy analyses (RDA) to determine genotype-environment and genotype-phenotype-associations. RDA identified 1909 outlier SNPs linked with six environmental predictors, which have the highest contributions as ecological drivers of adaptive phenotypic variation. The same method detected 2430 outlier SNPs that are associated with five traits. A large overlap has been observed between signatures of selection identified by[Formula: see text]and XP-EHH showing that both methods target similar selective sweep regions. Average genetic differences measured by [Formula: see text] are low between gradients, but XP-EHH signals are the strongest between agroecologies. Genes in the calcium signalling pathway, those associated with the hypoxia-inducible factor (HIF) transcription factors, and sports performance (GALNTL6) are under selection in high-altitude populations. Our study underscores the relevance of landscape genomics as a powerful interdisciplinary approach to dissect adaptive phenotypic and genetic variation in random mating indigenous livestock populations.

Morphometric differentiation of three chicken ecotypes of Ethiopia using multivariate analysis.

Twenty-one morphometric traits were measured on 770 extensively managed indigenous chickens in the western zone of Tigray, comprising 412 hens and 358 cocks in three agro-ecologies. The quantitative traits for male and female chicken ecotypes were separately analyzed using multivariate analysis with SAS 2008. Four and seven principal components accounted for about 74.26% and 69.77% of the total variability in morphometric traits for males and females, respectively. Earlobe length, wingspan, skull length, and shank length werethe most important traits for discriminating among female chicken ecotypes, while wingspan, neck length, earlobe length, spur length, body length, and shank length were the most important discriminatory traits among male chicken ecotypes. The discriminant analysis accurately classified 97.3% of female and 100% of male chicken ecotypes. Cluster analysis revealed the genetic heterogeneity of indigenous chicken populations in both sexes. This finding suggests the presence of morphological variations among the indigenous chicken populations in the different agro-ecological zones, classified as distinct indigenous chicken ecotypes (Lowland, Midland, and Highland). Further DNA-based studies are needed to confirm and complement these morphological variations for effective conservation and the development of sustainable genetic improvement strategies for indigenous chicken populations in the region.

Genomic analysis of Nigerian indigenous chickens reveals their genetic diversity and adaptation to heat-stress.

Indigenous poultry breeds from Africa can survive in harsh tropical environments (such as long arid seasons, excessive rain and humidity, and extreme heat) and are resilient to disease challenges, but they are not productive compared to their commercial counterparts. Their adaptive characteristics are in response to natural selection or to artificial selection for production traits that have left selection signatures in the genome. Identifying these signatures of positive selection can provide insight into the genetic bases of tropical adaptations observed in indigenous poultry and thereby help to develop robust and high-performing breeds for extreme tropical climates. Here, we present the first large-scale whole-genome sequencing analysis of Nigerian indigenous chickens from different agro-climatic conditions, investigating their genetic diversity and adaptation to tropical hot climates (extreme arid and extreme humid conditions). The study shows a large extant genetic diversity but low level of population differentiation. Using different selection signature analyses, several candidate genes for adaptation were detected, especially in relation to thermotolerance and immune response (e.g., cytochrome P450 2B4-like, TSHR, HSF1, CDC37, SFTPB, HIF3A, SLC44A2, and ILF3 genes). These results have important implications for conserving valuable genetic resources and breeding improvement of chickens for thermotolerance.

Genotype by Environment Interactions (G*E) of Chickens Tested in Ethiopia Using Body Weight as a Performance Trait.

Ethiopia is a developing nation that could highly benefit from securing food via improved smallholder poultry farming. To support farmer and breeding decisions regarding which chicken strain to use in which Ethiopian environment, G*E analyses for body weight (BW) of growing male and female chickens were conducted. Research questions were (1) if a G*E is present for BW and (2) which strain performs best in which environment in terms of predicted BW. Analyses were performed using predicted BW at four different ages (90, 120, 150, and 180 days) of five strains (Horro, Koekoek, Kuroiler, Sasso-Rhode Island Red (S-RIR), and Sasso) tested in five Ethiopian regions (Addis Ababa, Amhara, Oromia, South Region, and Tigray) that are part of three Agro-Ecological Zones (AEZ) (cool humid, cool sub-humid, and warm semi-arid). The indigenous Horro strain was used as a control group to compare four other introduced tropically adapted strains. The dataset consisted of 999 female and 989 male farm-average BW measurements. G*E was strongly present (p < 0.001) for all combinations of strain and region analyzed. In line with previous research, Sasso was shown to have the highest predicted BW, especially at an early age, followed by Kuroiler. Horro had the lowest predicted BW at most ages and in most regions, potentially due to its young breeding program. The highest predicted BW were observed in Tigray, Oromia, and Amhara regions, which are in the main part of the cool sub-humid AEZ.

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.

Morpho-biometric characterization of indigenous chicken ecotypes in north-western Ethiopia.

Morphological characterization of Animal Genetic Resources is the first step to documenting diversity and designing breed specific breeding programs. The current study characterized the morpho-biometric variation of indigenous chicken ecotypes prevailing in northwestern Ethiopia. A multi-stage purposive, stratified, and random sampling method was employed to select the study areas and chickens. A total of 1200 adult chickens were sampled and characterized for 12 qualitative and 11 quantitative traits. Univariate and multivariate data analysis methods were employed to analyze the data using SAS and R statistical software. Red plumage colour (33.2%), white and red earlobe colour (73.8%) and yellow shank colour (57.0%) were the most predominant colour trait categories. Sex, agro-ecology, location, and the interaction of sex and location had a highly significant (p<0.001) effect on all body measurements. Shank traits were found to have the highest discriminating power in both sexes. The overall classification rates for the female and male sample populations were 57.47% and 69.97%, respectively. The squared Mahalanobis distances between sites were significant (p<0.001) for both sexes. The longest distance was obtained between North Achefer and Banja (19.25) and between North Achefer and Dembecha (16.80) in female and male chickens, respectively. In female chickens, canonical variates 1 (CAN 1) and 2 (CAN 2) explained 82% of total variation and distinctly separated the sample populations of North Achefer and Jawi from others. In male chickens, 90% of the total variance is explained by CAN1, CAN2, and CAN3, which distinctly separate the sample populations of the North Achefer, Sinan, and Jawi, among others. Using cluster analysis, the indigenous chickens found in the study area could be classified into four ecotypes: ecotype 1 (Banja, Dembecha, and Aneded), ecotype 2 (North Achefer), ecotype 3 (Sinan), and ecotype 4 (Jawi).

Yolk Fatty Acid Content, Lipid Health Indices, and Oxidative Stability in Eggs of Slow-Growing Sasso Chickens Fed on Flaxseed Supplemented with Plant Polyphenol Extracts.

Previous attempts to increase the level of flaxseed in hens' diet for the production of n-3 polyunsaturated fatty acids (n-3 PUFAs)-enriched eggs have been commonly associated with undesirable effects on production efficiency, lipid health indices, and oxidative stability of eggs, requiring adequate research attention. This study investigated the effects of feeding a moderate level of flaxseed (FS) and plant polyphenol extracts (PPEs) on fatty acid content, oxidative stability, and lipid health indices in eggs of slow-growing Sasso T451A laying hens. One hundred and five hens were assigned to five groups (seven replicates of three) and fed on FS (75 g flaxseed and no antioxidants), VE8 (75 g flaxseed and 800 mg vitamin E), TS8 (75 g flaxseed and 800 mg Thymus schimperi), DA8 (75 g flaxseed and 800 mg Dodonaea angustifolia), and CD8 (75 g flaxseed and 800 mg Curcuma domestica) extract per kg diets. The egg yolk content of eicosapentaenoic acid (EPA, C20:5 n-3) in the DA8, TS8, and CD8 diets and docosahexaenoic acid (DHA, C22:6 n-3) in TS8 and CD8 diets significantly (p < 0.05) increased compared with the FS diet. The FS diet significantly increased the malondialdehyde (MDA) content in egg yolks, whereas the TS8 diet decreased it by 67% (p < 0.05). Little difference was observed in yolk fatty acid content between cooked and raw eggs. Production of n-3 PUFA-enriched eggs with favorable lipid health indices was possible through inclusion of PPEs extracted from local plant species grown in Ethiopia and a moderate dose of flaxseed in the diet of laying hens.

Quantifying morphometric and adaptive characteristics of indigenous cattle genetic resources in northwest Ethiopia.

Ethiopia is the gateway of livestock genetic resources to Africa and has a wide range of altitude. It is endowed with huge diverse cattle genetic resources. The aim of this research was to determine the morphometric and potentioally adaptive characteristics of cattle populations. Multi-stage purposive and random sampling methods were employed to select the study areas, households and animals. A total of 1200 adult cattle were sampled and characterized for 14 qualitative and eight morphometric variables. The comparison of marginal means, chi-square tests, canonical discriminant analysis, and clustering analysis were employed using SAS and SPSS statistical software. The sex of the animal, location and agro-ecology were fitted as fixed effects in the model and had highly significant (p<0.001) effects for most body measurements. The chi-square test values of all categorical variables were significantly different (p<0.001) and potentioally adaptive characteristics such as coat colour type, navel flap, and tail length had higher association (> 0.45) values. White with red, light red, black and dark red were the most predominant coat colour types of cattle. The maximum hit rates were recorded in Enebsie and Sinan cattle. From five extracted canonical variate, (can1 and can2) accounted 75.4% and 78.8% in the female and male cattle populations, respectively. The canonical class has separated cattle populations of Sinan from Banja at can1 and Mecha from Sinan populations at can2. The square Mahalanobis distances between sites were significant (p<0.001) and the largest distance was found between Banja and Sinan locations. Cluster analysis result classified the study populations into four major cattle groups. The cumulative analysis results showed that the cattle populations of the study area can be categorized into four breed types as Jawi Sanga, Gojjam Zenga, Banja cattle, and Sinan cattle. However, this morphology based grouping need to be confirmed by molecular data.

Ecological niche modelling as a tool to identify candidate indigenous chicken ecotypes of Tigray (Ethiopia).

The Tigray region is an ancient entry route for the domestic chickens into Africa. The oldest African chicken bones were found in this region at Mezber, a pre-Aksumite rural farming settlement. They were dated to around 800-400 BCE. Since then, the farming communities of the region have integrated chicken into their livelihoods. The region is also recognised for its high chicken-to-human population ratio and diverse and complex geography, ranging from 500 to 4,000 m above sea level (m.a.s.l.). More than 15 agro-ecological zones have been described. Following exotic chicken introductions, the proportion of indigenous chicken is now 70% only in the region. It calls for the characterisation of indigenous Tigrayan chicken ecotypes and their habitats. This study reports an Ecological Niche Modelling using MaxEnt to characterise the habitats of 16 indigenous village chicken populations of Tigray. A total of 34 ecological and landscape variables: climatic (22), soil (eight), vegetation, and land cover (four), were included. We applied Principal Component Analysis correlation, and MaxentVariableSelection procedures to select the most contributing and uncorrelated variables. The selected variables were three climatic (bio5 = maximum temperature of the warmest month, bio8 = mean temperature of the wettest quarter, bio13 = precipitation of the wettest month), three vegetation and land cover (grassland, forest land, and cultivated land proportional areas), and one soil (clay content). Following our analysis, we identified four main chicken agro-ecologies defining four candidates indigenous Tigrayan chicken ecotypes. The study provides baseline information for phenotypic and genetic characterisation as well as conservation interventions of indigenous Tigrayan chickens.

Whole genome sequences of 234 indigenous African chickens from Ethiopia.

Indigenous chickens predominate poultry production in Africa. Although preferred for backyard farming because of their adaptability to harsh tropical environments, these populations suffer from relatively low productivity compared to commercial lines. Genome analyses can unravel the genetic potential of improvement of these birds for both production and resilience traits for the benefit of African poultry farming systems. Here we report whole-genome sequences of 234 indigenous chickens from 24 Ethiopian populations distributed under diverse agro-climatic conditions. The data represents over eight terabytes of paired-end sequences from the Ilumina HiSeqX platform with an average coverage of about 57X. Almost 99% of the sequence reads could be mapped against the chicken reference genome (GRCg6a), confirming the high quality of the data. Variant calling detected around 15 million SNPs, of which about 86% are known variants (i.e., present in public databases), providing further confidence on the data quality. The dataset provides an excellent resource for investigating genetic diversity and local environmental adaptations with important implications for breed improvement and conservation purposes.

In Vitro Antioxidant Activities of Plant Polyphenol Extracts and Their Combined Effect with Flaxseed on Raw and Cooked Breast Muscle Fatty Acid Content, Lipid Health Indices and Oxidative Stability in Slow-Growing Sasso Chickens.

Adding flaxseed was found to decrease oxidative stability in feed and increase the antioxidant needs of chicken. This has also been associated with a decrease in the nutritional value and oxidative stability of meat if sufficient dietary antioxidants are not included. Furthermore, dietary flaxseed has been explored in fast-growing chickens as such studies are limited with slow-growing chickens. Thus, this study aimed to evaluate the effects of feeding plant polyphenol extracts as an antioxidant alongside flaxseed on fatty acid content, oxidative stability, and lipid health indices in breast muscle of slow-growing Sasso T451A dual-purpose chicken. A total of 126 chickens assigned to six groups (seven replicates of three) were fed on NC (control and no antioxidants), FS (75 g flaxseed and no antioxidants), VE8 (75 g flaxseed and 800 mg vitamin E), TS8 (75 g flaxseed and 800 mg Thymus schimperi), DA8 (75 g flaxseed and 800 mg Dodonaea angustifolia) and CD8 (75 g flaxseed and 800 mg Curcuma domestica) extract per kg diet. Feeding on CD8 and VE8 in raw and TS8, CD8 and VE8 diets in cooked breast muscle increased (p < 0.05) the C22:6n − 3 (DHA) and C20:5n − 3 (EPA) contents compared to the FS diet. Feeding FS increased (p < 0.05) the malondialdehyde (MDA) content in breast muscle, whereas TS8 in cooked and raw and CD8 and DA8 diets in raw breast muscle decreased it (p < 0.05). No added benefit was observed in feeding VE8 over plant extracts in terms of improving fatty acid composition and lipid health indices and reducing lipid oxidation in breast meat.

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.

Species and Phenotypic Distribution Models Reveal Population Differentiation in Ethiopian Indigenous Chickens.

Smallholder poultry production dominated by indigenous chickens is an important source of livelihoods for most rural households in Ethiopia. The long history of domestication and the presence of diverse agroecologies in Ethiopia create unique opportunities to study the effect of environmental selective pressures. Species distribution models (SDMs) and Phenotypic distribution models (PDMs) can be applied to investigate the relationship between environmental variation and phenotypic differentiation in wild animals and domestic populations. In the present study we used SDMs and PDMs to detect environmental variables related with habitat suitability and phenotypic differentiation among nondescript Ethiopian indigenous chicken populations. 34 environmental variables (climatic, soil, and vegetation) and 19 quantitative traits were analyzed for 513 adult chickens from 26 populations. To have high variation in the dataset for phenotypic and ecological parameters, animals were sampled from four spatial gradients (each represented by six to seven populations), located in different climatic zones and geographies. Three different ecotypes are proposed based on correlation test between habitat suitability maps and phenotypic clustering of sample populations. These specific ecotypes show phenotypic differentiation, likely in response to environmental selective pressures. Nine environmental variables with the highest contribution to habitat suitability are identified. The relationship between quantitative traits and a few of the environmental variables associated with habitat suitability is non-linear. Our results highlight the benefits of integrating species and phenotypic distribution modeling approaches in characterization of livestock populations, delineation of suitable habitats for specific breeds, and understanding of the relationship between ecological variables and quantitative traits, and underlying evolutionary processes.

Ethiopian indigenous goats offer insights into past and recent demographic dynamics and local adaptation in sub-Saharan African goats.

Knowledge on how adaptive evolution and human socio-cultural and economic interests shaped livestock genomes particularly in sub-Saharan Africa remains limited. Ethiopia is in a geographic region that has been critical in the history of African agriculture with ancient and diverse human ethnicity and bio-climatic conditions. Using 52K genome-wide data analysed in 646 individuals from 13 Ethiopian indigenous goat populations, we observed high levels of genetic variation. Although runs of homozygosity (ROH) were ubiquitous genome-wide, there were clear differences in patterns of ROH length and abundance and in effective population sizes illustrating differences in genome homozygosity, evolutionary history, and management. Phylogenetic analysis incorporating patterns of genetic differentiation and gene flow with ancestry modelling highlighted past and recent intermixing and possible two deep ancient genetic ancestries that could have been brought by humans with the first introduction of goats in Africa. We observed four strong selection signatures that were specific to Arsi-Bale and Nubian goats. These signatures overlapped genomic regions with genes associated with morphological, adaptation, reproduction and production traits due possibly to selection under environmental constraints and/or human preferences. The regions also overlapped uncharacterized genes, calling for a comprehensive annotation of the goat genome. Our results provide insights into mechanisms leading to genome variation and differentiation in sub-Saharan Africa indigenous goats.

Integrated Environmental and Genomic Analysis Reveals the Drivers of Local Adaptation in African Indigenous Chickens.

Breeding for climate resilience is currently an important goal for sustainable livestock production. Local adaptations exhibited by indigenous livestock allow investigating the genetic control of this resilience. Ecological niche modeling (ENM) provides a powerful avenue to identify the main environmental drivers of selection. Here, we applied an integrative approach combining ENM with genome-wide selection signature analyses (XPEHH and Fst) and genotype-environment association (redundancy analysis), with the aim of identifying the genomic signatures of adaptation in African village chickens. By dissecting 34 agro-climatic variables from the ecosystems of 25 Ethiopian village chicken populations, ENM identified six key drivers of environmental challenges: One temperature variable-strongly correlated with elevation, three precipitation variables as proxies for water availability, and two soil/land cover variables as proxies of food availability for foraging chickens. Genome analyses based on whole-genome sequencing (n = 245), identified a few strongly supported genomic regions under selection for environmental challenges related to altitude, temperature, water scarcity, and food availability. These regions harbor several gene clusters including regulatory genes, suggesting a predominantly oligogenic control of environmental adaptation. Few candidate genes detected in relation to heat-stress, indicates likely epigenetic regulation of thermo-tolerance for a domestic species originating from a tropical Asian wild ancestor. These results provide possible explanations for the rapid past adaptation of chickens to diverse African agro-ecologies, while also representing new landmarks for sustainable breeding improvement for climate resilience. We show that the pre-identification of key environmental drivers, followed by genomic investigation, provides a powerful new approach for elucidating adaptation in domestic animals.