Population Structure and Genomic Characterisation of the Ashanti Dwarf Pig of Ghana.

There is still limited information on the genomic structure and genetic diversity of African pigs. Genetic diversity studies can contribute significantly to the genetic improvement and conservation of African pigs. This study presents a genetic diversity analysis and population structure of pig breeds in Ghana, with a focus on the Ashanti Dwarf pig (ADP), an indigenous pig breed of Ghana. A total of 167 pigs sampled in Ghana and populations consisting of Ashanti Dwarf pigs (n = 106), exotics (mostly European pigs) (n = 11), crosses (between indigenous and exotic breeds) (n = 44), and unknown breeds (nondescript) (n = 6) were genotyped using Porcine SNP60K BeadChip. Moderate heterozygosity levels, ranging from 0.28 for Ashanti Dwarf pigs to 0.31 for exotic pigs (mostly European pigs), were observed. Principal component analysis of the pig populations within Ghana resulted in two distinct clusters of pigs: (i) Northern and (ii) Southern regional clusters. The PCA based on breed also resulted in four clusters: (i) ADPs; (ii) exotics (iii) crossbreeds between ADP and exotics; (iv) unknown breed types. The PCA demonstrated that the clustering was influenced by genetics, geographical location, production systems, and practices. ADMIXTURE-based analysis also showed that the populations within Ghana are admixed. FST analysis revealed SNPs associated with QTLs for traits such as disease resilience and growth among ADP populations within the different regional and ecological zones of Ghana.

Association of Phenotypic Markers of Heat Tolerance with Australian Genomic Estimated Breeding Values and Dairy Cattle Selection Indices.

Dairy cattle predicted by genomic breeding values to be heat tolerant are known to have less milk production decline and lower core body temperature increases in response to elevated temperatures. In a study conducted at the University of Melbourne's Dookie Robotic Dairy Farm during summer, we identified the 20 most heat-susceptible and heat-tolerant cows in a herd of 150 Holstein Friesian lactating cows based on their phenotypic responses (changes in respiration rate, surface body temperature, panting score, and milk production). Hair samples were collected from the tip of the cows' tails following standard genotyping protocols. The results indicated variation in feed saved and HT genomic estimated breeding values (GEBVs) (p ≤ 0.05) across age, indicating a potential for their selection. As expected, the thermotolerant group had higher GEBVs for HT and feed saved but lower values for milk production. In general, younger cows had superior GEBVs for the Balanced Performance Index (BPI) and Australian Selection Index (ASI), whilst older cows were superior in fertility, feed saved (FS), and HT. This study demonstrated highly significant (p ≤ 0.001) negative correlations (-0.28 to -0.74) between HT and GEBVs for current Australian dairy cattle selection indices (BPI, ASI, HWI) and significant (p ≤ 0.05) positive correlations between HT and GEBVs for traits like FS (0.45) and fertility (0.25). Genomic selection for HT will help improve cow efficiency and sustainability of dairy production under hot summer conditions. However, a more extensive study involving more lactating cows across multiple farms is recommended to confirm the associations between the phenotypic predictors of HT and GEBVs.

Assessment of phenotypic diversity within Goliath chickens population in Benin.

Goliath chickens are a new strain of poultry that originated in the department of Zou, commune of Agbangnizoun in the Republic of Benin. The characteristics of this chicken strain have not been well studied. The purpose of this study was to characterize the phenotypic diversity of Goliath chickens in departments of Zou and Couffo. A total of 140 birds made up of 92 females and 48 males were sampled using 18 morphological descriptors. The results showed a wide variation in plumage colour within overall population with the most dominant being black (18.57%), white (17.14%) and red (16.43%). Black (21.74%) and white (20.65%) plumage dominated in females and red in males (35.42%). Coloured beaks and shanks were common in both chicken sexes. Yellow eyes were more common in females (63.04%), while red eyes were the most prevalent in males (43.75%). Comb and wattle colours were red in both sexes. Morphometrically, sexual dimorphism is very marked most of the body measurements with male birds being significantly superior. The average body weight was 3.26 kg in males and 2.78 kg in females. The population was clustered in three morphotypes according to the gradient size. Chickens from Bohicon and Agbangnizoun on the one hand, and those from Zagnanado and Toviklin on the other, formed groups 1 and 2, respectively, while group 3 included individuals from Djidja. 77.96% of observed diversity was due to variation between individuals. Molecular characterization is recommended for a thorough knowledge of the Goliath chicken strain of Benin.

Assessment of the reproductive performances of native sows in Southern Benin.

Native sows contribute to a large extent to food security and poverty alleviation in Benin. However, their reproductive performance particularly under extensive systems is poorly characterized. The objective of this study was to fill this knowledge gap by selecting 284 multiparous sows based on hair color and some reproductive parameters. The results showed that native sows of Southern Benin can be clustered into three groups with group 3 showing the best reproductive performances including highest average litter size (LS, 10.31 piglets), live-born piglets (LBP, 10.31 piglets), number of functional teats (10.94), and shorter average farrowing interval (6 mo). The analysis of sows' performances based on their origin revealed that sows from agro-ecological zone 8 have the highest number of LBP and the lowest age at first mating and first farrowing. The analysis of sows' performances based on the hair color showed that those with black hair have the largest LS and the highest number of LBP. This study showed that Benin's native sows have good reproductive ability with enough variation to develop a sustainable pig industry for a better contribution to food security and wealth creation.

Impact of heat stress on the growth performance and retail meat quality of 2nd cross (Poll Dorset × (Border Leicester × Merino)) and Dorper lambs.

The present study investigated the impact of heat stress and genetics on lamb growth performance and meat quality. Forty-eight Dorper and 2nd cross [Poll Dorset × (Border Leicester × Merino)] lambs (38--42 kg; 4-5 months old) were allocated to either thermoneutral [TN; 18-21 °C, 45-55% relative humidity (RH)], or heat stress (HS; 28 °C-38 °C, 40-60% RH) conditions in a 2 × 2 factorial design for 2 weeks. Compared with 2nd cross, Dorper lambs had a lower respiration rate (RR) and rectal temperature (RT), and exhibited less decline in body weight under HS. 2nd cross lambs showed a higher body weight gain than Dorpers under TN conditions. HS increased a* and chroma of the Longissimus thoracis et lumborum (LTL) from 2nd cross lambs over 10 days of display, but had no impact on Dorper LTL. In conclusion, Dorpers showed higher heat tolerance compared with 2nd cross lambs during the 2 weeks HS.

Effect of slaughter age and post-mortem days on meat quality of longissimus and semimembranosus muscles of Boer goats.

This study investigated the effects of age of animal and days post-mortem (PM) on meat quality of Boer goats. Twenty-four (24) wether Boer goats of two age groups (2YO group: 2 years old and 9MO: 6-9 months, with 12 animals/group) were slaughtered in a commercial processing plant. The pH@Temp18 was estimated to be above 6 in both age groups with higher (P < 0.01) values in 2YO goats. The PM storage for 14 days reduced the shear force in both age groups (P < 0.01). 2YO goat muscles (longissimus and semimembranosus) exhibited higher (P < 0.01) Thiobarbituric acid reactive substance values (TBARS), indicating increased lipid oxidation. Glycogen (P < 0.01) and lactate content (20 min post-slaughter) in longissimus of 9MO were lower compared to 2YO, and total muscle glycogen concentration was lower (P < 0.01) in both age groups below the threshold levels. Hence, as hypothesized, age and days PM proved to play crucial roles on Boer meat quality.

Heat Stress Impacts on Lactating Cows Grazing Australian Summer Pastures on an Automatic Robotic Dairy.

The objective of this study was to measure the impacts of summer heat events on physiological parameters (body temperature, respiratory rate and panting scores), grazing behaviour and production parameters of lactating Holstein Friesian cows managed on an Automated Robotic Dairy during Australian summer. The severity of heat stress was measured using Temperature-Humidity Index (THI) and impacts of different THIs-low (≤72), moderate (73-82) and high (≥83)-on physiological responses and production performance were measured. There was a highly significant (p ≤ 0.01) effect of THI on respiratory rate (66.7, 84.7 and 109.1/min), panting scores (1.4, 1.9 and 2.3) and average body temperature of cows (38.4, 39.4 and 41.5 °C), which increased as THI increased from low to moderate to high over the summer. Average milk production parameters were also significantly (p ≤ 0.01) affected by THI, such that daily milk production dropped by 14% from low to high THI, milk temperature and fat% increased by 3%, whilst protein% increased by 2%. The lactation stage of cow had no significant effect on physiological parameters but affected (p ≤ 0.05) average daily milk yield and milk solids. Highly significant (p ≤ 0.01) positive correlations were obtained between THI and milk temperature, fat% and protein% whilst the reverse was observed between THI and milk yield, feed intake and rumination time. Under moderate and high THI, most cows sought shade, spent more time around watering points and showed signs of distress (excessive salivation and open mouth panting). In view of the expected future increase in the frequency and severity of heat events, additional strategies including selection and breeding for thermotolerance and dietary interventions to improve resilience of cows need to be pursued.

Comparative Assessment of Thermotolerance in Dorper and Second-Cross (Poll Dorset/Merino × Border Leicester) Lambs.

The objective of this study was to compare the thermotolerance of second-cross (SC; Poll Dorset × Merino × Border Leicester) and Dorper lambs. Dorper and SC lambs (4-5 months of age) were subjected to cyclic heat stress (HS) (28-40 °C). The temperature was increased to 38-40 °C between 800 and 1700 h daily and maintained at 28 °C for the remainder of the day (30-60% relative humidity (RH)) in climatic chambers for 2 weeks (n = 12/group), with controls maintained in a thermoneutral (TN) (18-21 °C, 40-50% RH) environment (n = 12/group). Basal respiration rate (RR), rectal temperature (RT) and skin temperature (ST) were higher (p < 0.01) in SC lambs than in Dorpers. HS increased RR, RT and ST (p < 0.01) in both genotypes, but the levels reached during HS were lower (p < 0.01) in Dorpers. HS increased (p < 0.01) water intake to a greater extent in SC lambs, while feed intake was reduced (p < 0.05) by HS in SC lambs but not in Dorpers. HS increased (p < 0.01) blood urea nitrogen and creatinine in SC lambs only. Plasma non-esterified fatty acid concentrations were reduced (p < 0.05) by HS in SC lambs but increased (p < 0.05) in Dorpers. There was no effect of HS on pO2, cHCO3- and cSO2, but higher (p < 0.01) blood pH and lower (p < 0.01) pCO2 were recorded under HS in both genotypes. Blood electrolytes and base excess were reduced (p < 0.01) under HS, while a genotype difference (p < 0.05) was only observed in blood K+ and hemoglobin concentrations. Basal plasma prolactin concentrations were lower (p < 0.01) in Dorpers but were elevated at a similar level during HS (p < 0.01) in both genotypes. Dorper lambs are more resilient to HS than SC lambs. Future research should focus on confirming whether the better heat tolerance of Dorpers is translated to better returns in terms of growth performance and carcass traits over the summer months.

Genetic Selection for Thermotolerance in Ruminants.

Variations in climatic variables (temperature, humidity and solar radiation) negatively impact livestock growth, reproduction, and production. Heat stress, for instance, is a source of huge financial loss to livestock production globally. There have been significant advances in physical modifications of animal environment and nutritional interventions as tools of heat stress mitigation. Unfortunately, these are short-term solutions and may be unsustainable, costly, and not applicable to all production systems. Accordingly, there is a need for innovative, practical, and sustainable approaches to overcome the challenges posed by global warming and climate change-induced heat stress. This review highlights attempts to genetically select and breed ruminants for thermotolerance and thereby sustain production in the face of changing climates. One effective way is to incorporate sustainable heat abatement strategies in ruminant production. Improved knowledge of the physiology of ruminant acclimation to harsh environments, the opportunities and tools available for selecting and breeding thermotolerant ruminants, and the matching of animals to appropriate environments should help to minimise the effect of heat stress on sustainable animal genetic resource growth, production, and reproduction to ensure protein food security.

Phenotypic characterization of beef cattle breeds and production practices in Liberia.

Phenotypic characterization of animal genetic resources (AnGR) involves identification of distinct breed populations, describing their external and production characteristics in a given environment and management, and taking into account the social and economic factors that affect them. A survey involving 346 livestock farmers was conducted in the 15 counties of Liberia to collect data on production practices and phenotypic characteristics of beef cattle. A pre-tested structured questionnaire, focus group discussions, and in-depth interviews were utilized in data collection. Phenotypic descriptors were measured using a measuring tape and weighing scale. The purpose for keeping beef cattle, preferred cattle traits, and challenges of beef cattle farmers were also assessed. Liberia's beef cattle are predominantly of Ndama (50%), Muturu (38%), and Zebu (11%) breeds. Beef cattle are mainly kept on free range with little investment in housing, feeding, and veterinary care. Beef cattle are raised mainly for income generation, with high cost and low availability of feed (32%), insufficient housing (25%), diseases (21%), and high costs of veterinary medicines (12%) being the main challenges faced by the farmers. Liberian beef cattle were characterized as being docile (53%) or moderate (33%) in temperament, with solid/uniform coat color pattern (61%), black coat color (26%), and non-pigmented skin (84%). The animals had mainly erect or lateral ears, straight back lines, and are sloped rumps. Disease (54%) and drought tolerance (30%) were the main adaptive traits reported. The body weight of beef cattle sampled ranged from 213 to 226 kg, the body length from 119 to 122 cm, and the heart girth from 134 to 140 cm. The government of Liberia should improve policies on local AnGR management and support stakeholder institutions to ensure their sustainable use and conservation.

Domesticated animals as hosts of henipaviruses and filoviruses: A systematic review.

Bat-borne viruses carry undeniable risks to the health of human beings and animals, and there is growing recognition of the need for a 'One Health' approach to understand their frequently complex spill-over routes. While domesticated animals can play central roles in major spill-over events of zoonotic bat-borne viruses, for example during the pig-amplified Malaysian Nipah virus outbreak of 1998-1999, the extent of their potential to act as bridging or amplifying species for these viruses has not been characterised systematically. This review aims to compile current knowledge on the role of domesticated animals as hosts of two types of bat-borne viruses, henipaviruses and filoviruses. A systematic literature search of these virus-host interactions in domesticated animals identified 72 relevant studies, which were categorised by year, location, design and type of evidence generated. The review then focusses on Africa as a case study, comparing research efforts in domesticated animals and bats with the distributions of documented human cases. Major gaps remain in our knowledge of the potential ability of domesticated animals to contract or spread these zoonoses. Closing these gaps will be necessary to fully evaluate and mitigate spill-over risks of these viruses, especially with global agricultural intensification.

Origin and phylogenetic status of the local Ashanti Dwarf pig (ADP) of Ghana based on genetic analysis.

BACKGROUND: The Ashanti Dwarf Pig (ADP) of Ghana is an endangered pig breed with hardy and disease resistant traits. Characterisation of animal genetic resources provides relevant data for their conservation and sustainable use for food security and economic development. We investigated the origin and phylogenetic status of the local ADP of Ghana and their crosses with modern commercial breeds based on mtDNA, MC1R, Y-chromosome sequence polymorphisms, and genome-wide SNP genotyping. RESULTS: The study involved 164 local pigs sampled from the three agro-ecological zones of Ghana. Analyses of the mitochondrial D-loop region and Y-chromosome sequences revealed both European and Asian genetic signatures, with differences between the geographical zones. Black coat colour is the most predominant within the breed, with black MC1R alleles of both Asian and European origin. European alleles for spotting are present at a low frequency in the sample set, and may account for the occurrence of spotted piglets in some APD litters. PCA analysis of SNP data revealed a strong location and breed effect on clustering of local Ghanaian pigs. On a global level, Ghanaian local pigs cluster closely with European pigs of commercial origin, but we identified intervals via FST analyses that may elucidate loci for ADP specific traits. CONCLUSIONS: The presence of both European and Asian contributions, with differences between geographical zones probably reflects trading and colonial influences. Understanding the effects of admixture on important adaptive and economic traits of the ADP and other local breeds in Africa is critical for developing sustainable conservation programmes to prevent the decline of these genetic resources.

Diversity and evolution of the highly polymorphic tandem repeat LEI0258 in the chicken MHC-B region.

The chicken major histocompatibility complex (MHC) is located on the microchromosome 16 and is described as the most variable region in the genome. The genes of the MHC play a central role in the immune system. Particularly, genes encoding proteins involved in the antigen presentation to T cells. Therefore, describing the genetic polymorphism of this region is crucial in understanding host-pathogen interactions. The tandem repeat LEI0258 is located within the core area of the B region of the chicken MHC (MHC-B region) and its genotypes correlate with serology. This marker was used to provide a picture of the worldwide diversity of the chicken MHC-B region and to categorize chicken MHC haplotypes. More than 1,600 animals from 80 different populations or lines of chickens from Africa, Asia, and Europe, including wild fowl species, were genotyped at the LEI0258 locus. Fifty novel alleles were described after sequencing. The resulting 79 alleles were classified into 12 clusters, based on the SNPs and indels found within the sequences flanking the repeats. Furthermore, hypotheses were formulated on the evolutionary dynamics of the region. This study constitutes the largest variability report for the chicken MHC and establishes a framework for future diversity or association studies.

Gene diversity, agroecological structure and introgression patterns among village chicken populations across North, West and Central Africa.

BACKGROUND: Chickens represent an important animal genetic resource for improving farmers' income in Africa. The present study provides a comparative analysis of the genetic diversity of village chickens across a subset of African countries. Four hundred seventy-two chickens were sampled in 23 administrative provinces across Cameroon, Benin, Ghana, Côte d'Ivoire, and Morocco. Geographical coordinates were recorded to analyze the relationships between geographic distribution and genetic diversity. Molecular characterization was performed with a set of 22 microsatellite markers. Five commercial lines, broilers and layers, were also genotyped to investigate potential gene flow. A genetic diversity analysis was conducted both within and between populations. RESULTS: High heterozygosity levels, ranging from 0.51 to 0.67, were reported for all local populations, corresponding to the values usually found in scavenging populations worldwide. Allelic richness varied from 2.04 for a commercial line to 4.84 for one population from Côte d'Ivoire. Evidence of gene flow between commercial and local populations was observed in Morocco and in Cameroon, which could be related to long-term improvement programs with the distribution of crossbred chicks. The impact of such introgressions seemed rather limited, probably because of poor adaptation of exotic birds to village conditions, and because of the consumers' preference for local chickens. No such gene flow was observed in Benin, Ghana, and Côte d'Ivoire, where improvement programs are also less developed. The clustering approach revealed an interesting similarity between local populations found in regions sharing high levels of precipitation, from Cameroon to Côte d'Ivoire. Restricting the study to Benin, Ghana, and Côte d'Ivoire, did not result in a typical breed structure but a south-west to north-east gradient was observed. Three genetically differentiated areas (P<0.01) were identified, matching with Major Farming Systems (namely Tree Crop, Cereal-Root Crop, and Root Crop) described by the FAO. CONCLUSIONS: Local chickens form a highly variable gene pool constituting a valuable resource for human populations. Climatic conditions, farming systems, and cultural practices may influence the genetic diversity of village chickens in Africa. A higher density of markers would be needed to identify more precisely the relative importance of these factors.

Age, genotype and sex effects on growth performance of local chickens kept under improved management in Ghana.

Characterisation of animal genetic resources has been recognised globally as an important step towards their sustainable use. Body weight data of local chickens (213 forest and 160 savannah chickens) and 183 French free-ranging SASSO T44 chickens kept under improved management were collected from hatch to 40 weeks of age and analysed to determine the effects of age, genotype and sex on their growth performance. At all ages, SASSO T44 chickens had significantly (P<0.05) higher weights (2.6-3.2 kg at 28 weeks) than the local chickens (1.2-1.7 kg at 28 weeks). The rate of growth at the earlier ages in the local genotypes (5.57-7.80 g/day) was lower than the range of 13.81-15.42 in SASSO T44 chickens. Except at hatch, savannah chickens were significantly heavier (P<0.05) than the forest chickens at all ages. Male chickens had significantly (P<0.05) superior growth rates than females across all genotypes except from the 20th to the 28th week. Growth trends in both sexes depicted linear increase in body weights; however, the rate of increase in body weights was higher in males as compared to females, thus showing clear sexual dimorphism. There were no significant (P>0.05) differences in the growth rates of SASSO T44 chickens and local genotypes at the later ages (20-28 weeks). Local chickens from the savannah zone had better growth rate than forest chickens. The significant effect of ecozone on the growth potential of local chickens is an indication that their productive potential could be improved through interventions in the environment such as provision of feed and some veterinary care.

Characterisation of local Ghanaian chickens: growth performance evaluation based on Richards growth model and genetic size scaling.

The Richards growth model was fitted to body weight-age data of local and SASSO T44 chickens to describe their growth performance. Males had higher (P < 0.05) asymptotic mature weights than females. Within the local chicken population, birds from the savannah zone had higher (P < 0.05) asymptotic mature weights compared to forest chicken which ironically had higher body weights at hatch. Male local chicken had lower maturing rates compared to the females. Female local chicken were superior to SASSO T44 females in terms of maturing rate. On the average, local chickens took relatively longer time (78.4-83.3 days) to reach the point of inflection than the SASSO T44 population (74.2-79.8 days). However, there were no significant differences (P > 0.05) in the age at inflection among local chicken populations. The shape parameter for SASSO T44 chicken (0.053-0.370) and maturation rate for local chicken (0.177-0.198) were the most critical parameters. Scaling the body weights into degree of maturity highlighted the degree to which genotypes matured over time. Female chickens had the highest (P < 0.05) degree of maturity at all ages. The local chicken populations were also metabolically older than SASSO T44 chickens. Results of this study provide an opportunity to develop breeding strategies for local chicken by modifying either management practices or their genetic makeup to positively affect their growth and productivity.

Genetic diversity of Forest and Savannah chicken populations of Ghana as estimated by microsatellite markers.

The characterization of indigenous animal genetic resources is a requisite step in providing needed information for the conservation of useful genotypes against future needs. Thus, in this study, 22 microsatellite markers were used to genotype 114 local chickens from the Forest (n = 59) and Savannah (n = 55) eco-zones of Ghana and the results compared to those of the ancestral red junglefowl (n = 15) and two European commercial chicken populations--a broiler (n = 25) and white leghorn (n = 25). A total of 171 alleles were observed, with an average of 7.8 alleles per locus. The local Ghanaian chickens showed higher diversity in terms of the observed number of alleles per locus (6.6) and observed heterozygosity (0.568) compared with the combined control populations (6.0 and 0.458, respectively). However, Wright's F-statistics revealed negligible genetic differentiation (F(ST)) in local Ghanaian chicken populations. In addition, 65% of the Savannah chickens were inferred to be more likely from the Forest, suggesting a south-north dispersal of chickens from their probable original location in the Forest zone to the Savannah areas. It is concluded that the Forest and Savannah chickens of Ghana are a single, randomly mating unselected population, characterized by high genetic diversity and constitute a valuable resource for conservation and improvement.