Application of multivariate discriminant analysis for differentiation between Saudi sheep (Ovis aries) breeds based on physical and histochemical meat characteristics.

Background and Aim: The multivariate discriminant (MVD) analysis was a successful statistical tool with a discriminatory capacity for tracing sheep breeds based on meat characteristics. Thus, this study aimed to identify three Saudi sheep breeds based on the physical and histochemical aspects of meat using MVD analysis. Materials and Methods: Eight male lambs from each breed, Najdi, Neami, and Harri, were selected randomly at 90 days of age and allocated into three groups for breeding in a completely randomized design. The feeding and rearing management were similar for an experimental period of 90 days. The experimental diet consisted of a concentrated mixture with identical amounts of calories and nitrogen. Fifty-one meat characteristics were measured in the preliminary MVD, representing hot and cold carcass weight, meat cuts and quality measures, body component weights, fat deposit weights, and histochemical characteristics. Results: Out of the total meat characteristics measured, only 19 characteristics had significant discriminant power. The most powerful characteristics were temperature, empty intestinal weight, pH24, external carcass length, heart weight, and L1, based on partial R-square and Wilks' lambda values. The phenotypic associations between the characteristics had strong associations. The obtained principal components efficiently classified the eight individuals of each breed into distinct groups using robust discriminant characteristics. Conclusion: This method allowed us to determine the breed of sheep carcasses and cuts by considering the physical characteristics of the meat. Therefore, butchers and consumers should use scientific techniques for assigning carcasses and meat to their sheep breed after slaughtering.

Power of phenotypes in discriminating Awassi sheep to pure strains and from other breeds.

The phenotypic description is the oldest method for animal taxonomic studies. In this study, we report phenotypic traits of discriminant power to assign sheep individuals into Awassi breed or other exotic breeds found in Jordan. Twenty-two and 19 phenotype traits for ewes and rams, respectively, were utilized using multivariate and discriminant analyses. Seven traits, out of them, for ewes and five for rams were qualitative traits: body color, nose shape, horn presence, ear shape, wattles presence, udder shape, and teat placement. The other 15 traits were quantitative traits: body weight, head width, head length, chest depth, chest girth, shoulder width, withers height, foreleg height, shin circumference, body length, rump width, rump length, rump height, rear leg height, and udder height. The traits were taken on 1697 and 652 adult ewes and rams of different breeds, respectively. The breeds were predefined as Awassi and three exotic breeds: Chios, Assaf, and improved Awassi sheep. The results indicated a significant relationship of the 21 and 16 studied traits in assigning and discriminating individual's sheep into their correct breed. The analysis revealed the clustering of the three strains of Awassi sheep in Jordan as the Baladi, the Naemi, and the Saqri. The genetic distances have also confirmed the findings. However, the potential of gene flow between Awassi strains and the exotic breed was reported. The phenotypic traits with discriminant power would be utilized in a guideline for sheep taxonomy in general and for Awassi sheep in particular.

The wild species genome ancestry of domestic chickens.

BACKGROUND: Hybridisation and introgression play key roles in the evolutionary history of animal species. They are commonly observed within several orders in wild birds. The domestic chicken Gallus gallus domesticus is the most common livestock species. More than 65 billion chickens are raised annually to produce meat and 80 million metric tons of egg for global human consumption by the commercial sector. Unravelling the origin of its genetic diversity has major application for sustainable breeding improvement programmes. RESULTS: In this study, we report genome-wide analyses for signatures of introgression between indigenous domestic village chicken and the four wild Gallus species. We first assess the genome-wide phylogeny and divergence time across the genus Gallus. Genome-wide sequence divergence analysis supports a sister relationship between the Grey junglefowl G. sonneratii and Ceylon junglefowl G. lafayettii. Both species form a clade that is sister to the Red junglefowl G. gallus, with the Green junglefowl G. varius the most ancient lineage within the genus. We reveal extensive bidirectional introgression between the Grey junglefowl and the domestic chicken and to a much lesser extent with the Ceylon junglefowl. We identify a single case of Green junglefowl introgression. These introgressed regions include genes with biological functions related to development and immune system. CONCLUSIONS: Our study shows that while the Red junglefowl is the main ancestral species, introgressive hybridisation episodes have impacted the genome and contributed to the diversity of the domestic chicken, although likely at different levels across its geographic range.

Renal efficiency underlies adaptive heterothermy of heat-stressed hypohydrated goats.

We investigated the thermotolerance of the F1 progeny (Black Bedouin × Damascus crossbreed) to summer conditions alongside that of two pure breeds. Male goats (n = 7 per breed) were used to conduct a summertime 28-day trial along with hypohydration. The animals were fitted with miniscule thermologgers, intraperitoneally and subcutaneously, to measure core (Tc) and peripheral (Tp) body temperatures (BT), respectively. All goats were kept under shaded housing for a 7-day basal period before being switched to unshaded pens for the next 21 days. During the first 14 days, animals had free access to water. However, during the third 7-day period, access to water was time-restricted (4 h/day). Finally, it was restricted to 40% of the third week's average daily intake over the last 7 days. Exposure to the unshaded conditions resulted in pronounced heat stress in all animals, as reflected by 0.42 and 1.44 °C rises for Tc and Tp, respectively. The F1 goats displayed a clear heterothermic adaptive response, especially after the water restriction bouts' initiation. Interestingly, the F1 goats displayed higher ratios of renal relative medullary thickness (77.7, 73.3, and 72.6 ± 1.1%) along with higher circulating concentrations of antidiuretic hormone (44.6, 31.6, and 11.6 ± 3.7 ng/mL), respectively, which suggested an improved water metabolism.

Microsatellite-Based Genetic Structure and Diversity of Local Arabian Sheep Breeds.

The genetic diversity of the sheep breeds in the Arab countries might be considered to be a mirror of the ecology of the region. In this study, the genetic structure and diversity of sheep breeds from Saudi Arabia (Harri, Najdi, Naemi, Arb, and Rufidi) and Awassi sheep from Jordan as an out-group were investigated using 19 microsatellites. All the breeds had high intra-population genetic diversity expressed as allelic number (7.33) and richness (2.9) and, expected heterozygosity (0.77). Structure analysis revealed three main gene pools underlying the ancestral genetic diversity of the study populations. The first pool had Harri, Najdi, and Rufidi breeds; the second had Naemi and Awassi breeds, and the third had the Arb breed which was significantly differentiated from the other breeds. Factorial correspondence analysis lent further support to the presence of the three gene pools. Although the outgroup Awassi sheep was more clearly differentiated, it still genetically close to Naemi sheep. The differentiation of the Arb breed could have been resulted from geographic and reproductive isolation. On the other hand, the genetic structure of the other two gene pools could be the result of the past and recent gene flow between individuals reared in the region known to be the center for animal husbandry and trading until the current time.

Whole-Genome Resequencing of Red Junglefowl and Indigenous Village Chicken Reveal New Insights on the Genome Dynamics of the Species.

The red junglefowl Gallus gallus is the main progenitor of domestic chicken, the commonest livestock species, outnumbering humans by an approximate ratio of six to one. The genetic control for production traits have been well studied in commercial chicken, but the selection pressures underlying unique adaptation and production to local environments remain largely unknown in indigenous village chicken. Likewise, the genome regions under positive selection in the wild red junglefowl remain untapped. Here, using the pool heterozygosity approach, we analyzed indigenous village chicken populations from Ethiopia, Saudi Arabia, and Sri Lanka, alongside six red junglefowl, for signatures of positive selection across the autosomes. Two red junglefowl candidate selected regions were shared with all domestic chicken populations. Four candidates sweep regions, unique to and shared among all indigenous domestic chicken, were detected. Only one region includes annotated genes (TSHR and GTF2A1). Candidate regions that were unique to each domestic chicken population with functions relating to adaptation to temperature gradient, production, reproduction and immunity were identified. Our results provide new insights on the consequence of the selection pressures that followed domestication on the genome landscape of the domestic village chicken.

Genetic origin of goat populations in Oman revealed by mitochondrial DNA analysis.

The Sultanate of Oman has a complex mosaic of livestock species and production systems, but the genetic diversity, demographic history or origins of these Omani animals has not been expensively studied. Goats might constitute one of the most abundant and important domestic livestock species since the Neolithic transition. Here, we examined the genetic diversity, origin, population structure and demographic history of Omani goats. Specifically, we analyzed a 525-bp fragment of the first hypervariable region of the mitochondrial DNA (mtDNA) control region from 69 Omani individuals and compared this fragment with 17 mtDNA sequences from Somalia and Yemen as well as 18 wild goat species and 1,198 previously published goat sequences from neighboring countries. The studied goat breeds show substantial diversity. The haplotype and nucleotide diversities of Omani goats were found equal to 0.983 ± 0.006 and 0.0284 ± 0.014, respectively. The phylogenetic analyses allowed us to classify Omani goats into three mtDNA haplogroups (A, B and G): haplogroup A was found to be predominant and widely distributed and accounted for 80% of all samples, and haplogroups B and G exhibited low frequencies. Phylogenetic comparisons with wild goats revealed that five of the native Omani goat populations originate from Capra aegagrus. Furthermore, most comparisons of pairwise population FST values within and between these five Omani goat breeds as well as between Omani goats and nine populations from nearby countries were not significant. These results suggest strong gene flow among goat populations caused by the extensive transport of goats and the frequent movements of human populations in ancient Arabia. The findings improve our understanding of the migration routes of modern goats from their region of domestication into southeastern Arabia and thereby shed light on human migratory and commercial networks during historical times.

Effects of concentration of corn distillers dried grains with solubles and enzyme supplementation on cecal microbiota and performance in broiler chickens.

With the increasing production of ethanol for biofuels, a by-product of corn-based ethanol fermentation, dried distillers grains with solubles (DDGS) is finding its way into the feed of agricultural animals including cattle, pigs, poultry, sheep, goats, aquaculture species and horses. Corn DDGS contains very high levels of non-starch polysaccharides and could be considered a good source of fibre. Despite knowledge of the role of the fibre in modulating intestinal microbiota and consequently influencing health, there is currently little information on the interactions between DDGS and intestinal microbiota. We assessed the changes in the cecal microbiota of broilers feed rations supplemented with DDGS (five concentrations: 0, 6, 12, 18 and 24% w/w) with and without presence of digestive enzymes. DDGS concentration was strongly positively correlated (P = 3.7e-17, r = 0.74) with feed conversion efficiency (FCR), diminishing broiler performance with higher concentrations. Additionally, DDGS concentrations positively correlated with Richness index (P = 1.5e-3, r = 0.5), increasing the number of detectable species in the cecum. Among the most affected genera, Faecalibacterium (P = 0.032, r = -0.34) and Streptococcus (P = 7.9e-3, r = -0.39) were negatively correlated with DDGS, while Turicibacter (P = 2.8e-4, r = 0.52) was positively correlated with the DDGS concentration. Enzymes showed minimal effect on cecal microbiota.

The effect of corn distiller's dried grains with solubles (DDGS) fortified with enzyme on growth performance of broiler.

The objective of the current study was to investigate the effect of corn distiller's dried grains with solubles (DDGS) and enzyme supplementation on growth performance and carcass yield in broiler chickens. The experiment was a 5 × 3 factorial design with 450 broiler chickens and with diets containing five levels of DDGS (0, 6, 12, 18, and 24%) and three levels of the enzymes (no supplementation, Rovabio® enzyme, and Tomoko® enzyme). Five pens with six chicks were fed an experimental diet from 0 to 35 days of age. Diets containing 12, 18, and 24% DDGS decreased performance (P < 0.05) at the start of the trial at 0-10 days. Inclusion of enzyme during 0-10 days improved body weight gain (BWG) and European production efficiency factor (EPEF) (P < 0.05). During the grower (11-24 days) and finisher (25-35 days) periods, chickens which had received 0, 6, or 12% DDGS converted feed to body weight more efficiently (P < 0.05). Enzyme supplementation improved feed conversion ratio (FCR) for the periods (11-24 and 25-35 days, respectively) (P < 0.05). The cumulative performance results (0 to 35 days of age) showed that Tomoko enzyme improved FCR as compared to no enzyme while Rovabio was intermediate (P < 0.05). Chickens which had received 0, 6, or 12% had better FCR (P < 0.05) compared to 18 or 24% DDGS. Chick's performance was depressed at early age when the diet contained 12% DDGS but later, they were able to tolerate higher levels of DDGS. The study indicate that a maximum level of DDGS to use in the starter diets is 6% and it could be increased in the grower and finisher period to 12% and enzyme supplementation to diets containing DDGS can improve FCR and growth performance in broilers.

A survey of mycotoxin contamination and chemical composition of distiller's dried grains with solubles (DDGS) imported from the USA into Saudi Arabia.

Distiller's dried grains with solubles (DDGS) is a source of nutritional feedstuff for poultry farmers and industry. The DDGS is a by-product of ethanol industry and an economical feed source of energy, amino acids, crude fiber, minerals, and vitamins. The use of DDGS as a feed ingredient is a novel idea and little information is available on its dietary composition. Many factors such as the type of plants, locality, year of production, and the conditions during distillation process affect the chemical composition of DDGS. In this paper, the chemical composition and the presence of mycotoxin in DDGS imported from the USA into Saudi Arabia as a feedstuff for poultry have been documented.

The differentiation of camel breeds based on meat measurements using discriminant analysis.

The meat productivity of camel in the tropics is still under investigation for identification of better meat breed or type. Therefore, four one-humped Saudi Arabian (SA) camel breeds, Majaheem, Maghateer, Hamrah, and Safrah were experimented in order to differentiate them from each other based on meat measurements. The measurements were biometrical meat traits measured on six intact males from each breed. The results showed higher values of the Majaheem breed than that obtained for the other breeds except few cases such dressing percentage and rib-eye area. In differentiation analysis, the most discriminating meat variables were myofibrillar protein index, meat color components (L* and a*, b*), and cooking loss. Consequently, the Safrah and the Majaheem breeds presented the largest dissimilarity as evidenced by their multivariate means. The canonical discriminant analysis allowed an additional understanding of the differentiation between breeds. Furthermore, two large clusters, one formed by Hamrah and Maghateer in one group along with Safrah. These classifications may assign each breed into one cluster considering they are better as meat producers. The Majaheem was clustered alone in another cluster that might be a result of being better as milk producers. Nevertheless, the productivity type of the camel breeds of SA needs further morphology and genetic descriptions.

The power of 28 microsatellite markers for parentage testing in sheep

Background In sheep breeding, there are situations where relationships recorded at the farm among pedigrees such as parent-offspring, full-sibs or half-sibs need to be tested. A panel of 28 microsatellite (MST) markers was tested to provide accurate pedigree information and resolve the common problem of significant error in pedigree records in Merino sheep. Three different flocks of Australian Merino sheep were investigated. A private farm flock represents a flock with no record availability. Two other flocks were maintained under good managements of full keeping records and being selected for high and low parasite resistances. Results In the studied panel, eight MSTs provided an average of Polymorphic Information content (PIC) equal to 0.65 or more in order to be sufficient to make an accurate and successful DNA-based parentage analysis. The panel of twenty-eight MST loci was obviously sufficient for providing 100% accurate pedigree and genotyping data. DNA-based pedigree records were constructed and all significant pedigree record errors were eliminated. Conclusions These results were used for further study of population genetic parameters such as recombination and haplotyping which heavily based on pedigree information. Nevertheless MST based parentage testing is still available and affordable in most countries and for each farmer with reasonable cost in comparison with fast growing SNP based parentage technologies.

Analysis of genetic diversity and differentiation of sheep populations in Jordan

Background Genetic diversity of sheep in Jordan was investigated using microsatellite markers (MS). Six ovine and bovine MS located on chromosomes 2 and 6 of sheep genome were genotyped on 294 individual from ten geographical regions. Results The number of alleles per locus (A), the expected heterozygosity (He) and observed heterozygosity (Ho) were measured. Overall A, He and Ho were 12.67, 0.820 and 0.684, respectively. On the other hand, genetic distances undoubtedly revealed the expected degree of differentiation among the studied populations. The finding showed closeness of three populations from south (Maan, Showbak and Tafeilah) to each other. Populations from the middle regions of Jordan (Karak, Madaba, Amman, AzZarqa and Mafraq) were found to be in one cluster. Only two populations of the middle region were an exception: AlSalt and Dead Sea. Finally, sheep populations from Irbid were located in separated cluster. It was clear that the studied predefined populations were subdivided from four populations and would be most probably accounted as ancestral populations. These results indicate that number of population is less than the predefined population as ten based on geographical sampling areas. Conclusions The possible inference might be that geographical location, genetic migration, similar selection forces, and common ancestor account for population admixture and subdivision of Awassi sheep breed in Jordan. Finally, the present study sheds new light on the molecular and population genetics of Awassi sheep from different regions of Jordan and to utilize the possible findings for future management of genetic conservation under conditions of climate changes and crossbreeding policy.

Phylogeny and evolutionary analysis of goat breeds in Jordan based on DNA sequencing.

Phylogeny and evolutionary analyses were performed for Jordan goat breeds based on DNA sequencing. DNA segment of 0.5-kb from sixteen goat individuals of four breeds was sequenced. The DNA sequencing was analyzed by both Arlequin and MEGA softwares. The results showed a quite evolutionary differentiation found within goat breeds between. Furthermore, phylogeny tree was reconstructed providing evidences for a close phylogenetic alliance among breeds. The resulted evolutionary sequencing and phylogeny trees provide evidences that sequencing data were worthy to describe the evolutionary and phylogeny genetics in goats breeds in Jordan. On other hand the data were given scopes for possible sequences of gene(s) and identify polymorphisms, given possibility to identify Caprine genes from other close species genome like cattle. In the future we intend, in order to clearly identify the genetic polymorphisms, to detect further genetic variation and to develop tests particularly suitable for specific interested genes genotyping.