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, eightMSTs 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

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

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 fromsouth (Maan, Showbak and Tafeilah) to each other. Populations from themiddle 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 themolecular and population genetics of Awassi sheep fromdifferent regions of Jordan and to utilize the possible findings for future management of genetic conservation under conditions of climate changes and crossbreeding policy

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

DIVERSITY OF INDIGENOUS LAYERS IN COMPARISON WITH EXOTICS IN JORDAN

ABSTRACT Genetic variation of a hundred indigenous layers chicken and its genetic relatedness to twenty exotic layers chickens of each Pakistani chicken and commercial layers were assessed in Jordan using six microsatellite markers. the microsatellite markers showed an average allele number of 5.8 per locus, expected heterozygosity of 55.8% and high polymorphism of 54% in Jordan indigenous chicken. on the other hand, the genetic relatedness between the three breeds, that were originally independent, was described by pairwise genetic distance. the genetic distance was the shortest (0.135) between indigenous chicken and Pakistani chicken, revealing indigenous chicken was more closely related to Pakistani layer chicken than the commercial layers. this result confirmed the historical information about their common origin. long genetic distance (0.205) was showed between indigenous chicken and commercial layers. this might be a result of gene flow by crossing individuals of both sometimes ago. finally, the longest genetic distance (0.288) was found between commercial layers and Pakistani chicken. the overall results are valuable for sustainable genetic conservation program to reserve indigenous Jordan layer chicken for its unique genetic sources

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

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

Extinction probabilities of Hassawi cattle from Saudi Arabia using population viability analysis

The sharp reduction in population size (N) of Hassawi cattle alarmed to estimate the possibility of extinction over a defined future time horizon. Two Hassawi cattle populations were considered for population viability analysis (PVA) in order to provide estimates of extinction probabilities (EPs). The EPs were estimated using Vortex® modeling program. The estimates of 2013 census and records on previous numbers were utilized in PVA models for two separated populations and their meta-population. The results of EPs and evolutionary growth rate were simulated for past and future, utilizing their demographic parameters and catastrophic events; like, feed scarcity, low production capability, crossbreeding and epidemic diseases. The simulated model concludes that the Hassawi cattle is facing extinction as the population size (N) and effective population size (Ne) were much less than those recommended to save endangerment. Therefore, the mimicked dynamic history of real Hassawi cattle population suggests that the assumed model was reasonable to mimic the likely fate faced by the Hassawi cattle population in the past. The future model concluded that the Hassawi cattle are indeed facing extinction after 21 years if assumptions of past model existed because both N and Ne were much lower than those recommended for escaping endangerment. Furthermore, PE increased with availability and severity of catastrophe events. The results of PVA and PEs should be considered into account to draw inferences about the expected future the Hassawi cattle dynamic because they are accurate data than those might extract from historical records. It is recommended that PVA may be considered in developing conservation strategy for the Hassawi cattle in order to conserve their valuable genetic resources, while the climate change is alarming

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

Influence of stocking density on welfare indices of broilers

The current study was conducted to identify the influence of short-term (five days) high stocking density (SD) on broilers' welfare by assessing several thermophysiological parameters in 32 birds of 43 days of age Ross male broiler chickens. Based on broiler's body weight, broilers were randomly allotted into two SD rates; control (26.5 kg/m2) or high (45.0 kg/m2). It appears evident that placing broilers at high SD as 45.0 kg/m2 had manifested noticeable impacts on their thermophysiological responses. This conclusion was demonstrated by the existence of results of the current study showed a major displacements in broilers' homeothermic status, high SD broilers experienced pronounced elevations of their body temperatures as well as head, body and shank surface temperatures over the control SD broilers. Additionally, this was further emphasized by the noticeable displacements of body internal, external and total thermal gradients as well as heat loss index of high SD broilers compared to the control broilers. Based on the presented evidences, short-term high SD markedly increased broilers stress and jeopardize their welfare. Measuring broilers' thermophysiological responses under different rates of SD can be adapted to assess their welfare. </p