High Levels of Genetic Variation in MHC-Linked Microsatellite Markers from Native Chicken Breeds

The major histocompatibility complex (MHC) is a highly polymorphic gene region that regulates cellular communication in all specific immune responses. In this study, we investigated 11 microsatellite (MS) markers in the MHC-B region of chicken populations from four countries: Sri Lanka, Bangladesh, South Korea, and Nigeria. The MS markers were divided into two sets. Set 1 included five novel MS markers, which we assessed using 192 samples from 21 populations. Set 2 included six previously reported markers, which we assessed using 881 samples from 29 populations. The Set 1 MS markers had lower polymorphism (polymorphic information content (PIC) < 0.5) than the Set 2 markers (PIC = 0.4–0.9). In all populations, the LEI0258 marker was the most polymorphic, with a total of 38 alleles (PIC = 0.912, expected heterozygosity (He) = 0.918). Local populations from Sri Lanka, Bangladesh, and Nigeria had higher allele diversity and more haplotypes for Set 2 MS markers than Korean and commercial populations. The Sri Lankan Karuwalagaswewa village population had the highest MHC diversity (mean allele number = 8.17, He = 0.657), whereas the white leghorn population had the lowest (mean allele number = 2.33, He = 0.342). A total of 409 haplotypes (89 shared and 320 unique), with a range of 4 (Rhode Island red) to 46 (Karuwalagaswewa village (TA)), were identified. Among the shared haplotypes, the B21-like haplotype was identified in 15 populations. The genetic relationship observed in a neighbour-joining tree based on the DA distance agreed with the breeding histories and geographic separations. The results indicated high MHC diversity in the local chicken populations. The difference in the allelic pattern among populations presumably reflects the effects of different genotypes, environments, geographic variation, and breeding policies in each country. The selection of MHC allele in domestic poultry can vary due to intensification of poultry production. Preserved MHC diversity in local chicken provides a great opportunity for future studies that address the relationships between MHC polymorphisms and differential immune responses.

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Comparison of two air sampling methods to monitor operating room air quality and assessment of air quality in two operating rooms with different ventilation systems in the national hospital of Sri Lanka

International Journal of Infection Control ◽

10.3396/ijic.v12i3.017.16 ◽

2016 ◽

Vol 12 (3) ◽

Cited By ~ 1

Author(s):

Tshokey Tshokey ◽

Pranitha Somaratne ◽

Suneth Agampodi

Keyword(s):

Air Quality ◽

Sri Lanka ◽

Operating Room ◽

Ventilation System ◽

Surgical Site Infections ◽

National Hospital ◽

Air Contamination ◽

Acceptable Method ◽

The Difference ◽

Laminar Air Flow

Air contamination in the operating room (OR) is an important contributor for surgical site infections. Air quality should be assessed during microbiological commissioning of new ORs and as required thereafter. Despite many modern methods of sampling air, developing countries mostly depended on conventional methods. This was studied in two ORs of the National Hospital of Sri Lanka (NHSL) with different ventilation system; a conventional ventilation (CV) and a laminar air flow (LAF). Both ORs were sampled simultaneously by two different methods, the settle plate and sampler when empty and during use for a defined time period. Laboratory work was done in the Medical Research Institute. The two methods of sampling showed moderate but highly significant correlation. The OR with CV was significantly more contaminated than LAF when empty as well as during use by both methods. Overall, the difference in contamination was more significant when sampled by the sampler. Differences in contamination in empty and in-use ORs were significant in both ORs, but significance is less in LAF rooms. The consistent and significant correlation between settle plate and sampler showed that the settle plate is an acceptable method. The LAF theatre showed less contamination while empty and during use as expected. Air contamination differences were more significant when sampled with sampler indicating that it is a more sensitive method. Both CV and LAF ORs of the NHSL did not meet the contamination standards for empty theatres but met the standards for in-use indicating that the theatre etiquette was acceptable.

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Rhode Island Red Poultry Production and Management in Halaba Special Woreda, Southern Ethiopia

10.22192/ijarbs.2017.04.12.023 ◽

2017 ◽

Vol 4 (12) ◽

pp. 219-225

Author(s):

Abdulwahab Temame Hussen ◽

◽

Abera Anja ◽

Keyword(s):

Rhode Island ◽

Southern Ethiopia ◽

Poultry Production

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High Genetic Diversity but Absence of Population Structure in Local Chickens of Sri Lanka Inferred by Microsatellite Markers

Frontiers in Genetics ◽

10.3389/fgene.2021.723706 ◽

2021 ◽

Vol 12 ◽

Author(s):

Amali Malshani Samaraweera ◽

Ranga Liyanage ◽

Mohamed Nawaz Ibrahim ◽

Ally Mwai Okeyo ◽

Jianlin Han ◽

...

Keyword(s):

Genetic Diversity ◽

Sri Lanka ◽

Microsatellite Markers ◽

Allelic Diversity ◽

Genetic Distances ◽

Population Substructure ◽

High Genetic Diversity ◽

Naked Neck ◽

Local Chicken ◽

Local Chickens

Local chicken populations belonging to five villages in two geographically separated provinces of Sri Lanka were analyzed using 20 microsatellite markers to determine the genetic diversity of local chickens. Population genetic parameters were estimated separately for five populations based on geographic locations and for eight populations based on phenotypes, such as naked neck, long legged, crested or crown, frizzle feathered, Giriraj, commercial layer, crossbreds, and non-descript chicken. The analysis revealed that there was a high genetic diversity among local chickens with high number of unique alleles, mean number of alleles per locus (MNA), and total number of alleles per locus per population. A total of 185 microsatellite alleles were detected in 192 samples, indicating a high allelic diversity. The MNA ranged from 8.10 (non-descript village chicken) to 3.50 (Giriraj) among phenotypes and from 7.30 (Tabbowa) to 6.50 (Labunoruwa) among village populations. In phenotypic groups, positive inbreeding coefficient (FIS) values indicated the existence of population substructure with evidence of inbreeding. In commercial layers, a high expected heterozygosity He = 0.640 ± 0.042) and a negative FIS were observed. The positive FIS and high He estimates observed in village populations were due to the heterogeneity of samples, owing to free mating facilitated by communal feeding patterns. Highly admixed nature of phenotypes was explained as a result of rearing many phenotypes by households (58%) and interactions of chickens among neighboring households (53%). A weak substructure was evident due to the mating system, which disregarded the phenotypes. Based on genetic distances, crown chickens had the highest distance to other phenotypes, while the highest similarity was observed between non-descript village chickens and naked neck birds. The finding confirms the genetic wealth conserved within the populations as a result of the breeding system commonly practiced by chicken owners. Thus, the existing local chicken populations should be considered as a harbor of gene pool, which can be readily utilized in developing locally adapted and improved chicken breeds in the future.

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Investigation of Major Ecto-Parasite Affecting Backyard Chicken in Bishoftu Town, Ethiopia

10.47363/jmhc/2021(3)143 ◽

2019 ◽

pp. 1-9

Author(s):

Wangelu Kebede ◽

Keyword(s):

Egg Production ◽

Age Groups ◽

Single Species ◽

Poultry Production ◽

Poultry Products ◽

Exotic Breed ◽

The Difference ◽

Young Chicken ◽

Pathogenic Agents ◽

And Control

Backyard poultry production are considered as sources of meat and egg production. However, Parasites are among the main pathogenic agents, threatening the health of poultry and poultry products. The current study was conducted to investigate the prevalence of ectoparasite of poultry managed under backyard system started from November 2019 to April 2020 in Bishoftu town, surroundings of four kebeles; Babogaya, Danbi, 01kebele and 05 kebele in Oromia region South east of Finfinnee. 384 chickens of different age groups, both sexes and breeds were examined. Overall, 228/384 (59.4%) of chickens were infested with species of ectoparasites that mainly grouped into lice 141(36.7%), flea 79 (20.6%), and mite 8(2.1%). The prevalence of ectoparasite infection was 56(14.6%), 51(13.3%), 58(15.1%) and 63(16.4)% in Bishoftu town, Babogaya, Danbi, 01kebele and 05 kebele respectively, the difference in the prevalence of the parasites among difference kebeles were not statistically significant (P>0.05). The prevalence of ectoparasites infestation was higher in male 128(33.33%) chickens than females 100(26.04%) and higher in adult 150 (39.1%) than young chicken 78 (20.3%), high in local breeds 129(33.6%) than exotic breed 99 (25.8%). Seven species were identified with their attachments site, namely; menacanthus stremineus(13.3%) was found on skin, menopon gallinae(12.5%) was found on skin, thigh, feather and breast, goniodes gigas(5.5%) was found on skin and body feather, gonicotes gallinae (2.9%) was found on feather, lipeurus caponus(2.6%) was found on wing, skin, tail feather and a single species of flea(Echidnophaga gallinacae) 20.6% was found on eye, comb and wattle. while a single species of mite (ornithonyssus sylviarum) 2.1% was found on base of feather particularly, the vent area. In conclusion, infestation of chicken with ectoparasites was important constraint in poultry production sector. Associated with lack of attention with respect to hygienic system, treatment and control practices. Based on the results it could be suggested that, good management, biosecurity and the education of farmers could be a vital measure to keep free from ectoparasites and improve the productivity of the chicken.

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Molecular characterization of wheat (Triticum aestivum L.) genotypes through SSR markers

Bangladesh Journal of Agricultural Research ◽

10.3329/bjar.v37i3.12082 ◽

2012 ◽

Vol 37 (3) ◽

pp. 389-398 ◽

Cited By ~ 3

Author(s):

S Islam ◽

MS Haque ◽

RM Emon ◽

MM Islam ◽

SN Begum

Keyword(s):

Genetic Diversity ◽

Triticum Aestivum ◽

Genetic Distance ◽

Microsatellite Markers ◽

Gene Diversity ◽

Polymorphic Information Content ◽

Allelic Diversity ◽

Triticum Aestivum L ◽

Allele Number ◽

Average Gene

A study was undertaken to examine the genetic diversity of 12 wheat (Triticum aestivum L.) genotypes, using 4 simple sequence repeats (SSRs). A total of 10 alleles were found. Allele number per locus ranged from 2 to 4 with an average of 2.5. The polymorphic information content (PIC) values ranged from 0.2755 to 0.5411 with an average of 0.3839. The average gene diversity over all SSR loci for the 12 wheat genotypes was 0.4688, ranging from 0.3299 to 0.6042. Cluster analysis based on microsatellite allelic diversity discriminated the varieties into different clusters. Genetic diversity was the highest between variety Gourab and Akbar as well as Gourab and BAW-1064, showing a genetic distance value of 0.4697. The genetic distance was lowest between Balaka and Aghrani as well as Triticale and BAW-1036. Positive correlations were found between gene diversity, number of alleles, the allele size range and the types of repeat motif of microsatellite markers. It was found from this study that microsatellite markers could characterize and discriminate all of the genotypes. More primers should be used for saturation of different regions in further studies. Bangladesh J. Agril. Res. 37(3): 389-398, September 2012 DOI: http://dx.doi.org/10.3329/bjar.v37i3.12082

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Evaluation of the genetic diversity of domain II of Plasmodium vivax Apical Membrane Antigen 1 (PvAMA-1) and the ensuing strain-specific immune responses in patients from Sri Lanka

Vaccine ◽

10.1016/j.vaccine.2011.07.029 ◽

2011 ◽

Vol 29 (43) ◽

pp. 7491-7504 ◽

Cited By ~ 17

Author(s):

Sajani Dias ◽

Maheshika Somarathna ◽

Aresha Manamperi ◽

Ananias A. Escalante ◽

Anusha M. Gunasekera ◽

...

Keyword(s):

Genetic Diversity ◽

Sri Lanka ◽

Immune Responses ◽

Plasmodium Vivax ◽

Apical Membrane ◽

Apical Membrane Antigen 1 ◽

Apical Membrane Antigen

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Immunomodulatory potential of polysaccharides from Coriolus versicolor against intracellular bacteria Neisseria gonorrhoeae

Veterinary World ◽

10.14202/vetworld.2019.735-739 ◽

2019 ◽

Vol 12 (6) ◽

pp. 735-739 ◽

Cited By ~ 2

Author(s):

Manikya Pramudya ◽

Sri Puji Astuti Wahyuningsih

Keyword(s):

Immune Response ◽

Immune Responses ◽

Neisseria Gonorrhoeae ◽

Positive Control ◽

Negative Control ◽

Coriolus Versicolor ◽

Innate Immune ◽

Intracellular Bacteria ◽

Treatment Level ◽

The Difference

Background and Aim: For many years, people use natural products from the plant and fungal to improve immune response against microorganism. This study aimed to investigate the immunomodulatory properties of polysaccharides (PS) from Coriolus versicolor in mice infected by intracellular bacteria Neisseria gonorrhoeae. Materials and Methods: Thirty-six female BALB/C mice were divided into six groups: Normal control, negative control, positive control, P1 (PS before infection), P2 (PS after infection), and P3 (PS before and after infection). PS were administrated for 10 days. N. gonorrhoeae was infected twice with 2 weeks gap from the first to second exposure with a dose of 106 cells. 1 week after the end of treatment, level of oxidants, innate immune responses, and adaptive immune responses were measured. Results: This study showed that PS administration could restore the number of leukocytes as normal but could not enhance the number of phagocytes and its activity. PS administration also showed immunosuppression activity by lowering nitric oxide levels in P2 and P3 groups (p<0.05). This result showed that PS prevent over-expression of pro-inflammatory cytokines by decreasing phagocytic activity. Contrast with innate immune response result; PS administration could significantly increase interferon-gamma level in P1, P2, and P3 groups (p<0.05). Level of antibodies was significantly increased in the P3 group (p<0.05). PS administration also showed an increased level of tumor necrosis factor-a, but the difference was not significant (p>0.05). Conclusion: PS enhance adaptive immunity due to the capability of N. gonorrhoeae that able to survive and replicate in phagocytes. Thus, PS from C. versicolor could be potentially be used as a natural immunomodulator against intracellular bacteria.

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Detection of genetic divergence among Putative Ethyl Methane Sulfonate Mutants of Super Basmati using Microsatellite Markers

10.21203/rs.3.rs-34720/v1 ◽

2020 ◽

Author(s):

Kiran Hameed ◽

Bushra Sadia ◽

Madiha Habib ◽

Zia ul Qamar ◽

Faisal Saeed Awan

Keyword(s):

Genetic Diversity ◽

Base Pair ◽

Polymorphic Information Content ◽

Rice Cultivar ◽

Ethyl Methane ◽

Allele Number ◽

Methane Sulphonate ◽

Ssrs Markers ◽

Mutagenic Effects ◽

Selection Of

Abstract Mutation is a resource of generating genetic diversity in crop plant for breeding as well as genetic analysis. Ethyl Methane Sulphonate (EMS) is frequently applied chemical agents in plants. The present study was completed to investigate the mutagenic effects of different concentration of EMS on yield contributing traits of super basmati. The seeds of rice cultivar (Super basmati) were mutagenized with different doses from 0-2% v/v of EMS with difference of 0.25% for determination LD50. The treated and non-treated plants were observed under different agronomic parameters. A total of 48 putative EMS mutants of super basmati were selected randomly to analyze genetic diversity using 25 SSR primers. These markers were located on twelve chromosomes of rice. SSRs analysis revealed that abroad level of genetic diversity was existed among mutants of super basmati. A sum of 91 alleles was identified of which 82 alleles were originated to be polymorphic and the rest of nine alleles were discovered as monomorphic. The range of allele number was 2-10 with mean of 3.64 alleles/locus. The value of polymorphic information content (PIC) was from 0.039 (RM5) to 0.878 (RM44) with mean of 0.439 for each locus. All mutants differentiated from each other in more than two set of primers due to presence or absence of unique bands on chromosomes at definite base pair. The size base pair range was 75-1000bp. Dendrogram located mutant indices into four major groups. Phylogenic analyses exposed 40-96% similarity. It is concluded that EMS induced genetic variability and SSRs markers (RM44, RM154, RM1, RM252, RM334, RM487, RM110 and RM257) could be employed for the selection of rice mutants throughout molecular breeding program.

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Assessment of Genetic Diversity and Population Structure of Tunisian Barley Accessions (Hordeum vulgare L.) Using SSR Markers

Acta Agrobotanica ◽

10.5586/aa.7343 ◽

2020 ◽

Vol 73 (4) ◽

Author(s):

Salem Marzougui ◽

Mohamed Kharrat ◽

Mongi Ben Younes

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Polymorphic Information Content ◽

Hordeum Vulgare L ◽

Software Analysis ◽

Average Value ◽

Allele Number ◽

Cultivar Development ◽

Principal Coordinates ◽

Ssr Loci

In barley breeding programs, information about genetic dissimilarity and population structure is very important for genetic diversity conservation and new cultivar development. This study aimed to evaluate the genetic variation in Tunisian barley accessions (Hordeum vulgare L.) based on simple sequence repeat (SSR). A total of 89 alleles were detected at 26 SSR loci. The allele number per locus ranged from two to five, with an average of 3.4 alleles per locus detected from 32 barley accessions, and the average value of polymorphic information content was 0.45. A cluster analysis based on genetic similarity was performed, and the 32 barley resources were classified into five groups. Principal coordinates (PCoA) explained 12.5% and 9.3% of the total variation, and the PCoA was largely consistent with the results of cluster separation of STRUCTURE software analysis. The analysis of genetic diversity in barley collection will facilitate cultivar development and effective use of genetic resources.

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The Impact of Aeolus wind observations on the West African Monsoon

10.5194/egusphere-egu21-9449 ◽

2021 ◽

Author(s):

Maurus Borne ◽

Peter Knippertz ◽

Martin Weissmann ◽

Michael Rennie ◽

Alexander Cress

Keyword(s):

Weather Prediction ◽

West African Monsoon ◽

West African ◽

Boreal Summer ◽

Horizontal Line ◽

The West ◽

Great Opportunity ◽

African Monsoon ◽

The Difference ◽

The Impact

Tropical Africa is characterized by the world-wide largest degree of mesoscale convective organisation. During boreal summer, the wet phase of the West African Monsoon (WAM), the midlevel African easterly jet (AEJ) over the Sahel allows for the formation of synoptic-scale African easterly waves (AEWs) with a maximum intensity close to the West African coast. AEWs interact with convection and its mesoscale organization through modifications in humidity, temperature and vertical wind shear, and often serve as initial disturbances for tropical cyclogenesis. In addition, rainfall can be modulated by other types of tropical waves such as Kelvin or mixed Rossby gravity waves. Upper-tropospheric conditions are dominated by the Tropical Easterly Jet (TEJ), whose variability appears to be connected to convective activity. Overall, our quantitative understanding of the WAM system is still limited. The observational network over the region is sparse and rainfall forecasts with current Numerical Weather Prediction models are hardly better than climatology.The Aeolus satellite launched in 2018 offers a great opportunity to further investigate the WAM with an unprecedented density of free-tropospheric wind data. Assimilating Aeolus wind observations in denial experiments using the current operational system of the European Centre for Medium-Range Weather Forecasts (ECMWF) shows that the main circulation features of the WAM are greatly impacted: the AEJ and the TEJ are systematically weaker and stronger respectively by~1m/s in the analysis fields including Aeolus data. As a consequence AEWs also show a weakening in the propagation amplitude. We are currently investigating the contributions of the HLOS (horizontal line-of-sight) Rayleigh and Mie wind observations to these observed differences. Mie observations (i.e., those related to backscatter from hydrometeors and aerosol particles) seems to contribute strongly to the difference in the AEJ, which lies within a convectively active region with a high aerosol load. On the other hand, the difference seen in the TEJ appears to originate mostly in the Rayleigh (i.e., clear air) observations. Surprisingly, the ascending and descending HLOS observations contribute differently to the data impact, possibly revealing a remaining bias or model problems with the diurnal cycle. Future work will include systematic comparisons between the operational systems of DWD and ECMWF to understand the influence of different data assimilation approaches as well as the impact on forecasts.

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