Copy number variation in livestock: A mini review

Review (Published online: 26-04-2018)

20. Copy number variation in livestock: A mini review

V. Bhanuprakash, Supriya Chhotaray, D. R. Pruthviraj, Chandrakanta Rawat, A. Karthikeyan and Manjit Panigrahi

Veterinary World, 11(4): 535-541

ABSTRACT

Copy number variation (CNV) is a phenomenon in which sections of the genome, ranging from one kilo base pair (Kb) to several million base pairs (Mb), are repeated and the number of repeats vary between the individuals in a population. It is an important source of genetic variation in an individual which is now being utilized rather than single nucleotide polymorphisms (SNPs), as it covers the more genomic region. CNVs alter the gene expression and change the phenotype of an individual due to deletion and duplication of genes in the copy number variation regions (CNVRs). Earlier, researchers extensively utilized SNPs as the main source of genetic variation. But now, the focus is on identification of CNVs associated with complex traits. With the recent advances and reduction in the cost of sequencing, arrays are developed for genotyping which cover the maximum number of SNPs at a time that can be used for detection of CNVRs and underlying quantitative trait loci (QTL) for the complex traits to accelerate genetic improvement. CNV studies are also being carried out to understand the evolutionary mechanism in the domestication of livestock and their adaptation to the different environmental conditions. The main aim of the study is to review the available data on CNV and its role in genetic variation among the livestock.

Keywords: copy number variation, copy number variation regions, livestock, single nucleotide polymorphisms, quantitative trait loci.

Molecular detection of Leptospira spp. from canine kidney tissues and its association with renal lesions

Research (Published online: 25-04-2018)

19. Molecular detection of Leptospira spp. from canine kidney tissues and its association with renal lesions

Biswajit R. Dash, Vitthal S. Dhaygude, Prashant D. Gadhave, Kaustubh V. Garud and Dattatarya P. Kadam

Veterinary World, 11(4): 530-534

ABSTRACT

Aim: The study aimed to detect the prevalence of Leptospira spp. in kidney tissues collected during necropsy and to establish its association with renal lesions in dogs of Mumbai region.

Materials and Methods: Kidney tissues from 40 dogs were collected during necropsy after gross examination and then fixed in neutral buffered formalin and Bouin's fluid for histopathology and histochemistry, respectively. Kidney tissues were also collected for the detection of Leptospira spp. by polymerase chain reaction (PCR) in a sterile container and stored at -80°C until further processing.

Results: Of 40 cases studied, 13 (32.5%) cases showed lesions of nephritis of varying histotype and severity. Glomerulonephritis was reported as the most common type of nephritis in 9 (69.23%) cases, and interstitial nephritis was recorded in 4 (30.76%) cases. Chronic and acute interstitial nephritis was observed in two cases each. Renal failure as a cause of death was found in 7 (17.5%) dogs. Of a total of 40 cases, 9 were found positive for pathogenic Leptospira spp. genome by PCR. However, of nine PCR-positive cases, only four cases showed lesions in kidneys as glomerulonephritis and interstitial nephritis in two cases each. The rest five cases positive for Leptospira spp. by PCR did not show any appreciable lesions in the kidneys.

Conclusion: Leptospiral DNA was detected in 9 (22.5%) cases by PCR. Of these nine cases, only four cases showed renal lesions. Other five cases which were positive for Leptospira spp. by PCR did not show any appreciable gross and microscopic lesions in the kidneys which might be carriers for Leptospira spp. Considering variable reports on types of nephritis in Leptospira spp. infection and also the prevalence of non-pathogenic Leptospira spp., it is important to conduct an extensive study on the prevalence of Leptospira spp. and its association with renal lesions involving batteries of tests.

Keywords: histopathology, kidneys, Leptospira spp., nephritis.

Pseudopregnancy in goats: Sonographic prevalence and associated risk factors in Khartoum State, Sudan

Research (Published online: 23-04-2018)

18. Pseudopregnancy in goats: Sonographic prevalence and associated risk factors in Khartoum State, Sudan

Areeg Mohamed Almubarak, Naglaa Abd Elhakeem Abass, Majdi Elnaim Badawi, Mohamed Tagelddin Ibrahim, Abdelhamid Ahmed Elfadil and Rihab Mohamed Abdelghafar

Veterinary World, 11(4): 525-529

ABSTRACT

Aim: This study was conducted to estimate the prevalence of pseudopregnancy in goats and to investigate potential risk factors associated with the condition in Khartoum State.

Materials and Methods: A cross-sectional study was carried out from March 2015 to February 2016. A total of 378 female goats which presented to the Veterinary Teaching Hospital, College of Veterinary Medicine, Sudan University of Science and Technology, for routine ultrasonographic pregnancy diagnosis were examined. Ultrasound scanning was performed using a real-time scanner equipped with dual-frequency (3.5-5 MHz) curvilinear transducer.

Results: The results showed that the prevalence of pseudopregnancy in goats in Khartoum State was 10.6%. Risk factors such as general body condition (χ2=5.974; p=0.05), age (χ2=11.760; p=0.0129), type of estrus (χ2=12.794; p=0.000), and previous reproductive performance (χ2=13.397; p=0.020) showed significant association (p≤0.05) with the occurrence of pseudopregnancy in the univariate analysis. Breed (χ2=12.627; p=0.082), milk yield (χ2=5.951; p=0.114), type of feeding (χ2=1.721; p=0.190), season (χ2=2.661; p=0.264), locality (χ2=7.66; p=0.264), parity number (χ2=0.451; p=0.767), and rearing system (χ2=1.593; p=0.451) were not significantly associated with pseudopregnancy.

Conclusion: The prevalence of pseudopregnancy in goats in Khartoum State was 10.6%. Pseudopregnancy in goats is significantly associated with age, type of estrus, general body condition, and previous reproductive performance. This study showed for the first time that pseudopregnancy is a real reproductive problem in goats in Khartoum State.

Keywords: goat, hydrometra, prevalence, risk factors, Sudan, ultrasound.

Isolation, identification, and serotyping of Avibacterium paragallinarum from quails in Indonesia with typical infectious coryza disease symptoms

Research (Published online: 23-04-2018)

17. Isolation, identification, and serotyping of Avibacterium paragallinarum from quails in Indonesia with typical infectious coryza disease symptoms

Agnesia Endang Tri Hastuti Wahyuni, Charles Rangga Tabbu, Sidna Artanto, Dwi Cahyo Budi Setiawan and Sadung Itha Rajaguguk

Veterinary World, 11(4): 519-524

ABSTRACT

Background and Aim: Infectious coryza (IC) or snot is an infectious upper respiratory disease affecting chickens and birds, including quails, and it is caused by Avibacterium paragallinarum. The symptoms of IC are facial swelling, malodorous nasal discharge, and lacrimation. This study aimed to isolate, identify, and serotype the A. paragallinarum of snot in quails and to determine the sensitivity and resistance to several antibiotics.

Materials and Methods: Nine quails from Yogyakarta, Indonesia with typical snot disease symptoms were used in this study. The nasal swab was obtained and directly streaked onto a chocolate agar plate and blood agar plate (BAP), then incubated in 5% CO2 at 37°C for 24-48 h. Staphylococcus spp. was cross-streaked onto the BAP to show the satellite growth. The observation of the morphology of the suspected colony, Gram staining, and biochemical tests (catalase test, oxidase test, urease test, peptone test, and carbohydrate fermentation such as maltose, mannitol, lactose, and sorbitol) are done to identify the species of bacteria. This research also detects the serovar of A. paragallinarum using hemagglutination inhibition test. The antibiotic sensitivity tests were also performed using several antibiotics against five A. paragallinarum isolates that were cultured on Mueller-Hinton Agar and added with antibiotic discs, then incubated in 5% CO2 at 37°C for 24-48 h.

Results: Five isolates out of nine suspected isolates (55.5%) were A. paragallinarum. The growth of isolates from quails did not depend on the nicotinamide adenine dinucleotide (NAD) (NAD-independent). Sensitivity test was done using the five identified A. paragallinarum isolates, results showed that they were 100% sensitive to amoxicillin (AMC) and ampicillin (AMP); 100% resistant toward amikacin (AK), erythromycin (E), gentamycin (CN), and tetracycline (TE); 80% resistant toward kanamycin (K) and trimethoprim (W); 60% resistant toward chloramphenicol (C); and 20% toward enrofloxacin (ENR). The antibiotics that have an intermediate sensitivity (in between sensitive and resistant) were ENR and K, 80% and 20%, respectively. Three out of five A. paragallinarum isolates were identified as serovar B of A. paragallinarum using HI test.

Conclusion: Five out of nine isolates (55.5%) from quails with typical IC disease symptoms identified as A. paragallinarum and sensitive toward AMC and AMP. Three out of five A. paragallinarum isolates were identified as serovar B.

Keywords: antibiotic sensitivity test, Avibacterium paragallinarum, infectious coryza, nicotinamide adenine dinucleotide-independent.

Seroprevalence and risk factors of caprine brucellosis in Khartoum state, Sudan

Research (Published online: 19-04-2018)

16. Seroprevalence and risk factors of caprine brucellosis in Khartoum state, Sudan

Eman Mohamed-Ahmed Mohamed, Abdelhamid Ahemd Mohamed Elfadil, Enaam Mohamed El-Sanousi, Hatim Hamad Ibrahaem, Saad El-Tiab Mohamed-Noor, Mohamed Abdelsalam Abdalla and Yassir Adam Shuaib

Veterinary World, 11(4): 511-518

ABSTRACT

Aim: This cross-sectional study was conducted from April to July 2012 in Khartoum state, Sudan, to determine the seroprevalence of brucellosis in goats and to investigate potential risk factors associated with this disease.

Materials and Methods: A total of 307 serum samples were collected from both sexes of goats in four different localities and were subjected to testing for brucellosis using rose bengal plate test (RBPT), serum agglutination test (SAT), and competitive enzyme-linked immunosorbent assay (cELISA).

Results: The overall seroprevalence was 11.4% (n=35) with a 95% confidence interval (CI) ranging from 7.80 to 15.0. Out of these 35 RBPT-positive samples, the positivity of 18 and 17 were confirmed by SAT and cELISA, respectively. A significant statistical variation was observed between brucellosis seroprevalences in goats purchased from local animal markets and goats that were raised at the farm. Conversely, such significant variations were not observed among the categories of other risk factors with seroprevalences ranging from 3.0% (95% CI between 0.40 and 7.20) to 16.3% (95% CI between 10.4 and 22.3). Location (χ2=9.33, df=3, p=0.02), breed (χ2=3.52, df=1, p=0.05), herd size (χ2=6.59, df=2, p=0.03), and herd expansion (χ2=5.39, df=1, p=0.02) were associated with RBPT-positive status for brucella in the two-tailed Chi-square test. In addition, Sharq an-Nil locality and goats raised at the farm had increased odds of being RBPT positive.

Conclusion: Brucellosis was detected in goats in all surveyed localities. An effort should be made to educate goat owners/herders about brucellosis as well as about the importance of vaccination.

Keywords: brucellosis, goats, risk factors, rose bengal plate test, seroprevalence, Sudan.

Viability test of fish scale collagen (Oshpronemus gouramy) on baby hamster kidney fibroblasts-21 fibroblast cell culture

Research (Published online: 18-04-2018)

15. Viability test of fish scale collagen (Oshpronemus gouramy) on baby hamster kidney fibroblasts-21 fibroblast cell culture

Chiquita Prahasanti, Denny Tri Wulandari and Noer Ulfa

Veterinary World, 11(4): 506-510

Aim: This study aims to examine the toxicity of collagen extracted from gouramy fish scales (Oshpronemus gouramy) by evaluating its viability against baby hamster kidney fibroblasts-21.

Materials and Methods: Collagen was extracted from gouramy fish scales (O. gouramy) with 6% acetic acid. Its results were analyzed using Fourier-transform infrared spectroscopy and freeze-dried technique. Its morphology then was analyzed with scanning electron microscope. Afterward, 3-(4.5-dimethylthiazole-2-yl)2.5-diphenyl tetrazolium bromide assay was conducted to compare cells with and without fish scale collagen treatment.

Results: Collagen extracted from gouramy fish scales had no influence statistically on cultured fibroblast cells with a statistical significance (2-tailed) value of 0.754 (p>00025).

Conclusion: Collagen extracted from gouramy fish scales has high viability against BHK21 fibroblast cells.

Keywords: bone graft, collagen, gouramy fish scale, viability, 3-(4.5-dimethylthiazole-2-yl)2.5-diphenyl tetrazolium bromide.

Genetic characterization of 11 microsatellite loci in Egyptian pigeons (Columba livia domestica) and their cross-species amplification in other Columbidae populations

Research (Published online: 17-04-2018)

14. Genetic characterization of 11 microsatellite loci in Egyptian pigeons (Columba livia domestica) and their cross-species amplification in other Columbidae populations

Sherif Ramadan, Ahmed Dawod, Osama El-Garhy, Amira M. Nowier, Marwa Eltanany and Miho Inoue-Murayama

Veterinary World, 11(4): 497-505

ABSTRACT

Aim: This study aimed to analyze the genetic diversity and relationships of 10 Egyptian pigeon populations belonging to Columba livia domestica species using 11 microsatellite markers and to investigate the success of these markers amplification across another eight pigeon species.

Methods: Genomic DNA was isolated from feather samples of 179 pigeon samples from 10 Egyptian breeds: Asfer Weraq (n=14), Austoraly (n=20), Reehani (n=21), Messawed (n=17), Nemssawy (n=27), Otatti (n=12), Morasla (n=17), Tumbler (n=22), Halaby Asfer (n=10), and Karakandy (n=19) in addition to Japanese feral pigeons (n=30). Genotyping was done using 11 specific polymorphic microsatellite makers. Moreover, 37 samples not belonging to C. livia domestica but belonging to another eight pigeon species were genotyped. The polymerase chain reaction (PCR) products were electrophoresed on an ABI 3130xl DNA Sequencer. The basic measures of genetic diversity and phylogenetic trees were computed using bioinformatics software.

Results: Across the 10 studied Egyptian populations, the number of alleles per locus ranged from 3 to 19 and the average number of alleles observed was 9.091. The lowest value of expected heterozygosity (0.373) was obtained for the Reehani breed, and the highest value (0.706) was found for Morasla breed. The overall expected heterozygosity of Egyptian pigeons was 0.548. The FST coefficient which indicates fixation coefficients of subpopulations within the total population for the 11 loci varied from 0.318 to 0.114 with a relatively high mean (0.226). In our study, the FIS showed a relatively high average (0.037). The pairwise Reynolds's genetic distance between the 11 studied pigeon populations recorded lower values between Otatti and Austoraly (0.025) and between Morasla and Japanese feral pigeons (0.054). These results are supported by clustering pattern either by the neighbor-joining phylogenetic tree or by a Bayesian clustering of STRUCTURE with the admixture method.

Conclusion: We confirm the applicability of the CliμD17, CliμT17, CliμD16, CliμD32, CliμT13, CliμD01, PG1, PG2, PG4, PG6, and PG7 microsatellite markers among Egyptian domestic pigeons and across other pigeon species using cross-species amplification method. The information from this study should be useful for genetic characterization and for developing conservation programs of this important species.

Keywords: Egyptian breed, genetic diversity, microsatellite, pigeon.