Iranian Buffalo Research Articles

Molecular identification of Sarcocystis cruzi isolated from Iranian buffaloes in Guilan province

Molecular identification of Sarcocystis cruzi isolated from Iranian buffaloes in Guilan province

Brucellosis in Iranian buffalo: prevalence and diagnostic methods

The water buffalo (Bubalus bubalis) in Iran represent an important source of meat and milk products with high biological value. Given the importance of water buffalo in Iran and the prevalence of brucellosis as one of the most important zoonotic diseases in this ruminant species, this study summarized available data on history, epidemiology, diagnosis, and control of brucellosis in water buffalo from previous studies that have been carried out in Iran. According to the documented data, there are three main groups of Iranian buffalo, including the Khuzestan ecotype (Khuzestan province); the Azary ecotype (Western/ Eastern Azarbaijan and Ardabil provinces); and the North ecotype (Gylan and Mazandaran provinces). Preliminary studies conducted on Iranian buffaloes either by serological or molecular tools reported that buffaloes' infection occurred due to natural exposure to a wild strain of Brucella abortus and Brucella melitensis. Previous studies dealing with brucellosis in Iranian buffalo are next to none. This review notifies the importance of reliable and detailed epidemiological investigations of Iranian buffaloes through continuous monitoring systems of the health status of buffalo populations. Continuous test and slaughter strategy, vaccination, and re-planning of veterinary activities are required to mitigate buffalo's role in disseminating and maintaining brucellosis in Iran.

A genome-wide scan of copy number variants in three Iranian indigenous river buffaloes

BackgroundIn Iran, river buffalo is of great importance. It plays an important role in the economy of the Country, because its adaptation to harsh climate conditions and long productive lifespan permitting its farming across the Country and to convert low-quality feed into valuable milk. The genetic variability in Iranian buffalo breeds have been recently studied using SNPs genotyping data, but a whole genome Copy Number Variants (CNVs) mapping was not available. The aim of this study was to perform a genome wide CNV scan in 361 buffaloes of the three Iranian river breeds (Azeri, Khuzestani and Mazandarani) through the analysis of data obtained using the Axiom® Buffalo Genotyping Array 90 K.ResultsCNVs detection resulted in a total of 9550 CNVs and 302 CNVRs identified in at least 5% of samples within breed, covering around 1.97% of the buffalo genome. and A total of 22 CNVRs were identified in all breeds and a different proportion of regions were in common among the three populations. Within the more represented CNVRs (n = 302) mapped a total of 409 buffalo genes, some of which resulted associated with morphological, healthy, milk, meat and reproductive traits, according to Animal Genome Cattle database.ConclusionsThis work provides a step forward in the interpretation of genomic variation within and among the buffalo populations, releasing a first map of CNVs and providing insights about their recent selection and adaptation to environment. The presence of the set of genes and QTL traits harbored in the CNVRs could be possibly linked with the buffalo’s natural adaptive history together to a recent selection for milk used as primary food source from this species.

Genetic Analysis of Persistency for Milk Fat Yield in Iranian Buffaloes (Bubalus bubalis).

This study aimed to estimate heritabilities and genetic trends for different persistency measures for milk fat yield and their genetic correlations with 270-day milk yield in Iranian buffaloes. The records of test-day milk fat yield belonging to the first three lactations of buffaloes within 523 herds consisting of 43,818 records were got from the Animal Breeding Center and Promotion of Animal Products of Iran from 1996 to 2012. To fit the lactation curves based on a random regression test-day model, different orders of Legendre polynomial (LP) functions were selected. Three persistency measures were altered according to the specific condition of the lactation curve in buffaloes: (1) The average of estimated breeding values (EBVs) for test day fat yield from day 226 to day 270 as a deviation from the average of EBVs from day 44 to day 62 (PM1), (2) A summation of contribution for each day from day 53 to day 247 as a deviation from day 248 (PM2), and (3) The difference between EBVs for day 257 and day 80 (PM3). The estimates of heritability for PM1, PM2, and PM3 ranged from 0.20 to 0.48, from 0.36 to 0.47, and from 0.19 to 0.35 over the first three lactations, respectively. The estimate of genetic trends for different persistency measures of milk fat yield was not significant over the lactations (P > 0.05). Genetic correlation estimates between various measures of persistency were generally high over the first three lactations. Also, genetic correlations estimates between persistency measures and 270-day milk yield were mostly low and varied from 0.00 to 0.24 (between PM1 and 270-day milk yield), from −0.19 to 0.13 (between PM2 and 270-day milk yield), and from −0.02 to 0.00 (between PM1 and 270-day milk yield) over the first three lactations, respectively. Persistency measures that showed low genetic correlations with milk fat yield were considered the most suitable measures in selection schemes. Besides, medium to high heritability estimates for different persistency measures for milk fat yield indicated that relevant genetic variations detected for these characters could be regarded in outlining later genetic improvement programs of Iranian buffaloes.

Genetic and genomic evaluation of different breeding strategies using stochastic simulation in Iranian buffalo (

Context Despite the importance of buffalos to income and food needs, there has been little attention to the simulation of breeding programs using different strategies in the Iranian buffalo population. Aims The present study aimed to evaluate different breeding strategies in Iranian native buffalo by using stochastic simulation, and to determine the most appropriate strategy for Iranian buffalo breeding. Methods Different breeding scenarios were simulated for sensitivity of outcomes to the nucleus population size and selection design. Two systems of closed and open nucleus breeding schemes were simulated. Three different nucleus sizes, the optimal fraction of nucleus dams born in the base, and the appropriate fraction of base sires born in the nucleus were considered. Four selection designs were considered: random, phenotypic, best linear unbiased prediction (BLUP), and genomic selection. Key results The results indicated that in different population sizes and both open and closed nuclei, the average total genetic value was higher in genomic selection than in other selection designs. The total genetic value was higher in open nucleus than closed nucleus breeding schemes regardless of selection design. The highest mean of total genetic value was estimated at 91.53 in the optimal nucleus size of 15% of base population for the genomic selection approach and the open nucleus breeding system. In all nucleus population sizes, the highest inbreeding was obtained for selection based on BLUP, followed by genomic, phenotype and then random selection. Conclusions Overall, the application of open nucleus breeding schemes along with genomic selection is recommended for improving buffalo productivity. Implications Selection strategies used in Iranian buffaloes have so far been based on phenotypic information; however, obtaining genetic information could improve genetic progress in the Iranian buffalo population.

Exploring novel single nucleotide polymorphisms and haplotypes of the diacylglycerol O-acyltransferase 1 (DGAT1) gene and their effects on protein structure in Iranian buffalo.

Diacylglycerol O-acyltransferase 1 (DGAT1) plays a key role in the synthesis of triglycerides. Recent studies have shown that a transition mutation resulting in substitutions of guanine by adenine in the DGAT1 gene in cattle has considerable effects on milk yield and composition. Currently, there is no systematic research reporting on the utilization of this gene segment in Iranian buffalo (Bubalus bubalis). In this study, the genetic differentiation of three indigenous Iranian buffalo populations was investigated in the region spanning exon 3 to exon 17 of the DGAT1 gene. A total of 200 buffaloes were genotyped, all the samples were sequenced directly in both directions with forward and reverse sequencing primers. Sequence analysis showed novel SNPs compared to the reference GenBank sequence (DQ886485) at nucleotide positions g.6097A>G, g.7036C>T, g.7338G>A, g.7710C>T, g.8087C>T, g.8259G>A, g.8275G>A, g.8367C>T, and g.8426C>T. No polymorphisms were found within exon 8. Therefore, the K232A position was thought to be a conserved and fixed region for high milk fat content (K allele) in Bos indicus and all buffalo breeds. Comparison with Indian buffalo revealed three exonic SNPs, one of which was nonsynonymous. A unique 22bp insertion was observed in intron 10 of DGAT1. Linkage disequilibrium analysis allowed the identification of nine haplotypes among the sampled animals. To our knowledge, this is the first report of sequencing analysis of the DGAT1 gene in Iranian buffalo. Our results suggest that genetic diversity exists and could be useful in examining the association between the DGAT1 gene and milk production traits in buffalo.

Economic values and selection indices for production and reproduction traits of Iranian buffaloes (Bubalus bubalis)

Iranian buffalo plays a critical role in supplying a portion of the income and the necessities of the rural population. The first step to design a breeding program is difinition of breeding goal (BG), a linear combination of breeding values for various traits and their economic values (EV). The current study was aimed at determining EVs for important traits of Iranian buffaloes, namely milk yield (MY), milk fat (MF), age at the first calving (AFC), and calving interval (CI), as well as at estimating the genetic response of applying various types of selection indices. Economic and management data of 50 buffalo herds from various main regions of buffalo rearing in Iran were collected. The EVs were estimated using a simple profit function. Five selection indices were constructed by combining information on various traits. The EVs for BG traits of MY, MF, AFC, and CI were 0.18, 4.66, - 0.36, and - 1.87 US$, respectively. The highest predicted genetic gain in BG was 16.95 and came from applying the selection index that included all traits. The smallest genetic gain (4.93) was predicted for the index with only AFC included. Predicted genetic gain from an index that included production traits and AFC as a reproduction trait (16.9) was higher than that from the index with only production traits (16.15). Results showed that inclusion of reproductive traits in the selection index had a positive effect on genetic gain for breeding goal.

A review on breeding and genetic strategies in Iranian buffaloes (Bubalus bubalis).

The aim of current study was to review breeding progress and update information on genetic strategies in Iranian buffaloes. Iranian buffalo is one of the vital domestic animals throughout north, north-west, south and south-west of Iran with measurable characteristics both in milk and meat production. The species plays an important role in rural economy of the country due to its unique characteristics such as resistance to diseases and parasites, having long productive lifespan and showing higher capability of consuming low-quality forage. In Iran, total production of milk and meat devoted to buffaloes are 293,000 and 24,700tons, respectively. Selection activities and milk yield recording are carrying out by the central government through the Animal Breeding Centre of Iran. The main breeding activities of Iranian buffaloes included the estimation of genetic parameters and genetic trends for performance traits using different models and methods, estimation of economic values and selection criteria and analysis of population structure. Incorporating different aspects of dairy buffalo management together with improved housing, nutrition, breeding and milking, is known to produce significant improvements in buffalo production. Therefore, identifying genetic potential of Iranian buffaloes, selection of superior breeds, improving nutritional management and reproduction and developing the education and increasing the skills of practical breeders can be useful in order to enhance the performance and profitability of Iranian buffaloes.

Genetic perspective of milk yield persistency in the first three lactations of Iranian buffaloes (Bubalus bubalis).

The objectives of this study were to estimate the genetic parameters and genetic trends for different measures of persistency (PM) for milk yield in Iranian buffaloes using a random regression test day model. Test day records of the first three lactations of buffaloes within 715 herds comprising 43 014, 38 941 and 33 937 records, respectively, were obtained from the Animal Breeding Center of Iran during 1992 to 2012. Legendre polynomial functions were chosen to fit the lactation curves in the framework of a random regression test day model for estimating (co)variance components. Three measures of persistency were modified based on the lactation curve conditions of buffaloes: (1) The average of estimated breeding values (EBVs) for test day milk yields from day 226 to day 270 as a deviation from the average of EBVs from day 44 to day 62 (PM1), (2) A summation of contribution for each day from day 53 to day 247 as a deviation from day 248 (PM2), (3) The difference between EBVs for day 257 and day 80 (PM3). The highest heritability estimates were observed for PM2 over the first three lactations (0·29, 0·80 and 0·42, respectively). Estimates of genetic correlations between persistency measures and milk yield varied from -0·48 to 0·29 (first lactation), from -0·12 to 0·48 (second lactation), and from -0·62 to 0·63 (third lactation). Estimate of genetic trend for first lactation PM2 was negative (-0·0088 ± 0·0043; P < 0·05). It is essential to include milk yield persistency in the breeding goal of Iranian buffaloes along with other important traits such as milk yield or reproductive traits.

Estimates of genetic parameters and genetic trends for production and reproduction traits in Iranian buffaloes (Bubalus bubalis)

Calving and milk production records from April 1992 to March 2012 comprising 5353 records of age at first calving (AFC), 2972 records of 305-days milk yield (MY) and 2349 records of interval between first and second calving (CI) from the first lactation buffaloes within 785 herds of Iran were analysed using a linear animal model to estimate variance components and heritability for these traits. A linear animal model including direct genetic effect was implemented by Gibbs sampling methodology. A single Gibbs sampling chain with 300 000 rounds was generated by the TM program. Genetic trends were obtained by regressing yearly mean estimates of breeding values on birth year. Posterior mean estimates of direct heritabilities for MY, AFC and CI were 0.46 ± 0.21, 0.20 ± 0.06 and 0.21 ± 0.14, respectively. The posterior means of direct genetic correlation between MY-AFC, MY-CI and AFC-CI were –0.31, 0.01 and –0.17, respectively. Estimates of direct genetic trends for MY, AFC and CI were negative and significant, and their corresponding values were –1.50 ± 0.05 (P &lt; 0.0001), –0.04 ± 0.001 (P &lt; 0.0001) and –0.02 ± 0.005 (P &lt; 0.001), respectively. Medium to high direct heritability estimates for productive and reproductive traits would be due to higher additive genetic variances for these traits and implied that applicable genetic variations observed for productive and reproductive traits could be applied in designing future genetic selection plans for Iranian buffaloes.

Estimation of genetic parameters for test-day milk yield and fat percentage in first calving Iranian buffaloes

Estimation of genetic parameters for test-day milk yield and fat percentage in first calving Iranian buffaloes

Identified factors influencing the occurrence of abnormal lactation curves in Iranian buffaloes

Atypical lactation curves (ALCs), mostly characterized by the lack of any distinguished peak, are the subject of this study. Logistic regression was used to assess the influences of some non-genetic factors on the occurrence of ALCs in Iranian buffaloes. The data set consisted of 24,679 lactation records from 11,478 buffaloes that calved during the years 1996 to 2012. As a reasonable statistical criterion, odds and odds ratio were used to evaluate the probable differences between the various levels of the factors. Genetic analysis of the ALC trait was also carried out using Bayesian approach to estimate heritability and repeatability parameters. The results revealed that almost 44% of the lactation curves were atypical. All factors but ecotype factor had significant effects on the occurrence of ALCs. The frequency of ALCs increased until the third parity and decreased afterward, therefore the highest and the lowest values of the trait were observed in the third and 10th parities, respectively. Unlike the parity effect, ageing of the buffaloes caused the odds values to be continually increasing. The incidence of the ALCs for buffaloes calved out of season (July to December) was more likely (almost 15%) than those calved in season (January to June). The structure of the data also affected the trait significantly, such that the lactations with 4 recorded test-days were 1.75 times more likely to have atypical curves than those with 8 recorded test-days. Heritability and repeatability of the occurrence of ALCs were estimated very low and were 0.020 and 0.036, respectively.

Analysis of population structure and genetic variability in Iranian buffaloes (Bubalus bubalis) using pedigree information

The objective of this study was to use pedigree analysis to evaluate the population structure, genetic variability and inbreeding in Iranian buffaloes. The analysis was based on the pedigree information of 42 285 buffaloes born from 549 sires and 6376 dams within 1697 herds. Pedigree information used in this study was collected during 1976 to 2012 by the Animal Breeding Centre of Iran. The CFC program was applied to calculate pedigree statistics and genetic structure analysis of the Iranian buffaloes. Also, the INBUPGF90 program was used for calculating regular inbreeding coefficients for individuals in the pedigree. The analysis of pedigree indicated that inbreeding coefficient ranged from 0% to 31% with an average of 3.42% and the trend of inbreeding was significantly positive over the years (P &lt; 0.0001). Average coancestry was increased in recent years and overall generation interval was 6.62 years in Iranian buffaloes. Founder genome equivalent, founder equivalent, effective number of founders and effective number of non-founders were increased from 1976 to 2002, but their values decreased from 2002 onwards. A designed mating system to avoid inbreeding may be applied to this population of buffalo to maintain genetic diversity.

Bayesian analysis of direct and maternal effects for birthweight in Iranian buffaloes using Gibbs sampling

Calving records from April 1994 to March 2010 comprising 8570 calving events from the first three parities of 734 buffalo herds of Iran were analysed using a linear animal model to estimate variance components and heritability for birthweight. A linear animal model including direct and maternal genetic effects with covariance between them and maternal permanent environmental effect was implemented by Gibbs sampling methodology. A single Gibbs sampling chain with 500 000 rounds was generated by the Threshold Model program. Posterior means of direct and maternal heritabilities and repeatability for birthweight were 0.21, 0.15 and 0.23, respectively. Estimate of correlation between direct and maternal genetic effects for birthweight was –0.71. Also, the ratio of permanent environmental variance to phenotypic variance was 0.02. Along with the direct genetic effects, the contribution of maternal effects to the phenotypic variance of birthweight may provide producers with information to optimally use the reported estimates when making selection decisions. The results of this study indicated that exploitable genetic variation observed for birthweight could be considered in designing future selection programs for Iranian buffaloes and improvement in birthweight could be attained by genetic selection.

Testicular lesions and epididymal sperm parameters in the Iranian river buffalo (Bubalus bubalis)

The aim of this study was to evaluate the testicular lesions and their effects on the epididymal sperm parameters in the Iranian river buffalo (Bubalus bubalis). Total numbers of 117 scrota from the pubertal buffalo were provided from the local slaughterhouse. The samples were evaluated for morphological parameters and any macro- or microscopic lesions. The sterile swabs from the testis parenchyma were subjected to microbiology culture. The epididymal spermatozoon was analysed for concentration, progressive motility and abnormalities. The results showed 34.2% fibrotic adhesions between parietal and visceral layers of tunica vaginalis that was significantly different among seasons (P<0.05). The cases of unilateral cryptorchidism and bilateral Sertoli cell tumour were detected, with no spermatozoa in the respected epididymides. Microscopic examination showed 13.25% (31/234) lesions including general (51.61%; 16/31) and multifocal (29.03%; 9/31) degenerations as well as interstitial orchitis (9.68%; 3/31) and the Sertoli cell tumour (6.45%; 2/31). No relationship between the lesions and the bacterial isolation (n=6) was detected. The sperm parameters and morphological parameters of the testis were under influence of microscopic lesions (P<0.05). In conclusion, the testicular macro- and microscopic lesions may have a noticeable contribution in the Iranian buffalo fertility.

Linear and threshold analysis of direct and maternal genetic effects for secondary sex ratio in Iranian buffaloes

The objective of this study was to estimate variance components and genetic parameters for secondary sex ratio (SSR) in Iranian buffaloes. Calving records from April 1995 to June 2010 comprising 15,207 calving events from the first three lactations of 1066 buffalo herds of Iran were analyzed using linear and threshold animal models to estimate variance components, heritabilities and genetic correlations between direct and maternal genetic effects for SSR. Linear and threshold animal models included direct and maternal genetic effects with covariance between them and maternal permanent environmental effects were implemented by Gibbs sampling methodology. Posterior means of direct and maternal heritabilities and repeatability for SSR obtained from linear animal model were 0.15, 0.10, and 0.17, respectively. Threshold estimates of direct and maternal heritabilities and repeatability for SSR were 0.48, 0.27, and 0.52, respectively. The results showed that the correlations between direct and maternal genetic effects of SSR were negative and high in both models. In addition, the ratios of maternal permanent environmental variance were low. Exploitable genetic variation in SSR can take advantage of sexual dimorphism for economically important traits which may facilitate greater selection intensity and thus greater response to selection, as well as reducing the replacement costs. Threshold animal model may be applied in selection programs where animals are to be genetically ranked for female rate.

Brucella abortus and Brucella melitensis in Iranian Bovine and Buffalo Semen Samples: The First Clinical Trial on Seasonal, Senile and Geographical Distribution Using Culture, Conventional and Real-time Polymerase Chain Reaction Assays

Conventional and real-time PCR assays were developed for detection and identification of Brucella species in bovine and buffalo semen samples. Totally, 91 bovine and buffalo semen samples were collected from 4 major provinces of Iran in various seasons. The animals which their semen samples were collected for this study had less than 1 year old, 1-2 years old, 2-3 years old and more than 3 years old. Samples were cultured and DNA was extracted and novel primers have been designed using the IS711 target of Brucella species for conventional PCR. Positive results of PCR have been studied for presences of Brucella abortus and Brucella melitensis. Totally, 21.56% and 14.28% of bovine and buffalo semen samples, respectively, were positive for Brucella species. Khozestan had the highest while Sistan Va Balochestan had the lowest incidences of Brucella species in studied regions. Samples which were collected in spring season had the highest rate of infection. Also, samples which were collected from less than 1 year old bovine and buffalo semen samples had the highest incidence of Brucella species. Totally, 25 (24.50%) and 4 (3.92%) bovine semen samples and 14 (15.38%) and 1 (1.09%) buffalo semen samples were positive for Brucella abortus and Brucella melitensis.

Random regression models to estimate genetic parameters for test-day milk yield and composition in Iranian buffaloes

Abstract. The objective of this study was to estimate genetic parameters for milk yield and milk percentages of fat and protein in Iranian buffaloes. A total of 9,278 test-day production records obtained from 1,501 first lactation buffaloes on 414 herds in Iran between 1993 and 2009 were used for the analysis. Genetic parameters for productive traits were estimated using random regression test-day models. Regression curves were modeled using Legendre polynomials (LPs). Heritability estimates were low to moderate for milk production traits and ranged from 0.09 to 0.33 for milk yield, 0.01 to 0.27 for milk protein percentage and 0.03 to 0.24 for milk fat percentage, respectively. Genetic correlations ranged from −0.24 to 1 for milk yield between different days in milk over the lactation. Genetic correlations of milk yield at different days in milk were often higher than permanent environmental correlations. Genetic correlations for milk protein percentage ranged from −0.89 to 1 between different days in milk. Also, genetic correlations for milk percentage of fat ranged from −0.60 to 1 between different days in milk. The highest estimates of genetic and permanent environmental correlations for milk traits were observed at adjacent test-days. Ignoring heritability estimates for milk yield and milk protein percentage in the first and final days of lactation, these estimates were higher in the 120 days of lactation. Test-day milk yield heritability estimates were moderate in the course of the lactation, suggesting that this trait could be applied as selection criteria in Iranian milking buffaloes.

Distribution of BoLA-DRB3 allelic frequencies and identification of two new alleles in Iranian buffalo breed.

The role of the major histocompatibility complex (MHC) in the immune response makes it an attractive candidate gene for associations with disease resistance and susceptibility. This study describes genetic variability in the BoLA-DRB3 in Iranian buffaloes. Heminested PCR-RFLP method was used to identify the frequency of BoLA-DRB3 alleles. The BoLA-DRB3 locus is highly polymorphic in the study herd (12 alleles). Almost 63.50% of the alleles were accounted for by four alleles (BoLA-DRB3.2 ∗48, ∗20, ∗21, and obe) in Iranian buffalo. The DRB3.2 ∗48 allele frequency (24.20%) was higher than the others. The frequencies of the DRB3.2 ∗20 and DRB3.2 ∗21 are 14.52 and 14.00, respectively, and obe and gbb have a new pattern. Significant distinctions have been found between Iranian buffalo and other cattle breed studied. In the Iranian buffaloes studied alleles associated with resistance to various diseases are found.

Gross morphology, histomorphology and histomorphometry of the jejunum in the adult river buffalo

Summary For this study the jejuni of 50 adult (2-4 years), apparently healthy Iranian river buffaloes were collected from the abattoir for gross morphology, histomorphology, and histomorphometry. Our statistical analysis revealed that, there are significant (P 0.05) in lengths as well as thicknesses of jejunal villi between the 3 different regions. The mast cells distributions were highly significant (P<0.001) between the superficial and deep regions of jejunal tunicae mucosae in all buffaloes. There were also highly significant (P<0.001) differences in the distribution of goblet cells between the superficial and deep regions of jejunal mucosa, and their population was more in the superficial than in the deep region.