Estimation of Inbreeding Coefficients Using Pedigree and Microsatellite Markers and Its Effects on Economic Traits of Shirvan Kordi Sheep

INTRODUCTION Intensive selection within a single population of finite size reduces the genetic variability and increases the rate of inbreeding KEY WORDS Research Article Estimation of Inbreeding Coefficients in Shirvan Kordi Sheep In the overdominance hypothesis, inbreeding depression is attributable to higher fitness of heterozygotes for the loci in question. For the partial recessive hypothesis, negative fitness consequences are due to the fixation of recessive or partially recessive deleterious alleles Microsatellites has been widely used as reliable molecular markers to study the genetic relationship of different populations and for indirect measures of inbreeding. They are codominant, highly polymorphic, highly abundant, heritable, locus specific, and easily analyzed and therefore suitable for studies on population phylogenesis constitution This study was carried out using microsatellite markers because they are powerful tools for tracking alleles through a population and to estimate genetic variability and inbreeding Marker data collected provides information on population structure, relatedness and inbreeding MATERIALS AND METHODS Data Pedigree information from 1989 to 2009 of a flock of Kordi sheep maintained at Shirvan Sheep Breeding Station was used. Pedigree file contained information on individual identification number, sex, type of birth, dam and sire as well as birth date and included 7170 registered animals (3332 males and 3838 females), progeny of177 sires and 2182 dams. Pedigree analysis Inbreeding coefficients of the animals were computed using the CFC program Microsatellite method Blood samples (5 mL) of 100 animals were collected from the jugular vein and transferred into vacutainer tubes containing 0.5 molar EDTA as anticoagulant and frozen at -20 ˚C. Total DNA was isolated from blood samples using the Diatom DNA Kit, according to the manufacturer instructions. The quantity and quality of the isolated DNA was determined using both spectrophotometry and by 0.8% agarose gel electrophoresis. Characteristics of the microsatellite markers used in this study are listed in Approximately, 100 ng DNA (adjusted concentration) was used as template for polymerase chain reaction (PCR). The PCR reaction cycle was carried out in a the rmocycler (Biorad) by denaturation at 95 ˚C for 4 min, denaturation at 95 ˚C for 45 sec, primer annealing for 45 sec at the desired temperature (55-60 ˚C) and an extension for 1 min at 72 ˚C, repeating the cycle 35 times. The final extension step was at 72 ˚C for 4 min. The PCR amplification was conducted in a 12 μL volume. PCR products were analyzed by vertical electrophoresis in 6% non-denaturing polyacrylamide gel (170 V, 3-4 h) and bands visualized by rapid silver staining Molecular data analysis Molecular data were analysed using the POPGENE V1.32 RESULTS AND DISCUSSION Pedigree analysis The analysis of pedigree revealed that mean level of inbreeding (F) of all animals acrossall years (1989-2009) was 0.668%. Moreover, the minimum and maximum coefficientsof inbreeding for the animals in the flock was 0 and 31.25%, respectively. The low average coefficient of inbreeding could be ascribed to breeding strategies at the station for preventing mating of relatives. Totally, 23.26% of the animals (1668 out of 7170) were inbred with a mean inbreeding coefficient of 2.87%. In the pedigree, 3332 and 3838 of the animals were males and females with mean inbreeding coefficients of 0.693% and 0.646%, respectively. Out of all, 1668 animals were inbred. These included 823 males and 845 females having average inbreeding coefficient of 2.81% and 2.93%, respectively. These results indicated that fewmatings of close relatives have occurred. Descriptive statistics for inbreeding coefficients for the entire population and the inbred portion of the population are shown in 135 Estimation of Inbreeding Coefficients in Shirvan Kordi Sheep Mean of all traits decreased and increased irregularly by increasing inbreeding coefficients. This could be due to fewer records in the numerically higher classes of inbreeding. Inbreeding depression Details of the data used for the estimation of inbreeding depression are given in Regression coefficients and their standard errors on inbreeding coefficients were -0.0013 ± 0.0003 kg for BWT, 0.080 ± 0.015 kg for WWT, 0.001 ± 0.0009 kg for BW6M, -0.065 ± 0.055 kg for BW9M, -0.092 ± 0.063 kg for BW12M, 0.008 ± 0.0066kg for Wool and -0.023 ± 0.012 lambs for LS. Pre-weaning growth traits BWT: birth weight trait; WWT: weaning weight trait; BW6M: body weight at 6 months of age trait; BW9W: body weight at 9 months of age trait; BW12M: body weight at 12 months of age trait; Wool: wool produced annually and LS: number of lambs per ewe lambing. Changes for every one percent increase in inbreeding coefficient for BWT and WWT were -0.0131 and 0.0795 kg, respectively. Regression coefficient estimate for BWT Regression coefficients for BW in the 9 th and 12 th month were more than all the other studied traits. Estimates of -0.0653 and -0.0921 kg per 1% increase in inbreeding coefficient for BW in 9 th month and BW in 12 th month, were more than the values reported in other studies. Annual wool production and number of lambs per ewe lambing The effect of inbreeding on wool produced annually and the number of lambs per ewe lambing amounted to 0.0083 kg and -0.023 lambs, respectively. For the annual wool production, the linear effect of individual inbreeding, regression was positive but non-significant. On the average, an increase in 1 percent in individual inbreeding increased the wool produced annually by 0.0083 kg. A review b

GENETIC POLYMORPHISM OF LEPTIN GENE USING PCR-RFLP METHOD IN THREE DIFFERENT POPULATIONS

ABSTRACT This investigation was conducted to identify polymorphism of the leptin gene in Holstein cows, Mazandarani native cattle and buffaloes by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP). The frequencies of A and B alleles were 0.4 and 0. 6 -in Holstein cows, 0.56 and 0.44 -in Mazandarani native cattle, 0.61 and 0.35 in buffaloes, respectively. The heterozygote genotype (AB) had the highest frequency in all three populations: 0.73, 0.622 and 0.509 in Holstein cows, Mazandarani cattle and buffaloes, respectively. Chi-square test showed that Mazandarani cattle and buffaloes were in HardyWeinberg equilibrium but Holstein cows were not in equilibrium

Genetic Analyses of Egg Quality in Khorasan Razavi Native Fowl Using the Bayesian Method

This study was conducted to estimate the genetic parameters influencing egg quality in Khorasan Razavi native fowl. (Co)Variance components were estimated by the Bayesian statistical method via Gibbs sampling in GIBBS3F90 software. 1000 eggs (28-29 weeks old) were collected from 775 hens of the ninth generation of Khorasan-Razavi Province native fowl breeding center. External (egg weight,specific gravity, long length, short length, shape index, shell strength, shell weight, shell thickness) and internal (yolk diameter, yolk height, yolk weight, yolk index, albumen diameter, albumen height, albumen weight, albumen index, Haugh unit) egg quality traits were measured. Six univariate animal models were used for estimation of genetic parameters and the best model for each trait was determined by deviance information criterion (DIC). Genetic and phenotypic correlations between traits were estimated using bivariate animal model. Direct heritability estimates ranged from 0.10 (egg width) to 0.39 (yolk index). For all traits except albumen diameter and albumen index, the inclusion of maternal effects in the model resulted in considerable reduction in direct heritability. Genetic correlations of egg weight with shell strength and shell thickness were negative. In conclusion, due to genetic correlations among external and internal egg quality traits, selection based on egg weight and shell thickness may improve external and internal egg quality traits. Also, including maternal effects in the form of genetic or permanent environment in the statistical model resulted in more accurate estimates for most traits

The Effect of Cinnamon Extract on Spermatogenesis and

Genotypes of Iranian Zel sheep for Calpastatin (CAST) locus were determined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) methods and for Calpain (CAPN) locus by PCR-SSCP. Blood samples were collected from 200 purebred Zel sheep of Zel Breeding Station located in Golestan province in northeast of Iran. Extraction of genomic DNA was based on modified salting out method. The digestion of PCR products of CAST gene by MspI and NcoI restriction enzymes revealed two alleles M and N, with frequencies 85.5 and 14.5%, respectively. Frequencies were 75, 21 and 4% for MM, MN and NN genotypes, respectively. Alternatively, using PCR-SSCP method, four genotypes including AA, AB, BB and AC with frequencies of 71, 21, 4 and 4%, respectively, were observed in this population. Analyzing CAPN gene by the PCR-SSCP method, revealed two different conformational patterns (AA and AB) with frequencies of 69 and 31% for AA and AB, respectively. Average heterozygosity for both loci was low (0.28 and 0.25% for CAST using PCR-SSCP and PCR-RFLP, and 0.26% for CAPN). Yearling weights (YW) were analyzed by a statistical model comprising PCR-SSCP and as a result CAPN genotypes had significant effect (P<0.01) on YW. A Chi-square test confirmed Hardy-Weinberg (H-W) equilibrium for the CAST locus using PCR-SSCP method but not for PRC-RFLP method and CAPN locus. Totally, the investigated herd had little genetic diversity and different factors disturb H-W equilibrium and PCR-RFLP and PCR-SSCP might be used successfully in these studies