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The genomes of domestic animals have been artificially selected during long periods of domestication and have led to many significant changes in their economic traits. Exploring these changes is useful to expand our knowledge about the domestication process, understand the complexity of genetic diversity in livestock, and make an appropriate breeding decision. The genotypic information of 23 individuals representing French and Swedish Holsteins was used to detect signature signs between these two breeds. Quality control and data filtering were performed using PLINK software. The principal component analysis was performed to determine genetic diversity. In addition, linkage disequilibrium (LD), ancestral, and recent effective population size (Ne) were separately estimated for each breed. The signature of selection was determined by the fixation index (FST) statistic. The corrected r2 (calculated statistics for LD) between single nucleotide polymorphisms (SNPs) decreased with increasing the physical distance from 100 Kb to 7.5 Mb (from about 0.3 to 0.09 in both breeds). These values were slightly smaller for the French breed. The effective population size was estimated at 1775 and 2120 individuals for French and Swedish Holsteins 900 generations ago to 31 and 39 in the recent generation, respectively. Overall, three regions with outlier FST values were identified as the signature of selection. The flanking SNP was mostly located on BTA2, BTA16, and BTA19. Candidate genes were found to be associated with SERTAD (liver metabolism and health), SYT14 (meat yield and marble levels), IRF6 (immune system), HSD11B19 (heat stress), LAMB3, and (fat deposition). Therefore, these potential genes can be considered invaluable genetic resources for future research to attempt to create generations of commercial breeds of cattle. [ABSTRACT FROM AUTHOR]

In recent years the Varroa destructor mite has been a dominant challenge for honey bee colonies, worldwide. Varroa- sensitive hygiene, a behavioral characteristic of honey bee, involves the detection and removal of Varroa larvae from the colony. It has been exploited as a recordable trait for Varroa resistance. The sense of smell is a key element in Varroa sensitive hygiene behavior. In this scenario, NorpA2 candidate gene, a putative olfactory receptor, is associated with vision and smell in honey bee and is known as a candidate gene for Varroa sensitive hygiene. With this motivation, the main goal of the current work was to determine some single nucleotide polymorphism (SNP) markers of NorpA2 candidate gene employing PCR sequencing in a case-control approach. To this end, after the identification of resistant (RES) and susceptible (SUS) colonies according to the percentage of infections of the drone pupae to Varroa mite, a total of 10 drone pupae (5 from SUS and 5 from RES) were selected and were subjected for DNA isolation. The polymerase chain reaction (PCR) was performed based on two pairs of specific primers for the amplification of 5' untranslated region (5' UTR) and promoter regions of NorpA2 gene. After expected size bands were observed, the purification process and Sanger sequencing of the PCR products were carried out. The sequencing results were quality checked and the alignment and clustering were done using the BLAST and MAFTT software, respectively. Sequences of both UTR and promoter regions displayed multiple variations (SNP, deletion). Interestingly, the results showed the existence of three specific differences in sequence in the form of SNP (C/T) at position 308 and the form of SNP/deletion at positions 504 and 563 of the nucleotide sequence region in the promoter between the SUS and RES groups. To our knowledge, this is the first report on the identification of biomarkers to control host-mite interaction in the honey bee Apis mellifera. Further research is required for the reported SNPs to be validated as biomarkers of resistance to Varroa. [ABSTRACT FROM AUTHOR]

Understanding the genomics aspect of curve variable allows for the combination of genomic regions of such model-based variables from multiple measurements into a few biologically meaningful variables. With this motivation, the aim of the current study was a model-based quantitative trait loci (QTL) detection for growth curve variables in Ghezel fat-tailed sheep. We tested the following items during research: 1) Determining the best nonlinear growth models using six nonlinear equations (Von Bertalanffy, Gompertz, Logistic, Richards, Weibull and Brody) according to 24905 obtained data sets collected from the Ghezel Sheep Breeding Center, Iran, during the 1994-2013 period; 2) Conducted partial genome scan to identify significant QTl controlling best growth model parameters in Ghezel sheep using three half-sib families (Family size=25-50) and 8 microsatellite markers distributed on ovine chromosome 1. In addition, QTL effects for two paternal half-sibs using two models, individual families and across families were calculated. Molecular data were analyzed using SAS and GridQTL programs. Observed results demonstrated the Brody model was the best growth model for growth data according to the lower values of RMSE, AIC and BIC and generally greater values of R² adj than other models. Thus, Brody model parameters (A, B, and C) were subjected to further QTL analysis. Also, our observation identified one significant QTL between the markers INRA11-CSSM004 associated with Brody model A variable (maturity) located in 123 CM in chromosome 1 (P<0.01). Analyses using more families and advance massive genotyping tools will be useful to confirm or to reject these findings. [ABSTRACT FROM AUTHOR]

Genetic diversity is essential and mirrors for diversity pattern and population evolution. With this motivation, the aim here is to investigate genetic similarities of three indigenous goats of Iran: Azerbaijan (n=50), Sarbisheh (n=50), Busher (n=29) using 9 microsatellites markers. We extracted genomic DNA and then employed routine polymerase chain reaction (PCR) protocol for amplification of nine specific microsatellite markers. The experimental raw genotype was applied to generate summary of statistics for molecular diversity criteria. From the results, 8 microsatellites visualized satisfactory electrophoresis pattern and reasonable degree of polymorphism. The ILSTS004 (0.42) and BM415 (1.8) microsatellite markers indicated highest and lowest value for Shannon index. We obtain 57-67% range for observed heterozygosity value regarding to Azerbaijan and Sarbisheh goat, respectively. From these results it is clear the high genetic similarity was found between the Sarbisheh and Busher populations. Overall, bottleneck based evidence using IAM and SMM models demonstrated normal 'L'-shaped distribution in investigated Azerbaijan and Sarbisheh goat. In conclusion, this analysis leads evidence for sufficient genetic variation within investigated goat. [ABSTRACT FROM AUTHOR]

Milking ability in goat farming is not particularly new, however, it has frameworks for receiving economic benefits from marketing of milk. For this reason, investigation of varied methods plays an important role to evaluate mammary gland structure in dairy animal. Hence, the overall objective of current work was to test the image processing tools as an alternative method for quantitative assessment of mammary gland structure in Mohabadi goat. Under this circumstance, survey data was collected from 72 Mohabadi does from research station of Department of Animal Science, University of Tehran. The fixed effects for each candidate animal consists of pedigree, birth date, milk characteristics as well as monitoring the history of record during assessment was monitored. Image process tools was based on two stages: First, three different camera photos were taken from different angels of mammary gland structure from both sides of each animal and next step, Digimizzer image processing software was employed for further analysis and estimation of seven morphological dimensions (udder length, teat length and teat angle at both sides and as well as udder height). To investigate this statistically, the descriptive statistics, correlation, different regression analysis, principal component analysis and as well as association study between linear mammary gland traits and milk were analyzed using SAS 9.3 software. The highest correlation was observed in the length of right and left udder (r=0.67 P<0.05). The results revealed that the milk yield was significantly influenced by the length of the right teat (P<0.05). In conclusion, digital image processing may be considered as alternative tools for linear morphological characterization that would provide more accurate observation and measurements on the indigenous goat population. [ABSTRACT FROM AUTHOR]

The present study was conducted to measure the genetic diversity and population genetic structure of four Iranian sheep breeds, namely; Ghezel, Makui, Kurdi and Baluchi (utilizing 20 animals per breed from both sexes) using 12 short tandem repeats markers. Our results demonstrated that the observed number of alleles and the median number of effective alleles for the Ghezel Makui, Kurdi, and Baluchi breeds were (50, 48, 44 and 43) and (2.49, 2.46, 2.45 and 2.47), respectively. Also, the mean Shannon Index was 0.982, 0.939, 0.965, and 0.959 values for Ghezel, Makui, Kurdi, and Baluchi breed, respectively. Moreover, the polymorphic information content (PIC) values were ranked from 0.09 (ILSTS011) to 0.75 (TGLA13). Additionally, the average inbreeding coefficient (FIS) was from 0.144 (Kurdi) to 0.306 (Makui). Furthermore, the lowest genetic distance was seen between Makui and Baluchi breeds (0.120), but the highest was between Ghezel and Kurdi breeds (0.884). The outcomes of this research showed the normal 'L'-shaped distribution of the mode-shift analysis test and the lack of bottleneck in the studied populations. On this basis, we conclude that the investigated Iranian sheep breeds carry reasonable within and between genetic diversity. [ABSTRACT FROM AUTHOR]

This study exploited the co-segregation of quantitative trait loci (QTL) affecting pre-weaning traits in Ghezal sheep. Two half-sib families (n=71) were genotyped for 8 informative microsatellite markers covering chromosome 1. Data for production traits (birth weight (BW), weaning weight (WW), average dairy gains (ADG) and Kleiber ratio (KBR) were collected. Investigated microsatellite loci were successfully amplified in progenies and allele numbers per locus ranged from 2 (CSSM11) to 10 (MAF109). Two models used for estimation of QTL effect were across families and individual families. QTL mapping were conducted using online GridQTL. The results show that two the QTL retained significance (P=0.01) for BW and KRB at the region of flanking markers CSSM019-CSSM032 and BM1312 respectively. Further studies will be useful using more families, animals and chromosome number for identification of co-segregation of QTL affecting pre-weaning traits in Ghezal sheep. [ABSTRACT FROM AUTHOR]

Varroa destructor is an ectoparasitic mite of the honey bee and is a primary cause of colony loss of apiculture in the world. The aim of this study was to determine infestation levels and the suppression of mite reproduction in drone brood cells of independent colonies. A number of East Azarbaijan native honey bee colonies were isolated for three years without treating against varroa. Then, seven genotypic groups were prepared with three colonies in each group: native survivors, F1 generation of Carniolan colonies, H1 generation of survivor x commercial, H1 generation of Carniolan x survivor and commercial native colonies originated from three different regions of Maragheh, Bostan-Abad, and Varzeghan in the East Azarbaijan province. A total of 3268 fifteen to eighteen-days old drone pupae from twenty-one colonies were assessed for infestation and suppression of mite reproduction. The mean of drone pupae infestation percentage, reproducing mite percentage, mites reproducing more than three offsprings percentage, and fecundity number were found to be 45.20%, 76.13%, 40.69%, and 2.215, respectively. Significant differences were observed in the four studied traits between the understudy groups. The survivor group had the lowest mite infestation level and fertility (14.2% and 68.6%, respectively). Native commercials originated from the above three mentioned regions in the East Azarbaijan province had lower fecundity and lower number of mites reproducing more than three offsprings than other groups. Our results suggest that establishing varroa surviving colonies from native colonies can reduce varroa infestation and enhance the levels of suppression of mite reproduction (SMR). Moreover, a significant variation was observed within and between understudy groups in the colonies. Therefore, it can be concluded that selective breeding programs can enhance the levels of SMR. [ABSTRACT FROM AUTHOR]

To determine chemical composition as well as apparent metabolizable energy corrected to zero nitrogen balance (AMEn) estimates of Amaranth grain in adult roosters by regression method, firstly, a specie of Amaranthus hybridus chorostachys were cultivated in a farm pilot at agriculture research station (Khalat Poushan-Tabriz- East Azarbaijan- Iran). After harvesting, amaranth grain was sifted and milled. Finally, the chemical composition of amaranth grain produced in the Advanced Animal Nutrition Laboratory was analyzed. Adult roosters 96-week-old Leghorn in individual metabolic cages for nine days used to determine AMEn content by the regression method. The basal diet was based on corn-soybean with 3200 kcal/kg metabolizable energy and 12% protein. Two experiments with raw amaranth grain (RAG) and processing amaranth grain (PAG), started separately using 40 leghorn roosters in the form of completely random by factorial method (2-5), that each experiment consisted of two levels of Rovabio multi-enzyme (0 and 0.055%) and five amaranth grain levels (0, 15, 30, 45, 60% of replacement or embedment of energizing part of the diet). Each experiment included four replicates that included one bird, it was subjected to biological experiments in metabolic cages by total excreta collection method. The obtained results of regression equations in adult roosters showed that AMEn content for raw amaranth without enzyme (RAG-e), raw amaranth with an enzyme (RAG+e), processed amaranth without enzyme (PAG-e), and processed amaranth with an enzyme (PAG+e) were 3250.24, 3433.18, 3242.18 and 3438.09 kcal/kg, respectively. The total results of this study showed that according to amaranth's adaptable and nutritious agricultural features, it can have a good potential in supplementation of poultry diets with enzymes for improving the energy and nutrition quality. [ABSTRACT FROM AUTHOR]

Regardless of reasonable reproductive performance of ewe lambs of many breeds, Ghezel ewe lambs have a very poor fertility rate, but Ghezel yearling ewes have a high fertility rate. So, comparing ewe lambs with yearling ewes can help us to understand the reason of this difference. Accordingly, this study was designed to evaluate body weight, body biometrical parameters, serum metabolites, progesterone concentration, and trait correlations of Ghezel ewe lambs and yearling ewes. During the breeding season, Ghezel ewe lambs (n=36, 7 months old) and yearling ewes (n=39, 18 months old) were weighed, their body biometrical parameters were measured, blood samples were collected, and serum metabolites and progesterone concentrations were measured. Then, all data were analyzed by the general linear model procedure of SAS software. The results of this study indicated higher relative body weight, all body biometrical parameters (except head length), and progesterone concentration in yearling ewes in comparison with ewe lambs (P<0.01). However, serum urea and glucose concentrations were lower in yearling ewes in comparison with ewe lambs (P<0.05). Also, results indicated a positive correlation of relative body weight and age with progesterone concentration of yearling ewes (P<0.01). On the other hand, results indicated a negative correlation of serum progesterone, relative body weight and age with urea concentration of yearling ewes (P<0.05). The overall results of this study indicated that Ghezel ewe lambs had lower relative body weight, body parameters, and progesterone concentration, but higher blood glucose and urea concentrations in comparison with yearling ewes. [ABSTRACT FROM AUTHOR]

Two experiments were conducted to determine: first, the best time of excreta collection after force feeding of broilers to yield the maximal amount of excreta, and second, nitrogen-corrected true metabolizable energy contents of some poultry feedstuffs including yellow corn, soybean meal, corn gluten meal, canola meal and poultry by-product meal by a new precision-fed chick assay using 3-week-old broiler chicks. In experiment one, thirty-five 21-d-old male broiler chicks, with the same body weight were randomly assigned in to 7 experimental groups with 5 birds per each. Seven experimental treatments were designed with different excreta collection times. All chicks were precision-fed with 10 g of corn-soybean meal (60:40) mixture. Excreta were collected at 2, 4, 6, 8, 10, 12, and 14 h after precision feeding. In experiment two, thirty 21-d old male broiler chicks with 5 chicks per each feed ingredients were precision-fed by 10 g of experimental feedstuffs and 5 chicks fasted for determining endogenous energy losses. The maximum time of excreta collection for 3-week-old male broiler chicks was approximately 12 h after precision feeding. The average nitrogen-corrected true metabolizable energy values of yellow corn, soybean meal, corn gluten meal, canola meal and poultry by-product meal, were 3527.55, 2572.4, 4183.25, 1806.38 and 2678.06 kcal/kg, respectively. In conclusion, nitrogen-corrected true metabolizable energy values of feedstuffs can be determined in 3-week-old broiler chicks by using a precision-fed assay. This research suggests using energy values obtained on young broiler chicks in formulating diets for the same birds. [ABSTRACT FROM AUTHOR]

Development of genomic selection can be a new strategy in breeding of native chicken. The main aim of this study was to evaluate application of a genomic selection program in Iranian native chickens from economic and genetic points of view. In this study, two scenarios including conventional scenario with 3360 and 3380 animals and genomic scenario were compared using ZPLAN+ software. The traits in the selection index were egg number, body weight, mean weight of egg and age at sexual maturity. In genomic scenario different reference population size were considered. In this scenario the genomic information from cocks (800 cocks were genotyped) was added to available information in conventional scenario based on selection index method. The generation interval was 14.5 months for all conventional and genomic scenarios. In comparison of scenarios, genetic gain and the economic profit increased by increasing reference population size in genomic scenario (€126.88-€147.45 with 80 cocks) and (€140.20 to €160.77 with 60 cocks) per animal unit. The reliability of selection index was 0.33 for cocks in conventional scenario. The reliabilities of genomic scenarios were 0.61-0.84 for 80 selected cocks and 0.66-0.87 for 60 selected cocks and that were high in comparison to conventional scenario. This study showed that genomic selection can increase the genetic improvement rate of native chickens. However, the costs of genomic scenarios were higher than conventional scenario, but genomic information increased accuracy of selection and genetic gain in breeding goals traits. [ABSTRACT FROM AUTHOR]

Genome-wide evaluation uses the associations of a large number of single nucleotide polymorphism (SNP) markers across the whole genome and then combines the statistical methods with genomic data to predict the genetic values. Genomic predictions relieson linkage disequilibrium (LD) between genetic markers and quantitative trait loci (QTL) in a population. Methods that use all markers simultaneously may therefore result in greater reliabilities of predictions of the total genetic merit, indicating that a larger proportion of the genetic variance is explained. This is hypothesized that the genome-wide methods deal differently with genetic architecture of quantitative traits and genome. The genomic nonlinear Bayesian variable selection methods (BayesA, BayesBand Bayesian LASSO) are compared using the stochastic simulation across three effective population sizes (Ne). Thereby, a genome with three chromosomes, 100 cM each was simulated. For each animal, a trait was simulated with heritability of 0.50, three different marker densities (1000, 2000 and 3000 markers) and number of the QTL was assumed to be either 100, 200 or 300. The data were simulated with two different QTL distributions which were uniform and gamma (α=1.66, β=0.4). Marker density, number of the QTL and the QTL effect distributions affected the genomic estimated breeding value accuracy with different Ne (P<0.05). In comparison of three methods, the greatest genomic accuracy obtained by BayesB method for traits influenced by a low number of the QTL, high marker density, gamma QTL distribution and high Ne. [ABSTRACT FROM AUTHOR]

The success of genomic selection mainly depends on the extent of linkage disequilibrium (LD) between markers and quantitative trait loci (QTL), number of QTL and heritability (h2) of the traits. The extent of LD depends on the genetic structure of the population and marker density. This study was conducted to determine the effects of marker density, level of heritability, number of QTL, and to compare the accuracy of predicting breeding values using two diverse approaches: GBLUP and BayesA using simulated data under two different distributions of the QTL effect. Thereby, three traits (milk production, carcass weight and mature body weight) were simulated with the heritability of 0.10, 0.30 and 0.50, respectively; for each ovine animal, a genome with three chromosomes, 100 cM each. Three different marker densities was considered (1000, 2000 and 3000 markers) and the number of QTL was assumed to be either 100, 200 or 300. Data were simulated with two different distributions of the QTL effect which were uniform and gamma (α=1.66 and β=0.4) the marker density, number of the QTL, the QTL effect distributions and heritability levels significantly affected the accuracy of genomic breeding values (P<0.05). The BayesA produced estimates with greater accuracies in traits influenced by a low number of the QTL and with the gamma QTL effects distribution. Based on the findings of this simulation, heritability, as well as dense marker panels, aiming to increase the level of LD between the markers and QTL, is likely to be needed for successful implementation of the genomic selection. [ABSTRACT FROM AUTHOR]

The aim of the present study was to estimate the genetic parameters and genetic trends of somatic cell score (SCS) in the first 3 lactations of Iranian Holstein cows by random regression (RR) animal model by using Restricted Maximum Likelihood (REML) method. The data set used in this analysis included observations of 340318 test-day records of 41526 cows in 288 herds; 89969 test-day of 11750 cows in 127 herds and 20010 test-day of 2461 cows in 60 herds in the first-, second- and third-parity, respectively, during the period from 2002 to 2010. Fixed effects considered were: year of calving, age-season of calving (by applying a fixed regression for each subclass of this effect) and herd-test date. Estimates of additive genetic variances for all parities, with only small changes, show a similar trend. Heritability estimates for first parity (0.03 to 0.07) were lower than those for second (0.07 to 0.11) and third (0.08 to 0.17) parities. Genetic correlations between daily SCS within parity were high for adjacent tests and low between the beginning and the end of lactation and decreased with increase parity number. Genetic correlations between parities were higher than 0.70 but environmental correlations between parities were in range of 0.22 to 0.51. Genetic correlations between parity demonstrate that genes that control SCS in parities are same and selection animal for SCS in first parity would have affected SCS in other parity. The genetic trend for SCS was favorable until 1995 and unfavorable since then. The relatively high level of SCS and positive genetic trends (0.431 to 0.701 cells/mL/year) would suggest that genetic improvement of SCS is at unacceptable level in Iran. [ABSTRACT FROM AUTHOR]