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(A) Frequency of combined interaction scores from the String database [21] and (B) Frequency of TOM connectivity in BGCN. (PDF 648Â kb)

Functional analysis of the light green module genes. Over-represented GO/pathway terms were grouped based on kappa statistics. The size of each category within a pie chart represents the number of included terms. Only the most significant GO/terms within groups were labeled. GO/pathway terms are represented as nodes, and the node size represents the term enrichment significance, while the edges represent significant similarity between categories. (A) Representative biological processes interactions among module genes. (B) Representative molecular function interactions among module genes. (C) Representative Ractome analysis interactions among module genes. (PDF 2605Â kb)

The objective of present study was to derive the economic values for number of inseminations to conception, calving interval, milk yield and stillbirth, using economic data of 10 Iranian Holstein herds. The economic values were derived by using the profit function methods and differentiating a profit equation with respect to the traits of interest. The cow fertility costs herd amortization or replacement cost and cow feed cost were included in the profit function. The average of feed cost per cow per day was 8.65 USD. The total feed cost comprised 61 percent of milk production, 23 percent of maintenance, 12 percent of pregnancy and 4 percent of growth. In calculation of cow feed cost, the estimated cost for each Mcal and per g protein of feed were 0.0006 and 0.165 USD, respectively. The replacement cost of each heifer per cow herd was 1719 USD. The average cost of each insemination was 30 USD. The estimated economic values for the number of insemination, calving interval, milk yield and one percent unit of stillbirth, were -82, -2.08, 0.193 and -1.27 USD per cow/per year, respectively. The results of the current study suggested that improving the number of inseminations, calving interval, milk yield and stillbirth will have a positive effect on the profitability of Iranian Holstein cows. © 2010 Copyright by Islamic Azad Univerty, Rasht Branch, Rasht, Iran.

Functional analysis of the red module genes. Over-represented GO/pathway terms were grouped based on kappa statistics. The size of each category within a pie chart represents the number of included terms. Only the most significant GO/terms within groups were labeled. GO/pathway terms are represented as nodes, and the node size represents the term enrichment significance, while the edges represent significant similarity between categories. (A) Representative biological processes interactions among module genes. (B) Representative molecular function interactions among module genes. (C) Representative Ractome analysis interactions among module genes. (PDF 3753Â kb)

Genetic and non-genetic parameters were estimated for early growth traits of Iranian Baluchi lambs using univariate and multivariate models. The investigated traits were: birth weight (BWT), weaning weight (WWT), 6-month weight (6MW) and pre-weaning average daily gain (ADG). Data and pedigree information used in this research were collected at the Abbasabad Sheep Breeding Station during a period between 1973 and 2003 on 15,568 lambs descended from 326 sires and 4737 dams. Twelve models including different combination of direct and maternal effects (additive genetic, permanent environmental and common environmental) as well as additive genetic relationship between direct and maternal effects were used to analyze data. For each trait, the most appropriate model was chosen based on likelihood ratio tests. In addition, multivariate analysis was performed using the most appropriate models obtained in univariate analysis. Based on the most appropriate fitted models, estimates of direct heritabilities were 0.12 ± 0.02, 0.10 ± 0.02, 0.06 ± 0.01 and 0.09 ± 0.02 for BWT, WWT, 6MW and ADG, respectively. Estimates of maternal additive genetic and maternal permanent environmental variances, as a proportion of phenotypic variance (m 2 and pe 2 , respectively) were 0.08 ± 0.02 and 0.08 ± 0.01 for BWT, 0.04 ± 0.01 and 0.09 ± 0.01 for WWT, 0.03 ± 0.01 and 0.03 ± 0.01 for 6MW, and, 0.01 ± 0.01 and 0.08 ± 0.01 for ADG, respectively. Maternal common environmental component was significant only on BWT and was estimated to be 0.19 ± 0.02. The estimate of maternal common environmental variances as a proportion of phenotypic variance (c 2 ) was significant only for BWT (0.19 ± 0.02). Direct genetic correlations among studied traits were positive and ranged from 0.37 (BWT–6MW) to 0.98 (WWT–ADG). Maternal genetic correlation estimates between studied traits were positive varying from 0.11 (BWT–ADG) to 0.64 (ADG–6MW). The estimates of phenotypic and environmental correlations were positive and generally lower than those of genetic correlations. Results indicated that besides direct genetic effects, maternal effects should be included in the statistical model to obtain accurate estimates of genetic parameters for early growth traits.

Native chicken breeding station of Mazandaran was established in 1988 with two main objectives: genetic improvement through selection programs and dissemination of indigenous Mazandarani birds. (Co)variance components and genetic parameters for economically important traits were estimated using (bi) univariate animal models with ASREML procedure in Mazandarani native chicken. The data were from 18 generations of selection (1988-2009). Heritability estimates for body weight at different ages [at hatch (bw1), 8 (bw8), 12 (bw12) weeks of ages and sex maturation (wsm)] ranged from 0.24 ± 0.00 to 0.47 ± 0.01. Heritability for reproductive traits including age at sex maturation (asm); egg number (en); weight of first egg (ew1); average egg weight at 28 (ew28), 30 (ew30), and 32 (ew32) weeks of age; their averages (av); average egg weight for the first 12 weeks of production (ew12); egg mass (em); and egg intensity (eint) varied from 0.16 ± 0.01 to 0.43 ± 0.01. Generally, the magnitudes of heritability for the investigated traits were moderate. However, egg production traits showed smaller heritability compared with growth traits. Genetic correlations among egg weight at different ages were mostly higher than 0.8. On the one hand, body weight at different ages showed positive and relatively moderate genetic correlations with egg weight traits (ew1, ew28, ew30, ew32, ew12, and av) and varied from 0.30 ± 0.03 to 0.59 ± 0.02. On the other hand, low negative genetic correlations were obtained between body weight traits (bw1, bw8, bw12, and wsm) and egg number (en). Also, there is low negative genetic correlation (-24 ± 0.04 to -29 ± 0.05) between egg number and egg weight. Therefore, during simultaneous selection process for both growth and egg production traits, probable reduction in egg production due to low reduction in egg number may be compensated by increases in egg weight.

Embryo transfer is a reproductive technique that has a major impact on the dissemination of economically important genes and the rate of genetic gain in breeding schemes. In recent years, there has been increasing interest in the use of sexed and genotyped embryos in commercial embryo transfer programs. Marker/gene assisted selection (MAS/GAS) projects can be performed in the pre-implantation stage through mass production of characterized embryos. Biopsy of a few cells in the morulla stage is essential for pre-implantation genetic diagnosis (PGD), in which sex determination, evaluation of disease genes, and genotyping for candidate genes are performed. Limited quantity of cells and low amount of DNA restrict the use of multiple molecular analyses in PGD programs. Recently, whole genome amplification (WGA) techniques promise to overcome this problem by providing sufficient input DNA for analysis. Among several techniques proposed for WGA, the primer extension pre-amplification (PEP) and the improved-primer extension pre-amplification (I-PEP) methods are the most commonly used. However, these methods are time-consuming and need more than 12 h amplification cycles. Since the time is a critical parameter in the successful characterized embryo transfer, the shortening of diagnosis time is highly desirable. In this study, we developed a short and simple I-PEP procedure (~3 h) and evaluated its performance for the amplification of bovine genomic DNA. We assessed short WGA procedure by polymerase chain reaction (PCR) amplification of 7 specific loci. The results indicated that the short procedure possesses enough sensitivity for the molecular genetic analysis of 1 input cell. Although the efficiency of the method was 100%, there was an inconsistency between genomic DNA (gDNA) and whole genome amplification product (wgaDNA) genotypes for kappa-casein locus; that is, however, most likely due to allele drop-out (ADO) or false homozigocity. The results of this study indicate that with the application of reliable methods, WGA-amplified bovine DNA will be a useful source for sexing and genotyping bovine embryos in several quantitative trait locus (QTL) markers.

The objectives of this study were to quantify the errors in economic values (EVs) for traits affected by cost or price thresholds when skewed or kurtotic distributions of varying degree are assumed to be normal and when data with a normal distribution is subject to censoring. EVs were estimated for a continuous trait with dichotomous economic implications because of a price premium or penalty arising from a threshold ranging between -4 and 4 standard deviations from the mean. In order to evaluate the impacts of skewness, positive and negative excess kurtosis, standard skew normal, Pearson and the raised cosine distributions were used, respectively. For the various evaluable levels of skewness and kurtosis, the results showed that EVs can be underestimated or overestimated by more than 100% when price determining thresholds fall within a range from the mean that might be expected in practice. Estimates of EVs were very sensitive to censoring or missing data. In contrast to practical genetic evaluation, economic evaluation is very sensitive to lack of normality and missing data. Although in some special situations, the presence of multiple thresholds may attenuate the combined effect of errors at each threshold point, in practical situations there is a tendency for a few key thresholds to dominate the EV, and there are many situations where errors could be compounded across multiple thresholds. In the development of breeding objectives for non-normal continuous traits influenced by value thresholds, it is necessary to select a transformation that will resolve problems of non-normality or consider alternative methods that are less sensitive to non-normality.

The present study was undertaken to genetically evaluate Turkmen horses for genetic diversity and to evaluate whether they have experienced any recent genetic bottlenecks. A total of 565 individuals from Turkmen horses were characterized for within breed diversity using 12 microsatellite markers. The estimated mean allelic diversity was (9.42 ± 1.78) per locus, with a total of 131 alleles in genotyped samples. A high level of genetic variability within this breed was observed in terms of high values of effective number of alleles (4.70 ± 1.36), observed heterozygosity (0.757 ± 0.19), expected Nei's heterozygosity (0.765 ± 0.13), and polymorphism information content (0.776 ± 0.17). The estimated cumulative probability of exclusion of wrongly named parents (PE) was high, with an average value of 99.96% that indicates the effectiveness of applied markers in resolving of parentage typing in Turkmen horse population. The paternity testing results did not show any misidentification and all selected animals were qualified based on genotypic information using a likelihood-based method. Low values of Wright's fixation index, F(IS) (0.012) indicated low levels of inbreeding. A significant heterozygote excess on the basis of different models, as revealed from Sign and Wilcoxon sign rank test suggested that Turkmen horse population is not in mutation-drift equilibrium. But, the Mode-shift indicator test showed a normal 'L' shaped distribution for allelic class and proportion of alleles, thus indicating the absence of bottleneck events in the recent past history of this breed. Further research work should be carrying out to clarify the cause of discrepancy observed forbottleneck results in this breed. In conclusion, despite unplanned breeding in Turkmen horse population, this breed still has sufficient genetic variability and could provide a valuable source of genetic material that may use for meeting the demands of future breeding programs.

An experiment was conducted to investigate the effect of short-term selection for 4 week breast weight (4wk BRW), and to estimate genetic parameters of body weight, and carcass traits. A selection (S) line and control (C) line was randomly selected from a base population. Data were collected over two consecutive hatches for four generations. A total of 1 135 records from 156 sires and 218 dams were used to estimate the genetic parameters. The genetic improvement of 4wk BRW was 3.5, 2.7 and 0.6 g in generation 2, 3 and 4, respectively. The estimated heritability by using pedigree information was 0.35±0.06. There were a significant difference for BW, and carcass weights but not for carcass percent components between lines (P

A stochastic bio-economic model has been used to determine the effects of new reproductive technologies over a 15-year period. A strategy of using conventional artificial insemination (AI) or embryo transfer (ET) using two sex-controlled embryos at different conception rates (CRs) and herd sizes resulted in a 24 state model. The genetic means of AI population increased over the years, and the genetic means of milk production for all of the embryo strategies were greater than those of AI. In addition, the genetic means of milk yield using different embryo-based scenarios in the expanding herds were greater than those for the fixed herds. The net profit of using sexed ET in the expanding herds was greater (P < 0.05) than that of fixed size herds. In general, there was a roughly consistent trend in net profit per cow for sexed ET strategies in the expanding herds over the years, but there was an increasing trend in net profit per cow for sexed ET strategies in the fixed herds over the years. Medium to high CRs for ET and the use of sex-controlled embryo systems, especially for induction of twin births to produce dairy replacements, will be critical elements of a system that produces significant numbers of female calves. The greater number of female calves produced in the sex-controlled scenarios allows the farmer to select animals with the best genetic potential as dairy replacement heifers; therefore, the rate of genetic gain increased in the dairy herd. Results of sensitivity analyses showed that a significant decrease in the production costs and increase in the ET performance are essential for embryo-based technologies to be profitable.

The objective of this study was to develop a method for calculating economic values of clinical mastitis (CM) and somatic cell score (SCS) for inclusion in a dairy cattle breeding goal in the context of a country where farm production and economic data are scarce. In order to calculate the costs and derive economic values for SCS, a new model, 'milk collection method', has been developed and was compared with the Meijering model with individual and average SCS distributions. For the population, estimated economic values using the milk collection method were 1.3 and 2.4 times higher than those of Meijering method with average and individual SCS, respectively. The milk collection method needs no assumptions about normality of the distribution of SCS and because of a lack of normality in Iranian data for SCS, the Meijering method resulted in economic values that were biased downwards. Failing to account for the fact that milk price penalties for SCS are applied at milk collection rather than individual cow level resulted in a further large downward bias in the economic value of SCS. When the distribution of data is unknown or difficult to approximate or when a transformation to normality is not straightforward, the milk collection method would be preferable. Inclusion of SCS and CM in the breeding goal for Iranian dairy cattle is justified based on these results. The model to calculate mastitis costs proposed here could be used to estimate economic values for CM in other developing countries where farm production and economic data are generally poor.

Accuracy of multiple-trait genetic evaluation based on allelic relationships with traditional best linear unbiased prediction (BLUP) was compared through computer simulation. Firstly, a base population (N = 100) was simulated; the population was half male/half female. After reaching linkage disequilibrium between marker and QTL, phenotypic and genotypic records were simulated for the last generation. For each animal in the base population, three chromosomes (each one Morgan in length) was created; on each chromosome, 200 markers and 50 QTLs were randomly located. Mutation rate in each generation was 2.5 × 10-5. Total allelic relationships consider variety of genetic relationships among relatives and employ information of non-relatives as well. In evaluation using total allelic relationships, three separate allelic matrixes were required. To form such matrixes, firstly, marker effects were estimated for each trait using mixed model of BLUP. Then, based on these effects, particular markers of each trait as well as common markers among two traits were determined and used to form allelic relationship matrixes. Correlation between actual and estimated breeding values in the last generation was evaluated based on 10 iterations. Statistical comparison was performed using t-student test. A significant difference was observed between evaluation accuracy of studied two methods.Keywords: Marker, allelic relationships, multiple-trait evaluation

The current study was conducted to investigate the effect of short-term selection in Japanese quail for 4-wk BW and estimate genetic parameters of BW, carcass traits, and egg weight. A selected line and control line were randomly selected from a base population. In each generation, 39 sires and 78 dams were used as parents for the next generation. Data were collected over 2 consecutive hatches for 4 generations, and 1,554 records from 151 sires and 285 dams were used to estimate the genetic parameters. The genetic improvement of 4-wk BW was 9.6, 8.8, and 8.2 g in generations 2, 3, and 4, respectively. There was a significant effect of sex, generation, and line (P < 0.001). There was a significant difference for BW and carcass weights but not for carcass percentage components between sexes (P < 0.01). Females showed higher figures than males. The realized heritability for 4-wk BW was 0.55, reflecting the accuracy of selection. However the estimated heritability by using pedigree information was 0.26 ± 0.05. The genetic correlation among BW and carcass traits was relatively high (ranging from 0.85 to 0.91). Inbreeding caused a decline in the mean for all of the traits, but its effect was only significant for 4-wk BW and carcass weight (P < 0.05). Selection for 4-wk BW improved feed conversion ratio 0.16 units over the selection period. Results showed there was a strong genetic correlation between 4-wk BW and carcass traits that suggests that early 4-wk BW can be used as a selection criterion to improve carcass traits. Also, intense selection resulting in high rates of inbreeding might result in decreased response to selection due to inbreeding depression.

A stochastic bio-economic model was used to determine the effects of applying artificial insemination (AI) with conventional or sexed semen at different conception rates and herd sizes on the genetic progress of productive trait and net profit over a 15-year period. The genetic means of the cattle population was predicted to increase over the years and the rate of genetic progress in the population program using sexed semen was significantly greater than the rate of progress in the population using conventional semen. The theoretical genetic gain was greater than the realized genetic gain for milk yield for all the AI scenarios. In addition, the genetic means for milk yield in the expanding herds were greater than in the fixed sized herds. The trend in net profit generated by using AI strategies with conventional semen over the time horizon was greater when herds were expanding (P < 0.01). The trend in net profit for fixed sized herds was generally negative, however, expanding herds experienced positive net profits over the years. Also, the net profit of using AI strategies with sexed semen was greater when dairy herds were expanding. On the other hand, the net profit of using AI with sexed semen was greater than that of AI with conventional semen at the end of the time horizon. The results of sensitivity analyses indicated that a 20% increase or decrease in milk sales income and feed costs have significantly modified the net profit of AI strategies using either sexed or conventional semen.

The objectives of this study were to estimate economic values (EVs) for three production traits (milk, fat and protein yields) and longevity and to develop a national selection index. The proposed Iranian selection index was compared with selection indices of three other countries in the world. A simple and appropriate model was used to describe the Holstein dairy cattle industry under an Iranian production system. Production parameters and economic data were collected from two Holstein dairy farms in Tehran province. The EVs were estimated at farm level for three breeding perspectives (maximized profit, minimized costs, and economic efficiency) and two restrictions in production system (fixed herd size and fixed total input). The average absolute EVs on profit perspective and herd size restriction for milk, fat, and protein yields (based on $/kg) and longevity ($/month) were 0.11, 0.89, -0.20, and 6.20, respectively. The average absolute EVs under minimized costs per unit of product interest for milk, fat, protein yields and longevity were -0.30, -3.43, 0.88 and -20.40, respectively. The average absolute EVs under maximized economic efficiency for milk, fat and protein yields and longevity were 0.34, 2.73, -0.99 and 36.33, respectively. Relative emphasis for three production traits and longevity were 59.7, 14.3, -3.0 and 23.1, respectively. The comparison of the proposed Iranian index with those countries where most of the semen and embryos are imported points out that developing a national selection index to improve cow profitability and optimum generic trends is necessary. Sensitivity analysis indicated that the influence of milk payment changes on EVs was the greatest as its influence on fat and protein EVs is substantial. EVs for milk and fat yields, with respect to price changes (milk, feed and non-feed), were the least sensitive and most sensitive, respectively.

Signal transducer and activator of transcription 5A (STAT5A) was chosen because of its involvement in the development of the mammary gland and it is a key mediator of prolactin signaling and can activate transcription of milk protein genes in response to prolactin. Semen samples from 134 Iranian Holstein proven bulls were obtained from the Animal Breeding Center of Iran. A 215 bp fragment, located within exon 7 of bovine STAT5A gene was amplified. PCR product was digested with Ava I enzyme. Gene frequencies of T and C alleles were 0.131 and 0.869 respectively. Genotypes are distributed according to the Hardy–Weinberg equilibrium. Least squares means between the two genotypes for protein yield were significant ( P P

In this study, direct and maternal heritabilities were estimated for growth traits and carcass characteristics in Lori-Bakhtiari sheep. Data for birth weight (BW; n=5826), weaning weight (WW; n=5408), body weight at six months of age (6MW; n=4237), body weight at slaughter (SW; n=396), cold carcass weight (CCW; n=291), lean weight (LW; n=204), bone weight (WB; n=291), fat weight (WF; n=204) and fat-tail weight (FTW; n=396) were used to estimate the heritabilities. The data for first three traits had been collected during seventeen years, 1990 to 2006, while for other traits had been collected during six years, 2000 to 2006. Genetic parameters including both direct and maternal genetic effects were estimated using multivariate animal models, and a Derivative Free Restricted Maximum Likelihood (DFREML) approach. The direct heritability for BW, WW, 6MW, SW, CCW, LW, WB, WF and FTW were 0.30 ? 0.03, 0.13 ? 0.03, 0.20 ? 0.03, 0.24 ? 0.06, 0.16 ? 0.06, 0.16 ? 0.06, 0.20 ? 0.11, 0.23 ? 0.11, and 0.27 ? 0.11, respectively. Maternal heritability estimates were 0.22, 0.17, 0.06, 0.10, 0.09, 0.15, 0.26, 0.06 and 0.07 for BW, WW, 6MW, SW, CCW, LW, WB, WF and FTW, respectively. Consequently, genetic progress is possible for growth traits and carcass composition by selection.

The main objective of this study was to estimate the genetic and phenotypic relationships between calving difficulty (CD) and fertility traits, including success at first service (SF), number of inseminations to conception (INS), interval from calving to first service (CTFS), interval between first and last service (IFL) and days open (DO), in first-parity Iranian Holsteins under standard (SMMs) and recursive (RMMs) mixed models. The data analysed in this paper included 29 950 records on CD and fertility traits, collected in the time period from 1995 to 2014 by the Animal Breeding and Improvement Center of Iran. Under all observed SMMs and RMMs, five bivariate sire-maternal grandsire models (ten bivariate analyses in total) were used for the analyses. Recursive models were applied with a view to consider that CD influences the fertility traits in the subsequent reproductive cycle and the genetic determination of CD and fertility traits by fitting CD as covariate for any of the fertility traits studied. The existence of such cause-and-effect is considered in RMMs but not in SMMs. Our results implied a statistically non-zero magnitude of the causal relationships between CD and all the fertility traits studied, with the former influencing the latter. The causal effects of CD on SF (on the observed scale, %), INS, CTFS, IFL and DO were -2.23%, 0.10 services, 1.93 days, 3.76 days and 5.61 days, respectively. Direct genetic correlations between CD and the fertility traits under both models were not statistically different from zero (95% HPD interval included zero), except for the correlation between CD and CTFS, which were 0.197 and 0.134 under SMM and RMM, respectively, indicating that genes associated with difficult births also increase intervals between calving and the first insemination afterwards. Comparison of both models by the deviance information criterion (DIC) demonstrated the plausibility of RMMs over SMMs.

Genetic profiles of Iranian Holstein young bulls at the national artificial insemination station were determined on the basis of individual genotypes at 13 ISAG's recommended microsatellites, the most useful markers of choice for parentage identification. In the present study a total of 119 individuals were genotyped at 13 microsatellite loci and for possible parent-offspring combinations. A high level of genetic variation was evident within the investigated individuals as assessed from various genetic diversity measures. The mean number of observed alleles per microsatellite marker was 9.15 and the number of effective alleles as usual was less than the observed values (4.03). The average observed and expected heterozygosity values were 0.612 and 0.898, respectively. The mean polymorphic information content (PIC) value (0.694) further reflected a high level of genetic variability. The average exclusion of probability (PE) of the 13 markers was 0.520, ranging from 0.389 to 0.788. The combined exclusion of probability was 0.999, when 13 microsatellite loci were used for analysis in the individual identification system. Inbreeding was calculated as the difference between observed and expected heterozygosity. Observed homozygosity was less than expected which reflects inbreeding of -3.7% indicating that there are genetic differences between bull-sires and bull-dams used to produce young bulls. The results obtained from this study demonstrate that the microsatellite DNA markers used in the present DNA typing are useful and sufficient for individual identification and parentage verification without accurate pedigree information. (Asian-Aust. J. Anim. Sci. 2006. Vol 19, No. 4 : 463-467)

Particulates in microscope imagery can interfere with cell boundary tracking algorithms. In this paper, we present an automated way of identifying and tracking particulates. We also demonstrate a way of ‘removing’ the particulates from the image to obtain a more accurate segmentation and demonstrate this using a previously-developed active contour-based segmentation algorithm. We also demonstrate some pitfalls of using particulate tracking, especially when the particulates are near cell boundaries.

Three machine learning algorithms: Random Forests (RF), Boosting and Support Vector Machines (SVM) as well as Genomic Best Linear Unbiased Prediction (GBLUP) were used to predict genomic breeding values (GBV) and their predictive performance was compared in different combinations of heritability (0.1, 0.3, and 0.5), number of quantitative trait loci (QTL) (100, 1000) and distribution of QTL effects (normal, uniform and gamma). To this end, a genome comprised of five chromosomes, one Morgan each, was simulated on which 10000 bi-allelic single nucleotide polymorphisms were distributed. Pearson’s correlation between the true and predicted GBV and Mean Squared Error of GBV prediction were used, respectively, as measures of the predictive accuracy and the overall fit achieved with each method. In all methods, an increase in accuracy of prediction was seen following increase in heritability and decrease in the number of QTL. GBLUP had better predictive accuracy than machine learning methods in particular in the scenarios of higher number of QTL and normal and uniform distributions of QTL effects; though in most cases, the differences were non-significant. In the scenarios of small number of QTL and gamma distribution of QTL effects, Boosting outperformed other methods. Regarding Mean Squared Error of GBV prediction, in most cases Boosting outperformed other methods, although the estimates were close to that of GBLUP. Among methods studied, SVM with 0.6 gigabytes (GIG) was the most efficient user of memory followed by RF, GBLUP and Boosting with 1.2-GIG, 1.3-GIG and 2.3-GIG memory requirements, respectively. Regarding computational time, GBLUP, SVM, RF and Boosting ranked first, second, third and last with 10 min, 15 min, 75 min and 600 min, respectively. It was concluded that although stochastic gradient Boosting can predict GBV with high prediction accuracy, significantly longer computational time and memory requirement can be a serious limitation for this algorithm. Therefore, using of other variants of Boosting such as Random Boosting was recommended for genomic evaluation.

Different fertility indices were constructed for improving fertility performance in Iranian Holstein dairy cows. Number of inseminations per conception and days from calving to first insemination, each weighted by its economic value, were included as breeding goals in the aggregate genotype definition. Different fertility indices (FI) were constructed with different combinations of available fertility traits number of inseminations to conception (INS), days from calving to first service (DFS), interval between first and last insemination (IFL), and days open (DO). The fertility index (FI1) that included INS and DFS had the greatest genetic gain for INS (−0.39 insemination), DFS (−7.47 days), and profit ($4.3) per generation. Genetic gain for profit, DFS, and INS including only DO showed slight differences regarding FI1. A selection index that included only INS (DFS) presented the larger (smaller) genetic gains for INS and smaller (larger) for DFS, which were −0.40 (−0.034) and −0.975 (−11.18) inseminations and days, respectively. The result of this study showed that recording INS and DFS are preferable traits for including in a fertility subindex. DO can be used in the absence of other fertility traits. © 2014, Springer Science+Business Media Dordrecht.

The genetic architecture of a quantitative trait refers to the number of genetic variants, allele frequencies, and effect sizes of variants that affect a trait and their mode of gene action. This study was conducted to investigate the effect of four shapes of allelic frequency distributions (constant, uniform, L-shaped and U-shaped) and different number of trait-affecting loci (50, 100, 200, 500) on allelic frequency changes, long term genetic response, and maintaining genetic variance. To this end, a population of 440 individuals composed of 40 males and 400 females as well as a genome of 200 cM consisting of two chromosomes and with a mutation rate of 2.5 × 10(-5) per locus was simulated. Selection of superior animals was done using best linear unbiased prediction (BLUP) with assumption of infinitesimal model. Selection intensity was constant over 30 generations of selection. The highest genetic progress obtained when the allelic frequency had L-shaped distribution and number of trait-affecting loci was high (500). Although quantitative genetic theories predict the extinction of genetic variance due to artificial selection in long time, our results showed that under L- and U-shapped allelic frequency distributions, the additive genetic variance is persistent after 30 generations of selection. Further, presence or absence of selection limit can be an indication of low (50) or high (100) number of trait-affecting loci, respectively. It was concluded that the genetic architecture of complex traits is an important subject which should be considered in studies concerning long-term response to selection.

On the basis of the potential benefits to human health there is an increased interest in producing milk containing lower-saturated fatty acid (SFA) and higher unsaturated fatty acid (FA) concentrations, including cis-9 18:1 and cis-9, trans-11-conjugated linoleic acid (CLA). Twenty-four multiparous Holstein cows were used in two experiments according to a completely randomized block design, with 21-day periods to examine the effects of incremental replacement of prilled palm fat (PALM) with sunflower oil (SFO) in high-concentrate diets containing 30 g/kg dry matter (DM) of supplemental fat (Experiment 1) or increases in the forage-to-concentrate (F : C) ratio from 39 : 61 to 48 : 52 of diets containing 30 g/kg DM of SFO (Experiment 2) on milk production, digestibility and milk FA composition. Replacing PALM with SFO had no effect on DM intake, but tended to increase organic matter digestibility, yields of milk, protein and lactose, and decreased linearly milk fat content. Substituting SFO for PALM decreased linearly milk fat 8:0 to 16:0 and cis-9 16:1, and increased linearly 18:0, cis-9 18:1, trans-18:1 (��4 to 16), 18:2 and CLA concentrations. Increases in the F : C ratio of diets containing SFO had no effect on intake, yields of milk, milk protein or milk lactose, lowered milk protein content in a quadratic manner, and increased linearly NDF digestion and milk fat secretion. Replacing concentrates with forages in diets containing SFO increased milk fat 4:0 to 10:0 concentrations in a linear or quadratic manner, decreased linearly cis-9 16:1, trans-6 to -10 18:1, 18:2n-6, trans-7, cis-9 CLA, trans-9, cis-11 CLA and trans-10, cis-12 CLA, without altering milk fat 14:0 to 16:0, trans-11 18:1, cis-9, trans-11 CLA or 18:3n-3 concentrations. In conclusion, replacing prilled palm fat on with SFO in high-concentrate diets had no adverse effects on intake or milk production, other than decreasing milk fat content, but lowered milk fat medium-chain SFA and increased trans FA and polyunsaturated FA concentrations. Increases in the proportion of forage in diets containing SFO increased milk fat synthesis, elevated short-chain SFA and lowered trans FA concentrations, without altering milk polyunsaturated FA content. Changes in fat yield on high-concentrate diets containing SFO varied between experiments and individual animals, with decreases in milk fat secretion being associated with increases in milk fat trans-10 18:1, trans-10, cis-12 CLA and trans-9, cis-11 CLA concentrations.

Summary The objective was to assess goodness of fit and predictive ability of subsets of single nucleotide polymorphism (SNP) markers constructed based on minor allele frequency (MAF), effect sizes and varying marker density. Target traits were body weight (BW), ultrasound measurement of breast muscle (BM) and hen house egg production (HHP) in broiler chickens. We used a 600 K Affymetrix platform with 1352 birds genotyped. The prediction method was genomic best linear unbiased prediction (GBLUP) with 354 564 single nucleotide polymorphisms (SNPs) used to derive a genomic relationship matrix (G). Predictive ability was assessed as the correlation between predicted genomic values and corrected phenotypes from a threefold cross-validation. Predictive ability was 0.27 � 0.002 for BW, 0.33 � 0.001 for BM and 0.20 � 0.002 for HHP. For the three traits studied, predictive ability decreased when SNPs with a higher MAF were used to construct G. Selection of the 20% SNPs with the largest absolute effect sizes induced a predictive ability equal to that from fitting all markers together. When density of markers increased from 5 K to 20 K, predictive ability enhanced slightly. These results provide evidence that designing a low-density chip using low-frequency markers with large effect sizes may be useful for commercial usage.

Efficient reproductive performance is an important prerequisite for sustainable dairy production systems. Moreover, reproductive performance has become one of the most important functional traits in the dairy cattle industry, because of its economic importance, as well as its effect on animal welfare. The objective of present study was to evaluate the consequence of alternative selection strategies to improve fertility performance of Holstein cows in Iran. The traits milk production (. M), number of inseminations per conception (INS), days from calving to first insemination (DFS), maternal calving difficulty (MCD) and direct calving difficulty (DCD) were included in an aggregate genotype (. H). The selection indices in each strategy were a different combination of fertility traits and milk production. Although fertility traits were included in the aggregate genotype, in the first selection strategy, in which selection was based on milk production, unfavorable genetic gain for fertility traits occurred. In the second strategy, in which genetic gain for milk production was restricted to zero, in comparison to the other strategies, the genetic gains for profit and fertility traits were lowest and highest, respectively. In the third strategy, in which genetic gain for fertility traits was restricted to zero, the genetic gains for milk production and profit differed little compared to the first strategy. Favorable genetic gains were obtained for both fertility traits and milk production in the fourth strategy, in which proportional restriction was used. Although the genetic gain for milk production in this strategy was lower than in the first strategy, genetic gain for profit showed slightly differed. © 2012 Elsevier B.V.

One important question about genomic evaluation is how distance between generations of individuals in reference population and selection candidates, would affect the accuracy of genomic estimated breeding value of selection candidates. There were two schemes in the present study. In first scheme, for each individual a genome consisting 30 chromosomes each with 100 equally spaced single nucleotide polymorphisms (SNPs) and in second scheme a genome consisting 3 chromosomes each with 1000 equally spaced SNPs was simulated. To generate enough linkage disequilibrium between loci, random mating for 50 generations was done in a finite population. In generation 51, population size was expanded to 250 individuals. This structure was continued until generation 55. Individuals in generation 55 were juvenile and did not have phenotypic records and were selection candidates. Heritability was assumed to be 0.3. Our results showed using information from more distant generations would decrease accuracy of genomic estimated breeding values of selection candidates but in scheme in which marker distance was 1 centimorgan, increasing generation number between reference population and selection candidates would decrease accuracy more than scheme in which marker distance was 0.1 centimorgan. According to our results using EBVs of reference population instead of phenotypic records would increase accuracy extremely.

Data including 219 105 test day records of 22 569 first parity Holstein cows in 56 herds were analysed for milk yield, fat content and protein content. Legendre polynomials were used in a random regression model to explain traits curves, additive genetic and permanent environmental effects along days in milk (DIM). Legendre polynomials of order 3 were used to describe additive genetic effects on the traits. For permanent environmental effects, for milk the order of 6 and for fat and protein content the order of 4 were used. Heterogeneity of residual variance was considered. Restricted maximum likelihood (REML) methodology was used to estimate the required parameters. Variations in genetic, permanent environment and residual effects and heritability changes along DIM were computed and illustrated. Daily heritability estimates averaged as 0.22, 0.14 and 0.23 for milk, fat and protein contents, respectively. Minimum correlations between DIM for additive genetic effects were as 0.49, −0.01 and 0.34 for milk, fat and protein contents. There were higher genetic correlations between test day milk yield and protein content compared to fat content. The genetic trend of milk yield has increased over the years from 1971 to 2005, while the genetic trend for fat and protein content declined.

Neuropeptide Y (NPY) and gonadotrophin-releasing hormone receptor (GnRHR) are two candidate genes with a wide variety of physiological functions in growth and especially in reproduction processes. We examined the association of one SNP from each of these genes with growth- and egg production-related traits in Mazandaran native chickens. Two hundred and six individuals were genotyped by PCR-RFLP. Marker-trait association analyses were performed using both breeding value and phenotypic information. The data came from 18 successive generations of selection at a Mazandaran native chicken breeding station in Iran. Data were analyzed with a univariate animal model in an ASREML procedure to estimate breeding values of the birds for these traits. Two alleles were found for both genes, A and a alleles for GnRHR, with frequencies of 0.614 and 0.386, B and b alleles for NPY, with frequencies of 0.780 and 0.221, respectively. The additive genetic effects of the GnRHR gene on egg number and egg mass were significant. Also, body weight at sexual maturity was significantly influenced by the NPY gene. We conclude that GnRHR and NPY genes are associated with egg production and growth traits, respectively.

Stochastic simulation was used for studying the impacts of sexed semen on genetic progress and reproductive performance of dairy cows. Three strategies were compared: WSS (use unsexed semen in cows and heifers), SSH (use sexed semen in heifers and unsexed semen in cows) and SSCH (use sexed semen in both cows and heifers). Conception rate (CR) of unsexed semen was considered to be 35% and 65% in cows and heifers, respectively. CR of sexed semen was considered to be 15 (20% in cows and 50% in heifers), 10, 5 and 0 percentage points lower than unsexed semen. Thus, four subschemes were compared under SSCH (SSCH15, SSCH10, SSCH5, SSCH0) and SSH (SSH15, SSH10, SSH5, SSH0). Moreover, the effect was studied in four distinct paths of selection: active sires (AS), young bulls (YB), bull dams (BD) and milking cows (CW). The average genetic superiority of CW was 12% and 9.5% in SSCH15 and SSH15 strategies relative to a base scheme, respectively. The average genetic superiority of CW was 19% and 10.5% in SSCH0 and SSH0, respectively. Regression analysis showed that genetic superiority of CW increased significantly, that is, 0.5% and 0.1% per every 1% increase in CR in SSCH and SSH, respectively. The result showed that there is a significant difference between genetic superiority of cows in SSCH and SSH schemes. Widespread and limited use of sexed semen in commercial dairy herds resulted in a large genetic advantage in CW. The genetic advantage of gender control was minimal in the selection paths of AS, YB and BD. Open days and services per conception reached to 153 v. 125 days and 5 v. 2.86 under SSCH15 compared with WSS. The age at first calving increased from 774 to 790 days in SSH15 and SSCH15 strategies. Mean of parities decreased to 2.26 v. 2.42 by using sexed semen. The widespread use of sexed semen increased the age average of cows in all parities. Sexed semen increased selection intensity in the CW path, and this contributed to the genetic merit of future cows. On the other hand, sexed semen had a negative effect on the reproductive performance of dairy cows. Generally, although the effect of widespread use of sexed semen (SSCH) on genetic progress is significantly more than limited use of sexed semen (SSH), SSCH decreased reproductive performance of dairy herds dramatically, and this suggests that SSH scenarios might be more appropriate in animal breeding programs. Finally, to make a decision of which schemes are more convenient, it is necessary to compare the economic aspects of schemes.

A hypothesis was tested that providing the breeder hens with exogenous thyroxine (T(4)) would help their offspring to better survive the ascites-inducing condition during the growing period. In total, 132 broiler breeder hens were randomly assigned to one of 3 treatments: control (CON), hypothyroid [HYPO; 6-N-propyl-2-thiouracil (PTU)-treated], and hyperthyroid (HYPER; T(4)-treated). The hens were artificially inseminated, and the hatching eggs (n = 1,320) were incubated. No eggs in the HYPO group hatched. The 1-d-old male chicks (n = 288) from other groups were reared for 42 d under standard or low ambient temperature to induce ascites. Blood samples were drawn from the hens, embryos, and broilers for determination of T(4) and triiodothyronine (T(3)). The hematocrit was also determined in broilers. The PTU-treated hens had an increased BW along with lower plasma T(3) and T(4) concentrations. Plasma T(4) was higher in the HYPER hens compared with CON hens, but T(3) concentration was not different between these groups. The fertility rate was not affected by either hypo- or hyperthyroidism. The embryos in the HYPO group had lower plasma T(3) and T(4) concentrations at d 18 of embryonic development and internal pipping. Higher plasma T(4) was recorded in the HYPER birds at internal pipping, although plasma T(3) concentration was not affected at this stage. Maternal hyperthyroidism decreased the overall incidence of ascites in the cold-exposed chickens (10.0 vs. 33.4% for HYPER and CON groups, respectively). Although the effect of maternal PTU or T(4) treatment on plasma thyroid hormones and on the right ventricle-to-total ventricular weight ratio in the broilers was not significant, the cold-exposed healthy CON chicks showed higher hematocrit values, compared with the HYPER birds. It was concluded that maternal hyperthyroidism could decrease the incidence of cold-induced ascites in broiler chickens; however, probable causal mechanisms remain to be elucidated.

New molecular techniques focused on genome analysis, open new possibilities for more accurate evaluation of economiclly important traits in farm animals. Milk production traits are typical quantitative characteristics controlled by a number of genes. Mutations in their sequences may alter animal performance as well as their breeding values. In this study, we investigated the effect of Kpn2I restriction fragment length polymorphisms in the leptin gene, on bull breeding values for milk yield, fat, and protein yield, and their percentage. In order to test for an association between the leptin single-nucleotide polymorphism in exon 2 and milk productivity, we genotyped 134 Iranian Holstein bulls. Breeding values for milk-related traits (milk yield, fat, and protein yield and percentage) were estimated using the BLUP based on an animal model. The effect of the genotypes of Kpn2I polymorphism on the breeding values for milk-related traits was examined using least square methods. The T allele frequency was 0.425. Genotypes were distributed according to the Hardy-Weinberg equilibrium. Bulls with TT genotype had higher milk, fat and protein yield compared with TC and CC bulls (P < 0.05). Bulls with CC genotype had higher protein percentage compared with TT and TC bulls (P < 0.05). The association between leptin polymorphism with milk production traits suggests that this marker may be useful for selection based on molecular information.

In recent years, there has been an increasing interest toward the use of bovine genotyped embryos for commercial embryo transfer programs. Biopsy of a few cells in morulla stage is essential for preimplantation genetic diagnosis (PGD). Low amount of DNA have limited performing the several molecular analyses within PGD analyses. Whole genome amplification (WGA) promises to eliminate this problem. We evaluated the possibility and performance of an improved primer extension preamplification (I-PEP) method with a range of starting bovine genomic DNA from 1-8 cells into the WGA reaction. We optimized a short and simple I-PEP (ssI-PEP) procedure (~3h). This optimized WGA method was assessed by 6 loci specific polymerase chain reactions (PCRs), included restriction fragments length polymorphism (RFLP). Optimized WGA procedure possesses enough sensitivity for molecular genetic analyses through the few input cells. This is a new era for generating characterized bovine embryos in preimplantation stage.