Genome-wide study of linkage disequilibrium, population structure, and inbreeding in Iranian indigenous sheep breeds.

Knowledge of linkage disequilibrium (LD), genetic structure and genetic diversity are some key parameters to study the breeding history of indigenous small ruminants. In this study, the OvineSNP50 Bead Chip array was used to estimate and compare LD, genetic diversity, effective population size (Ne) and genomic inbreeding in 186 individuals, from three Iranian indigenous sheep breeds consisting of Baluchi (n = 96), Lori-Bakhtiari (n = 47) and Zel (n = 47). The results of principal component analysis (PCA) revealed that all animals were allocated to the groups that they sampled and the admixture analysis revealed that the structure within the populations is best explained when separated into three groups (K = 3). The average r2 values estimated between adjacent single nucleotide polymorphisms (SNPs) at distances up to 10Kb, were 0.388±0.324, 0.353±0.311, and 0.333±0.309 for Baluchi, Lori-Bakhtiari and Zel, respectively. Estimation of genetic diversity and effective population size (Ne) showed that the Zel breed had the highest heterozygosity and Ne, whereas the lowest value was found in Baluchi breed. Estimation of genomic inbreeding using FROH (based on the long stretches of consecutive homozygous genotypes) showed the highest inbreeding coefficient in Baluchi and the lowest in Zel breed that could be due to higher pressure of artificial selection on Baluchi breed. The results of genomic inbreeding and Ne showed an increase in sharing haplotypes in Baluchi, leading to the enlargement of LD and the consequences of linkage disequilibrium and haplotype blocks confirmed this point. Also, the persistence of the LD phase between Zel and Lori-Bakhtiari was highest indicating that these two breeds would be combined in a multi-breed training population in genomic selection studies.

Detecting selection signatures in three Iranian sheep breeds.

The objective of genome mapping is to achieve valuable insight into the connection between gene variants (genotype) and observed traits (phenotype). Part of that objective is to understand the selective forces that have operated on a population. Finding links between genotype-phenotype changes makes it possible to identify selective sweeps by patterns of genetic variation and linkage disequilibrium. Based on Illumina 50KSNP chip data, two approaches, XP-EHH (cross-population extend haplotype homozygosity) and FST (fixation index), were carried out in this research to identify selective sweeps in the genome of three Iranian local sheep breeds: Baluchi (n = 86), Lori-Bakhtiari (n = 45) and Zel (n = 45). Using both methods, 93 candidate genomic regions were identified as harboring putative selective sweeps. Bioinformatics analysis of the genomic regions showed that signatures of selection related to multiple candidate genes, such as HOXB9, HOXB13, ACAN, NPR2, TRIL, AOX1, CSF2, GHR, TNS2, SPAG8, HINT2, ALS2, AAAS, RARG, SYCP2, CAV1, PPP1R3D, PLA2G7, TTLL7 and C20orf10, that play a role in skeletal system and tail, sugar and energy metabolisms, growth, reproduction, immune and nervous system traits. Our findings indicated diverse genomic selection during the domestication of Iranian sheep breeds.

Short communication: Effects of diets containing supplemental fats on ruminal fermentation and milk odd- and branched-chain fatty acids in dairy cows.

There is a growing interest in odd- and branched-chain fatty acids (OBCFA) in milk following reports that several branched-chain fatty acids (FA) have health promoting effects, and certain milk OBCFA could serve as a biomarker to assess ruminal function. Twenty-four Holstein cows were fed 3 low-forage diets containing 30 g/kg of dry matter of prilled palm fat (PPF), sunflower oil (SO), or an equal mixture of both fats (experiment 1) or 3 diets containing 30 g/kg of dry matter of SO with a forage-to-concentrate ratio of 39:61, 44:56, or 48:52 (Experiment 2); diets were fed to investigate milk OBCFA composition and to explore the relationships between ruminal VFA and milk OBCFA using principal component analysis. Including SO in diets decreased yields of milk 13:0 anteiso, 15:0 anteiso, 15:0, 17:0, cis-9 15:1, and cis-9 17:1 compared with PPF. The molar proportion of ruminal propionate was the lowest and the yields of milk 14:0 iso and 16:0 iso were the greatest with the diet containing both fat supplements. Replacing concentrate with forages linearly increased ruminal acetate and yields of milk 13:0 iso, 14:0 iso, 15:0 iso, 16:0 iso, 17:0 iso, 13:0 anteiso, 15:0 anteiso, 15:0, 17:0, cis-9 15:1, and cis-9 17:1. The principal component analysis revealed that ruminal molar proportion of acetate related to concentrations of milk iso FA containing <17-carbon, whereas ruminal propionate related to milk 15:0, 17:0, cis-9 15:1, and cis-9 17:1, with the stronger correlations between milk OBCFA and ruminal acetate than propionate. No associations were found between ruminal molar proportion of butyrate and milk OBCFA concentrations. The results suggest that complete replacement of PPF with SO at 30 g/kg of dry matter in low-forage diets is not an effective strategy to enhance bioactive branched-chain FA in milk, rather this feeding practice lowers anteiso FA in milk; however, increasing forage proportion in diets containing SO enhances several iso and anteiso FA in milk. The milk OBCFA concentrations have stronger correlations with ruminal acetate molar proportion than with propionate or butyrate in cows fed diets containing supplemental fats.

Effect of tert-butyl hydroquinone on bull semen cryopreservation.

BACKGROUND: Many studies have been shown that freezing induced oxidative stress has detrimental effect on post-thaw sperm quality. OBJECTIVE: This study was conducted to investigate the effect of tert-butyl hydroquinone (tBHQ) on bull semen crtopreservation. MATERIALS AND METHODS: In this study, four different levels of tBHQ [Optidyl containing zero (T0), 2.5 (T2.5), 5 (T5), and 7.5 µM (T7.5) tBHQ] was used to study the effect of tBHQ on freezability of bull semen. On each collection day, four ejaculates were collected (a total of 24 ejaculates from four bulls), pooled and divided to four equal parts. Each part was diluted with one of the above-mentioned extenders and frozen. After thawing, sperm motility, plasma membrane functionality and integrity, apoptosis status and mitochondrial activity were assessed. RESULTS: The results show that total sperm motility was significantly higher in T5 compared to other groups. The value of VSL was significantly lower in T5 compared to T0. Also, T5 resulted in lower LIN and STR versus T0 and T2.5 groups. All extenders containing tBHQ resulted in a significantly higher percentage of sperm with functional membrane compared to T0 groups. Finally, Apoptosis related parameters and mitochondrial activity were not significantly difference between the groups. CONCLUSION: adding 5 µM tBHQ to the bull semen extender can be beneficial for post-thaw sperm quality. Also, in vivo or in vitro fertility test is recommended to test fertilizing ability of tBHQ exposed sperm.

Relationship between calving difficulty and fertility traits in first-parity Iranian Holsteins under standard and recursive models.

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 DIVERSITY, PARENTAGE VERIFICATION AND GENETIC BOTTLENECKS EVALUATION IN IRANIAN TURKMEN HORSE BREED.

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.

Effect of allele frequencies, effect sizes and number of markers on prediction of quantitative traits in chickens.

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.

Dissection of additive genetic variability for quantitative traits in chickens using SNP markers.

The aim of this study was to separate marked additive genetic variability for three quantitative traits in chickens into components associated with classes of minor allele frequency (MAF), individual chromosomes and marker density using the genomewide complex trait analysis (GCTA) approach. Data were from 1351 chickens measured for body weight (BW), ultrasound of breast muscle (BM) and hen house egg production (HHP), each bird with 354 364 SNP genotypes. Estimates of variance components show that SNPs on commercially available genotyping chips marked a large amount of genetic variability for all three traits. The estimated proportion of total variation tagged by all autosomal SNPs was 0.30 (SE 0.04) for BW, 0.33 (SE 0.04) for BM, and 0.19 (SE 0.05) for HHP. We found that a substantial proportion of this variation was explained by low frequency variants (MAF <0.20) for BW and BM, and variants with MAF 0.10-0.30 for HHP. The marked genetic variance explained by each chromosome was linearly related to its length (R(2) = 0.60) for BW and BM. However, for HHP, there was no linear relationship between estimates of variance and length of the chromosome (R(2) = 0.01). Our results suggest that the contribution of SNPs to marked additive genetic variability is dependent on the allele frequency spectrum. For the sample of birds analysed, it was found that increasing marker density beyond 100K SNPs did not capture additional additive genetic variance.

Fat source and dietary forage-to-concentrate ratio influences milk fatty-acid composition in lactating cows.

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.

Economic values under inappropriate normal distribution assumptions.

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.

Association of neuropeptide Y and gonadotrophin-releasing hormone receptor gene SNPs with breeding value for growth and egg production traits in Mazandaran native chickens.

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.

Effect of widespread and limited use of sexed semen on genetic progress and reproductive performance of dairy cows.

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.

Breeding objectives for Holstein dairy cattle in Iran.

Trait-by-trait and multiple trait bioeconomic modeling were used to derive farm-specific economic weights (EW) for a wide range of traits under different production and economic circumstances to define breeding objectives for Holstein dairy cattle in Iran. Production parameters and economic data were gathered on 10 dairy farms from March 2008 to February 2010. The EW (economic values multiplied by gene expressions, in US dollars per unit of trait per calf born from sires of self-replacing females in planning horizon of 20 yr) were estimated to be $0.15 per kilogram of milk yield; $1.36 per kilogram of fat yield; -$1.02 per kilogram of protein yield; $4.59 per month of longevity; -$1.22 per kilogram of mature cow weight; -$105.67 for combined somatic cell score and clinical mastitis; -$1.35 and -$0.28 for percentage direct and maternal calving difficulties, respectively; -$3.98 for percentage direct stillbirth; -$0.76 per day of age at first calving; -$0.72 per calving interval day; and $0.91 for percentage 56-d nonreturn rate on averages across investigated farms. The coefficient of variation of economic weights across the 10 farms was lowest for direct calving difficulty and highest for calving interval. The proposed Iranian selection index was compared with selection indices of major countries exporting semen to Iran. Average relative emphasis for production, durability, and health and reproduction, across all exporter countries, was 41, 37.5, and 21.5%, respectively, whereas the respective values were 50, 14, and 36% for the Iranian index. Significant differences in selection indices may potentially decrease the utility of importation of semen as a means of achieving sustainable genetic progress in Iran. Results obtained in this study provide important information about economic values of traits that can be used to improve the Iranian national progeny testing program as well as importation rules for semen to Iran.

Maternal hyperthyroidism is associated with a decreased incidence of cold-induced ascites in broiler chickens.

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.

A short and simple improved-primer extension preamplification (I-PEP) procedure for whole genome amplification (WGA) of bovine cells.

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.

Bio-economic model to evaluate twinning rate using sexed embryo transfer in dairy herds.

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.

Estimation of economic values and financial losses associated with clinical mastitis and somatic cell score in Holstein dairy cattle.

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.

Genetic parameters for feed utilization traits in Japanese quail.

Feed costs substantially affect the efficiency of poultry operations, justifying genetic improvement of feed utilization by selection. The current research was conducted to estimate genetic variance for the 4-wk feed conversion ratio (FCR) and its genetic correlations with BW, BW gain (WG), feed intake (FI), and residual feed intake (RFI) in Japanese quail. The data analyzed originated from a line selected for low FCR for 3 generations. In each generation, 35 sires and 70 dams were used as parents for the next generation. Body weight and WG were recorded on a total of 1,226 individuals, whereas FCR, RFI, and FI were recorded on 505 family groups. The results showed that heritability estimates (±SE) of BW at 28 d of age and WG between 7 and 28 d of age were 0.22 ± 0.05 and 0.28 ± 0.06, respectively. For FI, FCR, and RFI, significant genetic variances were estimated. Genetic correlations of FCR between 7 and 28 d of age with WG and FI between 7 and 28 d of age were -0.45 ± 0.09 and 0.24 ± 0.08, respectively. This implies that a low FCR is genetically related to a high WG and low FI. The genetic correlation between FCR from 7 to 28 d of age and RFI from 7 to 28 d of age was 0.26 ± 0.08, indicating that the 2 alternative feed efficiency traits are genetically different traits, and that the correlated genetic response in one of them in response to selection on the other is likely to be only moderate. Genetic correlations of RFI from 7 to 28 d of age with WG and FI between 7 and 28 d of age were 0.08 ± 0.04 and 0.74 ± 0.11, respectively. This reflects the fact that RFI is phenotypically independent of WG, which tends to make the genetic correlation between RFI and WG low as well. In conclusion, all the traits analyzed displayed significant genetic variance, allowing their genetic improvement by selection, yet the alternative feed utilization traits, FCR and RFI, displayed different genetic characteristics.

Response to selection and genetic parameters of body and carcass weights in Japanese quail selected for 4-week body weight.

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.

Response to selection for feed conversion ratio in Japanese quail.

We investigated the effect of selection for 4-wk feed conversion ratio (FCR) on genetic improvement of FCR, BW, weight gain (WG), feed intake (FI), and residual FI (RFI) in Japanese quail. The F line was selected for reduced FCR and the C line was maintained as a randombred control. In each generation, 35 sires and 70 dams were used as parents for the next generation. Three generations of selection were performed. Realized heritability for FCR was calculated as the ratio of cumulative selection response to the cumulative selection differential, and additionally, genetic response was quantified as the difference between the means of selection and control lines. The results showed that realized heritability for FCR after 3 generations of selection was 0.67. The mean FCR in F line and C line in the last generation was 2.13 and 2.61, respectively. This is 18.4% cumulative genetic improvement, or 6.1% improvement per generation. In the last generation, the means of F and C lines were 193 and 166 g for BW at age 28 d (16.4% total increase, or 5.5% per generation), 184 and 158 g for WG (17.2% total higher gain and 5.7% per generation), 393 and 413 g for FI (4.9% total higher consumption and 1.6% per generation), and -24.5 and 10.2 for RFI (-34.7 g of cumulative gain; -11.6 g per generation), respectively. These results show that selection to decrease FCR increases BW and WG and decreases FI and RFI as a correlated response.