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.

Association of pituitary specific transcription factor-1 (POU1F1) gene polymorphism with growth and biometric traits and blood metabolites in Iranian Zel and Lori-Bakhtiari sheep.

The pituitary-specific positive transcription factor 1 (POU1F1) gene has been the subject of many recent studies because of its important roles in growth and development of mammals. In this study, we investigated the single nucleotide polymorphisms (SNPs) at the third exon of POU1F1 gene and its association with growth and biometric traits and blood metabolites in two Iranian sheep breeds, Zel and Lori-Bakhtiari. Blood samples from 90 Lori-Bakhtiari and 90 Zel sheep were collected to extract DNA and the 295-bp fragment of the POU1F1 gene was amplified and the restriction fragment length polymorphism (RFLP) technique was adopted for genotyping. A SNP was identified in both Lori-Bakhtiari and Zel sheep breeds, which represents a non-synonymous single base mutation at restriction site for endonuclease AciI. The results revealed differential frequencies of alleles between the two studied breeds, where A allele was more frequent in Lori-Bakhtiari breed, while G allele was more frequent in Zel breed. When POU1F1 genotypes were tested, the animals with AA genotype had a higher weaning weight than those with GG genotype (p < 0.05), however there were not significant association between genotypes and birth weight, biometric traits (body length, body height, heart girth, thigh girth and abdominal girth) and blood metabolites (triglyceride and cholesterol) of the studied breeds (p > 0.05). These findings imply that the POU1F1 polymorphism may affect weaning weight, thus can be used as a molecular marker for this production trait.

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.

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.

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.

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.

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.

Effects of 6 times daily milking during early versus full lactation of Holstein cows on milk production and blood metabolites.

An experiment was conducted to determine the effects of different milking frequencies on entire lactation production performance in Holstein cows. One hundred twenty Holstein cows were assigned to 3 milking treatments (35 multiparous and 5 primiparous cows in each): 1) milking 6 times daily for the entire lactation (6x); 2) milking 6 times daily for the first 90 d in milk (DIM) and switching to 3 times daily milking afterward (6x-3x); and 3) milking 3 times daily for the entire lactation (3x). Milk yield was recorded every other day during the first 60 DIM and on 2 consecutive days per week subsequently. Cows were weighed and scored for their body condition immediately after parturition and monthly afterward. Blood and milk samples were taken from each cow on 30, 60, 90, 120, 150, 210, and 270 DIM, with an additional blood sampling on 15 DIM. Milk and fat corrected milk yield was greater for 6x and 6x-3x cows than for 3x cows (36.82, 37.32, and 36.1, 36.75 versus 34.56, 35.33 kg/d, respectively) during the experimental period. Milk fat and lactose percentage were not different among treatments, but milk protein was lower in 6x cows than in 6x-3x and 3x cows. Blood glucose concentration was higher and blood nonesterified fatty acids and beta-hydroxybutyrate concentration were lower in 3x cows than in 6x and 6x-3x cows during early lactation. Dry matter intake was greater in 6x cows than in 6x-3x and 3x cows (23.05, 22.58, and 22.45 kg/d, respectively). The 3x cows began to gain weight earlier than the 6x and 6x-3x cows, but there was no difference among groups for BW change regarding the entire experimental period. These results indicate that increasing milking frequency to 6 times daily increases milk yield only during early lactation and that there are no advantages of milking 6 times daily compared with 3 times daily during the mid and late lactation periods. Given the results of this study and the economical aspects of production, milking 6 times daily until 90 DIM and subsequently switching to milking 3 times daily is preferred.

Monitoring inbreeding trends and inbreeding depression for economically important traits of Holstein cattle in Iran.

Pedigree information of 852,443 registered Holstein cows and bulls, collected by the Animal Breeding Center of Iran from 1971 to 2007, was used to calculate inbreeding coefficients and their effect on production, reproduction, somatic cell count, calving ease, and longevity traits. The average inbreeding coefficient for the entire population was 2.90%, ranging from zero to 47.03%. The rates of inbreeding from 1989 to 2007 were 0.22 and 0.15% per year for females and males, respectively. The rates were higher after 2000, being 0.31 and 0.21% per year for females and males, respectively. Inbreeding had a deleterious effect on most traits. For the first 3 lactations, the inbreeding depression per 1% increase in inbreeding was -18.72, -16.19, and -27.38 kg for milk yield, -0.443, -0.367, and -0.690 kg for fat yield, and -0.476, -0.425, and -0.66 kg for protein yield, respectively. For all reproductive traits, the observed undesirable effect of inbreeding was not significant, except for the calving interval (0.53 d per 1% increase in inbreeding) in the third parity and age at first calving (0.45 d per 1% increase in inbreeding). Calving ease in heifers and cows was significantly influenced by the inbreeding of the dam, indicating that highly inbred cows had a higher incidence of difficult calvings. The estimate of inbreeding depression for somatic cell score was low and significant only for the third lactation. However, animals with high inbreeding coefficient tended to have higher somatic cell scores than animals with low inbreeding coefficients. For type traits, the influence of inbreeding was significant only for stature, chest width, body depth, size, rear udder height, suspensory ligament, udder depth, and front and rear teat placement. Cows with high levels of inbreeding coefficient were at higher relative risk of being culled.