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.

Effects of dietary curcumin supplementation on seminal quality indices and fertility rate in broiler breeder roosters.

1. Decreased semen quality is an underlying contributor to age-related subfertility in broiler breeder roosters. This study investigated the effects of dietary curcumin (derived from turmeric) supplementation as an antioxidant source on semen quality and fertility in broiler breeder roosters. 2. Twenty-eight Ross 308 roosters were randomly allotted to four groups with seven birds in each and were fed a standard diet supplemented with different levels of curcumin at 0 (C0), 10 (C10), 20 (C20) and 30 (C30) mg/bird per day from 48 through to 61 weeks of age. Body weight and semen quality traits were evaluated on a weekly basis and seminal concentrations of malondialdehyde (MDA) as a measure of antioxidation status were quantified at one-week intervals during the first 11 weeks of the trial (48-59 weeks of age). Semen samples from last 2 weeks (60 and 61 weeks of age) were used to artificially inseminate to assess the sperm-egg penetration (SP) in perivitelline membrane and fertility rates. 3. Except for body weight and ejaculate volume, other characteristics, including semen concentration, total sperm production, progressive motility and plasma membrane integrity were linearly improved by the increasing levels of curcumin supplementation (P < 0.01). However, dietary curcumin levels were linearly and quadratically associated with decreased seminal concentration of MDA (P < 0.01 and P < 0.03), percentage of abnormal sperm (P < 0.01 and P < 0.07) and increased plasma membrane functionality (P < 0.01 and P < 0.04), respectively. The SP holes in perivitelline membrane were increased in a linear and quadratic manner in response to increasing levels of curcumin (P < 0.01). Moreover, fertility rate was linearly improved (P < 0.01) as the dosage of curcumin increased, and resulted in 8, 12 and 14% improvements in the birds fed C10, C20 and C30, compared to C0, respectively. 4. In conclusion, the results showed that increasing levels of dietary supplementation of curcumin was associated with beneficial effects on semen quality indices and fertility rate in aged broiler breeder roosters.

The evolutionary history of the DMRT3 'Gait keeper' haplotype.

A previous study revealed a strong association between the DMRT3:Ser301STOP mutation in horses and alternate gaits as well as performance in harness racing. Several follow-up studies have confirmed a high frequency of the mutation in gaited horse breeds and an effect on gait quality. The aim of this study was to determine when and where the mutation arose, to identify additional potential causal mutations and to determine the coalescence time for contemporary haplotypes carrying the stop mutation. We utilized sequences from 89 horses representing 26 breeds to identify 102 SNPs encompassing the DMRT3 gene that are in strong linkage disequilibrium with the stop mutation. These 102 SNPs were genotyped in an additional 382 horses representing 72 breeds, and we identified 14 unique haplotypes. The results provided conclusive evidence that DMRT3:Ser301STOP is causal, as no other sequence polymorphisms showed an equally strong association to locomotion traits. The low sequence diversity among mutant chromosomes demonstrated that they must have diverged from a common ancestral sequence within the last 10 000 years. Thus, the mutation occurred either just before domestication or more likely some time after domestication and then spread across the world as a result of selection on locomotion traits.

Worldwide frequency distribution of the 'Gait keeper' mutation in the DMRT3 gene.

For centuries, domestic horses have represented an important means of transport and served as working and companion animals. Although their role in transportation is less important today, many horse breeds are still subject to intense selection based on their pattern of locomotion. A striking example of such a selected trait is the ability of a horse to perform additional gaits other than the common walk, trot and gallop. Those could be four-beat ambling gaits, which are particularly smooth and comfortable for the rider, or pace, used mainly in racing. Gaited horse breeds occur around the globe, suggesting that gaitedness is an old trait, selected for in many breeds. A recent study discovered that a nonsense mutation in DMRT3 has a major impact on gaitedness in horses and is present at a high frequency in gaited breeds and in horses bred for harness racing. Here, we report a study of the worldwide distribution of this mutation. We genotyped 4396 horses representing 141 horse breeds for the DMRT3 stop mutation. More than half (2749) of these horses also were genotyped for a SNP situated 32 kb upstream of the DMRT3 nonsense mutation because these two SNPs are in very strong linkage disequilibrium. We show that the DMRT3 mutation is present in 68 of the 141 genotyped horse breeds at a frequency ranging from 1% to 100%. We also show that the mutation is not limited to a geographical area, but is found worldwide. The breeds with a high frequency of the stop mutation (>50%) are either classified as gaited or bred for harness racing.

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.

Associations of growth hormone secretagogue receptor (GHSR) genes polymorphisms and protein structure changes with carcass traits in sheep.

Growth hormone secretagogue receptor (GHSR), a G protein-coupled receptor that binds ghrelin, plays an important role in the central regulation of pituitary growth hormone secretion, food intake, and energy homeostasis. Ghrelin receptor (GHSR) modulates many physiological effects and therefore is a candidate gene for sheep production performance. Polymorphism of the GHSR gene was detected by PCR-SSCP and DNA sequencing methods in 463 individuals. Two different structures in protein and nine single nucleotide polymorphisms (SNPs) were identified. The evaluation of the associations between these SSCP patterns with carcass traits suggests a positive effect of genotype TT and B structure on carcass weight, and body length (P<0.05). In addition, the animal with TC had greater abdominal fat than those with TT and CC (P<0.05) while CC genotype contributed to low blood cholesterol (P=0.04). The results confirm the hints suggesting that GHSR is a preferential target for further investigation on mutations that influence carcass trait variations.

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.

Determining the optimum replacement policy for Holstein dairy herds in Iran.

The objective of this study was to determine the optimum replacement policy for Holstein dairy herds in Iran using a dynamic programming model. Cows were described in terms of state variables that included milk production class, parity, pregnancy status, and month in milk with a 1-mo stage length. The objective function maximized the net present value of cows over a 15-yr planning horizon. Markov simulation was used to estimate expected herd dynamics under the optimal decision plan determined by dynamic programming. Stochastic elements included probabilities of pregnancy and abortion, production level, and involuntary culling. The optimum annual culling rate was estimated to be 31.4%, and cows had an expected herd life (time from first calving until culling) of 3.18 yr. High replacement cost and low carcass value resulted in only 2.87% voluntary culling (i.e., optimal model-based replacement). Assuming a heat detection rate of 0.4, cows averaged 2.8 services per lactation under the optimal policy. Sensitivity analyses were carried out to evaluate the effect of milk price, herd-average production, feed cost, heifer price, and carcass value on optimum replacement decisions. Herd-average production, replacement cost, and risk of involuntary culling were important factors affecting the optimal culling policy. Changes in the price of feed, calves, and milk and the probability of pregnancy had no considerable effect on the optimal policy considering the market situation in Iran during 2008.

Comparison of four induced molting methods based on subsequent performance and welfare of Single Comb White Leghorn hens.

A total of 400 Single Comb White Leghorn hens at 80 weeks of age were used in present study. Four treatment groups that were consisted of six replications with 10 hens per each replication were considered. In the first treatment, food and water were removed for the first 2, 4, 6 and 8 days. However, on days 3, 5, 7, 9 and on day 10 until day 28 hens were fed 45 g of food per hen (ON-OFF group). In the second and third groups, food was withdrawn for 10, 14 days, respectively and oyster shell and water were provided for ad libitum until day 28 (California and North Carolina treatments (CAL, NC groups)). The last group (full-food treatments (FF group)) was the hens that were non-food-deprived and were fed corn molt diet for 28 days ad libitum. In all treatment groups at day 29, hens were returned to a full food layer ration and received 16 h of light day(-1). Body weight, egg production, egg weight, relative eggshell weight, internal egg quality, egg specific gravity and mortality were determined. Differential leukocyte count and antibody response were also measured. The results demonstrated that induced molting increased egg production according to pre-molt egg production. There was not a significant difference in the rate of egg production during the peak period of post molt production for treatments. No significant differences were detected in differential leukocyte counts and antibody response against Sheep Red Blood Cell (SRBC) between treatments at pre molt and post molt of the experiment. This study indicated that diets with high corn level (FF groups) are effective and simplified nonfood removal procedure for welfare molting hens.

Animal model estimation of genetic parameters for most important economic traits in Iranian native fowls.

(Co)Variance components and genetic parameters for economic traits in Iranian native fowls were estimated using multivariate animal model analysis with DFREML procedure. The data of four stations of native fowls breeding (Mazandaran: 49536, Esfahan: 23108, West Azarbaijan: 24890 and Fars: 30279) was containing records of cocks and hens collected during period of 1988 to 2006. The recorded traits were Body weight (at 8 weeks or 12 weeks), Age at first egg, egg number at 12 first weeks of production and mean egg weight between 28 to 32 weeks. The most estimated heritabilites, except egg number, were more than 0.20. The highest heritabilites for all traits were related to Fars station, whereas most heritabilites in West Azarbaijan were less than other stations. The heritability for egg number was estimated 0.099+/-0.018 for Esfahan to 0.322+/-0.012 for Fars. The estimated heritabilities of body weight were medium to high and varied from 0.228+/-0.014 for Esfahan to 0.548+/-0.014 for Fars, While, the heritabilities of mean egg weight were high and ranged from 0.223+/-0.021 for West Azarbaijan to 0.638+/-0.013 for Fars. The heritability for age at first egg was estimated 0.270+/-0.021 for Esfahan to 0.520+/-0.014 for Fars. The most estimated genetic correlations, except between Body weight and Egg weight and between age at first egg and egg weight, were negative. The direct genetic correlations between maturity age and egg number were high and negative, ranging from -0.384+/-0.033 to -0.987+/-0.003 for Mazandaran and Fars, respectively.

Detection of quantitative trait loci affecting milk production traits on 10 chromosomes in Holstein cattle.

Sons (n = 71 to 75) of each of six Holstein sires were genotyped at 69 microsatellite loci covering a total of 676 cM on chromosomes 3, 5, 9, 10, 13, 15, 17, 20, 23, and 26. Estimates of quantitative trait loci (QTL) effect and location were made using a least squares interval mapping approach based on daughter yield deviations of sons for 305 d milk, fat, and protein yield and fat and protein percentage. Thresholds for statistical significance of QTL effects were determined from interval mapping of 10,000 random permutations of the data across the bull sire families and within each sire family separately. Analyses combining data across sires indicated the presence of QTL affecting milk, fat, and protein yield on chromosomes 20 and 26 and a QTL affecting fat and protein percentage on chromosome 3. Analyses within each sire family separately indicated the presence of segregating QTL in at least one family on 7 of the 10 chromosomes. Statistically significant estimates of QTL effects on breeding value ranged from 438 to 658 kg of milk, from 17.4 to 24.9 kg of fat, 13.0 to 17.0 kg of protein, 0.04 to 0.17% fat, and 0.07 to 0.10% protein.

The effect of using different culling regimens on genetic response with two-trait, two-stage selection in a nucleus broiler stock.

Stochastic simulation was used to study the effect on genetic response and inbreeding of various two-stage two-trait culling strategies. Four different parameter sets were considered for the two traits, BW and egg number. Selection of replacement animals was based on animal model best linear unbiased prediction (BLUP) to obtain estimated breeding values (EBV) at the second stage. Culling at Stage 1 was based on either animal model BLUP or phenotypes, and information from culled animals was either available or not available for calculation of second stage EBV. Besides founder individuals, six discrete generations were considered. Culling based on BLUP of two traits at Stage 1 produced higher response than culling on phenotypic evaluations. It was found that culling based on phenotypic evaluation and not carrying information to the second stage reduce rates of response by 9 to 17% and produced inbreeding higher than or close to that of BLUP selection. This study clearly shows that a double penalty of less response and higher inbreeding is generally paid for not using all information. Optimum selection schemes will depend on relative costs and benefits of collecting and processing the extra information required for full BLUP selection schemes.

Using recent versus complete pedigree data in genetic evaluation of a closed nucleus broiler line.

Stochastic simulation was used to study the effect of using full data and pedigree structure vs more recent data and pedigree structure to obtain best linear unbiased predictors (BLUP) of breeding values for single trait selection. Simulations used heritabilities of 0.10 and 0.50, with a population structure of 20 sires each mated to two dams, each producing 10 progeny, with 11 hatches from an unselected base population under both discrete and overlapping generations. Selection of parents was based on BLUP of breeding values using an animal model. The use of the last two generations of data and pedigrees gave the same selection response as when using full data and pedigree structure, for both heritabilities. Under discrete generations with use of only the last generation data and pedigree, which is similar to phenotypic evaluation, response to selection decreased by 21 and 3.8% at Generation 10 compared to selection response when using the full data and pedigree for heritabilities of 0.10 and 0.50, respectively. Corresponding decreases in inbreeding were 72 and 37%. The amount of central processing unit time for genetic evaluation when using the last six, four, and two generations of data and pedigree was reduced to 70, 40, and 11% of that when using the full data set, for a heritability of 0.10 and discrete generations. Very similar values were observed for a heritability of 0.50 and also under overlapping generations.