j. shodja

Copy number variation (CNV) consist of deletion, insertion, and duplications. It is an important source of genetic variation in organisms and thus influences on the gene expression and phenotypic variation. Copy number variation (CNV) is one of the structural variant with an intermediate size class larger than 50bp which involves unbalanced rearrangements that increase or decrease the amount of DNA (Pirooznia et al 2015, Alkan et al 2011). The size of CNVs is larger than 50bp, while smaller segments are known as insertions or deletions (indels). Thereupon these structural variations comprise more polymorphic than SNPs because of enormity, detection of them and their effect on phenotype has caught the attention of many researchers recently. It has been reported that CNVs changes in gene dosage and regulation as well as in transcript structure, and thus contribute to phenotypic variability (Pirooznia et al 2015, Alkan et al 2011). The pea-comb phenotype is caused by a CNV mapping to intron 1 of the SRY (sex determining region Y)-box 5 (SOX5) gene (Wright et al. 2009). Late feathering in chickens is due to incomplete duplication in PRLR and SPEF2 genes (Elfrink et al. 2008). In swine, dominant white colour has been related with a duplication of a 450-kb fragment of the KIT gene (Giuffra et al. 1999) and a splice mutation causing the skipping of exon 17 (Giuffra et al. 1999). In sheep, doubling in the ASIP gene results in the regulation of pigment in body coat (Norris et al. 2008). Doubling the 4.6 k base pair into the six introns of the STX17 gene results in a gray body color in the horse with age. Deletion of the intergenic region with a length of 11.7 kbp in the goat genome leads to the removal of horns (Clop et al. 2012). Chicken is the most intensively farmed animal on earth and is a major food source with billions of birds used in meat and egg production each year. A big share of chicken CNVs involves protein coding or regulatory sequences. A comprehensive study of chicken CNV can provide valuable information on genetic diversity and assist future analyses of associations between CNV and economically important traits in chickens. Unique chicken genome with macro and micro chromosomes and its biology make it an ideal organism for studies in development and evolution, as well as applications in agriculture and medicine (Burt 2005). In the last several years, There has been an increasing interest in the study of CNVs in the chicken. This study focuses on comparison of CNV between the broilers and layers chicken to find evidence of domestication on the genome using whole genome sequencing.

we used n=90 female birds of two commercial broiler (n=40) and layer (n=50) chicken. The broilers (BRs) were represented by 20 DNA samples of each of two lines (BRA and BRB) established independently and previously collected as part of the AVIANDIV project. In the layer group (LRs), data from 25 birds each from purebred white (WL) and brown (BL) egg laying populations, sequenced in the frame of the SYNBREED project (http://www.synbreed.tum.de/index.php?id=2 ,(were included. The paired-end reads with a read length of 101bp were mapped against the current reference genome assembly Galgal6 using the Burrows-Wheeler aligner (bwa, 0.6.2-r126 Version, with default parameters. Duplicate reads were masked during post-processing using the Picard tool set (version 2.9.2, http://picard.sourceforge.net). Finally, Genome Analysis Toolkit-3.3.0 was used to realign reads for correcting errors caused by InDels. Using GATK software package and Depth Of Coverage function (McKenna et al 2010), the depth of readings was calculated for each sample. Then filter out reads with mapping quality below 20. Because comparing the genomes of individuals in different groups was time consuming and computationally difficult for all parts of the genome, the genomes of each individual were divided into 1000 bp non-overlapping windows and the average reading depth per window was calculated. Then the results were normalized against the BL sample that showed highest average depth. In short, we created a correction factor per population and applied it on the depth of coverage value for each window. For all the contrasts, we performed an analysis of variance (ANOVA) as described (Carneiro et al 2014). For the Broilers-Layers contrast we scanned 935247 windows. 70372 windows showed significant by FDR with P < 0.001, with ANOVA using the Benjamini-Hochberg FDR method for multiple corrections (Benjamini and Hochberg 1995).

Mapping sequencing data to galGal6 assembly showed an average 98.61% mapping rate and 11.51 depth. Manhattan plot was plotted for regions of the genome that differed significantly between the two groups (FDR = 0.001). The points above the hypothetical line were identified and examined in a 25 Kbp confidence interval to identify possible genes. 39 regions were identified that half of them dose not contain any genes. Although Long noncoding RNAs are under lower selective pressure than protein-coding genes (Batista and Chang 2013), The other 11 regions contained 16 genes related to long non-coding RNAs. Long noncoding RNAs (lncRNAs) play a critical role in organizing the 3-dimensional genome architecture and regulating gene activity in cis or in trans through multiple mechanisms (Zhang et al 2019, Batista and Chang 2013). 6 othere regions also contained 12 coding genes. Most of the identified genes were somehow linked to the immune system disease or cancer. Genes such as DEDs and TNFAIP8 are involved in programmed cell death (apoptosis) and two genes NPAL3 and RCAN, which are involved in the immune system, had a copy number variation in the studied samples. In addition RCAN is involved in Down syndrome. The PFDN gene, located on chromosome 25, is also involved in Alzheimer's and Parkinson's disease.

The longevity of cows is crucial to the profitability of a dairy farm, and the culling of cows as a result of major health disorders is a significant risk that threatens production systems today. The possibility of taking diseases into account in the selection of dairy cows depends on the economic importance of the diseases. Mastitis and metritis are common diseases among dairy cows that are considered as risk factors for culling cows. The onset of these disorders can be attributed to factors such as environmental and managerial factors, but there is also evidence of a genetic component to each. Many genes are associated with resistance or susceptibility to mastitis and metritis in cattle, and their alleles have been reported. Subclinical mastitis seems to be one of the most important and damaging diseases threatening dairy cattle herds along with reproductive diseases, lameness and possibly some other common diseases such as Para-tuberculosis. Obviously, reducing production costs supports the profitability of dairy farms. By studying the relationship between the incidence rate and health disorders, in order to minimize the deaths due to health disorders, more emphasis has been placed on the health management of cows. The direct and adverse effects of mammary gland disorders (mastitis and nipple injury) on culling are well documented, while there are differences of results on the correlation between reproductive disorders and culling. Contradictory results may be due to differences in the purpose of the study, population, or the methods used. Many factors such as age, breed, production level, and calving season can play a role in the incidence of diseases.

The purpose of this study is to report the prevalence of clinical mastitis and metritis, moreover to investigate environmental and genetic factors affecting these diseases, to estimate the heritability of disease traits and to measure the correlation between disease and production traits in a Holstein cattle herd. Due to the fact that health records are not recorded in the country's farms in a regular and uniform manner, conducting this research is an experiment to collect this type of information so that in the future models can be provided for all Holstein cows in Iran to consider disease relating traits.

Data of 5052 milk yield from 1796 Holstein-Frisian cows has been gathered that had parturition from 2005 to 2009. In this study, using the 305-day milk production variables, parity, year of calving, the frequency of occurrence of clinical mastitis and metritis in cattle diseases using SAS software, using logistic procedure is estimated. The cows have been studied for all the diseases that occurred in all milking period. In logistic regression analysis, the effect of 305 days of milk and other factors in the occurrence of the disorder was investigated as a binary model. The effect of the lactation period in which the disorder was created was included in all analyzes and the fixed effects included milk for 305 days, calving period, calving year and calving season.Log [p. (1-p)] = b0 + b1 * milk305 + b2 * parity + b3 * calveyear + b4 * calve seasonA coefficient of b1 is assigned for the risk factor of milk production, a coefficient of b2 is assigned for the parturition, a coefficient of b3 is assigned for the factor of calving year and a coefficient of b4 is assigned for the factor of calving season. b0 is the logistic regression estimate if there is no predictor other than the response variable in the model. For each estimate of regression coefficients, the probability level, standard error and 95% confidence interval are also calculated. For a particular disease b1, b2, b3 and b4 are regression coefficients. Estimated genetic parameter in this research was heritability of diseases traits that has been done with ASReml software.

Metritis incidence rate is lower than mastitis. The percentage of animals with mastitis and metritis in the herd was 3.11% and 1.67%, respectively. The average calving interval for metritis incidence was 167.3 days and 129.5 days for mastitis. Data analysis of correspondence of metritis and 305 milk yield, parity, the year and the season of calving showed none of the risk factors had relation with the occurrence of clinical mastitis. The heritability of clinical mastitis and metritis were estimated to be 0.27 and 0.23, respectively. We could not find a relationship between milk production and metritis. Can we consider the increase in milk production as a risk factor for disease occurrence? It is very difficult to prove and explain this relationship and there are many contradictions between the results of other studies. From the lack of a proven correlation between milk production and the occurrence of diseases, it can be concluded that if proper management and nutrition provided based on the biological needs of high-yielding cows, then cows with high milk production will not necessarily suffer from diseases in comparison with low-yielding cows.Genetic studies have shown a positive correlation between mastitis and milk production. Erb (1987) and Dehu and Martin (1984) concluded that high milk production could not be a risk factor for mastitis. A study of Ayrshire cows in Finland found that cows with higher milk production during the previous lactation period were at increased risk for mastitis (Grun et al. 1989 and Grun et al. 1990). There are few documented findings on the association between milk production and the incidence of disease. Of course, it should be borne in mind that "milk production" is not the only risk factor for the disease. Concerning diseases in Holstein dairy cattle it seems the occurrence of the disease can also be the result of breeding and nutrition conditions and management. However, identifying all relevant factors and determining their quality and relative importance is difficulty accessible. It is also not easy to estimate all possible interactions between production and disease traits, even with the efficiency of today's computer technology.

In dairy cattle genetic improvement programs, we suggest to record and estimate the breeding values for disease traits and consider them in multi-trait selections among elite sires. The estimated heritability of metritis was lower than clinical mastitis. Keywords: Holstein-Friesian cows, clinical mastitis, metritis, milk 305 days, heritability.

Cashmere is a very fine fiber that is produced by secondary hair follicles in cashmere goat. Based on American test and material association description, cashmere is fine fiber in Asian Indian goat hair follicles with diameter lower than 30 microns. Cashmere is growing as “under coat” in cold season and it shedds during the time from late winter until early spring. It is estimated that 68 goat breeds produce cashmere fibers in the world. Cashmere goats are originated from Asia. The important countries that can produce a large amount of cashmere are China, Mongolia, Iran, Turkey, and India. Total production of cashmere is estimated to be 5mt. During the last decades, due to the economic importance of cashmere, USA, Australia, and NewZealand joined to the cashmere producing countries. Many researchers reported that cold climate is suitable for production of quality cashmere. In this research, effects of nutrition and age on histological characteristics of Raeini Cashmere goat were studied in Tabriz, East Azerbaijan.

For this research, 24 female Raeini cashmere goats were selected. The goats were selected from Baft Raeini cashmere goat breeding and husbandry station. Goats were fed individually   and were treated for 8 months of study based on feeding levels (Maintenance, 0.7 M, 1.4 M, and 1.8M) and age (6 months and 18 months) on fleece growth. The trial was conducted at the khalat-Pushan Research Station, University of Tabriz. The goats allocated to four feeding levels: M (goats fed to maintain live weight, 0.7M (goats fed to lose 3Kg live weight from February to September), 1.4M, and 1.8M (goats fed to gain live weight). Patches of fleece from defined areas were repeatedly shorn at 4 weekly intervals from the right mid side of each goat. For follicle study, in the fist, 120cm2 of left side of animals was marked firstly; then, these region fibers shaved by electrical shaver. Shaving was repeated monthly (for four weeks). Skin biopsy was taken monthly from left mid side of skin of abdomen. samples were fixed in 10% formalin. Paraffinized block were prepared and then, they are sectioned as serial section in 8-micron thickness. Histological sections were stained by sak pic method (reference ????). Results were analyzed by analyses variance and paired t-test.   

This research results, showed that there was no significant effect of feeding level or age on weight of cashmere and hair per area, secondary follicle activity, cashmere length, and yield (P<0.05). Fleece and live weight for young goats were significantly less than that of old goats (P<0.05). Result were appeared that mean cashmere diameters of patch shorn in September of goats fed M, 1.4M and 1.8M were significantly greater than that of goats fed 0.7M (P<0.05). In group feeding more than maintenance requirements, results indicated no increase in cashmere production. Average fiber diameter of cashmere in June was higher than in May. Results of this research indicated that there are not any significant differences between different levels of feeding and age on fiber growth rate (P<0.05). The highest fiber production and the maximum mean of fiber growth rates (1.64 and 1.48 g/120cm2 / 28 days) were observed in June and July. Secondary to primary follicle ratio of all goats was 12.60. Study of secondary follicles ratio showed that different levels of feeding cannot reduce number of secondary follicles. Many researchers reported that increase in feeding levels to over maintenance rate cannot increase cashmere growth rate. This research results confirmed by previous studies. it was reported that feeding limitation can reduce diameter of cashmere, but there is not any increasable effect during over maintenance feeding and an increase in dietary protein. This research indicated that cashmere diameter was more in two-years old goat than one-year old goat cashmere diameter. These   results were similar with reports of Klor et al. (1993), Rafat (1997), and Salehi (1997). Increase in diameter of wool fibers with increasing in the age of animals was reported in sheep and goat. In other studies, it is shown that effect of age on diameter of Norway cashmere goats was significant (P<0.05). Results of our research show that diameter of cashmere in Raeini goats increases at June. Similar results are illustrated in Kerman (with the same age and sex). The weight of produced fibers / body surface was the same in four feeding treatment groups, but diameter of cashmere was different. Numbers of secondary follicles   increased in April. Minimum weight of fibers was observed in April in all of the treatments, which may be because of low activity of follicles in this month. Variation of cashmere diameter and cashmere growth rate can explain differences in total cashmere production. Changes of feeding level from under maintenance to high levels cause increase in cashmere diameter. This study appeared that diameter of cashmere fibers can have reaction to feeding rate. Accordingly, energy has important effect on growth of hair and cashmere. The animals with low energy diet produce low amount of cashmere, Other researchers have opposite idea. According to their statement, there are not any difference in partition for nutrient between primary and secondary follicles. This research result showed that increase feeding cannot increase cashmere production. Jia et al (1995) reported that increase of diet net protein has not any important effect on cashmere goats production in Spain. In other study using unpregnant goat it has been indicated follicular activity and fiber growth is not under influence of pregnancy and milking. However, some researches showed that reproduction condition of animal, as pregnancy and milking, has effect on cashmere fiber growth.  

Generally, results of this study showed Raeini cashmere goats in East – Azarbayjan climate did not show any fundamental changes in diameter and length of cashmere in comparison with Raeini cashmere goats which reared in Kerman province.

Arkharmerino sheep breed is a fine wool type. Crossbreeding can lead to combination of favorable characteristics from the breeds involved. The greatest part of the wool produced by the indigenous sheep breeds in Iran is used in the hand woven carpets. It is estimated that 5.1 million m2 hand woven carpets is produced in Iran annually; therefore, the country needs 28 thousand tons of washed wool. Approximately 8 thousand tons of wool is imported as merino wool from Australia and New Zealand. Iranian wool is suitable for use in coarse-carpet industry, but it has some difficulties for use in the fine carpets. Fine carpet makers usually utilize imported wool, which has more uniformity of diameter. For finding suitable sheep breed to produce more uniform wool, we interest to Arkhar-Merino breed at University of Tabriz. The Kazakh Arkhar-Merino breed was produced at Kurmektinski experiment station of the Academy of Sciences of the Kazakh.  The purpose of research was to introduce a new breed of fine wool sheep which would combine the good production characteristics of the Merino with adaptability of local Arkhar. The breed is based on crossbreeding of wild Arkhar rams with ewes of the Novocaucasian Merino, Précoce and Rambouillet breeds. Crossbreeding between Iranian wool sheep and foreign wool breeds can lead to the production of a genetic combination with the better wool fibers. In order to evaluate fleece characteristics, wool samples of 451 yearlings of Arkharmerinos×Ghezel (ArGh) were collected by Mokhber et al. (2008). At first generation of ArGh, mean (± standard error) of fiber diameter, fiber diameter variability, staple length and percentage of true wool, medulla and kemp percentage were 27.10 ± 3.36 μ, 36.60 ± 7.84 %, 11.81 ± 4.06 cm, 91.31 ± 9.32%, 7.27 ± 6.90%, and 1.40 ± 3.03 %, respectively. At second generation of ArGh, the same traits were 26.33 ± 3.41μ, 34.64 ± 9.36 %, 10.15 ± 3.99 cm, and 95.41 ± 4.70 %, 3.39 ± 5.85 % and 2.01 ± 2.65 %, respectively.  The main aim of this work was to study the morphological and structural properties of breed wools of first and second generation of Arkharmerino ×Ghezel with breed Arkharmerino as a father's base and comparing with their parent's wool characteristics. The aim was to obtain information about crossbreeding of local fat tail rams with Arkhar-Merino ewes regarding the wool traits. Arkhamerino breed has been imported from Kazakhstan. For this purpose, the wool fibers were sampled from the middle region of the sheep's body. The physical properties of the wool fibers, such as fiber diameter, staple length, Kemp fiber percentage and modulation fiber percentage were measured. For study the morphological properties of fibers, surface image of the fibers was prepared using a scanning electron microscope. In order to measure the structural properties of the fibers, which is one of the important factors in the production of textile products, the infrared spectrum of each fiber was obtained according to the relevant standards. The chemical structure (such as the components of the main and side chains, functional groups, various linking bonds, etc.) and the chain conformation in wool fiber play a crucial role in its mechanical, other physical, and service properties. The effect of wool breeding on the chemical structure and chain conformation of wool samples, which were from Ghezel sheep and Arkharmerino Sheep in first and second generations, were investigated by employing an FT-IR spectrometer (IR Affinity-1s ATR-FTIR, Shimadzu, Japan) in a spectral range from 500 to 4000 cm-2. The infrared spectra of the control sample of wool in Fig. 1 indicate that the strong peak with absorption band at 3399.5 cm-1 was assigned to the combined stretching vibrations of N-H and O-H (νN-H, νO-H), and the absorption bands at 2960.2 cm-1, 2930.0 cm-1, 2870.0 cm-1were assigned to the asymmetrical and symmetrical stretching vibrations of C-H in CH3 and -CH2- groups, respectively. Moreover, the strong peak with absorption band at 1639.8 cm-1was due to the stretching vibration of C=O from amide Ι (νC = O), which was essentially relative and indicative to the α-helix conformation of the main chains of wool (Wojciechowska et al. 2002). The medium peaks with absorption bands at 1540.1 cm-1 and 1239.9 cm-1 were attributed to the bending vibration of N-H (δN-H) from amide ΙΙ and the stretching vibration of C-N (δC-N) from amide ΙΙΙ, respectively. Moreover, the stretching vibration of C-N (δC-N) from amide ΙΙΙ was considered to be relative and indicative to the β-sheet conformation in wool fiber (Cai and Singh 1999). The peak at 1079.3 cm-1 was due to the vibration of sulfur-containing group of cystine in wool. Table 2 shows the average and standard deviation of absorption band of the functional groups in the wool fibers. The results showed that the fiber scales in crossbreed and Arkharmerino fibers have a telescopic and regular state that are different from the irregular structure of the Ghezel fiber scales. The measurement of structural properties showed that the wave number of amide, amine, hydroxyl and C-N bonds in the second generation was more similar to Arkharmerino and it can be concluded that in the second generation of Arkharmerino × Ghezel, genetic structure of fibers has the most similarity to Arkarmerino breed. In general, the results show that the second-generation fibers of the Arkharmerino × Ghezel have a good structural and superficial quality for usingin textile products.

About 6 million heads of cows in Iran are native cattle, but their characteristics and production potential remains unknown. Inbreeding is one of the important factors which must be considered in the herd and can be of considerable economic loss to producers. In this research, we tried to investigate the occurrence of inbreeding and its effects on the production traits of Serabi native cattle in a breeding center related to agricultural ministry located in Sarab. The aim of this study was to evaluate inbreeding effects on milk yield, fat percentage, protein percentage, and birth weight of Sarabi dairy cattle. In this research, the effects of inbreeding and environmental factors on production traits and birth weight of Sarabi cows have been studied. The data were collected from 1250 Sarabi cows during 1992- 2012 years by Sarabi Breed Center in East Azerbaijan province. In the present study, a pedigree file containing 1250 head (764 females and 486 males) of dairy cows was used, including data about the registration number of the livestock, date of birth, gender, father's registration number, and registration number of the mother, date of birth, parity, and production records. After the removal of animals with unknown and unregistered parents in the flock, the pedigree was arranged using pedigree software. Pedigree software was used to calculate the inbreeding coefficient for each animal. The principles of this software in the calculation of inbreeding coefficient is based on the formation of a kinship matrix among the individuals. The inbreeding coefficients of animals were considered as a discrete trait in 4 groups. In this herd, inbreeding coefficient was estimated between 0- 0.28. Average inbreeding coefficients of all cows and inbred cows are 0.0109 and 0.0574, respectively. Totally, 19% of all animals were inbred. In this study, inbreeding coefficient has been included in the model either as a continuous variable or as a classification variable. When inbreeding factor considered as continuous variable in the model, its effect on milk yield, fat and protein percentage, and birth weight was significant (P<0.01). When inbreeding considered as a continuous trait, 1% increase in inbreeding coefficient had an effect equal to -2.69 kg, 1.59%, and +18.1% on milk yield, fat, and protein percentage, respectively. Miglior et al. (1995a) reported a 1% increase in inbreeding coefficient in Holstein cows reduced calf weaning by 0.44 kg and reduced milk production by 25 kg. Mohammadkarim (2006) using a univariate model reported for 1% increase in inbreeding coefficient, changes in milk yield, fat yield, open days and length of first lactation equal to -14.02, -0.349 kg, + 0.4839 and + 0.148 days, respectively. Inbreeding has a negative effect on production traits and birth weight. Results showed that the effects of year-season of calving and parity on production traits and birth weight were significant (P<0.01). The regression coefficient of milk, fat and protein percentages and birth weight on inbreeding, when inbreeding considered as a discrete variable, were -0.129kg, +0.093%, +0.072% and -0.564 kg, respectively. In this study, when inbreeding traits considered as a continuous variable, did not show any linear or nonlinear relation with birth weight trait of Sarabi cows. It can be concluded that in order to maintain the genetic reserves of Sarabi cattle breed, it is necessary to carefully monitor the reproduction breedings in this native cattle population. In the case of endangered breeds, such as Sarabi breed, these breeds have beneficial properties, particularly in relation to resistance to diseases, and tolerance to stressful environments. These desirable traits can be transferred to future genetic composition cattle breeds. Preserving the genetic resources of the country's livestock and pay attention to similar breeds of Sarabi should be taken into consideration by decision makers at livestock breeding centers. In Holstein cows it has been found that high milk production is associated with a genetic susceptibility to disease (Khaleghi & Rafat 2018), so the desirable characteristics of the Sarabi breed should be studied in this regard of susceptibility to diseases. The existence of a complete family tree in computer registrations is the first step in controlling inbreeding. The existence of this pedigree will help breeders to avoid breeding between close-up animals, like a brother-sister and a father -daughter, which will increase the incidence of inbreeding in the population. For this purpose, it is recommended to use optimal mixing softwares that controls inbreeding. There are programs for managing the breeding to identify animals as soon as possible and calculate their relativeness in the herd. By this method, it is possible to prevent the occurrence of high inbreeding in the herd and produce calves with high profitability. The prospect of this research is to carry out further research on the issue of inbreeding and effective population size on local breeds of dairy cattle to prevent the replacement of these breeds with Holstein. It is imperative to prevent the replacement of the foreigner breeds (Holstein generally) instead of Sarabi breed and its extinction as much as possible.

Average daily gain (ADG) is the most economically important trait in sheep industry.
In genome wide association study and genomic selection, determining of extent and level of linkage
disequilibrium (LD) and haplotype block structure are critical in sample size and marker density. Haplotype blocks are defined as long stretches of SNPs along a chromosome that have low recombination rates, which characterized by relatively few haplotypes. Understanding haplotype structure in genome can greatly facilitate LD analysis. Haplotype-based association analysis can offer a powerful approach for mapping functional genes (Gabriel et al., 2002). Therefore, the objective of this research were to study LD pattern, determine haplotype block structure and genome wide haplotype association study in Zandi sheep for identifying the genomic region associated with pre-weaning (AGW) and post-weaning daily gain (PWG). A total of 96 Iranian Zandi sheep were used in the study. The following two traits were analyzed: pre-weaning daily gain and post-weaning daily gain. Animals were genotyped using 50 K SNPChip panel. Quality control of the genotype data consisted in removing SNPs with a call rate less than 95 %, SNPs with a minor allele frequency (MAF) less than 5 %, individual with more than 10 % missing genotypes, and SNPs that deviated strongly from Hardy–Weinberg equilibrium (P < 10−6). LD between all pairs were calculated with r2 by PLINK v1.07. Haplotype blocks were identified on base algorithm Gabriel et al. (2002) for all autosomes, using Haploview software (Barrett et al. 2005), based on estimates of D' for all pairwise combinations of SNPs within each chromosome. Following Gabriel et al. (2002), a pair of SNPs is defined to be in “strong LD” if the upper 95% confidence bound of D' is > 0.98 (consistent with no historical recombination) and the lower bound is > 0.7. Using the Haploview default values for blocks (Gabriel et al. 2002), a haplotype block is defined as a region over which 95 % of informative SNP pairs show “strong LD”. The PLINK was used to generate the matrix using the GLM algorithm. In this analysis, because of the previous selection history of the flock, it was important to identify and correct for population stratification. To evaluate whether estimates were overinflated, we used the genomic inflation factor λ using the PLINK software (Purcell et al., 2007). We also assessed their deviation from the expected distribution of no SNPs being associated with the trait of interest using a quantile-quantile (Q-Q) plot, which is commonly used to analyze population stratification in GWAS. We use SNPEVG tool to show the (Q-Q) plot. The Bonferroni method was used to adjust for multiple testing from the number of SNP loci detected. We declared a significant SNP at the genome-wide significance level if the raw P-value was, 0.05/N, here N is the number of SNP loci tested in the analyses. Therefore, for each trait, the threshold P-value for declaring genome-wide significance was (0.05)/40,879=1.2×10-6. The exact positions of the annotated genes were extracted from the latest sheep genome Oar_v4.0 assembly along with the NCBI annotation release 102 of the sheep genome. To investigate whether the
significant SNPs detected in this study were within the range of previously identified QTL for relevant traits, we searched for meat or production QTL in the Animal QTLdb within a 1-Mb region on both sides of each significant haplotype. After quality control, 2 individuals were excluded, leaving 94 sheep for the association analysis. Additionally, we removed 1070 SNPs with call rates less than 95% and 7717 SNPs with MAF less than 0.05. A total of 40,879 SNPs passed these quality-control filters and were retained in the dataset. These SNPs were distributed across 26 autosomes, with the number of SNPs per chromosome ranging from 747 to 5694, and with a mean distance between adjacent SNPs ranging from 50.4 to 68.7 kb. Also, in this study, the extent of LD was 40 kb with r2=0.2. Overally, 1472 blocks were observed in the 7.58% of all SNPs were classified into haplotype blocks, covering 1.45% of the total autosomal genome size. The results showed a reduction in LD level with the increase in distance between markers. The average pre-weaning daily gain was 0.197±0.04 kg with an individual sheep range of 0.08-0.34 kg. Average post-weaning daily gain was 0.126±0.07 kg with an individual sheep range of 0.03-0.41 kg. The result from genomic control showed weak population stratification for AGW and PGW in between population of Zandi sheep. The genomic inflation factors (λgc) for the two traits were equal to 1.039 and 1.073, for AGW and PGW, respectively. However, as the Q-Q plots clearly show, there is no evidence of any systematic bias (λgc˂1.1) due to population structure or analytical approach in our case. Considering the significant fixed effects in the genomic wide association analysis, four haplotypes on chromosomes 3, 5, 6 and 7 identified to affect significantly AGW and PWG traits. The results of this study could provide a suite of novel SNP markers and candidate genes associated with growth traits and hence, may play an important role for understanding the biology of average daily gain in sheep.

Identifying of genes with large effects on economically important traits, has been one of the important goals in sheep breeding. Over the last decade, by the advent of genome-wide panels of single nucleotide polymorphisms (SNPs), it has become possible to identify and localize QTLs for complex traits in many livestock species. One important obstacle in association studies is the confounding effect of population structure. Because this effect generally increases in proportion to population size, population structure remains a major concern in association analyses. To date, 98 QTLs for wool traits have been reported via genome scan based on marker-QTL linkage analyses (http://cn.animalgenome.org/cgi-bin/QTLdb/OA/index, 27 Aug, 2017). Compared with traditional QTL mapping strategies, a GWAS has major advantages both in its power to detect causal variants with modest effects and in defining narrower genomic regions harboring causal variants for economically important traits. In this study, we assessed population stratification and performed a genome-wide association study (GWAS) of wool quality traits in Zandi sheep. Material and

A total of 96 Iranian Zandi sheep was used in the study. The following four traits were analyzed: staple length (SL), mean fiber diameter (MFD), fiber diameter coefficient of variation (FDCV), and the proportion of fiber that was equal or more than 30 µm (F≥30). Animals were genotyped using 50 K SNPChip panel. Quality control of the genotype data consisted in removing SNPs with a call rate less than 95 %, SNPs with a minor allele frequency (MAF) less than 5 %, SNPs with more than x % missing genotypes, and SNPs that deviated strongly from Hardy– Weinberg equilibrium (P < 10−6). The PLINK was used to generate the matrix using the GLM algorithm. In this study, although the resources of this breed were very clear, we still examined the distribution of the test statistics obtained from the numerous association tests. We also assessed their deviation from the expected distribution of no SNPs being associated with the trait of interest using a quantile-quantile (Q-Q) plot, which is commonly used to analyze population stratification in GWAS. We use SNPEVG tool to show the (Q-Q) plot. The Bonferroni method was used to adjust for multiple testing from the number of SNP loci detected. We declared a significant SNP at the genomewide significance level if the raw P-value was0.05/N, here N is the number of SNP loci tested in the analysis. The exact positions of the annotated genes were extracted from the latest sheep genome Oar_v4.0 assembly along with the NCBI annotation release 102 of the sheep genome. To investigate if the significant SNPs detected in this study were within the range of previously identified QTL for relevant traits, we searched for meat or production QTL in the Animal QTLdb within a 1-Mb region on both sides of each significant haplotype.

After quality control, 2 individuals were excluded, leaving 94 sheep for the association analysis. Additionally, we removed 1070 SNPs with call rates less than 95% and 7717 SNPs with MAF less than 0.05. A total of 40,879 SNPs passed these quality-control filters and were retained in the dataset. These SNPs were distributed across 26 autosomes, with the number of SNPs per chromosome ranging from 747 to 5694, and with a mean distance between adjacent SNPs ranging from 50.4 to 68.7 kb. Wool MFD was 29.85±0.03 µm with an individual sheep range of 22.4-39.04 µm. The overall coefficient of variation of fiber diameter was 43.12%±0.7% with an individual sheep range of 19.7%–68.0%. The average percentages of fiber that had equal or more than 30 µm were 27.04±0.03% with an individual sheep range of 12.04-43.10%. Average wool staple length was 11.25±0.03 cm with an individual sheep range of 6-19 cm. The result from genomic control showed weak population stratification for SL, MDF, FDCV and F≥30 between populations of Zandi sheep. The genomic inflation factors (λgc) for the four traits were equal to 1.127, 1.101, 1.059, and 1.009 for MDF, FDCV, FD≥30 and SL, respectively. However, the Q-Q plots clearly showed there was no evidence of any systematic bias due to population structure or analytical approach in our case. Overally, two significant SNPs at the genome-wise level were identified for FD, and FDCV. No significant SNPs was identified for SLor FD≥30. Two Haplotype region within ERBB2 and GNAS genes previously reported in human growth and development hair and skin. Haplotypes were located with previously QTL reported to affect fiber diameter and fiber diameter coefficient of variation in Merino and INRA401 breed sheep. The functions of all of the above genes are directly or indirectly related to skin and hair development. Hair follicles are skin appendages and produce hair; therefore, we hypothesize that these genes control hair follicle development and fiber diameter trait.

The results of this study could provide a suite of novel SNP markers and candidate genes associated with wool traits and hence, may play an important role in understanding the biology of wool traits in fat-tailed sheep.