goat

The identification of selection targeted genomic regions is one of the main aims of biological research. Domestication and selection have significantly changed the behavioral and phenotypic traits in modern domestic animals. The selection of animals by humans has left detectable signatures on the genome of modern cattle. The identification of these signals can help us to improve the genetic characteristics of economically important traits in cattle. The interest in the detection of genes or genomic regions that are targeted by selection has been growing over the last decade. Identifying the signatures of selection can provide valuable insights about the genes or genomic regions that are or have been under selection pressure, which in turn leads to a better understanding of genotype-phenotype relationships. This study aimed to identify effective genes and genomic regions on positive signatures of selection in Beetal goats using selection signature and gene ontology methods.

In this study, data from 631 Beetal goats genotyped using the Caprine 50 K Bead Chip were used to identify genomic regions under selection associated with important traits in Beetal goats. Quality control measures were performed in Plink by setting an animal call rate of 0.90, SNP call rate of 0.95, and SNPs with minor allele frequencies (MAF) lower than 0.05 or that do not conform to the Hardy–Weinberg expectation (p-value ≤ 0.000001) and unknown positions. After quality control of the initial data using Plink software (v1.90; http://pngu.mgh.harvard.edu/purcell/plink), 36,861 SNP markers in 594 animals of cattle were finally entered for further analysis. To identify the signatures of selection, the statistical method iHS was used under REHH software packages. Candidate genes were identified by SNPs located at 1% upper the range of iHS using Plink v1.9 software and the gene list of Illumina in R. Additionally, the latest published version of Animal Genome Database was used for defining QTLs associated with economically important traits in identified locations. In addition, the DAVID database (http://david.abcc.ncifcrf.gov) was used to determine biological routes. At this stage, it is assumed that genes belonging to a functional class can be considered a group of genes that have some specific and common characteristics. GeneCards (http://www.genecards.org) and UniProtKB (http://www.uniprot.org) databases were also used to interpret the function of the obtained genes. Moreover, gene ontology analysis for identified genes was performed using the DAVID online database.

After quality control filters, 36,861 SNPs were left while 9761 SNPs were removed due to Hardy-Weinberg Equilibrium, 1342 SNPs were removed due to unknown positions, 3963 were removed due to a minor allele threshold, and 1342 were removed due to missing genotypes. Besides 37 individuals were removed after quality control measures. Using the iHS approach, 10 genomic regions were identified on chromosomes 4, 6, 7, 11 (two regions per chromosome), 13, 14, 15, 17, and 18. Some of the genes located in identified regions under selection were associated with body size (SPP1, SCN9A, and TNPO2), fat metabolism (SDCBP), skeletal development (IBSP and MEPE), and energy metabolism (UCP2, TRPC3, and FBP1). Some of the genes under selection were found to be consistent with some previous studies. Results of the gene ontology analysis identified two biological pathways, namely skeletal system development and a calcium channel complex, with two important KEGG pathways, including the glucagon signaling pathway and the AMPK signaling pathway, which play an important role in glucose metabolism, homeostasis, and skeletal system development.

Overall, various genes found within these regions can be considered the candidates under selection based on function. Most of the genes under selection were found to be consistent with some previous studies and to be involved in several processes, such as growth, body weight, metabolic pathways, and domestication-related changes, including system development and immune systems. Furthermore, a survey on extracted QTLs showed that these QTLs were involved in some important economic traits in goats, such as feed conversion ratio, subcutaneous fat, Marbling score, meat tenderness, body weight, average daily gain, conformation traits, the length of productive life, carcass traits, and composition carcass traits. However, it will be necessary to carry out more association and functional studies to demonstrate the implication of these genes and surveys on QTLs related to selected regions. However, will be necessary to carry out more association and functional studies to demonstrate the implication of genes obtained from association analyses. Using these findings can accelerate genetic progress in breeding programs and can be used to understand the genetic mechanism controlling this trait. The results of our research can be used to understand the genetic mechanism controlling growth traits. Since this study supported previous results from the genome scan of production traits and revealed additional regions, using these findings could potentially be useful for genetic selection in goats for a better body weight.

 Understanding the genomic features of livestock is essential for successful breeding programs and conservation. Artificial selection is one of the major forces modifying the genetic composition of livestock populations. The identification of selection targeted genomic regions is one of the main aims of biological research. Domestication and selection have significantly changed the behavioral and phenotypic traits in modern domestic animals. The selection of animals by humans left detectable signatures on the genome of modern goat. Understanding the genomic features of livestock is essential for successful breeding programs and conservation. Artificial selection is one of the major forces modifying the genetic composition of livestock populations. Identifying genes under selection could be useful to elucidate their impact on phenotypic variation. Over the last decade, interest in the detection of genes or genomic regions that are targeted by selection has been growing. Identifying signatures of selection can provide valuable insights about the genes or genomic regions that are or have been under selection pressure, which in turn leads to a better understanding of genotype-phenotype relationships. This study aimed to identify effective genes and genomic regions on positive signature of selection in Murciano-Granadina and Barki goats using selection signature method.

In this study, data from 923 Murciano-Granadina and 68 Barki goats genotyped using Caprine 50 K Bead Chip were used to identify genomic regions under selection associated with important traits. Quality control measures were performed in Plink by setting an animal call rate of 0.90, SNP call rate of 0.95, and SNPs with minor allele frequencies (MAF) lower than 0.05 or that do not conform to the Hardy–Weinberg expectation (P value ≤ 0.000001) and unknown position. After quality control of the initial data using Plink software (v1.90; http://pngu.mgh.harvard.edu/purcell/plink), 43,170 SNP markers were finally entered for further analysis. To identify the signatures of selection, the statistical method FST was used under R software packages. Candidate genes were identified by SNPs located at 1% upper range of FST using Plink v1.9 software and the gene list of Illumina in R. Additionally, the latest published version of Animal genome database was used for defining QTLs associated with economically important traits in identified locations. GeneCards (http://www.genecards.org) and UniProtKB (http://www.uniprot.org) databases were also used to interpret the function of the obtained genes.

Using FST approach, we identified seven genomic regions on chromosomes 4, 6, 14, 15 (two regions per chromosome), 17, and 23 chromosomes. Candidate genes were detected. Some of the genes located in identified regions under selection were associated with milk yield, fat yield and fat metabolism, milk protein percentage and cholesterol milk content. Some of the genes under selection were found to be consistent with some previous studies|. Results of gene ontology analysis identified two biological pathways namely skeletal system development and calcium channel complex with two important KEGG pathways including glucagon signaling pathway and AMPK signaling pathway which play an important role in glucose metabolism and homeostasis and skeletal system development.

By the way, various genes that were found within these regions can be considered as candidates under selection based on function. Most of the genes under selection were found to be consistent with some previous studies and to be involved in several processes such as milk yield and metabolic pathways. Also, a survey on extracted QTLs showed that these QTLs involved in some economical important traits in goat such as milk yield and milk composition traits. However, it will be necessary to carry out more association and functional studies to demonstrate the implication of these genes. However, it will be necessary to carry out more association and functional studies to demonstrate the implication of these genes and survey on QTLs related to selected regions. However, will be necessary to carry out more association and functional studies to demonstrate the implication of genes obtained from association analyses. Using these findings can accelerate the genetic progress in the breeding programs and can be used to understand the genetic mechanism controlling this trait. The results of our research can be used to understand the genetic mechanism controlling milk and composition traits and considering, this study supported previous results from genome scan of production traits, also revealed additional regions, using these findings could potentially be useful for genetic selection in goat for better milk yield.

Over the last decade, interest in detection of genes or genomic regions that are targeted by selection has been growing. Identifying signatures of selection can provide valuable insights about the genes or genomic regions that are or have been under selection pressure, which in turn leads to a better understanding of genotype-phenotype relationships. The aim of this study was to identify candidate genes and genomic region related to litter size trait in Murcia-Granadina goats using the selective sweep methods.

In this study, data from 643 Murcia-Granadina goat genotyped using Caprine 50 K BeadChip were used. Quality control measures were performed in Plink by setting animal call rate of 0.90, SNP call rate of 0.90 and SNPs with minor allele frequencies (MAF) lower than 0.01. To identify the signatures of selection, two statistical methods of FST and hapFLK were used. Candidate genes were identified by SNPs located at 1% upper range of FST and hapFLK. Finally, GeneCards and UniProtKB databases were also used to interpret the function of the obtained genes.

Using FST approach, we identified nine genomic regions on chromosomes 4, 5, 6, 8, 12, 13, 14, 15, and 22 chromosomes. The identified candidate genes associated with litter size trait in these genomic regions included KMT2E, CAMK2D, CTNNAL, DACH1, DNMT3B, STK3. Some of the genes located in identified regions under selection were associated with the oocyte growth, development and differentiation of ovarian follicles, fertility and growth and development of granulosa cells, which can be directly and indirectly related to the trait of the litter size. Also, survey on extracted QTLs was shown that these QTLs in cow orthologous associated sperm count and calf size. The results of hapFLK statistics in this research led to the identification of four genomic regions on chromosomes 1, 2, 5, and 11. The identified candidate genes associated with the litter size trait in these genomic regions included EDA2R, KCNH7 and CNOT11. It was determined that they had different functions in folliculogenesis and spermatogenesis. Also, survey on extracted QTLs was shown in cow orthologous associated calving interval.

  By the way, various genes that were founded within these regions can be considered as candidates under selection based on function. However, will be necessary to carry out more association and functional studies to demonstrate the implication of genes obtained from association analyses. Finally, the results of our research can be used to understand the genetic mechanism controlling litter size trait.

Molecular markers that reveal polymorphisms at the DNA level now play a key role in animal genetics. However, the selection of molecular markers is crucial depending on the purpose, viz. this depends on different molecular biology techniques and their effects. Over the last decade, interest in identifying genes or genomic regions targeted by selection has grown. Identifying selection signatures can provide valuable insights into the genes or genomic regions that are or have been under selection pressure, which in turn leads to a better understanding of genotype-phenotype relationships. Type characteristics are important for breed identification and classification and are also positively correlated with body weight. This study aimed to identify effective genes and genomic regions under positive selection signatures in different goat breeds using selection signature methods. For this purpose, FST and hapFLK analyses were performed using the genome-wide single nucleotide polymorphisms (SNPs).
In this research, the information from 728 goats of four different breeds was used to identify genomic regions associated with type traits. To determine the genotype of the samples, Illumina caprine Bead Chip 50K was used. The genomic information of goat breeds was extracted from the Figshare database. Quality control was performed using the Plink software. The markers or individuals were excluded from further study based on the following criteria: unknown chromosomal or physical location, call rate <0.95, missing genotype frequency >0.05, minor allele frequency (MAF) <0.05, and a P-value for Hardy-Weinberg equilibrium test less than 10-3. After quality control, 36861 SNPs from goat SNP chip 50K from 691 goats remained for further analysis. To identify the signatures of selection, two statistical methods of FST and hapFLK were used under the software packages FST and hapFLK, respectively. Candidate genes were identified using the Plink v1.9 software and the Illumina gene list in R by SNPs located in the highest  FST and hapFLK values. In addition, the latest published version of the animal genome database was used to define QTLs associated with economically important traits at identified loci. The GeneCards (http://www.genecards.org) and UniProtKB (http://www.uniprot.org) databases were also used to interpret the function of the obtained genes.
The FST and hapFLK statistics were used to identify genomic regions subjected to positive selection associated with type traits in four goat breeds. Using the FST approach, we identified eight genomic regions on chromosomes 3, 4, 7, 13, 15, 18, 20, and 29. The identified candidate genes associated with type traits in these genomic regions included TGFBR3, CALCR, ACAD8, BCAR1, and ADAMTS6. Some of the genes located in the identified selection regions were directly and indirectly related to cell differentiation and proliferation, skeletal muscle growth and development, body length, calcium channel regulation, muscle fiber homeostasis, protein synthesis, and muscle cell size. Some of these genes in the selected regions were consistent with previous studies. The results of the reported QTLs in the selected regions and the bovine orthologous regions were QTLs located in the identified regions that were related to average daily gain, body weight, trunk width, and metabolic body weight. Furthermore, the results of the hapFLK statistics in this research led to the identification of five genomic regions on chromosomes 1, 5, 6, 13, and 30, and they were in the 99.9th percentile of all hapFLK values. The identified candidate genes associated with the type trait in these genomic regions included FNDC3B, STAB2, and CCNY. They were found to have different functions in fibroblast proliferation and bone cell differentiation.
Various/different genes that emerged in studied regions can be considered candidates for selection based on their function. By the way, various genes found in these regions can be considered candidates for selection based on their function. Most of the selected genes were found to be consistent with some previous studies and to be involved in production traits. A survey of extracted QTLs also found that these QTLs are involved in some economically important traits in goats, such as average daily gain and body weight in yearlings. However, further association and functional studies are required to demonstrate the importance of the genes obtained from association analyses. Leveraging these findings can accelerate genetic progress in breeding programs and help understand the genetic mechanism that controls these traits.
In this research, to identify genomic regions under selection associated with type traits were used the information obtained from 728 goats of different breeds including Beetal, Daira Deen Panah, Barbari, Teddi, In order to determine the genotype of the samples, Illumina caprine Bead Chip 50K were used. The genomic information of goat breeds was extracted from the figshare database. Quality control was conducted using the Plink software. The markers or individuals were excluded from the further study based on the following criteria: unknown chromosomal or physical location, call rate <0.95, missing genotype frequency >0.05, minor allele frequency (MAF) < 0.05, and a P-value for Hardy–Weinberg equilibrium test less than 10-3. After quality control, 36,861 SNPs from Goat SNP chip 50K on 691 goats were remained for the future analysis. To identify the signatures of selection, two statistical methods of FST and hapFLK were used under FST and hapFLK software packages, respectively. Candidate genes were identified by SNPs located at 1% upper range of FST and hapFLK using Plink v1.9 software and the gene list of Illumina in R. Additionally, the latest published version of Animal genome database was used for defining QTLs associated with economic important traits in identified locations. GeneCards (http://www.genecards.org) and UniProtKB (http://www.uniprot.org) databases were also used to interpret the function of the obtained genes. We used the FST and hapFLK statistics to identify genomic regions that have been under positive selection associated with type traits in four goat breeds. Using FST approach, we identified eight genomic regions on chromosomes 3, 4, 7, 13, 15, 18, 20, and 29 chromosome. The identified candidate genes associated with type trait in these genomic regions included TGFBR3, CALCR, ACAD8, BCAR1, ADAMTS6. Some of the genes located in identified regions under selection were associated with the cell differentiation and proliferation, skeletal muscle growth and development, body length, calcium channel regulation, muscle fiber homeostasis, protein synthesis and muscle cell size which can be directly and indirectly related to the trait of the type traits. Some of these genes in the selected regions were consistent with previous studies. Result of the reported QTLs in the selected regions and the orthologous regions of cattle were located in the identified regions, QTLs related to average daily gain, body weight, rump width and body metabolic weight. Also, the results of hapFLK statistics in this research led to the identification of five genomic regions on chromosomes 1, 5, 6, 13, and 30, and they were in the 99.9 percentile of all hapFLK values. The identified candidate genes associated with the type trait in these genomic regions included FNDC3B, STAB2 and CCNY. It was determined that they had different functions in proliferation of fibroblasts and differentiation of bone cells. Result of the reported QTLs in the selected regions and orthologous cattle in the identified regions, QTLs related to metabolic body weight were located. various genes that were founded within these regions can be considered as candidates under selection based on function. Most of the genes under selection were found are consistent with some previous studies and to be involved in production traits. Also, survey on extracted QTLs was shown that these QTLs involved in some economical important traits in goat such as average daily gain and body weight in yearling. However, it will be necessary to carry out more association and functional studies to demonstrate the implication of these genes. However, it will be necessary to carry out more association and functional studies to demonstrate the implication of these genes and survey on QTLs related to selected regions. However, will be necessary to carry out more association and functional studies to demonstrate the implication of genes obtained from association analyses. Using these findings can accelerate the genetic progress in the breeding programs and can be used to understand the genetic mechanism controlling this trait.

Green fodder is one of the components that is given special attention when preparing animal rations, due to its palatability and high digestibility. Green fodder in the livestock ration has an effect on maintaining health and improving the productive and reproductive efficiency of livestock, and it may also affect the quality of meat. On the other hand, the main problem in fodder production in the world is the lack of access to sufficient water for the cultivation and growth of fodder. The occurrence of continuous drought in recent years in the country has made the production of green fodder a problem and has pushed opinions towards sustainable methods including the hydroponic method. In this method, agricultural soil is not used for growing plants and feeding is done in a solution that contains all the necessary elements for the plant. There is no report regarding the effect of this food source on the quality of meat of livestock. Since at the time of introducing a feed source for livestock, all its dimensions or in fact its nutritional value must be measured, so this study was conducted with the aim of investigating the effect of consumption of different levels of barley hydroponic fodder on the qualitative and sensory characteristics of goat meat.

This experiment was performed with 28 Fars native male goats that were placed in individual cages in four treatments and seven replicates in a completely random design. The experimental treatments included the replacement of barley hydroponic fodder at three levels of 25, 50 and 75% instead of alfalfa (in terms of dry matter) in the diet and a control treatment without replacement. The ration was balanced based on the standard tables of goat nutrients recommended by Nutrient Requirements Council for Small Ruminants. After 90 days from the start of the experiment, six goats from each treatment were slaughtered and after 24 hours of cooling of the carcass at four ºC, the Longissimus dorsi muscle was separated, divided into smaller pieces and labeled to determine physical, chemical, textural and sensory factors. Chemical tests including measurement of intermuscular fat, protein and ash in meat samples were carried out by standard methods and the amount of dry matter of the samples was measured by placing about three grams of the sample at a temperature of 102 ± 2 ºC for three hours. The Keldahl method was used to measure the total content of volatile nitrogen and a digital pH meter set at 25 ºC was used to measure the pH. Fat oxidation rate in meat samples was determined by malondialdehyde method. Digital imaging and plastic bag methods were used to evaluate color and loss weight after storage of meat samples, respectively. The water holding capacity was determined by centrifuging the sample placed in filter paper for 4 minutes at 1500 rpm and recording the weight and then placing it in the oven at 70 ºC for 24 hours. Loss after cooking was calculated by placing the sample for one hour in a water bath at 90 ºC. Texture factors, including hardness, adhesiveness, cohesiveness, springiness and chewiness were measured by preparing cubic pieces with dimensions of one centimeter from the meat samples and using a texture testing machine. This device was equipped with a steel cylindrical probe with a diameter of six mm and a height of 35 mm. The probe of the device was inserted into the tested sample twice at a speed of two millimeters per second and up to 50% of the probe height, and the results were recorded by the device software. Sensory characteristics of meat samples, including color, smell, tenderness and overall acceptance wad evaluated by a panel group who completed a designed questionnaire based on the hedonic test. One-way analysis of variance was used in order to investigate the physicochemical and tissue characteristics in different treatments. In cases where there was a significant difference between the treatments, the averages were compared with Duncan's test. The results of the panel test were analyzed with the Kruskal -Wallis test.

There was not significant difference in the amount of fat (range of 10.08-13.87%), dry matter (range of 29.08-31.55%), ash (range of 0.93-1.15%) and total volatile nitrogen (range of 20.25-25.33 mg/100g) between the control group and experimental treatments. The results showed that the replacement of barley hydroponic fodder by 25% instead of alfalfa in the diet caused a significant increase in the amount of meat protein (P=0.0136) and oxidation (P=0.0497) and a significant decrease (P=0.0132) in loss of cooking compared to control treatment and other experimental treatments. There was no statistically significant difference in the recorded values for the texture evaluation and sensory scores of the meat between the experimental treatments and the control group. The overall acceptance of the meat samples in all the investigated treatments had a score of more than five and were placed in the moderately favorable level.

Finally, it can be concluded that the replacement of hydroponic barley fodder instead of alfalfa in the ration of fattening goats up to the level of 75%, did not have negative effects on the chemical, physical and oxidative stability of the meat during storage in the refrigerator or freezer. Also, the use of barley hydroponic fodder in proportions of 25, 50, and 75% (instead of alfalfa and 10, 20, and 30% of dry matter of the ration) did not have adverse effects on the redness, tenderness, and smell of meat. The scores obtained for overall acceptance showed that there was no significant difference in terms of sensory characteristics between the meat of the experimental treatments and the control.

Milk production and reproductive traits are important economic traits in goat. The different approaches including candidate gene mapping and genome-wide association studies (GWAS) are now implemented in goats in an attempt to identify the molecular mechanisms affecting these economically important traits. The gene ontology (GO) analysis gives a controlled vocabulary for describing attributes of genes and gene products. Kyoto Encyclopedia of Genes and Genomes (KEGG) provides the mythology for the careful examination of gene functions in respect of networks of genes and molecules. Gene network analysis can also identify paths and processes shared by candidate genes. The purpose of the present study was to bioinformatics analysis (GO, path enrichment, and network analysis of the effects of protein-protein interaction) of genes effective in litter size and milk production in goat.

Candidate genes associated with studied traits were retrieved from literature review, review of candidate gene studies, GWAS and NCBI database. GO analysis and enrichment analysis of the signaling pathways of KEGG were performed using online database of G: Profiler. The String database was used to infer the network of protein-protein interactions (PPI) and the selection of performance module. Cytoscape software was used to draw the resultant networks of protein-protein interactions. Finally, cytoHubba was used to identify Hub genes.

GO analysis for litter size showed that, for molecular function the candidates genes enriched in signaling receptor binding, signaling receptor active activity, hormone activity, protein binding and transforming growth factor beta receptor activity. The effect of the transforming growth factor β (TGF-β) family on fertility and reproduction, embryonic development, organogenesis, and uterine growth and function is remarkable in a wide range of organisms. In mammals, even early stages of reproductive development, including male and female germline specification, are controlled by TGF-β-related proteins. Hormone binding play an important role in fertility and reproduction. Sex hormone-binding globulin (SHBG), specifically bound to the biologically active androgens and estrogens that are key regulators of the reproductive organs as well as other sex-differentiated tissues such as muscle, adipose tissue, and bone. KEGG analysis also identified some signaling pathways including ، PI3K-Akt signaling pathway، TGF-beta signaling pathway and ovarian steroidogenesis which are significantly associated with litter size. GO analysis for 33 candidate genes related to milk production traits identified only one GO category for biological process namely linoleic acid metabolic process.

In this study, we identified several significant biological and signaling pathways that can be used to better understand the biological processes associated with litter size and milk production in goats.

Seasonal breeding mammals are sensitive to changes in day length. Thus, in small ruminants from temperate and subtropical latitudes, photoperiod is the main environmental factor that modulates their pattern of reproductive activity (Duarte et al., 2010). However, natural oscillations in the photoperiod or alterations by artificial photoperiod can lead to changes in milk production in ruminants with seasonal and non seasonal reproduction (Dahl et al., 2000). Exposure to artificially shortened photoperiods during the dry period increased their milk yields in the subsequent lactation (Auchtung et al., 2005; Mabjeesh et al., 2007). In the 12 wk of subsequent lactation, greater milk yields have been reported for does that received artificial short days during the dry period than those that received long days (Mabjeesh et al., 2007). Many livestock breeders in cold regions keep their animals in closed places in late autumn and during winter. In the closed position, the amount and intensity of light can be controlled. Short day length at the end of the pregnancy period is associated with increased milk production in lactating animals, but there is no information in this field for native goats in the country. Therefore, the aim of this research was to investigate the effect of reducing the length of the lighting period in late pregnancy on milk production and related hormones in black goats native to Chaharmahal and Bakhtiari province.

The work was conducted in the Farsan city (50º and 35' minutes of longitude and 32º and 16' of latitude and 2020 meters above sea level) located in Chaharmahal and Bakhtiari provinces. 40 indigenous black goats were randomly assigned to one of the following two treatments. Treatment 1: control; Female goats that were exposed to natural day length during pregnancy (20 heads). Treatment 2: Female goats that were exposed to short day length (8 hours of light and 16 hours of darkness) during the last 45 days of pregnancy (20 head). The female goats of two different treatments were reared in two separate locations of the same size with the same environmental and management conditions during the late pregnancy period (experimental period). The quantity and quality of feed was similar for both groups. After giving birth, all female goats were exposed to natural day length. Hand milking was done at one week intervals from one week to one month after birth. Blood samples were taken from jugular vein at the beginning of the experiment, 20 days before parturition, at the time of parturition, 15 and 30 days after parturition.

In the first week, milk production in the experimental treatment was 11% more than the control treatment, but in the second, third and fourth weeks, this superiority reached 13, 16 and 21%, respectively. On average, milk production in the experimental treatment was 15% more than the control treatment. In dairy goats, it was reported that milk production in the subsequent lactation period was 26% higher in goats that were exposed to short day length conditions in the last third of their pregnancy than goats that were exposed to long day conditions at the same time (Mabjeesh et al., 2007).The interaction between the treatment and the milk measurement time was not statistically significant. Milk production peaked in the third week in the control group and in the fourth week in the experimental treatment. Changing the duration of lighting at the end of pregnancy did not have a significant effect on any of the milk compounds on the seventh, fourteenth, twenty-first and twenty-eighth days of lactation. Normally, the composition of milk is not affected by photoperiod (Mabjeesh et al., 2007).The amount of prolactin hormone in the control treatment 20 days before delivery was higher than the amount of prolactin hormone in the experimental treatment at the same time (p<0.05). It has been found that short day length reduces the secretion of prolactin (Smith 1998). In both treatments, the amount of prolactin hormone increased from 45 days before delivery to 30 days after delivery. At the time of parturition, the amount of prolactin hormone in female goats of both treatments was similar. Within each treatment, the amount of prolactin hormone in female goats 15 days after giving birth was higher than its value at the time of giving birth, and the amount of prolactin hormone at the time of giving birth was higher than its value at 20 days before giving birth, and these differences were statistically significant (p<0.01). However, within each treatment, the difference in the amount of prolactin hormone in female goats between the 30th and 15th days after birth was not significant. The interaction effect of treatment and prolactin measurement time was statistically significant (p<0.05). Within each treatment, the amount of prolactin hormone in female goats 15 days after giving birth was higher than its amount at the time of giving birth, and the amount of prolactin hormone at the time of giving birth was higher than its value at 20 days before giving birth, and this difference were statistically significant (p<0.01). However, within each treatment, the difference in the amount of prolactin hormone in female goats between the 30th and 15th days after birth was not significant. The interaction effect of treatment and prolactin measurement time was statistically significant (p<0.05). The average melatonin hormone before and during delivery in treatment 2 was higher than the control treatment (p<0.01), but after delivery the difference between the two treatments was not significant. The amount of IGF 1 hormone in female goats of both treatments decreased from 45 days before calving to the time of calving and then increased.The amount of IGF-1 hormone in the experimental treatment was higher than the control treatment in 20 days before delivery (p<0.01) and at the time of delivery (p<0.05).

As a result, reducing the length of the lighting period at the end of pregnancy increases the milk production of native black goats in the subsequent lactation period.

By aggregating the previous studies, the present study aimed to perform a meta-analysis to estimate the weighted average of the genetic parameters of fiber length, fiber diameter and percentage yield of fiber in cashmere goats to increase the accuracy of estimations. The data of 14 related published papers between 1989 and 2021 were used. A model with random effects was used to estimate the genetic parameters, standard error and 95% confidence range of traits by using Metafor package in R environment. The weighted average of heritability estimates for length, diameter and percentage yield were 0.24 ± 0.047, 0.42 ± 0.053 and 0.60 ± 0.103, respectively. The obtained results indicated that the studied traits have high heritability estimates and therefore the direct genetic selection can lead to the improvement of the performance of these traits. The highest estimate of genetic and phenotypic correlations were obtained between the percentage yield and the fiber length as 0.84 and 0.54, respectively. The lowest genetic and phenotypic correlations were obtained between the percentage yield and the fiber diameter as 0.38 and 0.35, respectively. Sharp reductions in the standard errors of the heritability estimates due to aggregating the results and increasing the sample size, improve accuracy of the corresponding estimates. The genetic parameters estimated in the present study may be used for developing the breeding programs to improve the fiber traits in Cashmere goats. Therefore, the results of meta-analysis study can improve the breeding programs, especially in breeds with insufficient records.

DNA Mitochondria is one of the most commonly molecular markers for phylogenetic studies in animals due to its simple genome structure, which presents an ideal model to study evolution and genetic similarity. The aim of the present study was to investigate the divergence and percentage of genetic similarity along with the phylogenetic analysis of the eight species of wild and domestic goat based on the complete sequence of the mitochondrial genome and the separate sequences of 13 protein-coding genes for each genome.

In the present study, complete mitochondrial genome sequences along with separate sequences of 13 protein-coding genes per each genome from seven wild species of goat including Markhor (C. falcoeri), Capra ibex, Capra nubiana, Capra pyrenaica, Capra sibirica, Capra caucasica, Capra aegagrus, and domesticated species of goat (Capra hircus) were retrieved from NCBI database and compared to each other. Mitochondrial genomes and genes alignment were accomplished by the MegAlign module of DNASTAR software and compared by the Clustal W method. The Sequence Distances sub-section of the MegAlign module of DNASTAR also was used for the analysis of complete genome and gene sequences divergence and similarity percentage. For phylogenetic analysis, complete mitochondrial genomes and protein-coding genes’ sequences were aligned using MEGA7 software.

Based on the analysis, it was found that the highest similarity between the nucleotide sequences of the complete genome (99.50) of domestic goat (Capra hircus) and wild Capra aegagrus goat and the lowest percentage of similarity (93.79) between the nucleotide sequences of the complete genome of the breed Capra nubiana) with wild goat Capra sibirica goat. Also, based on the results of the phylogenetic tree, it was found that domestic goat breeds (Capra hircus) and wild Capra aegagrus goat are divided into one group and wild Capra ibex and Capra pyrenaica breeds are divided into another distinct cluster.

In this study, all the results obtained from complete sequences of the mitochondrial genome analysis are consistent with the results obtained from the sequence of 13 protein coding genes per each genome, which indicates the correct clustering of wild and domestic goat breeds. Therefore, mitochondrial genome sequences could be used as a suitable genetic marker for accurate phylogenetic analysis and clustering of different species of sheep.

The selection of animals by humans left detectable signatures on the genome of modern goat. The identification of these signals can help us to improve the genetic characteristics of economically important traits in goat. Over the last decade, interest in detection of genes or genomic regions that are targeted by selection has been growing. Identifying signatures of selection can provide valuable insights about the genes or genomic regions that are or have been under selection pressure, which in turn leads to a better understanding of genotype-phenotype relationships. A run of homozygosity (ROH) is a consecutive tract of homozygous genotypes in an individual that indicates it has inherited the same ancestral haplotype from both parents. Run of homozygosity one of the most methods were used to detecting the genomic inbreeding. The locations of ROHs which are under positive selection, or laboring favorable allele in population, tend to be fixed in the genome and formation of ROH Island during long times. Genomic regions enriched with ROH may be indicative of selection sweeps and are known as ROH islands. As detecting the ROH Islands, the genomic regions contain economic traits could be detectable.

In this research, the amount of genomic inbreeding and the effective size of the population were investigated using the information obtained from 879 goats of different breeds including Beetal, Daira Deen Panah, Nachi, Barbari, Teddi, Pahari, and Pothwari. In order to determine the genotype of the samples, Illumina caprine Bead Chip 50K were used. The genomic information of goat breeds was extracted from the figshare database. Quality control was conducted using the Plink software. The markers or individuals were excluded from the further study based on the following criteria: unknown chromosomal or physical location, call rate <0.95, missing genotype frequency >0.05, minor allele frequency (MAF) < 0.05, and a P-value for Hardy–Weinberg equilibrium test less than 10-3. After quality control, 36,861 SNPs from Goat SNP chip 50K on 827 goats were remained for the future analysis. Inbreeding coefficient was calculated using four methods including, genomic relationship matrix (FGRM), excess of homozygosity (FHOM), correlation between uniting gametes (FUNI) using the GCTA 1.0 software and run of homozygosity (FROH) using the PLINK 1.9 software. The effective population size (Ne) was calculated from linkage disequilibrium data with SNeP software (version 1.1). GeneCards (http://www.genecards.org) and UniProtKB (http://www.uniprot.org) databases were also used to interpret the function of the obtained genes.

The lowest and highest inbreeding coefficient calculated by three methods (FGRM, FHOM, and FUNI) were related to Beetal and Barbari breed, respectively. The highest (0.159) and lowest (0.028) amount of FROH was estimated in the Barbari and Pothwari breeds, respectively. The average length of ROH ranged from 70.2 to 391.4 Mb, and the average number of ROH fragments varied between 8.19 and 48.65. Also, the highest and lowest number of ROH were observed on chromosome 2 and 29, respectively. The size of Ne in in the current generations (fifth generation) of the studied breeds was ranged from 35 to 365. The highest Ne was estimated in the Beetal breed (365 heads) and the lowest in the Barbari breed (35 heads). The average inbreeding coefficient in Beetal, Teddi, Pahari, Nachi, Barbari, Daira Deen Panah and Pothwari breeds was obtained 0.035, 0.081, 0.031, 0.052, 0.15, 0.11 and 0.02, respectively. In addition, the Ne of most of the studied populations has been decreased. The results of this study revealed that, the selection processes in different goat breeds for economic traits during several years, has led to the formation of many ROH islands in goat genome, therefore scanning these regions at the genome level can be an alternative strategy to identify genes and associated loci with economic traits.

our findings contribute to the understanding of genetic diversity and population demography, and help design and implement breeding and conservation strategies for study goat breeds. Therefore, it is necessary to economize production and planning a suitable mating scheme to control inbreeding and genetically conserve the remaining pure animals of these breeds.

Goat milk production is very important in Iran. Artificially extending day length affected milk production in several domesticated species. In the dairy cow industry, the use of photoperiod management is usual because it is a safe, non-expensive, and effective method to increase milk production. Dairy cows with late gestation exposed to short days produce more milk than cows exposed to long days. But, long-day photoperiod during early lactation increases daily milk yield. In contrast to cows, small ruminants such as goats have seasonal reproductive cycles and therefore their response to photoperiod may differ. To date, no study was conducted to evaluate the magnitude of the response of native goats of Iran to photoperiod. Therefore, the objective of this study was to compare the magnitude of the effect of artificially shortening and extending day length on milk yield in black native goats of Chaharmahal and Bakhtiari province in Iran.
Six weeks before the start of giving birth in the flock, 80 does whose parturition dates were close to each other were selected from a local black goat flock and each one was randomly assigned to one of the following four treatments (n=20 for each treatment). Treatment 1: Does exposed to natural day length during pregnancy and lactation (control); Treatment 2: Does exposed to natural day during the pregnancy period and exposed to long day length at the beginning of the lactation period; Treatment 3: Does exposed to short day length at the end of the pregnancy period and exposed to natural day length during the lactation period; Treatment 4: Does exposed to short day length at the end of the pregnancy period and exposed to long days at the beginning of the lactation period. Milk production and levels of prolactin, melatonin, and IGF-1 hormones were measured. The does were milked manually once a week at 07:00 starting one week after parturition. Before milking the does, their kids were separated for 12 hours. Blood samples (five mL) were collected at the start of the experiment, 20 days before parturition, parturition, 15 and 30 days after parturition from each doe via jugular venipuncture into a sterile evacuated tube and immediately placed on ice. Plasma was harvested by centrifugation at 2000 rpm for 20 min and stored at -20 °C until use.
In treatments 2, 3, and 4, the amount of milk obtained in each milking time increased until the third week of the lactation period, and then its increasing process slowed down. In the control treatment, the amount of milk obtained in each milking time increased until the third week, but the amount of milk obtained in the fourth week was less than that in the third week, although this difference was not statistically significant. The average milk obtained in four milking times for treatments 1, 2, 3, and 4 was equal to 868.5, 959.25, 1005, and 1085 mL, respectively. Over the monitored lactation period, the averages of milk yield in the second, third, and fourth treatments were 10%, 15%, and 24% more than that in treatment 1 (control). According to the results of this research, it was reported that milk production in goats that were placed in short-day length conditions in the last third of their pregnancy period was 26% higher than in goats that were in long-day length conditions at the same time. In another study, a 20% increase in milk production was reported in Saanen goats that were exposed to a long light period after giving birth. The amount of prolactin hormone in treatments 1 and 2 in 20 days before delivery was higher than in treatments 3 and 4 (P<0.05), but no significant difference was observed between treatments 1 and 2 as well as between treatments 3 and 4. At the time of parturition, the amount of prolactin hormone in all treatments was similar. At 15 and 30 days after delivery, the amount of prolactin hormone was higher in treatments 2 and 4 than in treatments 1 and 3 (P<0.01). Before giving birth, the amount of melatonin in female goats of treatments 3 and 4 was higher than in treatments 1 and 2 (P<0.01). Fifteen days after birth, the amount of melatonin hormone in female goats of treatment 2 was lower than that of female goats of treatment 1 (control treatment) (P<0.05), and the difference between other treatments was not significant. The amount of melatonin in different treatments was similar 30 days after birth. In the 20 days before parturition, the difference between the female goats of treatments 3 and 4 with those treated with natural day length (treatments 1 and 2) was significant (P<0.01) in terms of IGF-1 hormone levels. At 30 days after birth, the difference between female goats of treatment 4 and other treatments was significant in terms of the amount of IGF-1 hormone (P<0.05). According to the results of the present research, it has been reported that the long lighting period increases the concentration of prolactin and IGF-1 hormones. Decreased secretion of melatonin hormone with the increasing length of photoperiod has been reported in cattle and other animals. Increasing the duration of the light period reduces the time when melatonin secretion is at its peak.
In general, the application of a short light period before parturition and a long light period after parturition increased the amount of milk produced by female goats.

The main goal in the repair of tibial fractures is to create a bone unit and study the effect of this nano polymaterial in the process of bone repair. In this research, 10 adult goats were divided into two groups, and the middle part of the right tibia was considered to create a 30 mm defect. . poly(e-caprolactone)/Gelatin/Gehlenite was used to fill the gap after the fracture in the second group. Then, on days 0, 15, 30, and 60, the animals in both the experimental group and the control group are radiographically examined. The results obtained from these results are based on the Lin and Sandow classification system depending on the amount of callus found and the spatial amount of the defect filled by the callus, mineralized and compared, after analysis And statistical analysis shows. There was a statistically significant difference between the two groups (P < 0.05); This confirms the faster bone formation in the experimental group than the control group and more form of poly(e-caprolactone/Gelatin/Gehlenite) in tibial bone reconstruction.

Survival records and pedigree information from Rayeni kids born between 1993 and 2009 from breeding station of Rayeni Cashmere goat, located in the Baft city, were used. Also, by completing questionnaire from breeding station of Rayeni Chashmere goat and flock nongovernmental, in Kerman province environmental factors affecting survival and survival rate were obtained. 11 herds with geographical diversity and different herd sizes in Kerman province were selected. The highest and lowest percentages of kid removal were related to fattening surplus (54.2%) and defective removal (0.4%), respectively. Death due to disease after fattening surplus was the most common cause of kid removal (22.3%). Survival rate in these herds was 89.94 percent. according to the results overall mean of lifetime cumulative was 310.3 days. The effect of fixed factors year and month of birth, sex of kid and kid’s birth weight as quadratic were significant. The estimates of heritability in logarithmic scale were low to medium (0.14 to 0.40), original scale were medium to high (0.25 to 0.70) and effective heritability were medium (0.23 to 0.61). Since the estimated genetic parameters for survival of goats are moderate, to improve the survival of goats from birth to one year of age and increase the economic profit of the farmer, while improving nutritional and managerial conditions, genetic selection within the breed can be considered.

Global demand for goat milk and its products has been growing. The decreased pasture quality has led goat producers to use intensive production systems with economical fodder resources. Goat milk contains functional compounds that enhance human immune system and overall health. Goat milk is enriched with functional peptides, conjugated linoleic acid, and healthy oligosaccharides that can immensely benefit human immunity and health. Goats are usually capable in utilizing lower quality forages. In few recent studies, alfalfa hay was compared with different by-products and local feeds with no significant effects found on rumen fermentation and milk production or composition. Murciano-Granadina goats were capable to utilize low quality fiber sources towards milk production.The objective of this study was to determine effects of feeding various forage sources on milk production, nutritional behaviors, and blood parameters of Murciano-Granadina dairy goats in Iran.

  Thirty second-parity Murciano-Granadina goats (190 ± 3 days in milk; 2 ± 0.03 kg/d milk yield) were used in a completely randomized design study with three treatments (10 goats per treatment). Treatments were diets containing 1) wheat straw (WS), 2) alfalfa hay (AH), or 3) corn silage (CS). To enable sound comparisons among forage sources, treatment diets were balanced to be isoenergetic and isonitrogenous. The concentrate portion of the rations was similarly ground for all treatments. Feed and milk (from a.m. and p.m. milking) samples were collected weekly for later analytical measurements. To determine goat behavior time; eating, ruminating, and resting times were observed and recorded by technical individuals on days 30 and 50 of the experiment in two 24-h period. Blood samples were taken at 0800 h on d 1, 30, and 56. The data were analyzed using mixed models of SAS program.

 The dry matter intake (DMI) was significantly affected by treatments (P <0.001). Body weight and its changes were similar among treatments, suggesting that nutrient partitioning towards tissue accretion or depletion was not different among treatments during the study, since goats were in late lactation. However, DMI was 228 g higher for goats received diet containing corn silage than for those received AH (P < 0.05). Decreased DMI for diets with wheat straw and alfalfa hay compared with corn silage could at least partially be related to increased dietary fat and indigestible cell wall in the former diets. Ruminating, standing, and resting times were not different among treatments (P > 0.10). These data would suggest that despite the differences in forage nutritional characteristics, digestibility, and intake, ruminating time was similar among treatments.Goats fed CS had higher milk production than the other two groups (P <0.001). The percentage of milk fat in the alfalfa hay treatment was higher than in the other treatments (p> 0.05). Similar to milk volume, daily yields of milk protein, lactose, and total solids were also higher for corn silage than for other treatments. This could be a result of increased milk volume and unchanged milk contents of protein and lactose for corn silage. Milk fat content was higher (P < 0.01) for AH treatment but milk fat yield tended (P < 0.10) to be greater for CS treatments than for other treatments.Serum concentration of glucose, albumin and non-esterified fatty acids (NEFA) were not significant among experimental treatments. Glucose and NEFA values are usually interpreted as indices for energy status of experimental animals. Similar glucose and NEFE concentrations in blood for the three forage treatments could be evaluated in light of the fact that goats were in mid and late lactation and thus were not in negative energy balance. As a result, they may have not been metabolically sensitive enough to respond to treatments at this stage of lactation. Serum concentrations of total proteins were higher for AH than for other treatments (P < 0.05). Findings  of this study suggest that lactating Murciano-Granadina goats are capable to utilize different forage sources including alfalfa hay, corn silage and wheat straw. However, corn silage leads to higher raw and fat-corrected milk yields, whereas alfalfa hay increases milk fat content. For higher feed efficiency and lower feed cost and where more available, Wheat Straw may be used in Murciano-Granadina goat diets. To improve milk yield and fat content and yield simultaneously, certain combinations of alfalfa hay and corn silage may be required. Determining this will require future experimentation. Future experiments could also investigate forage choice effects on milk fatty acids profile and other functional compounds.

To date, sex determination technique in domestic animal has economic benefits. Recently, circulating free DNA (cfDNA) highlighted as suitable candidate for non-invasive sex determination in livestock and endangered wild life animals. Based on this motivation, the objective of this report was the potential usefulness of free fetal DNA in maternal blood for prenatal fetal gender determination in pregnant goats.

 In this respect, a total of 21 animals, including 17 pregnant females with a gestation period of six weeks, unborn goats and 2 males (negative controls) were selected. During the running experiment, estrous synchronization  was performed by intravaginal CIDR. The animals not returned to estrus was considered as an indicator of success in pregnancy. Also in the last months, ultrasound method was used to confirm pregnancy. In the next phase, cffDNA was extracted from the blood plasma of female goats using the available common experimental protocol. The primers in this experiment were designed based on AME gene located on X and Y chromosomes. The polymerase chain reaction was optimized based on available standard methods.

The observation addressed existence of two fragment in the male embryo (171 bp AMELX gene band and 111 bp AMELY gene band) and one fragment in the female embryo (171 bp AMELX gene band). Here, most of findings was in line of similar pervious literatures and sex determination based on AME gene in case of sensitivity, specificity and accuracy indices indicated 0.83, 0.93 and 0.93 respectively.

On this basis, the results opened a new horizon of the potential usefulness of free fetal DNA in maternal blood for prenatal fetal gender determination in pregnant goats.

Theileriosis is one of prevalent diseases among small ruminant population in Kurdistan province which is encountered serious problems both clinical and microscopic. The disease imposes heavy damages to the livestock industry. The aim of the study is to compare the clinical and microscopic features in sheep and goats infested with ticks, evaluation of microscopic method to identify Theileriosis and finally identification of technical impairments and finding confident approaches for diminished diagnostic errors in both methods.

in this study, after recording the clinical findings of 250 tick infested small ruminants (230 sheep and 20 goats), blood and lymphatic smears were taken.

the results have shown that Piroplasms and Koch blue bodies were presented in 229 blood samples and in 238 lymphatic smears respectively. Statistical analyses declared that there was a meaningful correlation between blood and lymphatic smears and also between clinical findings such as: heart rate, conjunctiva discoloration and temperature variation with both blood and lymphatic smears.

coordination of clinical and laboratory findings have confirmed that the main problem in clinical diagnosis of theileriosis in Kurdistan province was the involvement of animals with none-acute form of the disease (for i.e. T. ovis) in most population of small ruminants. Thus investigation of parasite both in blood smears and in lymphatic smears could lead to diminish laboratory errors.

The genetic divergence could define as a mechanism which two or more breeds within the same species with a common ancestor could differently evolutionary separated in genome structure. Molecular genetics may provide proper tools for estimation of the level of diversity and mutational events on this breed over time. Accordingly, the main objective of the present report was to evaluate and compare the candidate gene polymorphisms for two meat and dairy type of goat breeds using candidate gene polymorphism approach. For this purpose, in overall, 30 goat individuals for two meat and dairy goat breed were chosen for genotyping of six candidate genes (Calpastatin, Myostatin, Insulin growth like hormone, Leptin, Pituitary-specific transcription factor and SCD genes using PCR-RFLP techniques. Molecular descriptive Statistics such as genotype and allele frequencies observed and expected heterozygosity, Minor allele frequency ,and Hardy-Weinberg Equilibrium was calculated and compared using POPGENE software between populations. The Chi-square test was used for significant differences between the two populations for screened genes. The observed results interesting showed significant genotype and allele frequency pattern between the two studied breeds. Obtained outputs may insight to the understanding of Genetic divergence between well-known breeds due to domestication and artificial selection as well as geographical

Nutritional and hormonal programs are one of the important ways of improving goat reproductive performance. Therefore, the present study was conducted to investigate the effect of using barley seed and eCG at the same time on the reproductive performance of goat in nomadic breeding conditions. The number of 60 goats of two to three-year-old in the breeding season and 60 goats of three to four-year-old in out-breeding season were chosen. Then the goats were divided into six groups of 10 numbers. 1- Control group (without receiving barley seed and eCG); 2- Group receiving 400 grams of barley for eight days (short term); 3- Group receiving 400 grams of barley for 16 days (long term); 4- Group receiving 400 IU eCG; 5- Group receiving 400 IU eCG and 400 grams of barley for eight days and 6- Group receiving 400 IU eCG and 400 grams of barley for 16 days. The results indicated that in-breeding season twinning rate in groups receiving barley for short and long term with eCG were higher compared to the group without receiving eCG. At the same time, the minimum (five) and maximum (20) numbers of  born kids were observed in control and group six, respectively. The results also indicated that in out-breeding season none of the characteristics were influenced statistically by treatments. It can be concluded that using 400 IU of eCG and 400 grams of barley seed daily, can improve the twinning rate in breeding season but such an effect cannot be observed in out breeding season.