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Objective: Data generation in biology and biotechnology has greatly increased in recent years due to the very rapid development of high-performance technologies. These data are obtained from studying biological molecules, such as metabolites, proteins, RNA, and DNA, to understand the role of these molecules in determining the structure, function, and dynamics of living systems. Functional genomics is a field of research that aims to characterize the function and interaction of all the major components (DNA, RNA, proteins, and metabolites, along with their modifications) that contribute to the set of observable characteristics of a cell or individual (i.e., phenotype). Furthermore, in a breeding program, genetic improvement can be maximized through accurate identification of superior animals that are selected as parents of the next generation, thereby achieving breeding goals. Artificial neural networks have been proposed to alleviate this limitation of traditional regression methods and can be used to handle nonlinear and complex data, even when the data is imprecise and noisy. Omics data can be too large and complex to handle through visual analysis or statistical correlations. This has encouraged the use of machine intelligence or artificial intelligence. The objectives of this study was to review the main applications of artificial intelligence methods in functional genomics, cancer, agriculture, domestic animals and its intertwined fields, i.e. epigenomics, transcriptomics, epitranscriptomics, proteomics, and metabolomics, discuss important aspects of data management, such as data integration, cleaning, noise removal, balancing and ratio of missing data, functional genomicssystem modeling, artificial intelligence and systems biology, addressing legal, ethical and economic issues related to the application of artificial intelligence methods in the field of genomics and presenting a view of possible scenarios in the future. Materials and methods: In this review, all researches conducted in the field of artificial intelligence application in functional genomics, cancer, agriculture, domestic animals, and its intertwined fields, i.e. epigenomics, transcriptomics, epitranscriptomics, proteomics, and metabolomics, were tried, focusing on the applications of recent years after Increase production of big data to be studied and used. Results: The studies showed that the application of artificial intelligence in all fields, including functional genomics, cancer, agriculture, domestic animals, and its intertwined fields, i.e., epigenomics, transcriptomics, epitranscriptomics, proteomics, and metabolomics, is increasing rapidly and has many benefits. Conclusions: Considering the vital applications that are often addressed by biology and especially functional genomics, it is better to deal with artificial intelligence tools that are able to help mechanistic understanding of biological processes. In other words, enabling systems biology is important to reap the benefits of AI results in genomics. Interpretability can certainly help AI to be more easily adopted in practical applications such as medicine. In our opinion, increasing the volume and diversity of reliable big data and integrating it with theoretical modeling will help increase human trust in AI-based predictions and decisions in the future. On the one hand, model-based approaches can provide knowledge-based constraints. On the other hand, the results of artificial intelligence can help to create the parameters of models of biological systems. Functional genomics, as well as all fields of medicine, biology, agriculture, animal science, and other sciences that involve both individual and collective rights, is a complex field of research. Those who want to use AI in this field will find it difficult to navigate, as the field is sensitive to legal, ethical, and spiritual aspects. Artificial intelligence opens many opportunities that we should not refuse for fear of not understanding all the steps. The path that artificial intelligence will follow is just beginning to unfold. It has many promises and many potential dangers ahead. This path will probably be long and irreversible. Artificial intelligence will change our lives and we need to change our minds as soon as possible to adapt, accept, and manage the resulting changes in the best possible way, to ensure that they will bring as many benefits as possible and will cause the least possible negative consequences for us. [ABSTRACT FROM AUTHOR]

Objective Fennel (Foeniculum vulgare mill) from the Apiaceae family is one of the most important medicinal plants that has strong antimicrobial, liver protective and antioxidant properties and has been used by humans since ancient times. The results of various studies on domestic animals have proven that adding the fennel in the diet of animals, increases digestion and growth efficiency, improves the oxidative quality of meat, increases the volume of cell packing, increases the number of red blood cells and hemoglobin. It improves carcass efficiency and small intestine weight and length and reduces total bacterial counts, improves performance and health status, and improves feed conversion and body weight. Therefore, the aim of this study was to investigate the effect of fennel feeding (Foeniculum vulgare) on IGF1 gene expression in the rumen tissue of Kermani lambs. Materials and methods In this research, 30 Kermani male lambs weighing 27.5 ± 0.45 kg (eight months old) were used. Diets were grouped into three fennel levels based on g/kg dry matter (0, 10 or 1% and 20 or 2% fennel g/kg dry matter). After the end of the study period, the investigated animals were slaughtered for sampling and the rumen weight was recorded. Total RNA was extracted from the rumen tissue and then cDNA was synthesized. The quality of RNA and cDNA was measured using electrophoresis on agarose gel. The Pfaffl et al. (2002) method was used to analyze the real time PCR data. Results Empty rumen weight in animals fed with fennel (780 g) was lower than animals fed with diet without fennel (890 g) (P < 0.05). The extracted total RNA was of good quality, complete, and healthy, and had two bands with sizes of S28 and S18. Electrophoresis of the amplification results of target (IGF1) and reference (GAPDH) genes in rumen tissue on agarose gel showed that the band size for the target gene is 265 bp and for the reference gene is 76 bp. By increasing the level of feeding with fennel, there was a significant increase in IGF1 gene proliferation in rumen tissue (p<0.05). The maximum expression of IGF1 gene was when the animals were fed with a diet containing 2% fennel. Conclusions The findings of the present study show that fennel can be used with a beneficial effect on IGF1 gene expression in the rumen in the diet of sheep to improve functions of this tissue. Although according to the findings of the current research and other studies, it can be confirmed that fennel can be used for productive and reproductive purposes in sheep breeding, but in future research, in order to reach a definite result, it is better to consider diverse and more complex physiological and epigenetic conditions. [ABSTRACT FROM AUTHOR]

Objective: Although aquaculture is the fastest sector in terms of animal protein production in the world, breeding programs in aquatic species have been delayed compared to livestock and plants. Breeding improvement programs in aquaculture are mainly based on using phenotypic and pedigree information in quantitative genetics. However, approaches based on genomic information such as marker assistant selection (MAS) and genomic selection (GS) have been used to improve economic traits in recent years. The present paper aimed to investigate the breeding principles in aquaculture from phenotypic selection to genomic selection, their advantages and limitations, and recent advances in different aquatic species. Results: Genomic selection increases genetic gain in aquaculture through increasing accuracy of selection, decreasing generation interval, decreasing inbreeding rate, better control of genetic and environmental interactions, and selection of animals with less sensitivity to environmental variation. Especially, genomic selection is suitable for difficult-to-measure or low heritability traits such as disease resistance, feed intake, reproduction traits, and carcass quality. Reference population size, marker density, mating design, number and size of families, and a number of generations are effective factors in the accuracy of genomic selection in aquaculture. Continuous advances in cost-effective technologies for genotyping especially genotyping-by-sequencing (GBS) and bioinformatics will facilitate the faster application of genomic selection in aquaculture. Conclusions: Although genomic selection has been used for about 20 aquatic species in recent years and has provided opportunities for the improvement of genetic gain. However, the advantages of this method should be evaluated in commercial and economic aquatic breeding programs. It is expected that genomic selection will be widely used in aquatic breeding in the future and pave the way for the sustainable development of this industry. [ABSTRACT FROM AUTHOR]

Objective: It has been shown that mutation in DNAH1 (Dynein Axonemal Heavy Chain 1) gene is associated with MMAF (multiple morphological anomalies of the flagella) and PCD (primary ciliary dyskinesia) phenotypes. MMAF has been widely studied in male reproductive traits and is often associated with abnormal sperm, which seriously affects male reproductive traits and even leads to infertility. Indeed, as a MMAF-dependent gene, many studies have identified the DNAH1 gene as a key and essential player in male and female gonadal development and have investigated the clinical applications of the DNAH1 gene. PCD is often associated with ciliary motility disorder, which is also an autosomal recessive genetic disease. Animals with severe PCD show infertility. This study aimed to study the expression pattern of the DNAH1 gene in the testicular tissue of Raini Cashmere goat using Real-Time PCR. Materials and Methods: Sampling was done from the testicular tissue of three heads (3 replicates from each head) of Raini Cashmere goats in the slaughterhouse. The isolated samples were placed in 1.5 mL microtubes. Total RNA was extracted from testicular tissue. Agarose gel electrophoresis and UV spectrophotometry were used to evaluate the quality and quantity of extracted RNA. Then cDNA was made and Real-Time PCR was performed. Also, the GAPDH housekeeping gene was used as a control. Melting curves were analyzed and data obtained from Real-Time PCR were performed. Results: The results of Real-Time PCR curves and observing the results of electrophoresis of PCR products on 2% agarose gel showed that the DNAH1 gene is expressed in testicular tissue. For the DNAH1 gene, a band of 140 bp was observed and for the GAPDH gene, a band of 143 bp was observed, and the accuracy of the amplification test was confirmed. Conclusions; According to the results of the present study and the results of other researchers, it can be concluded that the DNAH1 gene plays an important role in fertility. In the present study, it was found that the DNAH1 gene is expressed in testicular tissue. Therefore, the DNAH1 gene is most likely essential for male fertility, and the results of this research have provided a way for future studies to describe the role of the DNAH1 gene as a candidate gene for better fertility and normal physiology in domestic animals, especially goats. [ABSTRACT FROM AUTHOR]

Objective Skeletal muscles make up about 40% of body weight and are responsible for many functions, such as maintaining required energy, maintaining body condition, and protecting tissues. Normal growth of skeletal muscles is a prerequisite for animals to maintain normal functions and metabolism, and any abnormal growth of muscles leads to disease. Based on the analysis of gene expression profiles in skeletal muscle, MYH7 gene has been identified as a candidate gene related to muscle contraction. The aim of this study was to investigate the expression of MYH7 gene in femur, humeral muscle and back muscle tissues of fattening lambs of Kermani breed. Materials and Methods In this research, six Kermani male lambs were sampled from femur, humeral muscle and back muscle tissues at the time of slaughter. The total number of samples was equal to 54 samples (6 animals, 3 tissues and 3 repetitions of each tissue). Total RNA was extracted using a standard extraction kit. The quality and quantity of extracted RNA was evaluated using electrophoresis on 2% agarose gel and using nanodrop device. Parstous cDNA synthesis kit was used for the cDNA synthesis from the extracted RNA. Syber Green real time PCR reaction was used to check the relative level of gene expression. The method of Pfaffl et al. (2002) was used to analyze the data obtained from real time PCR. Results The results of RNAs extracted at A260/A280 wavelength showed that the quality is suitable and desirable (1.9-1.8). In addition, the observation of two bands of 18S and 28S for RNA on agarose gel indicated that the RNA was intact and the absence of additional bands on the gel indicated that the extracted RNA was pure. The results of real time PCR curves and electrophoresis of PCR products on agarose gel (2%) showed that the MYH7 gene is amplified and expressed in the femur, humeral muscle and back muscle tissues of Kermani male lambs. For the studied tissues (femur, humeral muscle and back muscle), a band of 283 bp was observed for the MYH7 gene and a band of 112 bp was observed for the beta-actin gene in all samples. These observations indicated that the correct experiment was performed and the desired fragments were amplified correctly. The results of this research showed that this gene is expressed in the femur, humeral muscle and back muscle tissues. Conclusion In the present study, it was found that the MYH7 gene is expressed in the femur, humeral muscle and back muscle. Therefore, it can be concluded that MYH7 gene plays a role in different muscles, which are very necessary for more meat production in the sheep breeds. [ABSTRACT FROM AUTHOR]

Objective Cannabis seeds have high amounts of crude protein and energy, so they can better resist the microbial digestion of the rumen and pass through the intact rumen to a greater extent and be digested and absorbed in the intestine. This means they can improve livestock performance. Therefore, they can be used for this purpose. On the other hand, DLK1 gene plays an important role in controlling cell differentiation processes, including muscle and nerve differentiation, adipogenesis, hematopoiesis, and bone differentiation throughout fetal and adult life. Therefore, the aim of this study was to investigate the effect of cannabis seeds on DLK1 gene expression in the heart tissue of Kermani lambs. Materials and methods To carry out this research, 12 six-month-old Kermani lambs of equal weight were used in a completely randomized design in three experimental groups. After slaughter, sampling of heart tissue (with 3 repeats) was done from both groups. The samples were quickly placed in liquid nitrogen and then stored in a -80 freezer. Total RNA was extracted using a standard kit. The quality and quantity of extracted RNA was evaluated. cDNA synthesis kit of Fermentase Company was used for cDNA synthesis. Real time PCR reaction using Syber Green method was used to check the relative level of gene expression. To analyze the data obtained from real time PCR, the method of Pfaffl et al. was used. Results The ratio of A260/A280 for the extracted RNAs was equal to 1.9-1.8, which indicates their appropriate and desirable quality. The results of real time PCR curves and electrophoresis of PCR products on agarose gel showed that DLK1 gene is expressed in heart tissue. The results of the present study also showed that feeding cannabis at the level of 1% significantly (P<0.05) increases the expression of DLK1 gene in the heart tissue by 4.74 times compared to the control group. Conclusions Based on the results of the present study, it can be concluded that cannabis can be used in the diet of sheep to improve the structure of the heart through positive effects on the expression of the DLK1 gene. In addition, the interesting results of the present study in response to the use of Cannabis seeds in the diet of sheep open a new path for wider research in this field. [ABSTRACT FROM AUTHOR]