For more than a quarter of a century, sequencing technologies from Sanger's method to next-generation high-throughput techniques have provided fascinating opportunities in the life sciences. The continuing upward trajectory of sequencing technologies will improve livestock research and expedite the development of various new genomic and technological studies with farm animals. The use of high-throughput technologies in livestock research has increased interest in metagenomics, epigenetics, genome-wide association studies, and identification of single nucleotide polymorphisms and copy number variations. Such studies are beginning to provide revolutionary insights into biological and evolutionary processes. Farm animals, such as cattle, swine, and horses, have played a dual role as economically and agriculturally important animals as well as biomedical research models. The first part of this study explores the current state of sequencing methods, many of which are already used in animal genomic studies, and the second part summarizes the state of cattle, swine, horse, and chicken genome sequencing and illustrates its achievements during the last few years. Finally, we describe several high-throughput sequencing approaches for the improved detection of known, unknown, and emerging infectious agents, leading to better diagnosis of infectious diseases. The insights from viral metagenomics and the advancement of next-generation sequencing will strongly support specific and efficient vaccine development and provide strategies for controlling infectious disease transmission among animal populations and/or between animals and humans. However, prospective sequencing technologies will require further research and in-field testing before reaching the marketplace.

Transformation of animal genomics by next-generation sequencing technologies: a decade of challenges and their impact on genetic architecture

Perspectives on Biology

Molecular approaches to the diagnosis and monitoring of production diseases in pigs.

Oligodeoxynucleotides containing unmethylated CpG motifs (CpG ODN) mimic the immunostimulatory activity of microbial DNA by interacting with Toll-like receptor 9 (TLR9) to activate both the innate and adaptive immune responses in different species. However, few studies have been published to compare the effects of CpG ODN on different pig breeds. Therefore, in this study, whole blood gene expression profiles of DPL and Landrace pigs treated with CpG ODN were studied using RNA-seq technology. 500 differentially expressed genes (DEGs) were identified between the two breeds. DPL pigs had significantly higher number of immune-relevant DEGs than the Landrace pigs after CpG ODN treatment. Pathway analysis showed that cytokine-cytokine receptor interaction and chemokine signaling pathway were the major enriched pathways of the immune-relevant DEGs. Further in vitro experiments showed that PBMCs of the DPL pigs had significantly higher levels of TLR9 mRNA than those of the Landrace pigs, both before and after CpG ODN stimulation. Cytokine and chemokine induction in the PBMCs of both breeds were also measured after CpG ODN stimulation. Our data showed that mRNA levels of cytokines (IFNα, IL8, IL12 p40) and chemokines (CXCL9, CXCL13) were significantly higher in the PBMCs of the DPL pigs than those of the Landrace pigs. Taken together, our data provide new information regarding the pig breed difference in response to CpG ODN stimulation and that higher levels of TLR9 mRNA in DPL pigs may be a major contributor for disease resistance.

/pdf/cpg-oligodeoxynucleotides-induce-differential-cytokine-and-4hom21gbpq.pdf

CpG Oligodeoxynucleotides Induce Differential Cytokine and Chemokine Gene Expression Profiles in Dapulian and Landrace Pigs.

This study was performed to identify the non- synonymous polymorphisms in the myosin heavy chain 1 gene (MYH1) association with skeletal muscle development in economically important Jeju Native Pig (JNP) and Berkshire breeds. Herein, we present an in silico analysis, with a focus on (a) in silico approaches to predict the functional effect of non-synonymous SNP (nsSNP) in MYH1 on growth, and (b) molecular docking and dynamic simulation of MYH1 to predict the effects of those nsSNP on protein-protein association. The NextGENe (V 2.3.4.) tool was used to identify the variants in MYH1 from JNP and Berkshire using RNA seq. Gene ontology analysis of MYH1 revealed significant association with muscle contraction and muscle organ development. The 95 % confidence intervals clearly indicate that the mRNA expression of MYH1 is significantly higher in the Berkshire longissimus dorsi muscle samples than JNP breed. Concordant in silico analysis of MYH1, the open-source software tools identified 4 potential nsSNP (L884T, K972C, N981G, and Q1285C) in JNP and 1 nsSNP (H973G) in Berkshire pigs. Moreover, protein-protein interactions were studied to investigate the effect of MYH1 mutations on association with hub proteins, and MYH1 was found to be closely associated with the protein myosin light chain, phosphorylatable, fast skeletal muscle MYLPF. The results of molecular docking studies on MYH1 (native and 4 mutants) and MYLFP demonstrated that the native complex showed higher electrostatic energy (−466.5 Kcal mol−1), van der Walls energy (−87.3 Kcal mol−1), and interaction energy (−835.7 Kcal mol−1) than the mutant complexes. Furthermore, the molecular dynamic simulation revealed that the native complex yielded a higher root-mean-square deviation (0.2–0.55 nm) and lower root-mean-square fluctuation (approximately 0.08–0.3 nm) as compared to the mutant complexes. The results suggest that the variants at L884T, K972C, N981G, and Q1285C in MYH1 in JNP might represent a cause for the poor growth performance for this breed. This study is a pioneering in-depth in silico analysis of polymorphic MYH1 and will serve as a valuable resource for further targeted molecular diagnosis and population-based studies conducted for improving the growth performance of JNP.

/pdf/an-integrated-in-silico-approach-for-functional-and-46pulk74e9.pdf

An integrated in silico approach for functional and structural impact of non- synonymous SNPs in the MYH1 gene in Jeju Native Pigs

Summary

This study was carried out with the objective to investigate the differentially expressed genes (DEGs) between Jeju native pig (JNP) and Berkshire piglets. The RNA-Seq technique was used to investigate the transcriptomes in the fat, liver and longissimus dorsi muscle from these two breeds. Paired-end reads of the sequences that passed the quality filters were aligned to the Sus scrofa genome using tophat2 (v2.0.2). In this study, 65% of muscle, 20% of fat and 54% of liver genes showed higher expression in the piglets of JNP than in Berkshire. Gene Ontology and signaling pathways showed that immune response and lipid metabolisms were commonly enriched pathways in all three tissues. It was found that the genes pertaining to body growth and immune system are significantly (P < 0.01) more highly expressed in Berkshire piglets. DEGs explored between the piglets of the two breeds might influence the identification of the genetic markers for further breed improvement programs. Our findings provide a new perspective for understanding and identifying candidate genes that are involved in various biological functions. Moreover, transcriptome analysis makes it easier to understand the differences between genetic mechanisms of breeds.

Evaluation of body growth and immunity‐related differentially expressed genes through deep RNA sequencing in the piglets of Jeju native pig and Berkshire

Canine transmissible venereal tumor (CTVT) is a histiocytic tumor of the dog that mainly affects the external genitalia, commonly found at tropical and subtropical zones. In the present investigation, we undertook this work mainly to perform a computational analysis of snSNP in the BTNL2 to identify the possible mutations and proposed the model structure of the mutant protein. Four deleterious mutations were identified in BTNL2 in 109 and 319 residual positions. Moreover, we constructed the homolgus structure of native and mutant proteins to predicate the stability. I-Mutant was used for routine analysis of protein stability and for the single site mutation analysis. It was found that mutation of L to S at residual position 109 and A to T at 319 residue position has shown maximum negative effect on the protein stability and considered for further analysis. The mutational effect on the protein function was analyzed by project HOPE. It was found that the wild-type residue is very conserved, but a few other residue types have been observed at this position too. Based on conservation scores this mutation is probably damaging to the protein. The present investigation was further used for molecular expect of the CTVT infection which might be useful in diagnosis and prevention of CTVT in canine.

Identification and In-silico Annotation of Functional Single Nucleotide Polymorphisms (SNPs) of the Candidate Gene Association with the Canine Transmissible Venereal Tumor Disease

contractionsed glucose transport after muscle Role of kallikrein-kininogen system in

Characterization and In Vitro Differentiation of Korean Ring-Necked Pheasant (Phasianus colchicus) Male Germ Cells

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Papers

Evaluation of body growth and immunity‐related differentially expressed genes through deep RNA sequencing in the piglets of Jeju native pig and Berkshire

Identification and In-silico Annotation of Functional Single Nucleotide Polymorphisms (SNPs) of the Candidate Gene Association with the Canine Transmissible Venereal Tumor Disease

contractionsed glucose transport after muscle Role of kallikrein-kininogen system in

Characterization and In Vitro Differentiation of Korean Ring-Necked Pheasant (Phasianus colchicus) Male Germ Cells