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Molecular Genetics in Livestock Production and Disease Resistance

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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (25 May 2023) | Viewed by 8897

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Special Issue Editor

Dr. Syed Mudasir Ahmad

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Guest Editor

Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-K, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shuhama, India
Interests: livestock; disease resistance; genomics; proteomics

Special Issue Information

Dear Colleagues,

Nearly a billion people worldwide depend on livestock for their livelihoods and food security, accounting for 40% of the world's agricultural output. Since the need for food is anticipated to grow significantly in the coming decades, knowledge of animal health and production is becoming more important. To enhance the production techniques and boost performance, it will be necessary to have a greater understanding of the structure and function of animal genomes as well as how they interact with non-genetic elements of production systems (such as diet and the environment). Lately, a large portion of animal genomics research has been devoted to animal genomes sequencing, identifying and cataloguing sequence variants from individual animals, and evaluating genomic variation to select for expected genetic differences in attributes. In recent years, high-throughput sequence technologies, such as GWAS, EWAS, transcriptomics, proteomics, and metabolomics, have developed significantly in all areas of biology, including applications in the traits and production of cattle. Additionally, genome editing technologies have added a novel promising research dimension to the existing animal breeding programs. In farm animal production, we are still in the early phase of exploring and improving their genetic potential.

The purpose of the current Topic is to promote submissions of high-quality research papers in the areas of molecular genetics concerning animal health and production.

Dr. Syed Mudasir Ahmad
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

livestock
production
health
disease resistance
genetics
omics approaches
genome editing

Published Papers (6 papers)

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Research

14 pages, 3086 KiB

Open AccessArticle

Genome-Wide Single-Nucleotide Polymorphism-Based Genomic Diversity and Runs of Homozygosity for Selection Signatures in Equine Breeds

by Anuradha Bhardwaj, Gitanjali Tandon, Yash Pal, Nitesh Kumar Sharma, Varij Nayan, Sonali Soni, Mir Asif Iquebal, Sarika Jaiswal, Ram Avatar Legha, Thirumala Rao Talluri, Tarun Kumar Bhattacharya, Dinesh Kumar, Anil Rai and B. N. Tripathi

Genes 2023, 14(8), 1623; https://doi.org/10.3390/genes14081623 - 14 Aug 2023

Viewed by 1101

Abstract

The horse, one of the most domesticated animals, has been used for several purposes, like transportation, hunting, in sport, or for agriculture-related works. Kathiawari, Marwari, Manipuri, Zanskari, Bhutia, Spiti, and Thoroughbred are the main breeds of horses, particularly due to their agroclimatic adaptation and role in any kind of strong physical activity, and these characteristics are majorly governed by genetic factors. The genetic diversity and phylogenetic relationship of these Indian equine breeds using microsatellite markers have been reported, but further studies exploring the SNP diversity and runs of homozygosity revealing the selection signature of breeds are still warranted. In our study, the identification of genes that play a vital role in muscle development is performed through SNP detection via the whole-genome sequencing approach. A total of 96 samples, categorized under seven breeds, and 620,721 SNPs were considered to ascertain the ROH patterns amongst all the seven breeds. Over 5444 ROH islands were mined, and the maximum number of ROHs was found to be present in Zanskari, while Thoroughbred was confined to the lowest number of ROHs. Gene enrichment of these ROH islands produced 6757 functional genes, with AGPAT1, CLEC4, and CFAP20 as important gene families. However, QTL annotation revealed that the maximum QTLs were associated with Wither’s height trait ontology that falls under the growth trait in all seven breeds. An Equine SNP marker database (EqSNPDb) was developed to catalogue ROHs for all these equine breeds for the flexible and easy chromosome-wise retrieval of ROH along with the genotype details of all the SNPs. Such a study can reveal breed divergence in different climatic and ecological conditions. Full article

(This article belongs to the Special Issue Molecular Genetics in Livestock Production and Disease Resistance)

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12 pages, 2286 KiB

Open AccessArticle

Study on the Protective Immunity Induced by Pseudotyped Baculovirus Expressing the E Protein of Tembusu Virus in Ducklings

by Zheng Ni, Tao Yun, Liu Chen, Weicheng Ye, Jionggang Hua, Yinchu Zhu, Guangqing Liu and Cun Zhang

Genes 2023, 14(7), 1316; https://doi.org/10.3390/genes14071316 - 22 Jun 2023

Viewed by 1057

Abstract

The Duck Tembusu virus (DTMUV), a pathogenic flavivirus, has been causing significant economic losses in the Chinese poultry industry since 2010. This virus can severely decrease egg production and inhibit the growth of laying ducks and ducklings. While many vaccines have been developed to prevent DTMUV infection, fresh outbreaks continue to occur, as few effective vaccines are available. The E glycoprotein of DTMUV is the primary target for inducing protective immunity in the natural host. Therefore, we conducted an investigation and successfully developed a recombinant baculovirus containing the DTMUV E gene. Ducklings were then vaccinated with the purified protein derived from this virus as a potential vaccine candidate. Our findings demonstrated that the E glycoprotein of DTMUV was highly expressed in Sf9 cells. The vaccination of ducklings with the recombinant baculovirus Bac-E resulted in the induction of strong humoral and cellular immune responses. Most significantly, we observed that the vaccine provided 100% protective immunity against lethal challenges with the DTMUV YY5 strain. Full article

(This article belongs to the Special Issue Molecular Genetics in Livestock Production and Disease Resistance)

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13 pages, 2953 KiB

Open AccessArticle

Identification of SNPs Related to Salmonella Resistance in Chickens Using RNA-Seq and Integrated Bioinformatics Approach

by Mashooq Ahmad Dar, Basharat Bhat, Junaid Nazir, Afnan Saleem, Tasaduq Manzoor, Mahak Khan, Zulfqarul Haq, Sahar Saleem Bhat and Syed Mudasir Ahmad

Genes 2023, 14(6), 1283; https://doi.org/10.3390/genes14061283 - 17 Jun 2023

Viewed by 1660

Abstract

Potential single nucleotide polymorphisms (SNPs) were detected between two chicken breeds (Kashmir favorella and broiler) using deep RNA sequencing. This was carried out to comprehend the coding area alterations, which cause variances in the immunological response to Salmonella infection. In the present study, we identified high impact SNPs from both chicken breeds in order to delineate different pathways that mediate disease resistant/susceptibility traits. Samples (liver and spleen) were collected from Salmonella resistant (K. favorella) and susceptible (broiler) chicken breeds. Salmonella resistance and susceptibility were checked by different pathological parameters post infection. To explore possible polymorphisms in genes linked with disease resistance, SNP identification analysis was performed utilizing RNA seq data from nine K. favorella and ten broiler chickens. A total of 1778 (1070 SNPs and 708 INDELs) and 1459 (859 SNPs and 600 INDELs) were found to be specific to K. favorella and broiler, respectively. Based on our results, we conclude that in broiler chickens the enriched pathways mostly included metabolic pathways like fatty acid metabolism, carbon metabolism and amino acid metabolism (Arginine and proline metabolism), while as in K. favorella genes with high impact SNPs were enriched in most of the immune-related pathways like MAPK signaling pathway, Wnt signaling pathway, NOD-like receptor signaling pathway, etc., which could be a possible resistance mechanism against salmonella infection. In K. favorella, protein–protein interaction analysis also shows some important hub nodes, which are important in providing defense against different infectious diseases. Phylogenomic analysis revealed that indigenous poultry breeds (resistant) are clearly separated from commercial breeds (susceptible). These findings will offer fresh perspectives on the genetic diversity in chicken breeds and will aid in the genomic selection of poultry birds. Full article

(This article belongs to the Special Issue Molecular Genetics in Livestock Production and Disease Resistance)

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15 pages, 3279 KiB

Open AccessArticle

Identification of a Novel lncRNA LNC_001186 and Its Effects on CPB2 Toxin-Induced Apoptosis of IPEC-J2 Cells

by Kaihui Xie, Qiaoli Yang, Zunqiang Yan, Xiaoyu Huang, Pengfei Wang, Xiaoli Gao and Shuangbao Gun

Genes 2023, 14(5), 1047; https://doi.org/10.3390/genes14051047 - 6 May 2023

Viewed by 1488

Abstract

The Clostridium perfringens (C. perfringen) beta2 (CPB2) toxin produced by C. perfringens type C (CpC) can cause necrotizing enteritis in piglets. Immune system activation in response to inflammation and pathogen infection is aided by long non-coding RNAs (lncRNAs). In our previous work, we revealed the differential expression of the novel lncRNA LNC_001186 in CpC-infected ileum versus healthy piglets. This implied that LNC_001186 may be a regulatory factor essential for CpC infection in piglets. Herein, we analyzed the coding ability, chromosomal location and subcellular localization of LNC_001186 and explored its regulatory role in CPB2 toxin-induced apoptosis of porcine small intestinal epithelial (IPEC-J2) cells. RT-qPCR results indicated that LNC_001186 expression was highly enriched in the intestines of healthy piglets and significantly increased in CpC-infected piglets’ ileum tissue and CPB2 toxin-treated IPEC-J2 cells. The total sequence length of LNC_001186 was 1323 bp through RACE assay. CPC and CPAT, two online databases, both confirmed that LNC_001186 had a low coding ability. It was present on pig chromosome 3. Cytoplasmic and nuclear RNA isolation and RNA-FISH assays showed that LNC_001186 was present in the nucleus and cytoplasm of IPEC-J2 cells. Furthermore, six target genes of LNC_001186 were predicted using cis and trans approaches. Meanwhile, we constructed ceRNA regulatory networks with LNC_001186 as the center. Finally, LNC_001186 overexpression inhibited IPEC-J2 cells’ apoptosis caused by CPB2 toxin and promoted cell viability. In summary, we determined the role of LNC_001186 in IPEC-J2 cells’ apoptosis caused by CPB2 toxin, which assisted us in exploring the molecular mechanism of LNC_001186 in CpC-induced diarrhea in piglets. Full article

(This article belongs to the Special Issue Molecular Genetics in Livestock Production and Disease Resistance)

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13 pages, 1153 KiB

Open AccessArticle

Genome-Wide Association Studies of Live Weight at First Breeding at Eight Months of Age and Pregnancy Status of Ewe Lambs

by Emmanuelle Haslin, Emma J. Pettigrew, Rebecca E. Hickson, Paul R. Kenyon, Kristene R. Gedye, Nicolas Lopez-Villalobos, J. M. D. R. Jayawardana, Stephen T. Morris and Hugh T. Blair

Genes 2023, 14(4), 805; https://doi.org/10.3390/genes14040805 - 27 Mar 2023

Viewed by 1405

Abstract

This study estimated genetic parameters and identified candidate genes associated with live weight, and the occurrence of pregnancy in 1327 Romney ewe lambs using genome-wide association studies. Phenotypic traits considered were the occurrence of pregnancy in ewe lambs and live weight at eight months of age. Genetic parameters were estimated, and genomic variation was assessed using 13,500 single-nucleotide polymorphic markers (SNPs). Ewe lamb live weight had medium genomic heritability and was positively genetically correlated with occurrence of pregnancy. This suggests that selection for heavier ewe lambs is possible and would likely improve the occurrence of pregnancy in ewe lambs. No SNPs were associated with the occurrence of pregnancy; however, three candidate genes were associated with ewe lamb live weight. Tenascin C (TNC), TNF superfamily member 8 (TNFSF8) and Collagen type XXVIII alpha 1 chain (COL28A1) are involved in extracellular matrix organization and regulation of cell fate in the immune system. TNC may be involved in ewe lamb growth, and therefore, could be of interest for selection of ewe lamb replacements. The association between ewe lamb live weight and TNFSF8 and COL28A1 is unclear. Further research is needed using a larger population to determine whether the genes identified can be used for genomic selection of replacement ewe lambs. Full article

(This article belongs to the Special Issue Molecular Genetics in Livestock Production and Disease Resistance)

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22 pages, 5114 KiB

Open AccessArticle

Molecular Evolution of the Bactericidal/Permeability-Increasing Protein (BPIFA1) Regulating the Innate Immune Responses in Mammals

by Hafiz Ishfaq Ahmad, Faheem Ahmed Khan, Musarrat Abbas Khan, Safdar Imran, Rana Waseem Akhtar, Nuruliarizki Shinta Pandupuspitasari, Windu Negara and Jinping Chen

Genes 2023, 14(1), 15; https://doi.org/10.3390/genes14010015 - 21 Dec 2022

Cited by 7 | Viewed by 1482

Abstract

Bactericidal/permeability-increasing protein, a primary factor of the innate immune system of mammals, participates in natural immune protection against invading bacteria. BPIFA1 actively contributes to host defense via multiple mechanisms, such as antibacterial, surfactant, airway surface liquid control, and immunomodulatory activities. However, the evolutionary history and selection forces on the BPIFA1 gene in mammals during adaptive evolution are poorly understood. This study examined the BPIFA1 gene of humans compared with that of other mammalian species to estimate the selective pressure derived by adaptive evolution. To assess whether or not positive selection occurred, we employed several different possibility tests (M1 vs. M2 and M7 vs. M8). The proportions of positively selected sites were significant, with a likelihood log value of 93.63 for the BPIFA1 protein. The Selecton server was used on the same dataset to reconfirm positive selection for specific sites by employing the Mechanistic-Empirical Combination model, thus providing additional evidence supporting the findings of positive selection. There was convincing evidence for positive selection signals in the BPIFA1 genes of mammalian species, which was more significant for selection signs and creating signals. We performed probability tests comparing various models based on dN/dS ratios to recognize specific codons under positive selection pressure. We identified positively selected sites in the LBP-BPI domain of BPIFA1 proteins in the mammalian genome, including a lipid-binding domain with a very high degree of selectivity for DPPC. BPIFA1 activates the upper airway’s innate immune system in response to numerous genetic signals in the mammalian genome. These findings highlight evolutionary advancements in immunoregulatory effects that play a significant role in the antibacterial and antiviral defenses of mammalian species. Full article

(This article belongs to the Special Issue Molecular Genetics in Livestock Production and Disease Resistance)

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