Avian Genomics and Transgenesis

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

Deadline for manuscript submissions: closed (20 August 2023) | Viewed by 14591

Special Issue Editors

Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
Interests: avian biotechnology; genome editing; primordial germ cells; transgenesis
Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
Interests: genetics; transcriptomics; germ cells, genome editing

Special Issue Information

Dear Colleagues,

Avian species have become valuable animal models in various agriculture, veterinary, and life science disciplines. In the past two decades, the discipline of avian genomics has been undergoing advancements together with the advancements in high-throughput sequencing techniques, including the recent whole-transcriptome sequencing (bulk RNA-seq) and single-cell RNA sequencing (scRNA-seq). As a result, the genome/transcriptome profiling of different individual cells and tissues, and also comparative analyses of cells and tissues, have been widely reported in avian model animals, such as chickens, quails, and zebra finches. Additionally, the avian transgenic discipline has also been undergoing advancements in the past two decades with the development of genome editing tools, such as meganucleases, zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nucleases (CRISPR/Cas), and base editors. These tools enabled the precise genome editing of avian cells in vitro, as well as in vitro- or in vivo-mediated genome editing for the generation of transgenic avian species. Additionally, the developed genome editing techniques and transgenic birds are outspreading our capability to explain the contribution of genome-modified birds in a variety of fields, ranging from basic research to applied biotechnology and biomedical research. This Special Issue aims to collect research and review manuscripts that newly address the expression and/or functions of an extended set of genes/transcripts, genome editing methods, and the generation/analysis of transgenic avian species. 

Prof. Dr. Jae Yong Han
Dr. Deivendran Rengaraj
Guest Editors

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Keywords

  • genomics 
  • transcriptomics 
  • genome editing 
  • transgenic animals 
  • avian species

Published Papers (7 papers)

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Research

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7 pages, 1347 KiB  
Communication
Male Gonads Transplantation from Kadaknath Chicken to Chicken and Duck Surrogates
by Adnan Naim, Surya Kanta Mishra, Anjan Sahoo and Indra mani Nath
Genes 2023, 14(5), 1094; https://doi.org/10.3390/genes14051094 - 16 May 2023
Viewed by 1137
Abstract
Transplantation of the gonadal tissue of male and female avian species, such as chicken, onto suitable surrogates and production of live offspring has been successfully demonstrated as a strategy for the conservation and re-constitution of valuable chicken germplasm. The main objective of this [...] Read more.
Transplantation of the gonadal tissue of male and female avian species, such as chicken, onto suitable surrogates and production of live offspring has been successfully demonstrated as a strategy for the conservation and re-constitution of valuable chicken germplasm. The main objective of this study was to establish and develop the male gonadal tissue transplantation technology for the conservation of the indigenous chicken germplasm. The male gonads of the Indian native chicken breed, Kadaknath (KN), were transplanted from a day-old donor to a recipient white leghorn (WL) chicken, and Khaki Campbell (KC) ducks, as surrogates. All the surgical interventions were performed under permitted general anaesthesia, and the chicks, upon recovery, were reared with and without immunosuppressant. The recipient surrogates for the donor KN gonads were housed and reared for 10–14 weeks, and post-sacrifice, developed gonadal tissues were harvested to squeeze out the fluid to perform artificial insemination (AI). The AI-entailed fertility test using the recovered seminal extract from the transplanted KN testes from both surrogate species (KC ducks and WL males), used against KN purebred females, remained very close to the percent fertility realised from purebred KN chickens (controls). These initial results revealed from this trial study suggest definitively that, Kadaknath male gonads were readily accepted and grown inside the intra- and inter-species surrogate host, WL chicken and KC ducks, demonstrating a suitable intra- and inter-species donor-host system. Furthermore, the developed transplanted male gonads of KN chicken into the surrogates were found to have the potential to fertilise the egg and give rise to pure-line KN chicks. Full article
(This article belongs to the Special Issue Avian Genomics and Transgenesis)
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15 pages, 2444 KiB  
Article
Targeted Modulation of Chicken Genes In Vitro Using CRISPRa and CRISPRi Toolkit
by Brittany Chapman, Jeong Hoon Han, Hong Jo Lee, Isabella Ruud and Tae Hyun Kim
Genes 2023, 14(4), 906; https://doi.org/10.3390/genes14040906 - 13 Apr 2023
Cited by 1 | Viewed by 2234
Abstract
Engineering of clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-associated protein 9 (Cas9) system has enabled versatile applications of CRISPR beyond targeted DNA cleavage. Combination of nuclease-deactivated Cas9 (dCas9) and transcriptional effector domains allows activation (CRISPRa) or repression (CRISPRi) of target [...] Read more.
Engineering of clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-associated protein 9 (Cas9) system has enabled versatile applications of CRISPR beyond targeted DNA cleavage. Combination of nuclease-deactivated Cas9 (dCas9) and transcriptional effector domains allows activation (CRISPRa) or repression (CRISPRi) of target loci. To demonstrate the effectiveness of the CRISPR-mediated transcriptional regulation in chickens, three CRISPRa (VP64, VPR, and p300) and three CRISPRi (dCas9, dCas9-KRAB, and dCas9-KRAB-MeCP2) systems were tested in chicken DF-1 cells. By introducing guide RNAs (gRNAs) targeting near the transcription start site (TSS) of each gene in CRISPRa and CRISPRi effector domain-expressing chicken DF-1 cell lines, significant gene upregulation was induced in dCas9-VPR and dCas9-VP64 cells, while significant downregulation was observed with dCas9 and dCas9-KRAB. We further investigated the effect of gRNA positions across TSS and discovered that the location of gRNA is an important factor for targeted gene regulation. RNA sequencing analysis of IRF7 CRISPRa and CRISPRi- DF-1 cells revealed the specificity of CRISPRa and CRISPRi-based targeted transcriptional regulation with minimal off-target effects. These findings suggest that the CRISPRa and CRISPRi toolkits are an effective and adaptable platform for studying the chicken genome by targeted transcriptional modulation. Full article
(This article belongs to the Special Issue Avian Genomics and Transgenesis)
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22 pages, 2839 KiB  
Article
Transcriptome Response of Differentiating Muscle Satellite Cells to Thermal Challenge in Commercial Turkey
by Kent M. Reed, Kristelle M. Mendoza, Jiahui Xu, Gale M. Strasburg and Sandra G. Velleman
Genes 2022, 13(10), 1857; https://doi.org/10.3390/genes13101857 - 14 Oct 2022
Cited by 3 | Viewed by 1439
Abstract
Early muscle development involves the proliferation and differentiation of stem cells (satellite cells, SCs) in the mesoderm to form multinucleated myotubes that mature into muscle fibers and fiber bundles. Proliferation of SCs increases the number of cells available for muscle formation while simultaneously [...] Read more.
Early muscle development involves the proliferation and differentiation of stem cells (satellite cells, SCs) in the mesoderm to form multinucleated myotubes that mature into muscle fibers and fiber bundles. Proliferation of SCs increases the number of cells available for muscle formation while simultaneously maintaining a population of cells for future response. Differentiation dramatically changes properties of the SCs and environmental stressors can have long lasting effects on muscle growth and physiology. This study was designed to characterize transcriptional changes induced in turkey SCs undergoing differentiation under thermal challenge. Satellite cells from the pectoralis major (p. major) muscle of 1-wk old commercial fast-growing birds (Nicholas turkey, NCT) and from a slower-growing research line (Randombred Control Line 2, RBC2) were proliferated for 72 h at 38 °C and then differentiated for 48 h at 33 °C (cold), 43 °C (hot) or 38 °C (control). Gene expression among thermal treatments and between turkey lines was examined by RNAseq to detect significant differentially expressed genes (DEGs). Cold treatment resulted in significant gene expression changes in the SCs from both turkey lines, with the primary effect being down regulation of the DEGs with overrepresentation of genes involved in regulation of skeletal muscle tissue regeneration and sarcomere organization. Heat stress increased expression of genes reported to regulate myoblast differentiation and survival and to promote cell adhesion particularly in the NCT line. Results suggest that growth selection in turkeys has altered the developmental potential of SCs in commercial birds to increase hypertrophic potential of the p. major muscle and sarcomere assembly. The biology of SCs may account for the distinctly different outcomes in response to thermal challenge on breast muscle growth, development, and structure of the turkey. Full article
(This article belongs to the Special Issue Avian Genomics and Transgenesis)
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Review

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12 pages, 5552 KiB  
Review
A Bird’s-Eye View of Endangered Species Conservation: Avian Genomics and Stem Cell Approaches for Green Peafowl (Pavo muticus)
by Sittipon Intarapat, Woranop Sukparangsi, Oleg Gusev and Guojun Sheng
Genes 2023, 14(11), 2040; https://doi.org/10.3390/genes14112040 - 04 Nov 2023
Viewed by 1990
Abstract
Aves ranks among the top two classes for the highest number of endangered and extinct species in the kingdom Animalia. Notably, the IUCN Red List classified the green peafowl as endangered. This highlights promising strategies using genetics and reproductive technologies for avian wildlife [...] Read more.
Aves ranks among the top two classes for the highest number of endangered and extinct species in the kingdom Animalia. Notably, the IUCN Red List classified the green peafowl as endangered. This highlights promising strategies using genetics and reproductive technologies for avian wildlife conservation. These platforms provide the capacity to predict population trends and enable the practical breeding of such species. The conservation of endangered avian species is facilitated through the application of genomic data storage and analysis. Storing the sequence is a form of biobanking. An analysis of sequence can identify genetically distinct individuals for breeding. Here, we reviewed avian genomics and stem cell approaches which not only offer hope for saving endangered species, such as the green peafowl but also for other birds threatened with extinction. Full article
(This article belongs to the Special Issue Avian Genomics and Transgenesis)
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19 pages, 1673 KiB  
Review
Strategies for the Generation of Gene Modified Avian Models: Advancement in Avian Germline Transmission, Genome Editing, and Applications
by Young-Min Kim, Seung-Je Woo and Jae-Yong Han
Genes 2023, 14(4), 899; https://doi.org/10.3390/genes14040899 - 12 Apr 2023
Cited by 1 | Viewed by 2198
Abstract
Avian models are valuable for studies of development and reproduction and have important implications for food production. Rapid advances in genome-editing technologies have enabled the establishment of avian species as unique agricultural, industrial, disease-resistant, and pharmaceutical models. The direct introduction of genome-editing tools, [...] Read more.
Avian models are valuable for studies of development and reproduction and have important implications for food production. Rapid advances in genome-editing technologies have enabled the establishment of avian species as unique agricultural, industrial, disease-resistant, and pharmaceutical models. The direct introduction of genome-editing tools, such as the clustered regularly interspaced short palindromic repeats (CRISPR) system, into early embryos has been achieved in various animal taxa. However, in birds, the introduction of the CRISPR system into primordial germ cells (PGCs), a germline-competent stem cell, is considered a much more reliable approach for the development of genome-edited models. After genome editing, PGCs are transplanted into the embryo to establish germline chimera, which are crossed to produce genome-edited birds. In addition, various methods, including delivery by liposomal and viral vectors, have been employed for gene editing in vivo. Genome-edited birds have wide applications in bio-pharmaceutical production and as models for disease resistance and biological research. In conclusion, the application of the CRISPR system to avian PGCs is an efficient approach for the production of genome-edited birds and transgenic avian models. Full article
(This article belongs to the Special Issue Avian Genomics and Transgenesis)
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13 pages, 2013 KiB  
Review
Current Approaches to and the Application of Intracytoplasmic Sperm Injection (ICSI) for Avian Genome Editing
by Shusei Mizushima, Tomohiro Sasanami, Tamao Ono and Asato Kuroiwa
Genes 2023, 14(3), 757; https://doi.org/10.3390/genes14030757 - 20 Mar 2023
Cited by 1 | Viewed by 1835
Abstract
Poultry are one of the most valuable resources for human society. They are also recognized as a powerful experimental animal for basic research on embryogenesis. Demands for the supply of low-allergen eggs and bioreactors have increased with the development of programmable genome editing [...] Read more.
Poultry are one of the most valuable resources for human society. They are also recognized as a powerful experimental animal for basic research on embryogenesis. Demands for the supply of low-allergen eggs and bioreactors have increased with the development of programmable genome editing technology. The CRISPR/Cas9 system has recently been used to produce transgenic animals and various animals in the agricultural industry and has also been successfully adopted for the modification of chicken and quail genomes. In this review, we describe the successful establishment of genome-edited lines combined with germline chimera production systems mediated by primordial germ cells and by viral infection in poultry. The avian intracytoplasmic sperm injection (ICSI) system that we previously established and recent advances in ICSI for genome editing are also summarized. Full article
(This article belongs to the Special Issue Avian Genomics and Transgenesis)
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18 pages, 937 KiB  
Review
Fate Decisions of Chicken Primordial Germ Cells (PGCs): Development, Integrity, Sex Determination, and Self-Renewal Mechanisms
by Kennosuke Ichikawa and Hiroyuki Horiuchi
Genes 2023, 14(3), 612; https://doi.org/10.3390/genes14030612 - 28 Feb 2023
Cited by 1 | Viewed by 2340
Abstract
Primordial germ cells (PGCs) are precursor cells of sperm and eggs. The fate decisions of chicken PGCs in terms of their development, integrity, and sex determination have unique features, thereby providing insights into evolutionary developmental biology. Additionally, fate decisions in the context of [...] Read more.
Primordial germ cells (PGCs) are precursor cells of sperm and eggs. The fate decisions of chicken PGCs in terms of their development, integrity, and sex determination have unique features, thereby providing insights into evolutionary developmental biology. Additionally, fate decisions in the context of a self-renewal mechanism have been applied to establish culture protocols for chicken PGCs, enabling the production of genome-edited chickens and the conservation of genetic resources. Thus, studies on the fate decisions of chicken PGCs have significantly contributed to both academic and industrial development. Furthermore, studies on fate decisions have rapidly advanced owing to the recent development of essential research technologies, such as genome editing and RNA sequencing. Here, we reviewed the status of fate decisions of chicken PGCs and provided insight into other important research issues that require attention. Full article
(This article belongs to the Special Issue Avian Genomics and Transgenesis)
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