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Genetics and Breeding of Non-traditional Farm Animals, Companion Animals, Lab...
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Genetics and Breeding of Non-traditional Farm Animals, Companion Animals, Lab Animals and Wildlife

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 March 2023) | Viewed by 6896

Special Issue Editors

Dr. Xiang Li

E-Mail Website
Guest Editor
National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Huazhong Agricultural University, Wuhan, China
Interests: animal nutrition and reproduction
Prof. Dr. Wuzi Dong

E-Mail
Guest Editor
College of Animal Science and Technology, Northwest A&F University, Yangling, China
Interests: economic animals breeding and artificial domestication

Special Issue Information

Dear Colleagues,

The breeds and health of non-traditional farm animals, companion animals, and lab animals, along with the genetic diversity of wildlife, have been acknowledged as issues of global concern. New technologies and methods have been widely used in genetics for breeding non-traditional farm animals, companion animals and lab animals, and for the conservation of genetic diversity in other forms of wildlife. Consequently, it is necessary to display the great progress in the fields of genetics, breeding and genetic diversity conservation for these animals in order to improve the value of non-traditional farm animals, companion animals and lab animals, and enhance the level of wild animal protection and management.

This Special Issue will showcase researchers’ ongoing efforts to achieve these goals. Colleagues are encouraged to submit manuscripts in the form of original research papers or reviews on the topics of the genetics and breeding of non-traditional farm animals, companion animals and lab animals, and genetic diversity wildlife conservation, as well as discussions of limitations, challenges, and future directions within the field.

Dr. Xiang Li
Prof. Dr. Wuzi Dong
Guest Editors

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.

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Published Papers (3 papers)

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Research

14 pages, 1395 KiB  
Article
Defining Candidate Imprinted loci in Bos taurus
by Minou Bina
Genes 2023, 14(5), 1036; https://doi.org/10.3390/genes14051036 - 2 May 2023
Cited by 1 | Viewed by 2301
Abstract
Using a whole-genome assembly of Bos taurus, I applied my bioinformatics strategy to locate candidate imprinting control regions (ICRs) genome-wide. In mammals, genomic imprinting plays essential roles in embryogenesis. In my strategy, peaks in plots mark the locations of known, inferred, and [...] Read more.
Using a whole-genome assembly of Bos taurus, I applied my bioinformatics strategy to locate candidate imprinting control regions (ICRs) genome-wide. In mammals, genomic imprinting plays essential roles in embryogenesis. In my strategy, peaks in plots mark the locations of known, inferred, and candidate ICRs. Genes in the vicinity of candidate ICRs correspond to potential imprinted genes. By displaying my datasets on the UCSC genome browser, one could view peak positions with respect to genomic landmarks. I give two examples of candidate ICRs in loci that influence spermatogenesis in bulls: CNNM1 and CNR1. I also give examples of candidate ICRs in loci that influence muscle development: SIX1 and BCL6. By examining the ENCODE data reported for mice, I deduced regulatory clues about cattle. I focused on DNase I hypersensitive sites (DHSs). Such sites reveal accessibility of chromatin to regulators of gene expression. For inspection, I chose DHSs in chromatin from mouse embryonic stem cells (ESCs) ES-E14, mesoderm, brain, heart, and skeletal muscle. The ENCODE data revealed that the SIX1 promoter was accessible to the transcription initiation apparatus in mouse ESCs, mesoderm, and skeletal muscles. The data also revealed accessibility of BCL6 locus to regulatory proteins in mouse ESCs and examined tissues. Full article
(This article belongs to the Special Issue Genetics and Breeding of Non-traditional Farm Animals, Companion Animals, Lab Animals and Wildlife)
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10 pages, 1272 KiB  
Article
Identification of Circular RNAs of Testis and Caput Epididymis and Prediction of Their Potential Functional Roles in Donkeys
by Yan Sun, Yonghui Wang, Yuhua Li, Faheem Akhtar, Changfa Wang and Qin Zhang
Genes 2023, 14(1), 66; https://doi.org/10.3390/genes14010066 - 25 Dec 2022
Cited by 6 | Viewed by 2049
Abstract
Circular RNAs (circRNAs) are a class of noncoding RNAs with a covalently closed loop. Studies have demonstrated that circRNA can function as microRNA (miRNA) sponges or competing endogenous RNAs. Although circRNA has been explored in some species and tissues, the genetic basis of [...] Read more.
Circular RNAs (circRNAs) are a class of noncoding RNAs with a covalently closed loop. Studies have demonstrated that circRNA can function as microRNA (miRNA) sponges or competing endogenous RNAs. Although circRNA has been explored in some species and tissues, the genetic basis of testis development and spermatogenesis in donkeys remain unknown. We performed RNA-seq to detect circRNA expression profiles of adult donkey testes. Length distribution and other characteristics were shown a total of 1971 circRNAs were differentially expressed and 12,648 and 6261 circRNAs were detected from the testis and caput epididymis, respectively. Among these circRNAs, 1472 circRNAs were downregulated and 499 circRNAs were upregulated in the testis. Moreover, KEGG pathway analyses and Gene Ontology were performed for host genes of circRNAs. A total of 39 upregulated circRNA host genes were annotated in spermatogenesis terms, including PIWIL2, CATSPERD, CATSPERB, SPATA6, and SYCP1. Other host genes were annotated in the focal adhesion, Rap1 signaling pathway. Downregulated expressed circRNA host genes participated in the TGF-β signaling pathway, GnRH signaling pathway, estrogen signaling pathway, and calcium signaling pathway. Our discoveries provide a solid foundation for identifying and characterizing critical circRNAs involved in testis development or spermatogenesis. Full article
(This article belongs to the Special Issue Genetics and Breeding of Non-traditional Farm Animals, Companion Animals, Lab Animals and Wildlife)
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10 pages, 943 KiB  
Article
Association of HOXC8 Genetic Polymorphisms with Multi-Vertebral Number and Carcass Weight in Dezhou Donkey
by Xiaoyuan Shi, Yan Li, Tianqi Wang, Wei Ren, Bingjian Huang, Xinrui Wang, Ziwen Liu, Huili Liang, Xiyan Kou, Yinghui Chen, Yonghui Wang, Faheem Akhtar and Changfa Wang
Genes 2022, 13(11), 2175; https://doi.org/10.3390/genes13112175 - 21 Nov 2022
Cited by 6 | Viewed by 1970
Abstract
An increase in the number of vertebrae can significantly affect the meat production performance of livestock, thus increasing carcass weight, which is of great importance for livestock production. The homeobox gene C8 (HOXC8) has been identified as an essential candidate gene [...] Read more.
An increase in the number of vertebrae can significantly affect the meat production performance of livestock, thus increasing carcass weight, which is of great importance for livestock production. The homeobox gene C8 (HOXC8) has been identified as an essential candidate gene for regulating vertebral development. However, it has not been researched on the Dezhou donkey. This study aimed to verify the Dezhou donkey HOXC8 gene’s polymorphisms and assess their effects on multiple vertebral numbers and carcass weight. In this study, the entire HOXC8 gene of the Dezhou donkey was sequenced, SNPs at the whole gene level were identified, and typing was accomplished utilizing a targeted sequencing genotype detection technique (GBTS). Then, a general linear model was used to perform an association study of HOXC8 gene polymorphism loci, multiple vertebral numbers, and carcass weight for screening candidate markers that can be used for molecular breeding of Dezhou donkeys. These findings revealed that HOXC8 included 12 SNPs, all unique mutant loci. The HOXC8 g.15179224C>T was significantly negatively associated with carcass weight (CW) and lumbar vertebrae length (LL) (p < 0.05). The g.15179674G>A locus was shown to be significantly positively associated with the number of lumbar vertebrae (LN) (p < 0.05). The phylogenetic tree constructed for the Dezhou donkey HOXC8 gene and seven other species revealed that the HOXC8 gene was highly conserved during animal evolution but differed markedly among distantly related animals. The results suggest that HOXC8 is a vital gene affecting multiple vertebral numbers and carcass weight in Dezhou donkeys, and the two loci g.15179224C>T and g.15179674G>A may be potential genetic markers for screening and breeding of new strains of high-quality and high-yielding Dezhou donkeys. Full article
(This article belongs to the Special Issue Genetics and Breeding of Non-traditional Farm Animals, Companion Animals, Lab Animals and Wildlife)
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