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Featured Papers in the 'Animal Genetics and Genomics' Section
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Featured Papers in the 'Animal Genetics and Genomics' Section

A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (25 March 2024) | Viewed by 10065

Special Issue Editor

Prof. Dr. Michael E. Davis

E-Mail Website
Guest Editor
Department of Animal Sciences, The Ohio State University, Columbus, OH 43210, USA
Interests: beef; dairy; genetics; genetic engineering; animal breeding; biostatistics; animal genetics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

It is critical to understand the contributions of genetics and genomics as we strive to efficiently produce animal protein to feed an ever-increasing world population in an environmentally sustainable and humane manner. Genetics and genomics will play key roles in increasing the efficiency of production systems. Genetic selection and innovation must target animal production, product quality, reproduction, health, welfare, and sustainability, so that a high-quality, safe, healthful, and affordable food supply is readily available. Papers concerning a wide range of animal genetics topics, including those focusing on population genetics, quantitative genetics, conservation genetics, immunogenetics, genomics, epigenomics, and microbial genetics, are welcome to this Special Issue.

Prof. Dr. Michael E. Davis
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. Animals is an international peer-reviewed open access semimonthly 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 2400 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

  • animal
  • genetics
  • genomics
  • production
  • product quality
  • reproduction
  • fertility
  • health
  • welfare
  • sustainability

Published Papers (5 papers)

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Research

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16 pages, 2513 KiB  
Article
Chicken Hypothalamic and Ovarian DNA Methylome Alteration in Response to Forced Molting
by Tongyu Zhang, Chengfeng Li, Jianwen Deng, Yaxiong Jia, Lujiang Qu and Zhonghua Ning
Animals 2023, 13(6), 1012; https://doi.org/10.3390/ani13061012 - 10 Mar 2023
Cited by 4 | Viewed by 1453
Abstract
Epigenetic modifications play an important role in regulating animal adaptation to external stress. To explore how DNA methylation regulates the expression levels of related genes during forced molting (FM) of laying hens, the hypothalamus and ovary tissues were analyzed at five periods using [...] Read more.
Epigenetic modifications play an important role in regulating animal adaptation to external stress. To explore how DNA methylation regulates the expression levels of related genes during forced molting (FM) of laying hens, the hypothalamus and ovary tissues were analyzed at five periods using Whole-Genome Bisulfite Sequencing. The results show that methylation levels fluctuated differently in the exon, intron, 5′UTR, 3′UTR, promoter, and intergenic regions of the genome during FM. In addition, 16 differentially methylated genes (DMGs) regulating cell aging, immunity, and development were identified in the two reversible processes of starvation and redevelopment during FM. Comparing DMGs with differentially expressed genes (DEGs) obtained in the same periods, five hypermethylated DMGs (DSTYK, NKTR, SMOC1, SCAMP3, and ATOH8) that inhibited the expression of DEGs were found. Therefore, DMGs epigenetically modify the DEGs during the FM process of chickens, leading to the rapid closure and restart of their reproductive function and a re-increase in the egg-laying rate. Therefore, this study further confirmed that epigenetic modifications could regulate gene expression during FM and provides theoretical support for the subsequent optimization of FM technology. Full article
(This article belongs to the Special Issue Featured Papers in the 'Animal Genetics and Genomics' Section)
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14 pages, 3180 KiB  
Article
Overexpression of the QKI Gene Promotes Differentiation of Goat Myoblasts into Myotubes
by Sijia Chen, Shu Niu, Wannian Wang, Xiang Zhao, Yangyang Pan, Liying Qiao, Kaijie Yang, Jianhua Liu and Wenzhong Liu
Animals 2023, 13(4), 725; https://doi.org/10.3390/ani13040725 - 17 Feb 2023
Viewed by 1435
Abstract
The QKI genes encode RNA-binding proteins regulating cell proliferation, differentiation, and apoptosis. The Goat QKI has six isoforms, but their roles in myogenesis are unclear. In this study, the six isoforms of the QKI gene were overexpressed in goat myoblast. Immunofluorescence, qPCR and [...] Read more.
The QKI genes encode RNA-binding proteins regulating cell proliferation, differentiation, and apoptosis. The Goat QKI has six isoforms, but their roles in myogenesis are unclear. In this study, the six isoforms of the QKI gene were overexpressed in goat myoblast. Immunofluorescence, qPCR and Western blot were used to evaluate the effect of QKI on the differentiation of goat myoblast. An RNA-Seq was performed on the cells with the gain of the function from the major isoforms to screen differentially expressed genes (DEGs). The results show that six isoforms had different degrees of deletion in exons 6 and 7, and caused the appearance of different types of encoded amino acids. The expression levels of the QKI-1 and QKI-5 groups were upregulated in the biceps femoris and latissimus dorsi muscle tissues compared with those of the QKI-4, QKI-7, QKI-3 and QKI-6 groups. After 6 d of myoblast differentiation, QKI-5 and the myogenic differentiators MyoG, MyoD, and MyHC were upregulated. Compared to the negative control group, QKI promoted myotube differentiation and the myoblasts overexpressing QKI-5 formed large, abundant myotubes. In summary, we identified that the overexpression of the QKI gene promotes goat-myoblast differentiation and that QKI-5 is the major isoform, with a key role. The RNA-Seq screened 76 upregulated and 123 downregulated DEGs between the negative control and the QKI-5-overexpressing goat myoblasts after d 6 of differentiation. The GO and KEGG analyses associated the downregulated DEGs with muscle-related biological functions. Only the pathways related to muscle growth and development were enriched. This study provides a theoretical basis for further exploring the regulatory mechanism of QKI in skeletal-muscle development in goats. Full article
(This article belongs to the Special Issue Featured Papers in the 'Animal Genetics and Genomics' Section)
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12 pages, 3143 KiB  
Article
The Complete Mitochondrial Genome of Eurasian Minnow (Phoxinus cf. Phoxinus) from the Heilongjiang River, and Its Phylogenetic Implications
by Lei Cheng, Ezhou Wang, Weitao Li, Xiaoli Yu and Xiaolin Liao
Animals 2022, 12(21), 2960; https://doi.org/10.3390/ani12212960 - 27 Oct 2022
Cited by 1 | Viewed by 1518
Abstract
Over the past two decades, the genus Phoxinus has undergone extensive taxonomic revision and many new species or mitochondrial lineages have been found in Europe. However, Asian populations of Phoxinus spp. have received less attention and have rarely been compared with their European [...] Read more.
Over the past two decades, the genus Phoxinus has undergone extensive taxonomic revision and many new species or mitochondrial lineages have been found in Europe. However, Asian populations of Phoxinus spp. have received less attention and have rarely been compared with their European relatives. In this study, we deciphered the 16,789-nucleotide mitochondrial genome of Phoxinus cf. phoxinus from the Heilongjiang River (HLJ) and compared it with other known mitogenomes or partial mitochondrial DNA (mtDNA) sequences of Phoxinus spp. We discovered that all known mitochondrial genomes of Phoxinus had a typical mtDNA architecture across vertebrates, but their D-loop regions varied greatly in length. A repetitive motif of ~130 bp was identified in the D-loop regions of Phoxinus spp. The unusual repetitive structure was revealed at the beginning of D-loop regions of all known mitogenomes of Phoxinus spp. The length differences of the D-loop region were attributed mainly to the number of repetitive motifs and the inserted sequences among them. However, this repetitive structure was absent in the other Far East phoxinins. This is further evidence for the notion that Far Eastern phoxinins should be divided into two genera: Phoxinus and Rhynchocypris. All mtDNA sequences (including three mitogenomes) from South Korea represent the same genetic lineage, as there were only slight differences among them. The remaining six mtDNA sequences are highly divergent and represent different lineages of the genus, as supported by partial mtDNA sequences. The updated phylogeny of genus Phoxinus suggests that there are five distinct mtDNA lineages in Asia. The Asian lineages have diverged markedly from their European relatives and should not be included with the European minnow (P. phoxinus). Full article
(This article belongs to the Special Issue Featured Papers in the 'Animal Genetics and Genomics' Section)
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12 pages, 830 KiB  
Article
Genetic Analyses of Rabbit Survival and Individual Birth Weight
by Rafik Belabbas, Rym Ezzeroug, Ali Berbar, María de la Luz Garcia, Ghania Zitouni, Djamel Taalaziza, Zoulikha Boudjella, Nassima Boudahdir, Samir Diss and María-José Argente
Animals 2022, 12(19), 2695; https://doi.org/10.3390/ani12192695 - 07 Oct 2022
Cited by 3 | Viewed by 1327
Abstract
Genetic parameters of kit survival traits and birth weight were estimated on ITELV2006 synthetic line aimed at improving kit survival using a multiple trait linear and threshold model. Data on 1696 kits for survival at birth and at weaning, as well as individual [...] Read more.
Genetic parameters of kit survival traits and birth weight were estimated on ITELV2006 synthetic line aimed at improving kit survival using a multiple trait linear and threshold model. Data on 1696 kits for survival at birth and at weaning, as well as individual birth weight and litter size were analysed. Genetic effects of kit survival traits and birth weight were estimated based on threshold and Gaussian models, respectively, using a Bayesian approach. The statistical model included, as fixed effects, parity, lactation status, season of farrowing, nest status, cannibalism in kit, place of kit’s birth in the cage and gender, and adjustment for litter size. Posterior means of heritabilities for direct genetic effects of survival at birth and the entire nursing period, as well as birth weight, were 0.018, 0.023, and 0.088, respectively, and were increased when adjusted for litter size to 0.021, 0.027 and 0.146. Genetic correlation between survival traits was zero. Therefore, these traits can be treated genetically as different traits. Genetic correlation between direct effects of survival at birth and birth weight showed positive, but low, value (+0.134) and was increased to +0.535 when the traits were adjusted for litter size. No genetic correlation was found between survival at weaning and birth weight. These magnitudes of genetic parameter estimates suggested that there is substantial potential for the genetic improvement of kit survival at birth through selection for birth weight. Full article
(This article belongs to the Special Issue Featured Papers in the 'Animal Genetics and Genomics' Section)
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Review

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15 pages, 1502 KiB  
Review
Evolutionary and Genomic Diversity of True Polyploidy in Tetrapods
by Marcello Mezzasalma, Elvira Brunelli, Gaetano Odierna and Fabio Maria Guarino
Animals 2023, 13(6), 1033; https://doi.org/10.3390/ani13061033 - 12 Mar 2023
Cited by 3 | Viewed by 3466
Abstract
True polyploid organisms have more than two chromosome sets in their somatic and germline cells. Polyploidy is a major evolutionary force and has played a significant role in the early genomic evolution of plants, different invertebrate taxa, chordates, and teleosts. However, the contribution [...] Read more.
True polyploid organisms have more than two chromosome sets in their somatic and germline cells. Polyploidy is a major evolutionary force and has played a significant role in the early genomic evolution of plants, different invertebrate taxa, chordates, and teleosts. However, the contribution of polyploidy to the generation of new genomic, ecological, and species diversity in tetrapods has traditionally been underestimated. Indeed, polyploidy represents an important pathway of genomic evolution, occurring in most higher-taxa tetrapods and displaying a variety of different forms, genomic configurations, and biological implications. Herein, we report and discuss the available information on the different origins and evolutionary and ecological significance of true polyploidy in tetrapods. Among the main tetrapod lineages, modern amphibians have an unparalleled diversity of polyploids and, until recently, they were considered to be the only vertebrates with closely related diploid and polyploid bisexual species or populations. In reptiles, polyploidy was thought to be restricted to squamates and associated with parthenogenesis. In birds and mammals, true polyploidy has generally been considered absent (non-tolerated). These views are being changed due to an accumulation of new data, and the impact as well as the different evolutionary and ecological implications of polyploidy in tetrapods, deserve a broader evaluation. Full article
(This article belongs to the Special Issue Featured Papers in the 'Animal Genetics and Genomics' Section)
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