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Functional Genomics, Genetics Breeding and Improvement of Domestic Animals
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Functional Genomics, Genetics Breeding and Improvement of Domestic Animals

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

Deadline for manuscript submissions: closed (10 July 2024) | Viewed by 10179

Special Issue Editors

Dr. Yalan Yang

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Guest Editor
Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
Interests: animal breeding; functional genomics; epigenomics
Dr. Rong Zhou

E-Mail
Guest Editor
Institue of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
Interests: animal genetics; functional genomics; animal biotechnology

Special Issue Information

Dear Colleagues,

With the rapid advancement of high-throughput sequencing technologies and functional genomics in domestic animals, the integration of multi-omics data has emerged as an efficient approach to identify both coding and non-coding genes, along with regulatory elements associated with economical traits. Additionally, genome-wide association studies have successfully identified numerous loci and markers linked to important traits. However, the breeding values derived from these advancements remain poorly evaluated, and their practical applications in breeding are largely understudied. Fortunately, genomic selection and gene editing have been proven to significantly expedite the breeding process. As a result, there is a growing need to develop new algorithms, methods and tools for genomic selection and gene editing, making them a research hot topic in the field of animal genetics and breeding.

In this Special Issue, we invite original articles and reviews that contribute to our understanding of various aspects related to the identification of candidate genes and regulatory elements, the elucidation of molecular mechanisms underlying important economical traits, and the exploration of breeding methods and technologies for animal improvement. We eagerly anticipate your valuable contributions.

Dr. Yalan Yang
Dr. Rong Zhou
Guest Editors

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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

  • domestic animals
  • functional genomics
  • multi-omics
  • genome selection
  • genome-wide association study
  • gene editing
  • economical traits

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Published Papers (6 papers)

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Research

13 pages, 5522 KiB  
Article
Genomic Regions Associated with Growth and Reproduction Traits in Pink-Eyed White Mink
by Hongyu Shi, Linling Liu, Peter Foged Larsen, Yu Ding, Tietao Zhang, Haihua Zhang and Zongyue Liu
Genes 2024, 15(9), 1142; https://doi.org/10.3390/genes15091142 - 29 Aug 2024
Viewed by 684
Abstract
In mink breeding, balanced selection for growth and reproductive features is essential because these traits are contradictory. The variables of total number born (TNB), number born alive (NBA), and body weight (BW) are highly valuable in terms of their importance in mink production. [...] Read more.
In mink breeding, balanced selection for growth and reproductive features is essential because these traits are contradictory. The variables of total number born (TNB), number born alive (NBA), and body weight (BW) are highly valuable in terms of their importance in mink production. A comprehensive understanding of the molecular mechanisms that drive these features could offer vital insights into their genetic compositions. In the present study, the single-nucleotide polymorphism (SNP) genotypes of 219 minks were obtained via double digest restriction-site associated DNA sequencing (ddRAD-seq). Following several rounds of screening, about 2,415,121 high-quality SNPs were selected for a genome-wide association study (GWAS). The GWAS was used to determine BW and reproductive traits in pink-eyed white mink. It was suggested that SLC26A36, STXBP5L, and RPS 29 serve as potential genes for the total number of kits born (TNB), while FSCB, PDPN, NKX 2-1, NFKB 1, NFKBIA, and GABBR1 are key genes for the number born alive (NBA). Moreover, RTTN, PRPF31, MACROD1, and KYAT1 are possible BW genes based on association results and available functional data from gene and mammalian phenotype databases. These results offer essential information about the variety of mink and theoretical principles for applying mink breeds. Full article
(This article belongs to the Special Issue Functional Genomics, Genetics Breeding and Improvement of Domestic Animals)
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19 pages, 5021 KiB  
Article
Regulation of myo-miR-24-3p on the Myogenesis and Fiber Type Transformation of Skeletal Muscle
by Danyang Fan, Yilong Yao, Yanwen Liu, Chao Yan, Fanqinyu Li, Shilong Wang, Mei Yu, Bingkun Xie and Zhonglin Tang
Genes 2024, 15(3), 269; https://doi.org/10.3390/genes15030269 - 21 Feb 2024
Cited by 3 | Viewed by 1705
Abstract
Skeletal muscle plays critical roles in providing a protein source and contributing to meat production. It is well known that microRNAs (miRNAs) exert important effects on various biological processes in muscle, including cell fate determination, muscle fiber morphology, and structure development. However, the [...] Read more.
Skeletal muscle plays critical roles in providing a protein source and contributing to meat production. It is well known that microRNAs (miRNAs) exert important effects on various biological processes in muscle, including cell fate determination, muscle fiber morphology, and structure development. However, the role of miRNA in skeletal muscle development remains incompletely understood. In this study, we observed a critical miRNA, miR-24-3p, which exhibited higher expression levels in Tongcheng (obese-type) pigs compared to Landrace (lean-type) pigs. Furthermore, we found that miR-24-3p was highly expressed in the dorsal muscle of pigs and the quadriceps muscle of mice. Functionally, miR-24-3p was found to inhibit proliferation and promote differentiation in muscle cells. Additionally, miR-24-3p was shown to facilitate the conversion of slow muscle fibers to fast muscle fibers and influence the expression of GLUT4, a glucose transporter. Moreover, in a mouse model of skeletal muscle injury, we demonstrated that overexpression of miR-24-3p promoted rapid myogenesis and contributed to skeletal muscle regeneration. Furthermore, miR-24-3p was found to regulate the expression of target genes, including Nek4, Pim1, Nlk, Pskh1, and Mapk14. Collectively, our findings provide evidence that miR-24-3p plays a regulatory role in myogenesis and fiber type conversion. These findings contribute to our understanding of human muscle health and have implications for improving meat production traits in livestock. Full article
(This article belongs to the Special Issue Functional Genomics, Genetics Breeding and Improvement of Domestic Animals)
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16 pages, 6243 KiB  
Article
Exploring Multi-Tissue Alternative Splicing and Skeletal Muscle Metabolism Regulation in Obese- and Lean-Type Pigs
by Wei Wang, Wangchang Li, Weiwei Liu, Zishuai Wang, Bingkun Xie, Xiaogan Yang and Zhonglin Tang
Genes 2024, 15(2), 196; https://doi.org/10.3390/genes15020196 - 31 Jan 2024
Cited by 1 | Viewed by 1592
Abstract
Alternative splicing (AS) is a crucial mechanism in post-transcriptional regulation, contributing significantly to the diversity of the transcriptome and proteome. In this study, we performed a comprehensive AS profile in nine tissues obtained from Duroc (lean-type) and Luchuan (obese-type) pigs. Notably, 94,990 AS [...] Read more.
Alternative splicing (AS) is a crucial mechanism in post-transcriptional regulation, contributing significantly to the diversity of the transcriptome and proteome. In this study, we performed a comprehensive AS profile in nine tissues obtained from Duroc (lean-type) and Luchuan (obese-type) pigs. Notably, 94,990 AS events from 14,393 genes were identified. Among these AS events, it was observed that 80% belonged to the skipped exon (SE) type. Functional enrichment analysis showed that genes with more than ten AS events were closely associated with tissue-specific functions. Additionally, the analysis of overlap between differentially alternative splicing genes (DSGs) and differentially expressed genes (DEGs) revealed the highest number of overlapped genes in the heart and skeletal muscle. The novelty of our study is that it identified and validated three genes (PYGM, MAPK11 and CAMK2B) in the glucagon signaling pathway, and their alternative splicing differences were highly significant across two pig breeds. In conclusion, our study offers novel insights into the molecular regulation of diverse tissue physiologies and the phenotypic differences between obese- and lean-type pigs, which are helpful for pig breeding. Full article
(This article belongs to the Special Issue Functional Genomics, Genetics Breeding and Improvement of Domestic Animals)
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16 pages, 5179 KiB  
Article
Transcription Factor SATB2 Regulates Skeletal Muscle Cell Proliferation and Migration via HDAC4 in Pigs
by Fanqinyu Li, Chao Yan, Yilong Yao, Yalan Yang, Yanwen Liu, Danyang Fan, Junxing Zhao and Zhonglin Tang
Genes 2024, 15(1), 65; https://doi.org/10.3390/genes15010065 - 2 Jan 2024
Viewed by 1925
Abstract
Skeletal muscle development remarkably affects meat production and growth rate, regulated by complex regulatory mechanisms in pigs. Specific AT sequence-binding protein 2 (SATB2) is a classic transcription factor and chromatin organizer, which holds a profound effect in the regulation of chromatin [...] Read more.
Skeletal muscle development remarkably affects meat production and growth rate, regulated by complex regulatory mechanisms in pigs. Specific AT sequence-binding protein 2 (SATB2) is a classic transcription factor and chromatin organizer, which holds a profound effect in the regulation of chromatin remodeling. However, the regulation role of SATB2 concerning skeletal muscle cell fate through chromatin remodeling in pigs remains largely unknown. Here, we observed that SATB2 was expressed higher in the lean-type compared to the obese-type pigs, which also enriched the pathways of skeletal muscle development, chromatin organization, and histone modification. Functionally, knockdown SATB2 led to decreases in the proliferation and migration markers at the mRNA and protein expression levels, respectively, while overexpression SATB2 had the opposite effects. Further, we found histone deacetylase 4 (HDAC4) was a key downstream target gene of SATB2 related to chromatin remodeling. The binding relationship between SATB2 and HDAC4 was confirmed by a dual-luciferase reporter system and ChIP-qPCR analysis. Besides, we revealed that HDAC4 promoted the skeletal muscle cell proliferation and migration at the mRNA and protein expression levels, respectively. In conclusion, our study indicates that transcription factor SATB2 binding to HDAC4 positively contributes to skeletal muscle cell proliferation and migration, which might mediate the chromatin remodeling to influence myogenesis in pigs. This study develops a novel insight into understanding the molecular regulatory mechanism of myogenesis, and provides a promising gene for genetic breeding in pigs. Full article
(This article belongs to the Special Issue Functional Genomics, Genetics Breeding and Improvement of Domestic Animals)
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13 pages, 4840 KiB  
Article
Uncoupling Protein 3 Promotes the Myogenic Differentiation of Type IIb Myotubes in C2C12 Cells
by Ziwei You, Jieyu Wang, Faliang Li, Wei Hei, Meng Li, Xiaohong Guo, Pengfei Gao, Guoqing Cao, Chunbo Cai and Bugao Li
Genes 2023, 14(11), 2049; https://doi.org/10.3390/genes14112049 - 7 Nov 2023
Viewed by 1877
Abstract
Uncoupling protein 3 (Ucp3) is an important transporter within mitochondria and is mainly expressed in skeletal muscle, brown adipose tissue and the myocardium. However, the effects of Ucp3 on myogenic differentiation are still unclear. This study evaluated the effects of Ucp3 on myogenic [...] Read more.
Uncoupling protein 3 (Ucp3) is an important transporter within mitochondria and is mainly expressed in skeletal muscle, brown adipose tissue and the myocardium. However, the effects of Ucp3 on myogenic differentiation are still unclear. This study evaluated the effects of Ucp3 on myogenic differentiation, myofiber type and energy metabolism in C2C12 cells. Gain- and loss-of-function studies revealed that Ucp3 could increase the number of myotubes and promote the myogenic differentiation of C2C12 cells. Furthermore, Ucp3 promoted the expression of the type IIb myofiber marker gene myosin heavy chain 4 (Myh4) and decreased the expression of the type I myofiber marker gene myosin heavy chain 7 (Myh7). In addition, energy metabolism related to the expression of PPARG coactivator 1 alpha (Pgc1-α), ATP synthase, H+ transportation, mitochondrial F1 complex, alpha subunit 1 (Atp5a1), lactate dehydrogenase A (Ldha) and lactate dehydrogenase B (Ldhb) increased with Ucp3 overexpression. Ucp3 could promote the myogenic differentiation of type IIb myotubes and accelerate energy metabolism in C2C12 cells. This study can provide the theoretical basis for understanding the role of Ucp3 in energy metabolism. Full article
(This article belongs to the Special Issue Functional Genomics, Genetics Breeding and Improvement of Domestic Animals)
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15 pages, 2697 KiB  
Article
Genome-Wide Detection of Copy Number Variations Associated with Miniature Features in Horses
by Md. Panir Choudhury, Zihao Wang, Min Zhu, Shaohua Teng, Jing Yan, Shuwei Cao, Guoqiang Yi, Yuwen Liu, Yuying Liao and Zhonglin Tang
Genes 2023, 14(10), 1934; https://doi.org/10.3390/genes14101934 - 13 Oct 2023
Cited by 2 | Viewed by 1751
Abstract
Copy number variations (CNVs) are crucial structural genomic variants affecting complex traits in humans and livestock animals. The current study was designed to conduct a comprehensive comparative copy number variation analysis among three breeds, Debao (DB), Baise (BS), and Warmblood (WB), with a [...] Read more.
Copy number variations (CNVs) are crucial structural genomic variants affecting complex traits in humans and livestock animals. The current study was designed to conduct a comprehensive comparative copy number variation analysis among three breeds, Debao (DB), Baise (BS), and Warmblood (WB), with a specific focus on identifying genomic regions associated with miniature features in horses. Using whole-genome next-generation resequencing data, we identified 18,974 CNVs across 31 autosomes. Among the breeds, we found 4279 breed-specific CNV regions (CNVRs). Baise, Debao, and Warmblood displayed 2978, 986, and 895 distinct CNVRs, respectively, with 202 CNVRs shared across all three breeds. After removing duplicates, we obtained 1545 CNVRs from 26 horse genomes. Functional annotation reveals enrichment in biological functions, including antigen processing, cell metabolism, olfactory conduction, and nervous system development. Debao horses have 970 genes overlapping with CNVRs, possibly causing their small size and mountainous adaptations. We also found that the genes GHR, SOX9, and SOX11 may be responsible for the miniature features of the Debao horse by analyzing their overlapping CNVRs. Overall, this study offers valuable insights into the widespread presence of CNVs in the horse genome. The findings contribute to mapping horse CNVs and advance research on unique miniature traits observed in the Debao horse. Full article
(This article belongs to the Special Issue Functional Genomics, Genetics Breeding and Improvement of Domestic Animals)
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