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Molecular Genetics and Breeding Mechanisms in Domestic Animals: 3rd Edition

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: 20 September 2025 | Viewed by 3654

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Prof. Dr. Guiping Zhao

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Chinese Academy of Agricultural Sciences, Beijing, China
Interests: animal genetics and breeding; immunogenetics; breeding for disease resistance; interactions between microbe and host
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Special Issue Information

Dear Colleagues,

Alongside the continuous progress of biotechnology, molecular genetics, breeding theory and methods, scientists in the field have rapidly developed high-quality germplasms. The current Special Issue on “Molecular Genetics and Breeding Mechanisms in Domestic Animals” explores and disseminates the latest research trends and achievements in the scientific field of animal molecular genetics and breeding. This Special Issue also aims to explore the achievements in research concerning disease-resistance breeding, which is of great significance to the development of animal husbandry and human health.

We invite submissions that discuss the molecular biology, genetics and immunity of domestic animals, placing particular emphasis on the following topics:

Analysis of molecular mechanisms of character formation based on multiomics;
Genetic mechanism research about important functional genes in animals;
New breeding theory based on bio-informatics;
Effects of microbiota on immune development;
Molecular interactions between microbial products and host sensors.

Prof. Dr. Guiping Zhao
Guest Editor

Manuscript Submission Information

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Keywords

animal genetics
animal breeding
functional genomics
multiomics analysis
molecular immunity
interactions between microbe and host

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Published Papers (4 papers)

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Research

19 pages, 2340 KiB

Open AccessArticle

by Yue Xing, Siyuan Mi, Gerile Dari, Zihan Zhang, Siqian Chen and Ying Yu

Int. J. Mol. Sci. 2025, 26(6), 2506; https://doi.org/10.3390/ijms26062506 - 11 Mar 2025

Viewed by 539

Abstract

Staphylococcus aureus-induced mastitis is a significant cause of economic losses in the dairy industry, yet its molecular mechanisms remain poorly defined. Although ferroptosis, a regulated cell death process, is associated with inflammatory diseases, its role in bovine mastitis is unknown. In this study, 11 S. aureus strains were isolated from milk samples obtained from cows with clinical or subclinical mastitis. Transcriptome analysis of Mac-T cells challenged with isolated S. aureus identified differentially expressed genes (DEGs). Enrichment analysis revealed significant associations between DEG clusters and traits related to bovine mastitis. KEGG pathway enrichment revealed ferroptosis, Toll-like receptor, and TNF signaling as significantly enriched pathways. Weighted gene co-expression network analysis (WGCNA) further prioritized ferroptosis-related genes (HMOX1, SLC11A2, STEAP3, SAT1, and VDAC2) involved in iron metabolism. Notably, the expression levels of HMOX1 and SAT1 were significantly increased in S. aureus-challenged Mac-T cells, and this upregulation was consistent with trends observed in transcriptome data from mother–daughter pairs of cows with subclinical mastitis caused by S. aureus infection. Furthermore, Ferrostatin-1 treatment significantly reduced the expression of HMOX1 and SAT1 in S. aureus-challenged cells, confirming the involvement of ferroptosis in this process. This study reveals that ferroptosis plays a key role in S. aureus-induced mastitis and highlights its potential as a target for molecular breeding strategies aimed at improving bovine mastitis resistance. Full article

(This article belongs to the Special Issue Molecular Genetics and Breeding Mechanisms in Domestic Animals: 3rd Edition)

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19 pages, 5382 KiB

Open AccessArticle

Dynamic m⁶A Modification Landscape During the Egg Laying Process of Chickens

by Yushi Zhang, Yida Chen, Haigang Ji, Yufang Niu, Liyang He, Wentao Wang, Tong Yu, Ruili Han, Yadong Tian, Xiaojun Liu, Xiangtao Kang, Hanfang Cai and Zhuanjian Li

Int. J. Mol. Sci. 2025, 26(4), 1677; https://doi.org/10.3390/ijms26041677 - 16 Feb 2025

Viewed by 546

Abstract

RNA N6-methyladenosine (m⁶A) is one of the most common and widespread reversible epigenetic modifications of mRNAs, and m⁶A has been shown to play a positive role in regulating follicular development. However, the role of RNA m⁶A methylation in chicken ovaries and egg production has not been fully studied. In this study, we comprehensively analyzed the m⁶A transcriptome profiles of high- and low-yield Gushi chickens at 43 weeks of age (43 w). We found that m⁶A modification differed between the two groups. The m⁶A peak was positively correlated with the gene expression level, indicating that m⁶A may play an important role in regulating chicken egg production. In total, 9008 and 15,415 m⁶A peaks were separately identified in the two groups, including 2241 differential m⁶A peaks. In addition, seven candidate genes related to egg laying that were significantly enriched in the KEGG pathway related to ovary development and egg laying were identified. In summary, we constructed the first m⁶A modification map of ovarian tissue of Gushi chickens, and the differences in egg laying in 43 w Gushi chickens may originate from the effect of RNA methylation on the expression of egg-related genes. These findings provide new insights into the regulatory mechanisms of m⁶A methylation during egg production in Gushi chickens. Full article

(This article belongs to the Special Issue Molecular Genetics and Breeding Mechanisms in Domestic Animals: 3rd Edition)

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19 pages, 6911 KiB

Open AccessArticle

ADCY5 Gene Affects Seasonal Reproduction in Dairy Goats by Regulating Ovarian Granulosa Cells Steroid Hormone Synthesis

by Chenbo Shi, Fuhong Zhang, Qiuya He, Jianjun Man, Yuanpan Mu, Jianqing Zhao, Lu Zhu, Juan J. Loor and Jun Luo

Int. J. Mol. Sci. 2025, 26(4), 1622; https://doi.org/10.3390/ijms26041622 - 14 Feb 2025

Viewed by 619

Abstract

Follicle development in dairy goats is lower after induced estrus during the non-breeding season, reducing conception rates and challenging year-round milk supply. This study investigated follicle development during the breeding and non-breeding seasons and explored molecular mechanisms for variations in the proportions of follicles of different sizes using ovarian RNA-seq and in vitro experiments. Induced estrus during the non-breeding season used a simulated breeding season short photoperiod and male effect methods, while the male effect method was used during the breeding season. This study identified an increase in follicle size during the breeding season and performed RNA-seq on ovaries to explore the underlying causes. The RNA-seq analysis elucidated pathways associated with cellular and hormonal metabolism and identified adenylyl cyclase 5 (ADCY5) as a key differentially expressed gene. In vitro experiments demonstrated that interfering with ADCY5 in ovarian granulosa cells (GCs) reduced steroid synthesis. Conversely, the overexpression of ADCY5 increased steroid synthesis. ADCY5 affects the biological function of GCs and consequently influences follicle development through the cAMP-response element binding protein (CREB) and p38 mitogen-activated protein kinase phosphorylation (MAPK) pathways. Overall, our findings demonstrate that follicle development in dairy goats differs between the breeding and non-breeding seasons and that the differential expression levels of the ADCY5 gene contribute to this discrepancy. Full article

(This article belongs to the Special Issue Molecular Genetics and Breeding Mechanisms in Domestic Animals: 3rd Edition)

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15 pages, 6681 KiB

Open AccessArticle

A Single-Cell Atlas of Porcine Skeletal Muscle Reveals Mechanisms That Regulate Intramuscular Adipogenesis

by Zhong Xu, Junjing Wu, Yujie Li, Jiawei Zhou, Yu Zhang, Mu Qiao, Yue Feng, Hua Sun, Zipeng Li, Lianghua Li, Favour Oluwapelumi Oyelami, Xianwen Peng and Shuqi Mei

Int. J. Mol. Sci. 2024, 25(23), 12935; https://doi.org/10.3390/ijms252312935 - 1 Dec 2024

Cited by 2 | Viewed by 1542

Abstract

Porcine skeletal muscle development is closely linked to meat production efficiency and quality. The accumulation of porcine intramuscular fat is influenced by the hyperplasia and hypertrophy of adipocytes within the muscle. However, the cellular profiles corresponding to the two stages of muscle development remain undetermined. Single-nucleus RNA sequencing (snRNA-seq) can elucidate cell subsets in tissues, capture gene expression at the individual cell level, and provide innovative perspectives for studying muscle and intramuscular fat formation. In this study, a total of 78,302 nuclei and 9 clusters of cells, which included fibro/adipogenic progenitor (FAP), myonuclei, adipocytes, and other cell types, of Xidu black pigs, were identified on Day 1 and Day 180. The pattern of cell clustering varied between the two developmental stages. Notably, the percentage of adipocytes in the Day 180 group was higher than in the Day 1 group (0.51% vs. 0.15%). Pseudo-time sequence analysis indicated that FAPs could differentiate into adipocytes and myonuclei cells, respectively. The THRSP gene was identified as a biomarker for swine intramuscular fat cells, and its down-regulation resulted in significant reduction in lipid droplet formation in porcine preadipocytes. Our research provides new insights into the cellular characteristics of intramuscular fat formation, which may facilitate the development of novel strategies to enhance intramuscular fat deposition and improve pork quality. Full article

(This article belongs to the Special Issue Molecular Genetics and Breeding Mechanisms in Domestic Animals: 3rd Edition)

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