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Animals
Special Issues
Genetics and Breeding for Enhancing Production Traits in Ruminants
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Genetics and Breeding for Enhancing Production Traits in Ruminants

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

Deadline for manuscript submissions: 30 April 2026 | Viewed by 1924

Special Issue Editor

Prof. Dr. Guangxin E

E-Mail Website
Guest Editor
College of Animal Science and Technology, Southwest University, Chongqing 400715, China
Interests: genomic selection; genetic diversity; quantitative trait loci (QTL); whole-genome sequencing; candidate genes for production traits; genome-wide selection signals

Special Issue Information

Dear Colleagues,

Understanding the genetic architecture underlying economically important traits is essential for advancing ruminant breeding and sustainable livestock production. With the growing availability of high-throughput sequencing technologies, genome-wide analyses have enabled the identification of selection signals, functional variants, and key genes associated with traits such as growth, reproduction, disease resistance, and environmental adaptation. This research topic, ‘Genetics and Breeding for Enhancing Production Traits in Ruminants’, aims to highlight recent advances in genetic diversity assessment, population structure analysis, and the discovery of functional genes in both indigenous and commercial breeds. We welcome contributions that explore genome-wide selection signatures, functional genomics, and molecular breeding strategies, with a focus on enhancing genetic improvement and preserving valuable genetic resources in ruminants.

We warmly encourage you to submit your original research to this Special Issue.

In this Special Issue, original research articles and communication are welcome. Research areas may include (but are not limited to) the following:

  1. Analysis of genetic diversity and phylogenetic relationships in domesticated animals;
  2. Identification of key genes associated with important economic traits, phenotypes, adaptability, and disease resistance using multi-omics approaches and whole-genome sequencing technologies;
  3. In-depth investigation of the functional mechanisms of candidate genes;
  4. Meta-analysis based on large-scale farm datasets;
  5. Development of theoretical frameworks or computational tools for genomic data analysis and application.
  6. Gene editing and stem cell breeding technologies: development and application

We look forward to receiving your contributions.

Prof. Dr. Guangxin E
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 250 words) can be sent to the Editorial Office for assessment.

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

  • genomic selection
  • genetic diversity
  • quantitative trait loci (QTL)
  • whole-genome sequencing
  • candidate genes for production traits
  • genome-wide selection signals

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Published Papers (4 papers)

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Research

14 pages, 1334 KB  
Article
Transcriptome Sequencing and Identification of APOE Gene Polymorphisms, Their Expression and Their Relationship with Body Size Traits in Guizhou White Goats (Capra hircus)
by Wen-Ying Wang, Lin-Guang Dai, Jun-You Huang, Xing-Chao Song, Jin-Zhu Meng, Yuan-Yuan Zhao, Zhen-Yang Wu and Qing-Ming An
Animals 2026, 16(7), 1031; https://doi.org/10.3390/ani16071031 - 27 Mar 2026
Viewed by 154
Abstract
Carcass growth and development are crucial evaluation indicators influencing the economic efficiency of goats (Capra hircus). This study aimed to screen the nucleotide variation sites (SNPs) of the APOE gene in Guizhou white goats and explore the correlation between APOE gene [...] Read more.
Carcass growth and development are crucial evaluation indicators influencing the economic efficiency of goats (Capra hircus). This study aimed to screen the nucleotide variation sites (SNPs) of the APOE gene in Guizhou white goats and explore the correlation between APOE gene variations and body size traits, as APOE had been identified as a key candidate gene regulating growth and development in this breed through transcriptome sequencing screening. A total of 324 Guizhou white goats were used in this study for SNP detection, population genetic analysis, real-time fluorescence quantitative PCR (RT-qPCR) and association analysis. The results showed that one nucleotide mutation site (g.353 A > G) was detected in the APOE gene, which yielded two alleles (A and G) and three genotypes (AA, AG and GG). The site exhibited moderate polymorphism and conformed to Hardy–Weinberg equilibrium. The mRNA expression level of APOE in longissimus dorsi muscle was significantly higher in males than in females. Association analysis revealed a sex-specific effect of this locus on body size traits. The A allele and AA genotype were significantly associated with increased body weight and heart girth in females, whereas no significant effect was detected in males. Therefore, the identified APOE gene mutation site can serve as a candidate molecular marker for the early selection of growth traits in Guizhou white goats. Full article
(This article belongs to the Special Issue Genetics and Breeding for Enhancing Production Traits in Ruminants)
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14 pages, 3279 KB  
Article
Functional Characterization of IGF2BP1, CDC25A, and RXFP2 Genes: Implications for Ovarian Function and Reproductive Regulation in Goats
by Haiyan Yang, Qiancheng Ma, Zhiying Wang, Shan Zhang, Luqi Wang, Haijing Zhu, Xianyong Lan, Ke Wang and Chuanying Pan
Animals 2026, 16(5), 836; https://doi.org/10.3390/ani16050836 - 7 Mar 2026
Viewed by 237
Abstract
Goat reproductive performance is a key determinant of the productivity and economic value of goat farming, especially in meat and milk production. In a previous study, to investigate the genetic basis of prolificacy, we divided goats into groups according to their consistent reproductive [...] Read more.
Goat reproductive performance is a key determinant of the productivity and economic value of goat farming, especially in meat and milk production. In a previous study, to investigate the genetic basis of prolificacy, we divided goats into groups according to their consistent reproductive performance (producing either single kids or twins) over five consecutive kidding cycles, and performed whole-genome resequencing and RNA-seq analysis on their ovarian tissues. Through integrated analysis, we identified three candidate genes—IGF2BP1 (insulin-like growth factor 2 mRNA-binding protein 1), CDC25A (cell division cycle 25A), and RXFP2 (relaxin family peptide receptor 2)—as potential key regulators of reproductive capacity. Using goat ovarian granulosa cells, we systematically assessed the impact of each gene through gain- and loss-of-function experiments. Overexpression of IGF2BP1 promoted cell proliferation and suppressed apoptosis, underscoring its role in maintaining cellular viability. Conversely, its knockdown significantly impeded growth and induced cell death. Similarly, CDC25A enhanced granulosa cell proliferation, whereas its knockdown led to marked growth impairment and increased apoptosis. Proliferation was also enhanced by RXFP2 overexpression but impaired upon its knockdown, suggesting that RXFP2 is functionally important for follicular development. Collectively, these findings establish IGF2BP1, CDC25A, and RXFP2 as fundamental regulators of granulosa cell dynamics and ovarian follicular development, providing crucial functional insights and promising targets for genetic selection to enhance reproductive efficiency in goats. Full article
(This article belongs to the Special Issue Genetics and Breeding for Enhancing Production Traits in Ruminants)
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10 pages, 452 KB  
Article
Investigation of a Rare CSN1S101 Allele in Goats Using Allele-Specific PCR and Mathematical Expectation Analysis
by Jingxuan Wang, Yuta Yang, Yuhuan Gao, Ebadu Areb, Xianyong Lan, Haijing Zhu and Chuanying Pan
Animals 2026, 16(5), 730; https://doi.org/10.3390/ani16050730 - 26 Feb 2026
Viewed by 245
Abstract
The casein alpha s1 (CSN1S1) gene plays an important role in milk protein synthesis and has been associated with milk quality and calcium-related physiological processes in mammals. To date, 19 CSN1S1 variants have been reported. Among them, the CSN1S101 allele [...] Read more.
The casein alpha s1 (CSN1S1) gene plays an important role in milk protein synthesis and has been associated with milk quality and calcium-related physiological processes in mammals. To date, 19 CSN1S1 variants have been reported. Among them, the CSN1S101 allele has been described as a key “null” variant that may influence goat milk production traits through its effect on CSN1S1 gene expression. However, the association between this allele and economically important traits in goats remains poorly understood. Therefore, the present study aimed to investigate the CSN1S101 allele in goats using economical and rapid approaches, including mathematical expectation (ME) analysis and allele-specific PCR (AS-PCR), and to evaluate its association with economic traits in Chinese goat breeds. A total of 2319 goats from 11 breeds were analyzed. Compared with the “0” allele, the “1” allele showed a higher frequency across all populations and exhibited low genetic diversity. Significant associations were detected between CSN1S101 genotypes and body length, third parity, and average kidding number in Laoshan dairy goats (p < 0.05). In addition, the low-frequency distribution of the CSN1S1 “0” allele was further confirmed. Overall, this study provides population-based association evidence supporting the consideration of CSN1S101 genetic variation in goat breeding programs. Full article
(This article belongs to the Special Issue Genetics and Breeding for Enhancing Production Traits in Ruminants)
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18 pages, 9796 KB  
Article
Integrative Transcriptomic and Proteomic Analysis Reveals CaMK4-Mediated Regulation of Proliferation in Goat Skeletal Muscle Satellite Cells
by He Cong, Lu Xu, Yaolong Liu, Zixuan Wang, Tao Ren, Pengcheng Ruan, Haoyuan Zhang, Chengli Liu, Yanguo Han, Pengfei Hu, Yan Zeng, Simone Ceccobelli and Guangxin E
Animals 2025, 15(21), 3083; https://doi.org/10.3390/ani15213083 - 24 Oct 2025
Viewed by 851
Abstract
CaMK4, a calcium/calmodulin-dependent protein kinase, is an important mediator of cellular signal transduction, yet its role in the regulation of skeletal muscle satellite cells (MuSCs) in goats has remained unclear. In this study, CaMK4 overexpression and knockdown models were established, and integrated [...] Read more.
CaMK4, a calcium/calmodulin-dependent protein kinase, is an important mediator of cellular signal transduction, yet its role in the regulation of skeletal muscle satellite cells (MuSCs) in goats has remained unclear. In this study, CaMK4 overexpression and knockdown models were established, and integrated transcriptomic and proteomic analyses were performed to systematically elucidate its regulatory network. CaMK4 overexpression altered key pathways associated with cell proliferation and muscle development, including cAMP, PI3K-Akt, and actin cytoskeleton regulation, while proteomic data highlighted calcium signaling and JAK-STAT pathways. Conversely, CaMK4 knockdown enhanced MuSC proliferation by upregulating cell cycle-related genes and proteins. Integrated analyses further identified that Galectin-9 (LGALS9), Collagen triple helix repeat containing-1 (CTHRC1), Hyaluronan Synthase 1 (HAS1), and L-Threonine Dehydrogenase (TDH) may serve as potential key nodes regulating cell cycle, apoptosis, and metabolic control. This suggests a regulatory role for CaMK4. Collectively, these findings provide a mechanistic framework for understanding CaMK4 function in ruminant muscle development and may offer insights for improving goat muscle growth, meat quality traits, and production efficiency. Full article
(This article belongs to the Special Issue Genetics and Breeding for Enhancing Production Traits in Ruminants)
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