Advances in Molecular Genetics and Breeding of Cattle, Sheep, and Goats

Journal Name	Impact Factor	CiteScore	Launched Year	First Decision (median)	APC
Animals animals	2.7	5.2	2011	16.1 Days	CHF 2400	Submit
Current Issues in Molecular Biology cimb	2.8	3.7	1999	15.8 Days	CHF 2200	Submit
Genes genes	2.8	5.5	2010	14.9 Days	CHF 2600	Submit
International Journal of Molecular Sciences ijms	4.9	9.0	2000	16.8 Days	CHF 2900	Submit
DNA dna	-	-	2021	23.3 Days	CHF 1000	Submit

23 pages, 1279 KiB

Open AccessArticle

Functional and Genetic Insights into the Role of the NR4A1 Gene in the Litter Size of the Shaanbei White Cashmere Goat

by Ebadu Areb, Yutian Bi, Yangyang Bai, Qihui Zhu, Lingyuan Ma, Chuanying Pan, Xiaolei Chen and Xianyong Lan

Animals 2025, 15(12), 1729; https://doi.org/10.3390/ani15121729 - 11 Jun 2025

Abstract

Nuclear receptor subfamily 4 group A member 1 (NR4A1) plays a crucial role in regulating various physiological processes. As gene mining for reproductive traits is essential, this study aimed to investigate the mRNA expression, genetic variation, and association of the NR4A1 [...] Read more.

Nuclear receptor subfamily 4 group A member 1 (NR4A1) plays a crucial role in regulating various physiological processes. As gene mining for reproductive traits is essential, this study aimed to investigate the mRNA expression, genetic variation, and association of the NR4A1 gene with goat litter size. We examined the mRNA expression levels of the NR4A1 gene in eight different tissues of female Shaanbei White Cashmere (SBWC) goats (n = 6). Then, a novel 11-bp insertion/deletion (InDel) variant was genotyped in 1136 SBWC goats, 87 SNPs were identified through resequencing (n = 120), and selection signal analysis was undertaken. The NR4A1 gene was expressed in all examined tissues, including the ovary and the oviduct, suggesting its role in goat reproduction. Both the 11-bp InDel and 13 SNP variants showed significant association with litter size. Additionally, four potential transcription factor binding sites were predicted within the insertion allele, which may contribute to increased litter size. Selection signal analysis revealed strong pressure on the NR4A1 gene region in the Cashmere goat population. These findings suggest that NR4A1 is a promising candidate gene for improving litter size in goats and could be utilized as a genetic marker in breeding programs. Full article

(This article belongs to the Topic Advances in Molecular Genetics and Breeding of Cattle, Sheep, and Goats)

16 pages, 6350 KiB

Open AccessArticle

Loss of Myostatin Shapes the Transcriptomic and Epigenetic Landscapes Across Multiple Muscle Types in Cattle

by Chao Hai, Xuefei Liu, Chunling Bai, Guanghua Su, Lei Yang and Guangpeng Li

Curr. Issues Mol. Biol. 2025, 47(6), 431; https://doi.org/10.3390/cimb47060431 - 7 Jun 2025

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Abstract

Myostatin (MSTN) is a critical regulator of muscle development. This study aimed to investigate the transcriptional and epigenetic mechanisms by which MSTN gene editing affects skeletal, cardiac, and smooth muscle function in cattle. The results showed that the MSTN gene-edited (MT) [...] Read more.

Myostatin (MSTN) is a critical regulator of muscle development. This study aimed to investigate the transcriptional and epigenetic mechanisms by which MSTN gene editing affects skeletal, cardiac, and smooth muscle function in cattle. The results showed that the MSTN gene-edited (MT) cattle skeletal muscle exhibited significantly larger myofiber cross-sectional areas (p = 0.049), accompanied by reduced shear force (p = 0.044), cooking loss rate (p = 0.0029), and pH (p = 0.014). Transcriptomic and whole-genome bisulfite sequencing (WGBS) revealed distinct expression and methylation patterns across muscle types. Notably, axon guidance signaling was identified as a shared enriched pathway in both transcriptional and CG/CHG/CHH methylation profiles of the gluteus. Further, 102 differentially expressed genes (DEGs) were commonly identified across all three muscle types; their KEGG enrichment included immune-related and cellular interaction pathways (e.g., antigen processing and presentation, and cell adhesion molecules), many of which intersect with axon guidance functions. Core regulators such as SEMA3A, PLXNA1, and NTN1 were epigenetically modulated in MT gluteus and heart. These findings suggest that MSTN knockout remodels neuromuscular signaling through muscle-type-specific transcriptional and epigenetic reprogramming. Full article

(This article belongs to the Topic Advances in Molecular Genetics and Breeding of Cattle, Sheep, and Goats)

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11 pages, 847 KiB

Open AccessArticle

Assessment of Genetic Diversity and Productive Traits in Crossbreed Cattle in the Caribbean Region, Colombia

by Andrés Rodríguez-Serrano, Marcos Ahumada-Velasco and Jesús María Cárdenas Beltrán

Genes 2025, 16(6), 677; https://doi.org/10.3390/genes16060677 - 30 May 2025

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Abstract

Objectives: Evaluate the genetic diversity and productive traits of crossbred cattle in the Caribbean region of Colombia, through analyses derived from the assessment of the genome-wide single-nucleotide polymorphism (SNP). Methods: A total of 590 individuals and 66,098 SNPs were analyzed by principal components [...] Read more.

Objectives: Evaluate the genetic diversity and productive traits of crossbred cattle in the Caribbean region of Colombia, through analyses derived from the assessment of the genome-wide single-nucleotide polymorphism (SNP). Methods: A total of 590 individuals and 66,098 SNPs were analyzed by principal components analysis (PCA) and detection of runs of homozygosity (ROH). The population was composed of 531 heifers marked as crossbreed and a group of 59 heifers marked as purebred Gyr. Additionally, allele frequencies were calculated for commercially important traits (CSN2, CSN3, LGB, DGAT1, GH1, CAPN1_316, CAPN1_350, CAPN1_4751, CAST_282, CAST_2870, and CAST_2959). Results: Global differences in PCA were 7.35%, and principal components explained 1.94% and 5.41% of the variation. Five ROH islands were identified in crossbred animals on chromosomes 2, 5, 7, 8, and 12. The majority of observed ROH classes were shorter than 2 Mb, 54% in crossbreed cattle and 47% in Gyr cattle. Individual inbreeding was 5.2% in crossbreed and 12% in Gyr cattle. Both groups had similar allelic and genotypic frequencies for most of the evaluated commercial traits. Only a wide variation was observed in the genes related to growth hormone (GH1) and Calpastatin (CAST_2870 and CAST_22959). Crossbreed heifers had desired allele frequencies for better milk production and quality in the genes CSN2, LGB, DGAT1, and GH1, as well as in the genes CAST_2870 and CAST_2959. Conclusions: Crossbreed cattle in the Colombian Caribbean region possess high genetic diversity and desirable allele frequencies to implement breeding and intense selection programs aimed at improving production yields. Full article

(This article belongs to the Topic Advances in Molecular Genetics and Breeding of Cattle, Sheep, and Goats)

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13 pages, 238 KiB

Open AccessArticle

Genetic Evaluation of Early Growth Traits in Yunnan Semi-Fine Wool Sheep

by Yaqian Wang, Hongyuan Yang, Xiaoqi Zhao, Xiaojun Ni, Yuanchong Zhao, Zhengrong You, Qingwei Lu, Sen Tang, Guobo Quan and Xuefeng Fu

Animals 2025, 15(11), 1512; https://doi.org/10.3390/ani15111512 - 22 May 2025

Viewed by 255

Abstract

With economic development and improved living standards, the demand for mutton and wool continues to grow, and improving the production performance and genetic potential of sheep breeds has become the key to promoting the high-quality development of the sheep industry. Thus, this study [...] Read more.

With economic development and improved living standards, the demand for mutton and wool continues to grow, and improving the production performance and genetic potential of sheep breeds has become the key to promoting the high-quality development of the sheep industry. Thus, this study analyzes the influencing factors of the early production traits of Yunnan semi-fine wool sheep, optimizes the genetic evaluation model, and relies on accurate genetic parameter estimation to provide a theoretical basis for formulating a scientific and efficient breeding strategy for this breed. Data were collected from the Laishishan and Xiaohai breeding farms in Qiaojia, Yunnan, covering production records of the core flock from 2018 to 2022. Using the GLM procedure in SAS 9.4 software, this study analyzed the non-genetic influences on early production traits in Yunnan semi-fine wool sheep. Concurrently, Danish Milk Unit 5 (DMU 5) software estimated the variance components across various animal models for each trait. Employing the Akaike Information Criterion (AIC) and likelihood ratio test (LRT), six models were tested, incorporating or excluding maternal inheritance and environmental impacts, to identify the optimal model for deriving the genetic parameters. The results show that the birth year, dam age, sex, flock and litter size significantly affect both the Birth Weight (BWT) and Weaning Weight (WWT) (p < 0.01). Additionally, the birth month was found to exert a significant effect on Birth Weight (BWT) (p < 0.01), the weaning month has a significant effect on the Weaning Weight (WWT) (p < 0.05). No significant effects of farm location were observed on either trait (p > 0.05). The most accurate genetic evaluation model determined the heritability of the Birth Weight (BWT) and Weaning Weight (WWT) as 0.3123 and 0.3471. From a production perspective, improving lamb birth, Weaning Weight (WWT), feed composition, and maternal nutrition during gestation is vital for breeding efficiency. This study not only identified the optimal animal models for early growth traits in Yunnan semi-fine wool sheep, offering a precise basis for estimating genetic parameters but also provides theoretical guidance for genetic selection and breed improvement in this population. Full article

(This article belongs to the Topic Advances in Molecular Genetics and Breeding of Cattle, Sheep, and Goats)

21 pages, 3332 KiB

Open AccessFeature PaperReview

Innovations in Cattle Breeding Technology: Prospects in the Era of Gene Editing

by Yu Wang, Xiangshun Cui and Zhi Chen

Animals 2025, 15(10), 1364; https://doi.org/10.3390/ani15101364 - 8 May 2025

Viewed by 753

Abstract

As a core species in the global livestock industry, cattle play an irreplaceable role in human food security and economic development. Beef cattle and dairy cattle meet the dietary needs of billions of people around the world by providing high-quality protein and dairy [...] Read more.

As a core species in the global livestock industry, cattle play an irreplaceable role in human food security and economic development. Beef cattle and dairy cattle meet the dietary needs of billions of people around the world by providing high-quality protein and dairy products, respectively. With the growth in population and the intensification of the pressure of climate change, traditional breeding techniques may be unsuitable to meet the increasingly growing demands for sustainable and highly adaptable processes. In recent years, the rapid development of genomics, bioinformatics, and gene-editing technologies has provided unprecedented tools and perspectives for the genetic improvement of cattle, driving the precise design and efficient development of new cattle breeds. However, the development of new cattle breeds still faces multiple bottlenecks pertaining to scientific, ethical, and industrialization aspects, which can be addressed through interdisciplinary collaboration. In this review, we will systematically assess the technological progress in the genetic breeding of beef cattle and dairy cattle, analyze the integration path of traditional breeding and modern biotechnology, and explore the future directions of cattle breeding research under the sustainable development goals, with the aim of providing theoretical support for cattle breeding. Full article

(This article belongs to the Topic Advances in Molecular Genetics and Breeding of Cattle, Sheep, and Goats)

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18 pages, 2277 KiB

Open AccessArticle

The 2SP Site Mutation in the Bovine Natural Resistance-Associated Macrophage 1 Promoter Exhibits Antituberculosis Potential

by Yongke Wei, Mengke Yuan, Yong Zhang and Yuanpeng Gao

Int. J. Mol. Sci. 2025, 26(9), 4229; https://doi.org/10.3390/ijms26094229 - 29 Apr 2025

Viewed by 359

Abstract

Gene-edited cattle overexpressing natural resistance-associated macrophage 1 (NRAMP1) have demonstrated enhanced resistance to tuberculosis (TB). However, introducing synthetic sequences and selection markers may pose potential risks. The endogenous editing of target gene promoters could effectively mitigate these risks. To date, no available mutation [...] Read more.

Gene-edited cattle overexpressing natural resistance-associated macrophage 1 (NRAMP1) have demonstrated enhanced resistance to tuberculosis (TB). However, introducing synthetic sequences and selection markers may pose potential risks. The endogenous editing of target gene promoters could effectively mitigate these risks. To date, no available mutation sites in the bovine NRAMP1 promoter have been identified to enhance host resistance to TB. In this study, we identified a unique mutation editing site, designated as 2SP, within the bovine NRAMP1 promoter, using bioinformatics analysis and dual luciferase assays. The mutation at the 2SP site specifically increased NRAMP1 promoter activity by 2.3-fold after Mycobacterium tuberculosis H37Ra infection, without modifying promoter activity in non-infected groups. By using base editing techniques, an endogenously edited THP-1 cell line with a mutation at the homologous region of the 2SP site was generated, without introducing screening markers. In H37Ra infection experiments, the edited THP-1 cells specifically upregulated NRAMP1 expression and significantly inhibited H37Ra proliferation, while maintaining baseline NRAMP1 expression levels in the absence of infection. In this research, we identified a novel mutation site and provided a fundamental reference for the development of gene-edited cattle with enhanced resistance to TB. Full article

(This article belongs to the Topic Advances in Molecular Genetics and Breeding of Cattle, Sheep, and Goats)

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8 pages, 730 KiB

Open AccessArticle

Variation in Ovine KRTAP13-3 and Its Association with Wool Characteristics in Chinese Tan Sheep

by Lingrong Bai, Huitong Zhou, Jinzhong Tao and Jon G. H. Hickford

Animals 2025, 15(7), 1069; https://doi.org/10.3390/ani15071069 - 7 Apr 2025

Viewed by 281

Abstract

Understanding the genetic factors that influence wool quality is essential for enhancing wool quality and uniformity. This study investigated the KRTAP13-3 gene in Chinese Tan sheep, a breed known for its unique wool characteristics. We analysed 232 sheep and revealed five previously identified [...] Read more.

Understanding the genetic factors that influence wool quality is essential for enhancing wool quality and uniformity. This study investigated the KRTAP13-3 gene in Chinese Tan sheep, a breed known for its unique wool characteristics. We analysed 232 sheep and revealed five previously identified sequence variants of KRTAP13-3 and then modelled to ascertain whether there was any association between the nucleotide sequence variation and variation in mean fibre diameter (MFD), fibre diameter standard deviation (FDSD), coefficient of variation of fibre diameter (CVFD), and mean fibre curvature (MFC). Twelve genotypes were observed, with the five variants having frequencies that ranged from 64.0% to 1.1%. Among the four variants with frequencies above 5%, nucleotide sequence variation was associated with heterotypic hair fibre diameter variation. The most common variant (A) was linked to increased FDSD and CVFD, while two other variants (B and D) revealed trends towards being associated with decreased CVFD. No associations were found with variation in the fine wool fibres from the Tan sheep. This suggests that KRTAP13-3 plays a role in regulating heterotypic hair fibre diameter variability and that it could possibly be a gene marker for improving wool traits. Full article

(This article belongs to the Topic Advances in Molecular Genetics and Breeding of Cattle, Sheep, and Goats)

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17 pages, 6291 KiB

Open AccessArticle

CTNNB1 and CDH1 Regulate Trophoblast Cell Adhesion and Junction Formation in Yak Placental Tissue at Different Gestational Stages

by Bohao Zhang, Chen Song, Bin Zhou, Junjun Zhang, Weitao Dong, Yong Zhang, Xingxu Zhao and Quanwei Zhang

Animals 2025, 15(6), 876; https://doi.org/10.3390/ani15060876 - 19 Mar 2025

Viewed by 477

Abstract

Yaks (Bos grunniens), which are distributed across the Tibetan Plateau and other high-altitude regions, are vital livestock that provide essential resources for local herders and have significant economic and ecological value [...] Full article

(This article belongs to the Topic Advances in Molecular Genetics and Breeding of Cattle, Sheep, and Goats)

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16 pages, 3592 KiB

Open AccessArticle

Multi-Omics Analysis Revealed the Molecular Mechanisms Affecting Average Daily Gain in Cattle

by Mingjuan Gu, Hongyu Jiang, Fengying Ma, Shuai Li, Yaqiang Guo, Lin Zhu, Caixia Shi, Risu Na, Yu Wang and Wenguang Zhang

Int. J. Mol. Sci. 2025, 26(5), 2343; https://doi.org/10.3390/ijms26052343 - 6 Mar 2025

Cited by 1 | Viewed by 749

Abstract

The average daily gain (ADG) is a critical index for evaluating growth rates in cattle and is closely linked to the economic benefits of the cattle industry. Heredity is one of the factors affecting the daily gain of cattle. However, the molecular mechanisms [...] Read more.

The average daily gain (ADG) is a critical index for evaluating growth rates in cattle and is closely linked to the economic benefits of the cattle industry. Heredity is one of the factors affecting the daily gain of cattle. However, the molecular mechanisms regulating ADG remain incompletely understood. This study aimed to systematically unravel the molecular mechanisms underlying the divergence in ADG between high average daily gain (HADG) and low average daily gain (LADG) Angus cattle through integrated multi-omics analyses (microbiome, metabolome, and transcriptome), hypothesizing that the gut microbiota–host gene–metabolism axis is a key regulatory network driving ADG divergence. Thirty Angus cattle were classified according to their HADG and LADG. Fecal and serum samples were collected for 16S, fecal metabolome, and blood transcriptome analysis. The results showed that compared with the LADG group, the abundance of Firmicutes increased in the HADG group, while the abundance of Bacteroidetes and Proteobacteria decreased. Metabolomics and transcriptomic analysis revealed that KEGG pathways associated with differentially expressed genes (DEGs) and differentially abundant metabolites (DAMs) were enriched in bile acid metabolism. Spearman correlation analysis showed that Oscillospira was positively correlated with ZBTB20 and negatively correlated with RADIL. ZBTB20 was negatively correlated with dgA-11_gut_group. This study analyzed the regulatory mechanism of average daily gain of beef cattle from genetic, metabolic, and microbial levels, providing a theoretical basis for analyzing the mechanism of differential daily gain of beef cattle, and has important significance for improving the production performance of beef cattle. The multi-omics network provides biomarker foundations for machine learning-based ADG prediction models, offering potential applications in precision breeding. While these biomarkers show promise for precision breeding, their causal roles require further validation. The conclusions are derived from a single breed (Angus) and gender (castrated males). Future studies should include females and diverse breeds to assess generalizability. Full article

(This article belongs to the Topic Advances in Molecular Genetics and Breeding of Cattle, Sheep, and Goats)

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13 pages, 2313 KiB

Open AccessArticle

EPAS1 Variations and Hematological Adaptations to High-Altitude Hypoxia in Indigenous Goats in Yunnan Province, China

by Li Zhu, Lin Tang, Yunong Zhao, Shanshan Li, Xiao Gou, Weidong Deng and Xiaoyan Kong

Animals 2025, 15(5), 695; https://doi.org/10.3390/ani15050695 - 27 Feb 2025

Viewed by 637

Abstract

The EPAS1 gene plays a central role in hypoxia adaptation in high-altitude animals. Using over 400 blood samples from goats across elevations in Yunnan (500–3500 m), this study examined hematological traits, genetic polymorphisms, and protein structure. Red blood cell (RBC) and hemoglobin (HGB) [...] Read more.

The EPAS1 gene plays a central role in hypoxia adaptation in high-altitude animals. Using over 400 blood samples from goats across elevations in Yunnan (500–3500 m), this study examined hematological traits, genetic polymorphisms, and protein structure. Red blood cell (RBC) and hemoglobin (HGB) levels increased significantly with altitude (p < 0.05), reflecting improved oxygen transport. A non-synonymous SNP (g.86650 A>T, p.Gln556Leu) exhibited adaptive selection, with the T allele frequency rising at higher altitudes (p < 0.05). At 2500 m, TT genotype goats showed significantly higher RBC and HGB levels than AA genotypes (p < 0.05). Protein modeling revealed structural instability caused by the polymorphism, highlighting its role in enhancing hypoxia adaptation. These findings provide a foundation for improving high-altitude livestock genetics. Full article

(This article belongs to the Topic Advances in Molecular Genetics and Breeding of Cattle, Sheep, and Goats)

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