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	17.7 Days	CHF 2400	Submit
Current Issues in Molecular Biology cimb	3.0	3.7	1999	17.8 Days	CHF 2200	Submit
Genes genes	2.8	5.5	2010	14.6 Days	CHF 2600	Submit
International Journal of Molecular Sciences ijms	4.9	9.0	2000	20.5 Days	CHF 2900	Submit
DNA dna	-	-	2021	20.5 Days	CHF 1000	Submit

17 pages, 16152 KB

Open AccessArticle

Multi-Omics Insights into Postnatal Skeletal Muscle Development in Duroc Pigs

by Kaiming Wang, Xin Li, Xibing Liu, Sui Liufu, Lanlin Xiao, Bohe Chen, Wenwu Chen, Jun Jiang, Yan Liu and Haiming Ma

Animals 2025, 15(18), 2715; https://doi.org/10.3390/ani15182715 - 16 Sep 2025

Viewed by 151

Abstract

Skeletal muscles, accounting for 40% of mammalian body mass, exhibit pronounced heterogeneity due to their distinct anatomical locations. Animal husbandry has focused excessively on longissimus dorsi (LDM) development while neglecting other muscles. In this study, we integrated Bulk RNA Sequencing (bulk RNA-seq) and [...] Read more.

Skeletal muscles, accounting for 40% of mammalian body mass, exhibit pronounced heterogeneity due to their distinct anatomical locations. Animal husbandry has focused excessively on longissimus dorsi (LDM) development while neglecting other muscles. In this study, we integrated Bulk RNA Sequencing (bulk RNA-seq) and Liquid Chromatography–Mass Spectrometry (LC-MS) analyses of Soleus (SOL), Gastrocnemius (GAS), and Psoas major muscles (PMM) across three key stages in Duroc pigs. We identified nine critical genes (S100A1, MBOAT2, CA3, GYG2, ACTN3, ENO3, SLC3A2, SLC16A10, and GAPDH) and eight metabolites potentially involved in regulating both skeletal muscle development and fiber-type transformation. The heterogeneity between SOL and GAS was low at birth but increased gradually during development. In contrast, PMM exhibited higher heterogeneity than SOL and GAS from birth. Notably, expression levels of MYH7, MYH1, and MYH4 displayed stage-specific and muscle type-dependent variations. Moreover, we observed a developmental shift from the MAPK signaling pathway (1–21 d) to the regulation of the actin cytoskeleton (21–120 d). Pairwise comparisons between the SOL, GAS, and PMM revealed that the signaling pathways were enriched in muscle fiber-type switching. Collectively, through the integration of bulk RNA-seq and LC-MS data, this study provides novel molecular breeding strategies for the genetic improvement of meat-producing animals. Full article

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

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14 pages, 4649 KB

Open AccessArticle

Genomic Characterization of the Kazakh Fat-Tailed Coarse-Wool Sheep Breed Using ROH Analysis

by Altynay Kozhakhmet, Zhanerke Akhatayeva, Kairat Dossybayev, Marina Yermekova, Tilek Kapassuly, Kanagat Yergali, Aibyn Torekhanov, Utepbergen Bissenov, Xianyong Lan and Beibit Kulataev

Animals 2025, 15(18), 2714; https://doi.org/10.3390/ani15182714 - 16 Sep 2025

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Abstract

Sheep breeding is an important sector of livestock production in the Republic of Kazakhstan. The Kazakh fat-tailed coarse-wool sheep holds a prominent position among local breeds due to its high meat productivity, resilience to extreme climatic conditions, and efficient use of pasture resources. [...] Read more.

Sheep breeding is an important sector of livestock production in the Republic of Kazakhstan. The Kazakh fat-tailed coarse-wool sheep holds a prominent position among local breeds due to its high meat productivity, resilience to extreme climatic conditions, and efficient use of pasture resources. This study focuses on the analysis of runs of homozygosity (ROH) to evaluate the genetic diversity level, inbreeding and to detect selection signatures in the Kazakh fat-tailed coarse-wool sheep breed. A total of 500 animals were genotyped using the OvineSNP50 BeadChip (Illumina, San Diego, CA, USA). As a result, a total of 41,728 ROH segments were identified, with an average length of 1.59 Mb, distributed across the entire genome. The most prominent homozygous regions were detected on chromosomes OAR10, OAR13, and OAR22, which might be associated with selection signatures. Genomic inbreeding coefficients (F_ROH and F_GRM) showed a strong positive correlation (r = 0.58, p < 0.001), supporting the effectiveness of ROH-based analysis. Several candidate genes were detected, including MYF5, PRDM16, TGM3, SLC26A4 and SMAD5 which are notably involved in muscle formation, wool traits, and fat metabolism. The findings have substantial practical value for breeding programs and for managing genetic diversity in sheep farming enterprises in the Republic of Kazakhstan. 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, 4614 KB

Open AccessArticle

Screening of circRNAs Associated with Secondary Wool Follicle Development in Fine-Wool Sheep and Construction of Their ceRNA Network

by Yu Luo, Binpeng Xi, Yufang Song, Tong Xiao, Zengkui Lu, Jianbin Liu, Chao Yuan and Tingting Guo

Animals 2025, 15(17), 2629; https://doi.org/10.3390/ani15172629 - 8 Sep 2025

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Abstract

Various signalling molecules and pathways critical for wool production and quality regulate wool secondary follicle (SF) development. Circular RNAs (circRNAs) regulate SF morphogenesis through a competing endogenous RNA (ceRNA) mechanism; these novel cyclic non-coding RNAs are not known to regulate the development of [...] Read more.

Various signalling molecules and pathways critical for wool production and quality regulate wool secondary follicle (SF) development. Circular RNAs (circRNAs) regulate SF morphogenesis through a competing endogenous RNA (ceRNA) mechanism; these novel cyclic non-coding RNAs are not known to regulate the development of SFs in the foetal period of fine-wool sheep. Here, we analysed circRNA expression profiles in the foetal skin of Gansu Alpine fine-wool sheep at 10 developmental stages (E87, E90, E93, E96, E99, E102, E105, E108, E111, and E138) using RNA sequencing. Among the differentially expressed circRNAs (DE circRNAs), 173 were significantly enriched in signalling pathways related to hair follicle (HF) development, such as Wnt/β-catenin, transforming growth factor-β/Smad, Notch, and mitogen-activated protein kinase. Six HF-development-related circRNAs were expressed at different stages and potentially regulated SF development through the ceRNA network. In total, 16 DE circRNAs and their targets, 44 miRNAs, and 65 mRNAs were screened, and 88 ceRNA regulatory network pathways related to SF development were constructed. These key DE circRNAs could be candidate genes for further exploration of the molecular HF development mechanism, providing an important theoretical basis for unravelling the regulatory network of SF development in fine-wool sheep and genetic wool trait improvement. Full article

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

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12 pages, 647 KB

Open AccessArticle

Effects of COLQ Gene Missense Mutations on Growth and Meat Traits in Leizhou Black Goats

by Jing Huang, Ke Wang, Yuelang Zhang, Jiancheng Han, Hanlin Zhou and Qinyang Jiang

Animals 2025, 15(17), 2618; https://doi.org/10.3390/ani15172618 - 6 Sep 2025

Viewed by 1315

Abstract

As an indigenous goat breed unique to southern China, Leizhou Black Goats (LZBGs) are highly valued for their rapid growth, high reproductive performance, and superior meat quality. However, their offspring frequently exhibit symptoms of muscle atrophy and malnutrition, suggesting potential genetic defects underlying [...] Read more.

As an indigenous goat breed unique to southern China, Leizhou Black Goats (LZBGs) are highly valued for their rapid growth, high reproductive performance, and superior meat quality. However, their offspring frequently exhibit symptoms of muscle atrophy and malnutrition, suggesting potential genetic defects underlying these adverse phenotypes. As a unique extracellular matrix component, collagen Q (COLQ) is specifically enriched within the synaptic basal lamina at vertebrate neuromuscular junctions (NMJs), where it anchors acetylcholinesterase (AChE) to facilitate efficient acetylcholine hydrolysis, ensuring precise neuromuscular signaling. The current investigation sought to characterize the spectrum of genetic polymorphisms within the COLQ gene and assess their correlation with key production traits, including growth performance and meat quality parameters, in the LZBG population. Previously, through whole-genome sequencing and transcriptome sequencing analyses of an LZBG population, we identified four SNPs in the COLQ gene, namely, two missense mutations (SNP1: p.238A/S and SNP3: p.47G/S), one intronic variant (SNP2), and one synonymous mutation (SNP4: p.101P/P). Population genetic analysis revealed strong linkage disequilibrium between SNP1 and SNP2. Computational modeling of protein structures predicted that the identified missense mutations may lead to alterations in protein conformation. Association analyses demonstrated significant correlations of SNP1 and SNP3 with growth and meat quality traits (p < 0.05), where SNP3 reduced COLQ expression by 0.64-fold in homozygotes. Association analysis revealed that both SNP1 and SNP3 showed significant correlations with growth and meat quality traits in LZBGs (p < 0.05). Notably, SNP3 (p.47G/S) was found to regulate COLQ gene expression, reducing its levels by 0.64-fold in homozygous individuals, suggesting its potential as a genetic marker for selecting goats with superior growth performance and muscular development characteristics. The identified genetic variants establish a foundation for marker-assisted selection in LZBG breeding programs with particular relevance to growth performance enhancement, while also advancing the understanding of COLQ’s functional mechanisms in muscle development. 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, 2950 KB

Open AccessArticle

Molecular Insights into Intramuscular Unsaturated Fatty Acid Deposition in Lambs Through Multi-Omics Profiling

by Xuewen Han, Xudong Liu, Yu Fu, Jinlin Chen, Cuiyu Lai, Xiaofan Yang, Xuesong Shan, Yang Chen and Huaizhi Jiang

Animals 2025, 15(17), 2617; https://doi.org/10.3390/ani15172617 - 6 Sep 2025

Viewed by 487

Abstract

Unsaturated fatty acids are key contributors to the nutritional and sensory quality of lamb meat. To investigate the molecular basis of intramuscular unsaturated fatty acid variation, we selected lambs with divergent fatty acid profiles and performed integrated transcriptomic and untargeted metabolomic analyses of [...] Read more.

Unsaturated fatty acids are key contributors to the nutritional and sensory quality of lamb meat. To investigate the molecular basis of intramuscular unsaturated fatty acid variation, we selected lambs with divergent fatty acid profiles and performed integrated transcriptomic and untargeted metabolomic analyses of the longissimus dorsi muscle. The high unsaturated fatty acid group exhibited distinct gene expression patterns in pathways related to lipid metabolism, mitochondrial function, and immune responses. Metabolomic profiling revealed significant enrichment of metabolites involved in both the biosynthesis and degradation of fatty acids. Among the differentially expressed genes, MYH7 was markedly upregulated in lambs with higher unsaturated fatty acid content, suggesting a potential regulatory role in energy metabolism or lipid homeostasis. These findings provide new molecular insights into the mechanisms underlying unsaturated fatty acid deposition in lamb and identify MYH7 and other candidates as potential targets for improving meat quality through breeding or nutritional strategies. Full article

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

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23 pages, 4939 KB

Open AccessArticle

Transcriptome and Metabolome Profiles Reveal the Underlying Mechanism of Fat Deposition Changes in Three-Way Crossbred Yak for High-Quality Beef Production

by Xiukai Cao, Wenxiu Ru, Jie Cheng, Le Sun, Nan Zhang, Lawang Zhaxi, Renzeng Dunzhu, Fengbo Sun, Kai Yang, Yue’e Gao, Xixia Huang, Bizhi Huang and Hong Chen

Animals 2025, 15(17), 2599; https://doi.org/10.3390/ani15172599 - 4 Sep 2025

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Abstract

Yajiangxue cattle (XF) is three-way crossbred cattle developed specifically for producing high-quality beef in the Tibetan Plateau by introducing the bloods of Tibetan yellow cattle (HF) and Angus cattle into Tibetan yak (MF). In the present study, we mainly focused on fat deposition [...] Read more.

Yajiangxue cattle (XF) is three-way crossbred cattle developed specifically for producing high-quality beef in the Tibetan Plateau by introducing the bloods of Tibetan yellow cattle (HF) and Angus cattle into Tibetan yak (MF). In the present study, we mainly focused on fat deposition and metabolism changes and used RNA-seq and LC-MS/MS-based metabolomics to partially explain the meat quality improvement in Yajiangxue cattle. Differential expression analysis revealed 1762, 2949, and 2931 different expression genes in XF vs. HF, XF vs. MF, and XF vs. cattle–yak (PF), respectively, such as BMP2, WISP2, FGF1, IL1B, IL6, and WNT5B. Immune response, oxidation–reduction processes, and fatty acid metabolism were markedly enriched. Furthermore, an initial identification revealed 319 metabolites using positive ion mode and 289 metabolites using negative ion mode in bovine adipose tissue across four breeds/populations. Of these, 143 were differential metabolites in positive ion mode, while 166 were in negative ion mode. The main pathways of metabolism affected by breed/population were unsaturated fatty acid biosynthesis, tryptophan and tyrosine biosynthesis, primary bile acid biosynthesis, cholesterol metabolism, beta-alanine metabolism, etc. Similarly, both the transcriptome and the metabolome results highlighted fatty acid metabolism. These results could help elucidate the biological mechanisms involved in fat deposition and identify valuable biomarkers for specific metabolite accumulation. Full article

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

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12 pages, 1709 KB

Open AccessArticle

Identification of MAPK10 as a Candidate Gene for High Milk Production in Water Buffaloes Through a Genome-Wide Association Study

by Wangchang Li, Huan Chen, Duming Cao and Xiaogan Yang

Animals 2025, 15(17), 2567; https://doi.org/10.3390/ani15172567 - 31 Aug 2025

Viewed by 602

Abstract

Buffaloes are a vital genetic resource for dairy production, yet advancements in improving milk production have been somewhat limited. In this study, we performed an integrated analysis of genomic sequencing data from 78 water buffaloes and their milk production traits, with a focus [...] Read more.

Buffaloes are a vital genetic resource for dairy production, yet advancements in improving milk production have been somewhat limited. In this study, we performed an integrated analysis of genomic sequencing data from 78 water buffaloes and their milk production traits, with a focus on 305-day milk yield (MY). Leveraging advancements in sequencing technology alongside genome-wide association study (GWAS) methods such as cBLUP, GMATs, and BayesR, we aimed to identify genetic factors that could facilitate the breeding of high-quality buffaloes. Our analysis revealed two significant SNPs associated with milk production traits. Based on these markers, four candidate genes were identified within the surrounding genomic regions. These genes showed significant enrichment in lactation-related pathways, including the prolactin signaling pathway (mitogen-activated protein kinase 10, MAPK10), IL-17 signaling pathway (MAPK10), MAPK signaling pathway (MAPK10), and adipocytokine signaling pathway (MAPK10). The identification of these candidate genes, particularly MAPK10, provides a robust theoretical basis for molecular breeding strategies aimed at enhancing milk production in buffaloes. This work paves the way for more targeted and effective breeding programs in the future. 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, 13277 KB

Open AccessArticle

ENO1 Regulates Apoptosis Induced by Acute Cold Stress in Bovine Mammary Epithelial Cells

by Na Shen, Jie Wang, Jiayu Liao, Hengwei Yu, Wenqiang Sun, Xianbo Jia and Songjia Lai

Animals 2025, 15(17), 2559; https://doi.org/10.3390/ani15172559 - 31 Aug 2025

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Abstract

Low-temperature environments in cold regions pose a significant threat to cattle farming. Bovine mammary epithelial cells (BMECs) are highly sensitive to cold stress, and acute cold stress can induce apoptosis, adversely affecting lactation performance and health. To explore the mechanism of acute cold [...] Read more.

Low-temperature environments in cold regions pose a significant threat to cattle farming. Bovine mammary epithelial cells (BMECs) are highly sensitive to cold stress, and acute cold stress can induce apoptosis, adversely affecting lactation performance and health. To explore the mechanism of acute cold stress-induced apoptosis in BMECs, we established an in vitro acute cold stress model. Results showed that mRNA levels of HSP90 increased significantly in a time-dependent manner after 2 h of cold stress, confirming successful model establishment. Following 4 h of cold stress, pro-apoptotic genes (Caspase-3, Bax) exhibited significantly elevated mRNA levels, while the anti-apoptotic gene (BCL-2) showed significantly reduced mRNA levels. Concurrently, the apoptosis rate increased significantly, indicating that acute cold stress induces apoptosis and suggesting the 4 h mark may represent a critical transition point. Integrated transcriptomic and functional analyses identified ENO1 as a core metabolic regulator counteracting acute cold stress-induced apoptosis in BMECs. As a multifunctional protein, ENO1 (alpha-enolase) acts as a central enzyme in glycolysis while exerting additional roles in cellular signaling and apoptotic processes, thereby participating in various pathophysiological regulations. Both mRNA and protein levels of ENO1 were significantly elevated in cold-stressed cells compared to untreated controls. Importantly, interference with ENO1 expression aggravated the extent of cold stress-induced apoptosis, demonstrating the regulatory role of ENO1 in this process. To our knowledge, this is the first report elucidating the core regulatory function of ENO1 in acute cold stress-induced apoptosis in BMECs. These findings provide a theoretical basis for understanding apoptotic mechanisms under stress. 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, 2450 KB

Open AccessArticle

Activation of Focal Adhesion Pathway by CIDEA as Key Regulatory Axis in Lipid Deposition in Goat Intramuscular Precursor Adipocytes

by Peng Shao, Qi Li, Yu Liao, Yong Wang, Yaqiu Lin, Hua Xiang, Zhanyu Du, Changhui Zhang, Jiangjiang Zhu and Lian Huang

Animals 2025, 15(16), 2374; https://doi.org/10.3390/ani15162374 - 13 Aug 2025

Viewed by 455

Abstract

Intramuscular fat (IMF) content determines the quality of goat meat and is regulated by the comprehensive effect of the proliferation and adipogenesis of intramuscular preadipocytes. Our previous RNA-seq data revealed that cell death-inducing DNA fragmentation factor alpha (DFFA)-like effector (CIDE) A was upregulated [...] Read more.

Intramuscular fat (IMF) content determines the quality of goat meat and is regulated by the comprehensive effect of the proliferation and adipogenesis of intramuscular preadipocytes. Our previous RNA-seq data revealed that cell death-inducing DNA fragmentation factor alpha (DFFA)-like effector (CIDE) A was upregulated during the development of intramuscular fat in the longissimus dorsi muscle tissue, implying an important role in lipid homeostasis. However, the mechanism by which CIDEA, a member of the CIDE family, regulates intramuscular fat deposition in goat muscle is unknown, so we explored the function and underlying mechanism of CIDEA in goat intramuscular preadipocytes. To address this, we altered CIDEA in intramuscular preadipocytes and resolved the effect and mechanism of CIDEA in adipogenesis through RT-PCR, Western blot, triglyceride and LD determinations, CCK-8, and RNA-seq. It was found that CIDEA increased lipid droplets (LDs) and triglyceride contents and inhibited cell proliferation. Meanwhile, the lipid metabolism-related genes PPARγ, C/EBPα, SREBP1c, PLIN1, TIP47, ADFP, DGAT1, ACC, FASN, ACSL1, and FABP3 were upregulated, while the lipolysis and β-oxidation genes HSL, ACOX1, and CPT1B, as well as the proliferation marker gene CDK1, were all downregulated upon CIDEA overexpression. Differentially expressed genes in CIDEA dysregulation groups through RNA-seq were selected and were enriched in the apelin and focal adhesion signaling pathways. Specifically, the Western blot and rescue assays found that focal adhesion, but not apelin, was the key signaling pathway in CIDEA regulating lipid deposition in goat intramuscular preadipocytes. In summary, this study reveals that CIDEA promotes lipid deposition in intramuscular preadipocytes through the focal adhesion pathway and inhibits cell proliferation. This work clarifies the functional role and downstream signaling pathway of CIDEA in intramuscular fat deposition and provides theoretical support for improving meat quality by targeting key phenotype-related genes. 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, 873 KB

Open AccessArticle

Polymorphism of Keratin Gene KRT71 and Its Relationship with Wool Properties in Gansu Alpine Fine-Wool Sheep

by Fangfang Zhao, Zhaohua He, Hongxian Sun, Jiqing Wang, Xiu Liu, Zhiyun Hao, Mingna Li and Shaobin Li

Animals 2025, 15(14), 2028; https://doi.org/10.3390/ani15142028 - 10 Jul 2025

Viewed by 409

Abstract

Keratin plays a crucial role in wool formation. Conducting polymorphism studies on key keratin genes is helpful in identifying key SNP sites that might influence wool traits. In this research, kompetitive allele-specific PCR (KASP) genotyping and protein immunofluorescence techniques were used to explore [...] Read more.

Keratin plays a crucial role in wool formation. Conducting polymorphism studies on key keratin genes is helpful in identifying key SNP sites that might influence wool traits. In this research, kompetitive allele-specific PCR (KASP) genotyping and protein immunofluorescence techniques were used to explore the polymorphisms of the KRT71 gene in Gansu alpine fine-wool sheep, analyze the relationship between the gene polymorphisms and wool production traits, and examine the expression and localization of the KRT71 protein in the hair follicles of fine-wool sheep. The results indicated that there were two single-nucleotide polymorphisms (SNPs) in the 5′ UTR and exon 9 of the KRT71 gene, named SNP1 (C.-7G/C) and SNP2 (C.1500G/A), respectively. Regarding SNP1, the mean stable length (MSL) of GG genotype individuals was significantly longer than that of GC genotype individuals (p < 0.05). Similarly, for SNP2, the MSL of GG genotype individuals was significantly greater than that of GA genotype individuals (p < 0.05). Moreover, the KRT71 protein showed moderate positive expression in the cuticle, outer root sheath, and sebaceous gland. It had strong positive expression in the inner root sheath, while no positive expression was detected in the hair medulla and hair papilla. In summary, the sheep KRT71 gene could be an important candidate gene for improvements in wool length. 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, 1433 KB

Open AccessArticle

ASIP, AHCY and ITCH Genes Are Associated with the Coat Color of Local Goats (Capra hircus) of Southwestern China

by Linyun Zhang, Shengnan Zhao, Houmo Yu, Yixin Duan, Jipan Zhang, Naiyi Xu and Yongju Zhao

Animals 2025, 15(13), 1849; https://doi.org/10.3390/ani15131849 - 23 Jun 2025

Viewed by 530

Abstract

The local goat breeds of Chongqing represent the typical goat populations of Southwestern China and play a significant role in global goat research. However, studies on these goats remain limited. Chongqing goats exhibit diverse coat colors, a crucial economic trait essential for individual [...] Read more.

The local goat breeds of Chongqing represent the typical goat populations of Southwestern China and play a significant role in global goat research. However, studies on these goats remain limited. Chongqing goats exhibit diverse coat colors, a crucial economic trait essential for individual and breed identification. In this study, we performed genome-wide association analysis (GWAS) of Chongqing goats to identify candidate genes associated with coat color. The results of the GWAS revealed that the ASIP, AHCY, and ITCH genes on chromosome 13 are significantly associated with coat color variation in Chongqing goats. Furthermore, haplotype analysis, gene function annotation, and pathway analysis enrichment further confirmed that a significant region on chromosome 13 is associated with coat color in local Chongqing goats, and that ASIP and AHCY are related to black coat color, whereas ITCH is potentially associated with white coat expression. Additionally, we also identified TPK1 as being associated with coat color in goats, which has hardly been reported. The newly identified genes expand our understanding of the complex genetic architecture underlying pigmentation traits in livestock. Our study identifies the genes related to coat color in local goats, which enriches the genetic resource pool of goats and contributes to a deeper understanding of the genetic mechanisms underlying coat color in these breeds. Full article

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

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14 pages, 1678 KB

Open AccessArticle

The Identification of a New Gene KRTAP 6-3 in Capra hircus and Its Potential for the Diameter Improvement of Cashmere Fibers

by Jian Cao, Zhanzhao Chen, Jianmin Zhang, Liang Cao and Shaobin Li

Genes 2025, 16(6), 721; https://doi.org/10.3390/genes16060721 - 19 Jun 2025

Viewed by 646

Abstract

Background: Cashmere is one of the important economic products of goats, and the KRTAP gene family, as an important family of regulatory genes in the growth process of cashmere fiber, largely affects the quality of cashmere. Methods: In this study, the KRTAP6-3 gene [...] Read more.

Background: Cashmere is one of the important economic products of goats, and the KRTAP gene family, as an important family of regulatory genes in the growth process of cashmere fiber, largely affects the quality of cashmere. Methods: In this study, the KRTAP6-3 gene was identified and located on goat chromosome 1 using a goat genome homology search combined with a phylogenetic tree approach. The Longdong cashmere goat KRTAP6-3 gene variation and its effect on cashmere quality were explored by using the polymerase chain reaction single-stranded conformation polymorphism (PCR-SSCP) technique, in situ hybridization, and the allele presence/absence model. Results: The results identified a total of six SNPs in KRTAP6-3, three of which were located in the coding region and two of which were synonymous mutations, in addition to 45- bp deletion sequences detected in alleles C and F. Moreover, the KRTAP6-3 mRNA showed a strong expression signal in the cortical layer of the primary and secondary follicles in the inner root sheaths, as well as in the cells of the hair papillae and the matrices during the anagen phase, and signaling at the sites described above is attenuated during the telogen phase. The presence of allele C was associated with increased MFD (mean fiber diameter) (p < 0.01). The MFD of goats with allele C genotype (genotype AC) was significantly higher (p < 0.05) than that of goats without allele C genotype (genotypes AA and AB). Conclusions: This indicates that genetic variation in the KRTAP6-3 gene in goats is significantly associated with cashmere traits and can serve as a candidate gene for molecular markers of cashmere traits. Full article

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

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14 pages, 276 KB

Open AccessArticle

Genomic Selection for Early Growth Traits in Inner Mongolian Cashmere Goats Using ABLUP, GBLUP, and ssGBLUP Methods

by Tao Zhang, Linyu Gao, Bohan Zhou, Qi Xu, Yifan Liu, Jinquan Li, Qi Lv, Yanjun Zhang, Ruijun Wang, Rui Su and Zhiying Wang

Animals 2025, 15(12), 1733; https://doi.org/10.3390/ani15121733 - 12 Jun 2025

Viewed by 1030

Abstract

This study aimed to identify the best model and method for the genomic selection of early growth traits in Inner Mongolian cashmere goats (IMCGs). Using data from 50,728 SNPs, the phenotypes (birth weight, BW; weaning weight, WW; daily weight gain, DWG; and yearling [...] Read more.

This study aimed to identify the best model and method for the genomic selection of early growth traits in Inner Mongolian cashmere goats (IMCGs). Using data from 50,728 SNPs, the phenotypes (birth weight, BW; weaning weight, WW; daily weight gain, DWG; and yearling weight, YW) of 2256 individuals, and pedigree information from 14,165 individuals, fixed effects were analyzed using a generalized linear model. Four single-trait animal models with varying combinations of individual and maternal effects were evaluated using the ABLUP, GBLUP, and ssGBLUP methods. The best model was selected based on a likelihood ratio test. Five-fold cross-validation was used to assess the accuracy and reliability of the genomic estimated breeding values (GEBVs). Birth year and herd significantly affected BW (p < 0.05) and WW, DWG, and YW (p < 0.01), while sex, birth type, and dam age had highly significant effects on all traits (p < 0.01). Model 4, incorporating direct and maternal additive genetic effects, maternal environmental effects, and their covariance, was optimal. Additionally, ssGBLUP achieved the highest GEBV accuracy (0.61–0.70), outperforming the GBLUP and ABLUP methods. Thus, ssGBLUP is recommended for enhancing the genetic progress in IMCGs. Under the best method, the heritability estimates for BW, WW, DGW, and YW were 0.11, 0.25, 0.15, and 0.23, respectively. Full article

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

22 pages, 2689 KB

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

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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)

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16 pages, 6350 KB

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

Viewed by 821

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 KB

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

Viewed by 825

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 KB

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 621

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)

20 pages, 3332 KB

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

Cited by 1 | Viewed by 4550

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 KB

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 739

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 KB

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

Cited by 1 | Viewed by 490

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 KB

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 803

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 KB

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 1302

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 KB

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 1098

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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