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Open AccessFeature PaperArticle

Integrated Analysis of CRY1 Gene Expression and InDel Polymorphism Reveals Associations with Ovarian Morphological Traits in Chinese Holstein Dairy Cattle

by Xuanbo Chen, Enhui Jiang, Yuta Yang, Haotian Zhang, Zhaoyu Liu, Ebadu Areb, Yongsheng Wang and Xianyong Lan

Biomolecules 2026, 16(8), 1201; https://doi.org/10.3390/biom16081201 - 17 Aug 2026

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Abstract

Clock genes, such as cryptochrome 1 (CRY1), exhibit rhythmic expression in the reproductive organs. This gene is a key component of the circadian clock and is involved in various physiological processes, including reproduction, suggesting that it may be linked to ovarian [...] Read more.

Clock genes, such as cryptochrome 1 (CRY1), exhibit rhythmic expression in the reproductive organs. This gene is a key component of the circadian clock and is involved in various physiological processes, including reproduction, suggesting that it may be linked to ovarian activity via neuroendocrine pathways. However, the association between CRY1 variants and ovarian traits in dairy cows is unclear. In this study we used qRT-PCR to assay the mRNA expression of this gene, and found that CRY1 expression was highest in oocytes in several tissues; subsequently, we found that CRY1 expression was highest in the ovary in Chinese Holstein dairy cattle, followed by muscle and spleen tissues (p < 0.01). Next, we identified a six bp insertion/deletion (indel) locus within the CRY1 gene in Chinese Holstein dairy cattle. Only two genotypes were detected: II (n = 854, 83.7%) and ID (n = 166, 16.3%). Association analysis revealed that the identified indel was significantly associated with dominant follicle and corpus albicans diameters (p < 0.05) during metestrus. Specifically, individuals with the ID genotype exhibited smaller dominant follicles and corpus albicans than those with the II genotype. Our preliminary findings suggest that CRY1 is associated with specific ovarian morphological traits and may serve as a basis for further investigation of its potential role in bovine reproductive function. Full article

(This article belongs to the Special Issue Vertebrate Comparative Genomics)

22 pages, 1067 KB

Open AccessFeature PaperArticle

Genetic Diversity and Runs of Homozygosity in Three Masu Salmon (Oncorhynchus masou) Populations Based on Whole-Genome Resequencing Data

by Song Bai, Chenfan Geng, Wei Wang, Xiaoyu Yan, Tian Dong, Hailiang Song and Hongxia Hu

Biomolecules 2026, 16(8), 1187; https://doi.org/10.3390/biom16081187 - 14 Aug 2026

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Abstract

Masu salmon (Oncorhynchus masou) is an ecologically and economically important cold-water salmonid in East Asia that exhibits diverse life-history forms. To compare population-level genomic variation and patterns of homozygosity among fish from different sources, we analyzed whole-genome resequencing data from 465 [...] Read more.

Masu salmon (Oncorhynchus masou) is an ecologically and economically important cold-water salmonid in East Asia that exhibits diverse life-history forms. To compare population-level genomic variation and patterns of homozygosity among fish from different sources, we analyzed whole-genome resequencing data from 465 individuals representing one field-collected Tumen River population (TM) and two landlocked cultured populations from Chicheng (CC) and Yanji (YJ). After quality control, 6,220,980 high-quality SNPs were retained. Population-specific filtering identified 5,589,828, 3,545,209, and 4,975,751 polymorphic SNPs in CC, TM, and YJ, respectively; although SNP numbers differed, approximately 91% of variants in each population were located in intronic or intergenic regions. Principal component analysis, ADMIXTURE, and distance-based neighbor-joining analysis clearly distinguished the three populations, with CC and YJ showing the closest genetic relationship. Pairwise

F_{ST}

was lowest between CC and YJ and highest between TM and YJ. CC exhibited the highest linkage disequilibrium, whereas TM showed the fastest LD decay and the lowest nucleotide diversity and heterozygosity. Runs of homozygosity (ROH) burden was highest in TM, intermediate in CC, and lowest in YJ. TM had the highest number of ROHs, cumulative ROH length, and

F_{ROH}

, and ROHs longer than 5 Mb were detected only in this population. CC had an intermediate ROH burden dominated by short segments, whereas YJ had the lowest ROH-based genomic inbreeding. The high and heterogeneous ROH burden in TM indicates elevated genome-wide homozygosity among the sampled fish but does not, by itself, demonstrate recent inbreeding throughout the population. Candidate ROH islands and their annotated genes showed limited overlap among populations. Candidate genes in TM were primarily associated with ion regulation, neural processes, and energy metabolism, whereas those in CC and YJ shared broad functional categories involving development, muscle organization, nutrient transport, and neural regulation but differed in most specific genes. These regions and genes should be regarded as exploratory, hypothesis-generating candidates rather than evidence of selection or causality. Overall, this study reveals distinct population genomic characteristics and ROH patterns among masu salmon populations of different origins and provides a basis for future germplasm conservation and genetic management. Full article

(This article belongs to the Special Issue Vertebrate Comparative Genomics)

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14 pages, 11052 KB

Open AccessArticle

A Functional SNP Variant of the 3′ UTR Within the ELF5 Gene Affects Lactation Traits Through bta-miR-487a-Mediated Regulation in Holstein Dairy Cattle

by Lingyuan Ma, Li Sun, Haotian Zhang, Chuanying Pan, Mingxun Li, Xianyong Lan and Yang Li

Biomolecules 2026, 16(8), 1163; https://doi.org/10.3390/biom16081163 - 10 Aug 2026

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Abstract

The genetic and physiological variations among individuals of Holstein dairy cattle contribute to variations in milk yield. Selecting high-yield cows is critical for improving lactation performance. The present study aimed to identify functional genetic variants of the 3′ untranslated region (3′ UTR) in [...] Read more.

The genetic and physiological variations among individuals of Holstein dairy cattle contribute to variations in milk yield. Selecting high-yield cows is critical for improving lactation performance. The present study aimed to identify functional genetic variants of the 3′ untranslated region (3′ UTR) in the ELF5 gene associated with milk production traits and to elucidate their underlying molecular mechanisms. A total of 1314 Chinese Holstein cows were genotyped, and a novel single nucleotide polymorphism (SNP), ELF5 g.32793 G>T, was identified in the 3′ UTR of ELF5. This SNP was significantly associated with milk production, such as milk yield, milk fat percentage, milk protein percentage, and somatic cell score. Bioinformatic prediction and dual-luciferase reporter assays demonstrated that the ELF5 g.32793 G>T affects the interaction between bta-miR-487a and the ELF5 3′ UTR. Functional analyses in bovine mammary epithelial (MAC-T) cells showed that bta-miR-487a suppressed cell proliferation by inducing G0/G1 phase arrest and reduced the expression of proliferation-related proteins. Collectively, these findings suggested that bta-miR-487a participates in the regulation of MAC-T cell growth and that the ELF5 g.32793 G>T polymorphism may influence lactation performance through an miRNA-associated mechanism. Therefore, the variant can be used as a functional marker for marker-assisted selection in dairy cattle breeding. Full article

(This article belongs to the Special Issue Vertebrate Comparative Genomics)

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19 pages, 6785 KB

Open AccessArticle

Circular RNA circNID2 Promotes Bovine Adipogenesis via miR-339a/NNAT

by Yue Liu, Mengyang Zhang, Zhuoyuan He, Li Sun, Yangyang Bai, Chuanying Pan, Xiaomei Sun, Yang Li, Enhui Jiang and Xianyong Lan

Biomolecules 2026, 16(8), 1113; https://doi.org/10.3390/biom16081113 - 30 Jul 2026

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Abstract

Adipose tissue development significantly influences meat quality and economic traits in beef cattle. In this study, we identified a novel circular RNA derived from two exons (exons 3 and exons 9) of the NID2 gene, designated as circNID2, which exhibits high structural stability [...] Read more.

Adipose tissue development significantly influences meat quality and economic traits in beef cattle. In this study, we identified a novel circular RNA derived from two exons (exons 3 and exons 9) of the NID2 gene, designated as circNID2, which exhibits high structural stability and marked upregulation during bovine adipocyte differentiation. Functional assays demonstrated that circNID2 suppresses the proliferation and apoptosis of bovine preadipocytes while robustly promoting adipogenic differentiation and lipid accumulation. Although containing several putative open reading frames, circNID2 lacks protein-coding potential. Mechanistically, circNID2 functions as a competing endogenous RNA by sponging miR-339a, thereby relieving the post-transcriptional repression of its downstream target, Neuronatin (NNAT). Functional rescue experiments further validated that circNID2 partially neutralizes the regulatory effects of miR-339a on preadipocyte proliferation, apoptosis, and differentiation. Collectively, these findings demonstrate that circNID2 regulates bovine preadipocyte function through the newly established circNID2/miR-339a/NNAT axis. This study provides novel insights into the post-transcriptional mechanisms governing mammalian adipogenesis and highlights circNID2 as a potential molecular target for improving fat deposition traits in cattle. Full article

(This article belongs to the Special Issue Vertebrate Comparative Genomics)

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22 pages, 12692 KB

Open AccessArticle

Physiology and Multi-Omics Provide Insights into Sperm Activation and Movement in Euryhaline Spotted Seabass (Lateolabrax maculatus)

by Qinghua Wang, Yuxin Zhang, Weiwei Zhang, Yingxin Wu, Jiajie Li, Yizheng Zhang, Lu Li, Zhiming Zhu and Zining Meng

Biomolecules 2026, 16(7), 1021; https://doi.org/10.3390/biom16071021 - 13 Jul 2026

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Abstract

Sperm activation and movement are pivotal determinants of fertilization success in teleosts, yet the molecular mechanisms in euryhaline species remain largely unresolved. Here, we integrated physiology and multi-omics to elucidate the osmolality, ions, and regulatory networks underlying sperm activation and movement in spotted [...] Read more.

Sperm activation and movement are pivotal determinants of fertilization success in teleosts, yet the molecular mechanisms in euryhaline species remain largely unresolved. Here, we integrated physiology and multi-omics to elucidate the osmolality, ions, and regulatory networks underlying sperm activation and movement in spotted seabass (Lateolabrax maculatus). Spotted seabass sperm showed strong motility across a broad osmotic range of 500 to 1200 mOsm/kg, with Na⁺ and K⁺ promoting motility and Ca²⁺ exerting inhibitory effects. Integrated transcriptomics and proteomics identified 29 genes and 6 proteins as candidate molecules associated with Na⁺ and K⁺ signaling, Ca²⁺ signaling and apoptosis, and energy metabolism. Up-regulation of NHE1 suggested a potential involvement of Na⁺/H⁺ exchange that regulated Na⁺ influx, while K⁺ influx via activated K⁺ channels may depolarize membrane potential. The capn1 was up-regulated, which may be associated with Ca²⁺-mediated apoptosis. Euryhaline fishes exhibited a broader osmotic activation range than freshwater and marine species, underscoring the critical roles of osmotic adaptability in fish sperm physiology. Ionic regulation patterns of euryhaline fishes are generally consistent with their environmental adaptation, with seawater-adapted species resembling marine fishes and freshwater-adapted species resembling freshwater fishes. Our findings highlight the integrated roles of osmotic effects and ionic regulation, providing insights into sperm activation and movement in euryhaline spotted seabass. Full article

(This article belongs to the Special Issue Vertebrate Comparative Genomics)

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16 pages, 3354 KB

Open AccessArticle

The Involvement of Melatonin in the Dimorphism of Glucose and Lipid Metabolism of Tilapia

by Jingkai Qin, Chenguang Liu, Zongzhen Liao, Yang Yu, Caiyun Sun and Wensheng Li

Biomolecules 2026, 16(1), 15; https://doi.org/10.3390/biom16010015 - 21 Dec 2025

Cited by 1 | Viewed by 653

Abstract

In tilapia, males grow faster than females, but the metabolites/pathways behind this sexual dimorphism remain unclear. In this study, we first examined growth, feeding, serum biochemical parameters, and mRNA expression in tilapia under mono-sex and mixed-sex cultures. Tilapia raised mono-sexually grow faster than [...] Read more.

In tilapia, males grow faster than females, but the metabolites/pathways behind this sexual dimorphism remain unclear. In this study, we first examined growth, feeding, serum biochemical parameters, and mRNA expression in tilapia under mono-sex and mixed-sex cultures. Tilapia raised mono-sexually grow faster than those raised in mixed-sex environments. We conducted a combined analysis of the gas chromatography–mass spectrometry (GC-MS)-based metabolome and digital gene expression (DGE) profile in the livers of immature and mature tilapia, with special reference to the sexual differences. The glucose and lipid metabolism pathways exhibited significant sexual dimorphism. The concentrations of melatonin, oxoadipate, and glucuronic acid in the tryptophan metabolism pathway showed sexual differences. Melatonin implantation inhibited food intake and growth in tilapia and impacted their glucose and lipid metabolism. After melatonin implantation, the glucose tolerance of tilapia improved, especially in females. This study generates comprehensive data elucidating the mechanisms underlying sexual dimorphism in glucose and lipid metabolism and establishes a reliable scientific basis for investigating the role of melatonin in the sexual dimorphism of tilapia. Full article

(This article belongs to the Special Issue Vertebrate Comparative Genomics)

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19 pages, 3536 KB

Open AccessArticle

Molecular Characterization and Nutritional Regulation of Two Fatty Acid Elongase (elovl8) Genes in Chinese Perch (Siniperca chuatsi)

by Yu He, Zhengyong Wen, Luo Zhou, Wanhong Zeng, Panita Prathomya, Tilin Yi and Qiong Shi

Biomolecules 2025, 15(4), 567; https://doi.org/10.3390/biom15040567 - 11 Apr 2025

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Abstract

Proteins for elongation of very long-chain fatty acids (ELOVLs) are critical for the synthesis of long-chain polyunsaturated fatty acids (LC-PUFAs), and they are one group of the rate-limiting enzymes responsible for the initial condensation reaction within the fatty acid elongation. Elovl8 is a [...] Read more.

Proteins for elongation of very long-chain fatty acids (ELOVLs) are critical for the synthesis of long-chain polyunsaturated fatty acids (LC-PUFAs), and they are one group of the rate-limiting enzymes responsible for the initial condensation reaction within the fatty acid elongation. Elovl8 is a newly identified member of the ELOVL protein family, and its evolutionary and functional characterizations are still rarely reported. Here, we identified two elovl8 paralogues (named Scelovl8 and Scelovl8b) from Chinese perch (Siniperca chuatsi), and then their molecular and evolutionary characteristics, as well as potential roles involved in LC-PUFA biosynthesis, were examined. The ORFs of both Scelovl8a and Scelovl8b genes were 810 bp and 789 bp in length, encoding proteins of 270 and 263 amino acids, respectively. Multiple protein sequence comparisons indicated that elovl8 genes were highly conserved in teleosts, showing similar structural function domains. Meanwhile, phylogenetic analysis showed that the elovl8 gene family was clustered into two subclades of elovl8a and elovl8b, and Scelovl8a and Scelovl8b shared close relationships with banded archerfish elovl8a and striped bass elovl8b, respectively. Genetic synteny and gene structure analyses further confirmed that elovl8b is more conserved in comparison to elovl8a in teleosts. In addition, Scelovl8a was found to be highly expressed in the liver, while Scelovl8b was most abundant in the gills. Long-term food deprivation and refeeding are verified to regulate the transcription of Scelovl8a and Scelovl8b, and intraperitoneal injection of fish oil (FO) and vegetable oil (VO) significantly modified their gene expression as well. In summary, our results in this study indicate that elovl8 genes were conservatively unique to teleosts, and both elovl8 genes might be involved in the endogenous biosynthesis of LC-PUFAs in Chinese perch. These findings not only expand our knowledge on the evolutionary and functional characteristics of both elovl8 genes but also lay a solid basis for investigating regulatory mechanisms of LC-PUFA biosynthesis in various teleosts. Full article

(This article belongs to the Special Issue Vertebrate Comparative Genomics)

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Review

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44 pages, 13101 KB

Open AccessReview

Neural Melanocortin Receptors in Fish: Insights into Growth Regulation and Aquaculture Advancement

by Ren-Lei Ji and Ya-Xiong Tao

Biomolecules 2026, 16(6), 839; https://doi.org/10.3390/biom16060839 - 8 Jun 2026

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Abstract

Understanding and regulating fish growth is vital for the economic sustainability of aquaculture. The melanocortin-3 and -4 receptors (MC3R/MC4R, known as neural MCRs), integral components of the leptin–melanocortin circuit, play crucial roles in vertebrate energy homeostasis and growth. Abnormal neural MCR signaling contributes [...] Read more.

Understanding and regulating fish growth is vital for the economic sustainability of aquaculture. The melanocortin-3 and -4 receptors (MC3R/MC4R, known as neural MCRs), integral components of the leptin–melanocortin circuit, play crucial roles in vertebrate energy homeostasis and growth. Abnormal neural MCR signaling contributes to human obesity. In teleosts, Mc4r was first comprehensively studied in goldfish in 2003. Since then, Mc4r has been characterized in various teleosts. Genetic and pharmacological reduction of neural Mcr signaling can increase feeding or growth in several fish models, although its aquaculture value must be evaluated using production endpoints such as feed conversion, body composition, reproduction, welfare, and biosafety. Furthermore, neural Mcrs also play a role in modulating reproductive processes and sexual function in teleosts. This review systematically examines recent progress on the roles of fish neural Mcrs, offering an overview of basic molecular characteristics, tissue distribution, and pharmacology. Physiological roles and mechanisms in growth regulation are reviewed. Finally, the potential and limitations of targeting neural Mcrs for aquaculture-relevant traits are discussed. This work contributes to our understanding of the evolution of energy homeostasis regulation in vertebrates, providing a foundation for healthier and more efficient aquaculture practices. Full article

(This article belongs to the Special Issue Vertebrate Comparative Genomics)

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