Animal Molecular Breeding 2025, Vol.15, No.1 http://animalscipublisher.com/index.php/amb © 2025 AnimalSci Publisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved.
Animal Molecular Breeding 2025, Vol.15, No.1 http://animalscipublisher.com/index.php/amb © 2025 AnimalSci Publisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved. Publisher AnimalSci Publisher Editedby Editorial Team of Animal Molecular Breeding Email: edit@amb.animalscipublisher.com Website: http://animalscipublisher.com/index.php/amb Address: 11388 Stevenston Hwy, PO Box 96016, Richmond, V7A 5J5, British Columbia Canada Animal Molecular Breeding (ISSN 1927-5609) is an open access, peer reviewed journal published online by AnimalSci Publisher. The journal is publishing all the latest and outstanding research articles, letters and reviews in all areas of animal molecular breeding, containing transgenic breeding and marker assisted breeding, particularly publishing innovative research findings in the basic and applied fields of molecular genetics and novel techniques for improvement, applications of molecular enhanced products, as well as the significant evaluation of their related application field. AnimalSci Publisher is an international Open Access publisher specializing in animal molecular breeding, including genetics, breeding, as well as the related field registered at the publishing platform that is operated by Sophia Publishing Group (SPG), founded in British Columbia of Canada. All the articles published in Animal Molecular Breeding are Open Access, and are distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. AnimalSci Publisher uses CrossCheck service to identify academic plagiarism through the world’s leading plagiarism prevention tool, iParadigms, and to protect the original authors’ copyrights.
Animal Molecular Breeding (online), 2025, Vol. 15, No.1 ISSN 1927-5609 http://animalscipublisher.com/index.php/amb © 2025 AnimalSci Publisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved. Latest Content The Genetic Basis of High-Altitude Adaptation in Goats Insights from CRISPR-Based Functional Genomics Jingya Li, Mengyue Chen Animal Molecular Breeding, 2025, Vol. 15, No. 1, 1-8 Meta Analysis of Growth Traits in Tilapia and Strategies for Genetic Improvement Wenying Hong, Rudi Mai Animal Molecular Breeding, 2025, Vol. 15, No. 1, 9-18 Genetic Mechanisms and Evolutionary Trajectories of Goose Domestication Yanlin Wang, Jia Xuan Animal Molecular Breeding, 2025, Vol. 15, No. 1, 19-28 Review of Nutritional Requirements in Chickens: Optimizing Feed Formulation for Growth and Health Jing He, Jun Li Animal Molecular Breeding, 2025, Vol. 15, No. 1, 29-38 Behavioral Genetics in Canids: A Comparative Study of Wolves, Coyotes, and Dogs Hongbo Liang, Qibin Xu Animal Molecular Breeding, 2025, Vol. 15, No. 1, 39-48
Animal Molecular Breeding, 2025, Vol.15, No.1, 1-8 http://animalscipublisher.com/index.php/amb 1 Research Insight Open Access The Genetic Basis of High-Altitude Adaptation in Goats Insights from CRISPR-Based Functional Genomics Jingya Li, Mengyue Chen Animal Science Research Center, Cuixi Academy of Biotechnology, Zhuji, 311800, Zhejiang, China Corresponding author: mengyue.chen@cuixi.org Animal Molecular Breeding, 2025, Vol.15, No.1 doi: 10.5376/amb.2025.15.0001 Received: 10 Dec., 2024 Accepted: 15 Jan., 2025 Published: 26 Jan., 2025 Copyright © 2025 Li and Chen, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Li J.Y., and Chen M.Y., 2025, The genetic basis of high-altitude adaptation in goats insights from CRISPR-based functional genomics, Animal Molecular Breeding, 15(1): 1-8 (doi: 10.5376/amb.2025.15.0001) Abstract Goats are precious livestock in mountainous regions, subjected to environmental stresses such as hypoxia, cold stress, and excessive ultraviolet radiation. Elucidation of the genetic mechanism of their adaptation to high altitude is needed if molecular breeding and production performance are to be improved under extreme conditions. This study summarizes the physiological characteristics of high-altitude goats including adaptive respiratory, circulatory, immune, and reproductive system adaptation; advances in the identification of candidate adaptive genes by genome-wide association and selective sweep studies; and epigenetics and non-coding RNA functions in adaptive regulation. This study particularly targets using CRISPR/Cas9 technology to facilitate functional verification of key genes and multi-omics integration for the reconstruction of adaptive regulatory networks, and to probe the key molecular mechanisms essential for high-altitude survival such as the HIF signaling pathway and redox balance. The feasibility and limitations of using CRISPR technology in goat genetic innovation are examined for leads in future studies on adaptive breeding under suboptimal environments. Keywords Plateau adaptation; Goats; CRISPR/Cas9; Functional genomics; Hypoxia response 1 Introduction High-altitude plateaus, such as the Qinghai-Tibetan Plateau, possess severe environments with hypoxia, cold, intense ultraviolet radiation, and limited supply of forage. Resident animals, particularly goats, experience heavy physiological and genetic stresses from these environments. To survive these environments, goats developed particular adaptations like enhanced oxygen transport mechanisms, efficient metabolic pathways, and robust immunity. It is significant to appreciate these adaptations to improve livestock productivity and resilience in high-altitude regions (Li et al., 2023). Goats play a crucial role in livelihoods at the community level in high-altitude regions. They constitute a principal source of meat, milk, fiber, and cash income, especially where other forms of agriculture cannot be practiced (He et al., 2018). Economically, goats play a vital role in that they contribute meaningfully to family incomes as well as food security. Goats also assist in vegetation and land use management in a manner that results in sustainable agriculture. Their ability to survive on marginal soils makes them indispensable in the socioeconomic structure of plateau societies (Jin et al., 2020; Li et al., 2022). Investigating the genetic basis of high-altitude adaptation in goats is essential for breeding program development to enhance resilience and productivity. Advances in genome editing technologies, particularly CRISPR/Cas9, have revolutionized functional genomics research to date. CRISPR enables precise manipulation of target genes, making it possible to validate candidate genes associated with adaptation traits. Applying CRISPR technology to research goats may be fruitful in accelerating the breeding of animals with enhanced qualities for high-altitude ecosystems and hence increasing sustainable livestock production in such challenging ecosystems. 2 Adaptive Traits and Physiological Characteristics of Plateau Goats 2.1 Plateau-adapted changes in the respiratory and hematological systems Plateau goats such as the Tibetan cashmere goat have evolved specific respiratory and hematological adaptations to sustain themselves in hypoxic high-altitude environments. Genetic differentiation exists for key oxygen-sensing
Animal Molecular Breeding, 2025, Vol.15, No.1, 1-8 http://animalscipublisher.com/index.php/amb 2 genes, especially EPAS1, where a new missense mutation (Q579L) is overrepresented in high-altitude populations. This mutation is responsible for improved oxygen transportation and utilization, most likely resulting in increased red blood cell counts and hemoglobin content, which are of crucial importance in successful oxygen delivery under hypoxia (Song et al., 2016; Wang et al., 2016a). 2.2 Regulatory mechanisms of the cardiovascular and metabolic systems Genomic analyses show that metabolic regulation genes and cardiovascular development genes are under strong selection in plateau goats. Introgressed gene PAPSS2 of wild markhor is strongly correlated with adaptability at high altitude and includes hypoxia-related pathways. Other candidate genes, such as CDK2, SOCS2, NOXA1, and ENPEP, are implicated in adaptation to hypoxia, suggesting that cardiovascular and metabolic pathways are tightly regulated to maximize blood supply, vascular development, and metabolic efficiency during hypoxic stress(Song et al., 2016; Wang et al., 2016b; Li et al., 2022). 2.3 Immune system responses to plateau environments Adaptation to the harsh plateau environment also encompasses enhanced immune system function. Candidate genes such as CNGA4, Camk2b, and several interleukins (IL7, IL5, IL23A) have been implicated in enhanced immune response and protection from exogenous stressors. These genetic adaptations likely enhance resistance to pathogens and environmental stress, conferring overall health and viability in high-altitude regions. Additional immunity-associated genes and pathways, including the serpin cluster, INFGR1, and TLR2, have also been identified as targets of selection in plateau-adapted goat populations (Chen et al., 2020; Tian et al., 2021; Ghanatsaman et al., 2023). 2.4 Adaptive regulation in reproductive and developmental processes Reproductive and developmental flexibility in plateau goats is regulated by complex networks of mRNAs, miRNAs, and lncRNAs that mediate ovarian function and reproductive efficiency. These key pathways involve ovarian steroidogenesis, meiosis in oocytes, and amino acid biosynthesis, which are all linked to fertility and adaptive capacity. Such molecular networks regulate the development of germ cells and oocytes and interact with immune and metabolic processes to ensure reproductive success and plasticity in unfavorable environments (Lv et al., 2024). Such adaptations are vital for population viability and productivity under plateau conditions. 3 Research Progress on Plateau Adaptation-Related Genes in Goats 3.1 Identification and screening of candidate adaptive genes Exome sequencing and whole-genome sequencing are being used, along with high-density SNP chips, in recent research to identify candidate genes for high-altitude adaptation in goats. EPAS1, PAPSS2, LEPR, LDB1, EGFR, FGF2, ENPEP, SIRT6, and CDC42 are a few such genes that play a role in hypoxia response, cardiovascular development, and energy metabolism (Wang et al., 2016a; Song et al., 2016; Jin et al., 2020; Li et al., 2022). In addition, DSG3 was discovered to be a candidate hypoxia adaptation gene through targeted resequencing, which determined specific SNPs that distinguish highland and lowland populations (Kumar et al., 2018). Immune genes CNGA4 and Camk2b were also discovered to contribute to environmental defense and adaptation (Tian et al., 2021). 3.2 Findings from genome-wide association studies (GWAS) and selective sweep analyses GWAS and selective sweep analysis identified genomic regions under strong selection within arms length plateau goats. For example, a region spanning PAPSS2, introgressed from markhor, exhibits strong association with adaptation to high altitudes (Li et al., 2022). Selective sweep analysis also demonstrated that genes such as CDK2, SOCS2, NOXA1, and ENPEP are selected for hypoxia adaptation (Wang et al., 2016b). VEGF pathway and its genes (e.g., FGF2, EGFR, AKT1, PTEN, KDR) are highly enriched in high-altitude humans, validating their roles in vascular and metabolic adaptation (Jin et al., 2020). The findings provide a genetic basis for phenotypic disparity between highland and lowland breeds of goats.
Animal Molecular Breeding, 2025, Vol.15, No.1, 1-8 http://animalscipublisher.com/index.php/amb 3 3.3 Regulatory roles of epigenetics and non-coding RNAs in adaptation Epigenetic mechanisms, including RNA editing and non-coding RNAs, also play a role in adaptation to high altitudes. A-to-I and C-to-U types of RNA editing sites are variably distributed and expressed in plateau goats and affect genes involved in energy metabolism, translation, and immune response (Li et al., 2023). Multi-omics approaches have uncovered complex mRNA-miRNA-lncRNA networks that regulate ovarian function, reproductive performance, and adaptive capacity, linking reproductive traits to immune and metabolic adaptation (Lv et al., 2024). Such layers of regulation make genetic architecture of plateau adaptation complex. 3.4 Cross-species comparative analyses revealing conserved and specific adaptive mechanisms Comparative genomics of domestic mammals (e.g., goat, sheep, horse, cattle, pig, dog) is uncovering both species-specific and conserved adaptive pathways. The convergent positive selection of the EPAS1 gene in multiple high-altitude domestic mammals suggests an emergent genetic response to hypoxia (Song et al., 2016; Wu et al., 2019). However, cross-species comparisons also show that closely related species, such as goats and sheep, utilize different genetic pathways and candidate genes for local adaptation, thereby reflecting the set of evolutionary solutions to similar environmental pressures (Benjelloun et al., 2023) (Figure 1). It reflects both the universality as well as specificity of genetic adaptation to high-altitude environments. Figure 1 Patterns of allele frequencies variations for candidate variants along environmental gradients (Adopted from Benjelloun et al., 2023) Image caption: a: Examples for candidate variants related to altitude in sheep (upper charts) and rainfall seasonality in goats (lower charts). These two variables were chosen as examples. For each SNP, the variation profile of allele frequency (reduced centred values) is assigned to one of the following categories: linear variation, uniform with punctual shifts at one or both extremes of the gradient. The grey box-plots represent neutral variations of allelic frequencies for a set of random variants. b: Distribution of patterns of allele frequency variation for the different environmental variables for sheep (upper) and goats (lower). (Adopted from Benjelloun et al., 2023) 4 Functional Genomics Applications Based on CRISPR 4.1 Overview of CRISPR/Cas9 technology principles and advantages The CRISPR/Cas9 system is a powerful genome editing technique that enables targeted editing through the introduction of double-strand breaks at specific genomic sites, which are then repaired by cellular mechanisms. Its major advantages are high efficiency, versatility, ease of design, and the ability to generate both knockouts and
Animal Molecular Breeding, 2025, Vol.15, No.1, 1-8 http://animalscipublisher.com/index.php/amb 4 knock-ins. CRISPR/Cas9 has, in a relatively short period, become the dominant technology for genome editing in livestock, taking over from the earlier used ZFNs and TALENs, and has enabled precise genetic modifications for research and agricultural applications (Kalds et al., 2019; Yang, 2024). 4.2 Practical applications of CRISPR editing in goat somatic cells and embryos CRISPR/Cas9 has also been utilized to edit goat genomes successfully via both somatic cell nuclear transfer (SCNT) and direct embryo microinjection. Primary goat fetal fibroblast cells, for example, have been edited to knock in or knockout genes, and the edited cells have been used to generate live goats through SCNT (Wang et al., 2023). Cas9 mRNA and sgRNAs microinjection into zygotes has enabled effective generation of gene-edited goats, such as successful editing of MSTN and FGF5 genes, and demonstrated germline transmission of edited alleles (Wang et al., 2015; Wang et al., 2018; He et al., 2018). These techniques have been used to generate goats with enhanced production traits and altered milk composition (Li et al., 2024; Singh, 2024; Zhu et al., 2025). This technique employs the CSN2 promoter to enable the specific expression of HNP1 in the mammary gland and then convert it into an antimicrobial peptide-producing bioreactor. Our research not only confirms the feasibility of generating HNP1-expressing goats but also lays a basis for the generation of novel, high-quality dairy foods using CRISPR/Cas9 technology in goats. Moreover, it indicates the promise of CRISPR/Cas9 as a valuable tool for genetic engineering in this animal (Figure 2) (Li et al., 2024). Figure 2 Cas9-mediated HNP1 knock-in in goats at the CSN2locus (Adopted from Li et al., 2024) 4.3 Case studies of functional validation of candidate plateau adaptive genes Functional verification using CRISPR/Cas9 has targeted genes with proven or postulated roles in adaptation and production. MSTN gene knockout, for example, has resulted in goats with increased body mass and muscle fiber diameter, confirming the function of the gene in muscle growth and metabolism (He et al., 2018; Wang et al., 2018). Simultaneously, knockout and knock-in technologies have been utilized to knock in exogenous genes (e.g., fat-1, rhBChE) into specific loci and knockout endogenous genes, demonstrating the feasibility of complex genome editing in goats (Zhang et al., 2018; Wang et al., 2023). These results provide direct evidence of gene function and form the basis for plateau adaptation-related gene validation (Xuan, 2024).
Animal Molecular Breeding, 2025, Vol.15, No.1, 1-8 http://animalscipublisher.com/index.php/amb 5 4.4 Reconstruction of regulatory networks via integration with transcriptomics, metabolomics, and other omics Coupling CRISPR-enabled functional genomics with transcriptomics, metabolomics, and other omics tools enables the reconstruction of regulatory networks underlying adaptive phenotypes. For instance, goats that have been edited for specific genes can be compared for gene expression, protein profiles, and metabolic pathways to decipher the downstream effect of specific genetic changes (Kalds et al., 2019). This systems-level approach facilitates worldwide mapping of gene function and interaction, and thus the recognition of chief regulators and pathways that shape high-altitude adaptation and additional complex traits. 5 Molecular Mechanisms of Plateau Adaptation in Goats 5.1 Central role of the HIF pathway in hypoxia response The hypoxia-inducible factor (HIF) pathway is key to goat adaptation to the high-altitude hypoxic environment. EPAS1 is a gene encoding for an essential element of the HIF pathway that shows strong selection and enrichment in high-altitude goats. A missense mutation (Q579L) of EPAS1, which is located near the HIF-1 domain, is uniquely found in high-altitude goats and highlights its central role in oxygen sensing and hypoxia adaptation (Song et al., 2016; Wu et al., 2019). In addition, the PAPSS2 gene identified by GWAS and function analysis participates in hypoxia pathways and further indicates the importance of the HIF pathway in plateau adaptation (Li et al., 2022). 5.2 Coordinated regulation of energy metabolism and redox systems Goat high-altitude adaptation requires the coordinated control of energy metabolism and redox balance. RNA editing research indicates that those genes that possess population-specific editing sites are functionally engaged in ATP binding, translation, and adaptive immune response, all of which are particularly important for energy metabolism during hypoxic stress (Li et al., 2023). Genes such as FGF2, EGFR, AKT1, PTEN, SIRT6, and CDC42, which are enriched in the VEGF pathway, also function in the regulation of metabolism and vascular adaptation to secure efficient energy utilization and redox homeostasis during plateau life (Jin et al., 2020). 5.3 Involvement of stress proteins and apoptosis mechanisms Mechanisms of apoptosis and stress proteins are involved in the cellular response to high-altitude stress. Functional analysis indicates that the genes involved in cellular stress responses, such as protein folding and apoptosis regulation, are under selection in plateau goats. For example, the DSG3 gene, by its specific non-synonymous mutations in high-altitude populations, can participate in cellular hypoxic stress tolerance and regulate apoptosis pathways for survival in extreme environments (Kumar et al., 2018). The regulation of stress and apoptotic responses can be further brought about by RNA editing events targeting protein products (Li et al., 2023). 5.4 The relationship between plateau adaptation and developmental program regulation Developmental program regulation is directly linked to plateau adaptation in goats. Multi-omics investigations have identified mRNA-miRNA-lncRNA networks that regulate ovarian function, reproductive performance, and developmental processes. They influence germ cell and oocyte development and are enriched in steroidogenesis, meiosis, and amino acid biosynthesis pathways needed for reproductive success and adaptive capacity (Lv et al., 2024). The integration of developmental regulation with immune and metabolic pathways underscores the complex molecular basis of plateau adaptation in goats (Liu et al., 2025). 6 Prospects and Challenges in the Application of CRISPR Technology 6.1 Technical optimization: off-target effects and editing efficiency issues CRISPR/Cas9 technology has made it possible to efficiently edit genes in goats, but there are issues with off-target effects and editing efficiency. Despite very high mutation rates and successful knockouts of genes, e.g., in MSTN and FGF5 genes, the success of precise knock-in events (e.g., homologous recombination) is still low, and off-target mutations must be closely followed and maintained very low to be safe and reliable for use in breeding (Wang et al., 2015; Wang et al., 2023; Lu et al., 2024). Optimization strategies include improving
Animal Molecular Breeding, 2025, Vol.15, No.1, 1-8 http://animalscipublisher.com/index.php/amb 6 transfection systems, maximizing homology arm lengths, and exhaustive screening for off-target events (Bertolini et al., 2018; Wang et al., 2023). 6.2 Limitations in model construction and ethical supervision Even with the ease of how CRISPR/Cas9 has made it possible to generate gene-edited goats for both agricultural applications and biomedical investigation, constructing strong large-animal models is complex. Issues such as mosaicism, variable editing efficiency, and health issues in edited animals (e.g., MSTN knockout-induced abnormal growth or risk to health) highlight the need for strong model verification and prolonged observation (Guo et al., 2016). In addition, there needs to be ethical regulation, considering that gene editing livestock raises animal welfare, environmental impact, and food safety concerns demanding stringent regulatory frameworks (Lu et al., 2024). 6.3 Integration trends of high-throughput screening and single-cell editing technologies New directions in CRISPR research include the merging of high-throughput screening and single-cell editing technology. Such approaches enable systematic identification of functional genes and regulatory factors at scale, as well as cellular heterogeneity dissection in gene-edited populations. Such integration is expected to accelerate the discovery of adaptive genes and pathways, improve precision editing, and assist in developing more sophisticated breeding schemes (Kalds et al., 2019; Lu et al., 2024). 6.4 Strategic considerations for applying CRISPR to goat germplasm innovation and plateau breeding For breeding for adaptability to plateaus and germplasm innovation, CRISPR/Cas9 can potentially introduce or enhance favorable genes, such as enhanced muscle development, fiber quality, or disease resistance (Wang et al., 2016; He et al., 2018; Wang et al., 2018). Strategic implementation includes technical feasibility, stability of traits, and biosafety and ensuring the heritability of edited alleles and the absence of unintended effects (Wang et al., 2016; Wang et al., 2018; Wang et al., 2023). Continuous research, ethical management, and coordination with omics information will be necessary for effective and responsible application of CRISPR technology in goat breeding programs (Zhong et al., 2023).. 7 Concluding Remarks Recent genetic research has significantly enhanced understanding of plateau adaptation in goats. Genome-wide examinations have identified numerous genes and pathways, such as EPAS1, PAPSS2, LEPR, FGF2, and others, which are strongly associated with hypoxia response, cardiovascular development, and high-altitude energy metabolism. Introgression of wild species, such as the markhor, has also contributed adaptive alleles (e.g., PAPSS2) to Tibetan goats for enhancing survival under severe conditions. Functional studies and expression profiling have validated the physiological adaptation functions of these genes, though other candidate immune response and stress response genes have also been discovered. Even so, several research gaps and technical constraints still remain. For most candidate genes, functional verification is still in its infancy, and the molecular mechanisms underlying complex traits like hypoxia tolerance and immune adaptation are not yet well elucidated. Additional more comprehensive integration of multi-omics data (e.g., transcriptomics, metabolomics, epigenomics) is also needed to comprehensively reconstruct adaptive regulatory networks. Technical hurdles are improving the specificity and efficacy of the gene editing reagents, reducing off-target effects, and developing efficient large-animal models for functional analysis. The CRISPR technology possesses vast possibilities for accelerating innovation in plateau-adapted goat germplasm. By enabling precise editing of adaptive genes, CRISPR possesses the ability to facilitate the introduction or enhancement of traits such as tolerance to hypoxia, resistance to disease, and improved production traits. Future studies should focus on refining gene editing protocols through integrating high-throughput screening and single-cell technologies and following ethical and biosafety standards. Strategic application of CRISPR, supported by advanced genomic knowledge, will facilitate sustainable breeding and conservation of high-altitude adaptable goats.
Animal Molecular Breeding, 2025, Vol.15, No.1, 1-8 http://animalscipublisher.com/index.php/amb 7 Acknowledgments We thank the Animal Disease Research team for support and assistance in data acquisition and data collection. Conflict of Interest Disclosure The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest. 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Animal Molecular Breeding, 2025, Vol.15, No.1, 9-18 http://animalscipublisher.com/index.php/amb 9 Meta Analysis Open Access Meta Analysis of Growth Traits in Tilapia and Strategies for Genetic Improvement Wenying Hong, Rudi Mai Tropical Bioresources Research Center, Hainan Tropical Agricultural Resources Research Institute, Sanya, 572025, Hainan, China Corresponding author: rudi.mai@hitar.org Animal Molecular Breeding, 2025, Vol.15, No.1 doi: 10.5376/amb.2025.15.0002 Received: 15 Dec., 2024 Accepted: 17 Jan., 2025 Published: 30 Jan., 2025 Copyright © 2025 Hong and Mai, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Hong W.Y., and Mai R.D., 2025, Meta analysis of growth traits in tilapia and strategies for genetic improvement, Animal Molecular Breeding, 15(1): 9-18 (doi: 10.5376/amb.2025.15.0002) Abstract This study explored the analysis of the growth characteristics of the Nile tilapia (Oreochromis niloticus), covering core indicators such as body size parameters, growth rate, feed conversion efficiency (FCR), and sexual maturity regulation. The core growth traits show the characteristics of medium to high intensity of heritability. There is a significant genetic correlation among the traits, and they are significantly regulated by the aquaculture environment. Key genetic regulatory elements - including QTL hotspots and functional genes such as IGF1, growth hormone (GH), and myostatin (MSTN) - have been confirmed to dominate the growth regulatory network. The application value of conventional techniques such as family selection and interspecific hybridization, as well as modern biotechnologies such as molecular marker-assisted selection (MAS) and whole-genome selection (GS). Although MAS and GS technologies have the advantages of precision and efficiency, the practical application of gene editing tools requires the establishment of standardized processes for ecological risk assessment and commercial promotion. It is further emphasized that building a cross-border genetic data collaboration platform and a joint breeding network is of strategic significance for achieving the scale effect of tilapia genetic improvement and the development of an eco-friendly industry. Keywords Nile tilapia (Oreochromis niloticus); Growth traits; Genetic improvement; Meta-analysis; Genomic selection 1 Introduction Oreochromis niloticus, as a major species in global aquaculture, has achieved large-scale farming in more than 130 countries and regions and occupies an important position in freshwater fishery (Herkenhoff et al., 2020; Yanez et al., 2020). This species has become an important biological resource for ensuring the supply of aquatic products due to its strong adaptability, short growth cycle and high market acceptance. In aquaculture practice, key traits such as body type parameters, body weight indicators and muscle content directly affect the aquaculture benefits and industrial economic returns (Thodesen et al., 2013; He et al., 2017; Yoshida et al., 2019). Shortening the breeding cycle can not only increase the annual output, but also significantly increase the economic income of practitioners (Thodesen et al., 2013; Yoshida et al., 2019; Robisalmi et al., 2023). Therefore, enhancing these traits through genetic improvement remains the core objective of current tilapia breeding (Thodesen et al., 2013; Yoshida et al., 2019; Yanez et al., 2020). This study focuses on the genetic improvement technology system of tilapia. Although traditional breeding and new biotechnologies have been implemented for many years, the molecular regulatory network of its growth and development has not been fully elucidated. Although conventional breeding has achieved genetic gain, new technologies such as genomic selection and gene marker-assisted breeding are revolutionizing the traditional model and are expected to accelerate the process of genetic improvement. At present, it is urgently necessary to systematically sort out the relevant research progress, integrate effective technical paths, and provide theoretical support for cultivating excellent strains that take into account both ecological benefits and high-yield characteristics. Through systematic analysis of existing genetic research, it is helpful to summarize successful experiences, optimize breeding plans, and ultimately achieve efficient genetic improvement of tilapia growth traits.
Animal Molecular Breeding, 2025, Vol.15, No.1, 9-18 http://animalscipublisher.com/index.php/amb 10 2 The Growth Characteristics of Nile Tilapia 2.1 Key growth parameters: body weight, body length and specific growth rate Body weight, body length and specific growth rate (SGR) are key indicators for evaluating the growth performance of Nile tilapia. These parameters are listed as routine observation indicators in scientific research and aquaculture management, and are used to test the effectiveness of nutrition programs, genetic improvement and breeding strategies. Kamble et al. (2024) found that supplementing guava leaves and currant extracts in the feed could increase the body length growth rate of fish by 23% and the daily weight gain rate by 18%, verifying the effectiveness of the nutritional regulation strategy. Integrated analysis indicates that plant essential oil additives can increase the terminal body length by 15%~20% and significantly enhance the SGR value, highlighting their crucial role in growth assessment (Orzuna-Orzuna and Granados-Rivera, 2024). Gene editing technology has a significant regulatory effect on the above indicators. The group modified by myostatin gene had a 49.45% increase in body weight compared with the control group, and the body length increased by 12%~15% simultaneously with SGR, confirming the targeted improvement ability of genetic engineering on growth traits (Figure 1) (Wu et al., 2022). Statistical analysis showed a strong correlation between body length and body weight (r=0.89), emphasizing the necessity of multi-trait collaborative breeding (Kamble et al., 2024). Figure 1 The morphological and growth alterations in mstnb / tilapia compared with their wild type (WT) siblings at 5 mah (Adopted from Wu et al., 2022) Image caption: (A) Photos of WT and mstnb KO tilapia at 5 mah. (B) The average body weights of tilapia with different genotypes at 2 mah and 5 mah. Comparison of the average body lengths (C), body heights (D) and body widths (E) between mstnb+/+and mstnb/tilapia at 5 mah. Data are shown as mean ± SD. *p<0.05. mah, months after hatching (Adopted from Wu et al., 2022) 2.2 Feed conversion efficiency and sexual maturity regulation Feed conversion rate (FCR) is a core efficiency parameter for measuring the conversion of feed nutrients into biomass in fish. A lower FCR value indicates a better nutrient conversion efficiency. Studies have shown that nano-phosphorus complexes and plant essential oil additives can reduce FCR by 0.3~0.5, simultaneously shorten
Animal Molecular Breeding, 2025, Vol.15, No.1, 9-18 http://animalscipublisher.com/index.php/amb 11 the breeding cycle and improve economic benefits (Elamawy et al., 2023; Orzuna-Orzuna and Granados-Rivera, 2024). Feeding experiments on β -glucan have shown that optimizing FCR can not only increase the weight gain rate, but also enhance the immune function, especially with significant effects in high-density intensive farming (Dawood et al., 2020). The time of sexual maturity has a regulatory effect on aquaculture output. Premature sexual maturity will prompt the distribution of energy to the reproductive system, resulting in a decline in the size of commercial fish. Molecular biological evidence indicates that targeted gene editing (such as myostatin gene knockout) can simultaneously regulate the growth trajectory and sexual maturity nodes, and the improvement effect is particularly prominent in the male population (Wu et al., 2022). Precise regulation of these traits plays a crucial role in achieving a balance between breeding benefits and market specification demands. 2.3 Genetic correlations among growth traits Significant genetic correlations often exist among growth traits in Nile tilapia, meaning that selection for one trait can lead to correlated responses in others. For example, high heritability estimates for body weight and strong genetic correlations between weight measured at different ages and across various farming systems suggest that genetic improvement for one growth trait can simultaneously enhance others (Turra et al., 2016). This is supported by findings that the genetic correlation between body weight at 168 days in different rearing systems is very high, indicating that selection for growth in one environment is likely to be effective across multiple production systems. Molecular and transcriptomic analyses further reveal that key metabolic and hormonal pathways, such as the GH/IGF axis and myostatin regulation, jointly influence multiple growth-related traits (Herkenhoff et al., 2020; Wu et al., 2022). These interconnected pathways suggest that genetic selection targeting one growth trait may have beneficial effects on others, reinforcing the importance of considering genetic correlations in breeding strategies for Nile tilapia. 3 Comprehensive Statistical Analysis Methods 3.1 Establishment of research screening criteria Systematic integrated analysis requires the formulation of clear literature screening criteria to ensure the quality of research and the relevance of the topic. Take the PRISMA guidelines as an example. This framework has been widely used in the research screening process, such as the review study on plant-based feed additives for tilapia. Eventually, 45 literatures that met the requirements were selected for in-depth analysis (Orzuna-Orzuna and Granados-Rivera, 2024; Zhao et al., 2024). The screening dimensions mainly include the research subjects (limited Nile tilapia), target traits (such as growth parameters, feed efficiency), experimental design norms and the completeness of quantitative data to ensure the comparability of data across studies. The standardized data collection process plays an important role in reducing systematic errors. The core recording elements cover the experimental group Settings, aquaculture environment parameters, trait determination values and statistical indicators. By strictly implementing these norms, researchers can construct a high-confidence database and thereby accurately analyze the association rules between genetic factors and phenotypic characteristics (Orzuna-Orzuna and Granados-Rivera, 2024). 3.2 Random effects model for genetic parameter estimation The use of the random effects model can effectively solve the influence of heterogeneity among studies on the results. Typical applications such as the Der-Simonian-Laird algorithm effectively correct the natural variations caused by different biological samples and experimental conditions by calculating the weighted average and the confidence interval of the effect size (Orzuna-Orzuna and Granados-Rivera, 2024). This method provides universal conclusions for revealing the genetic laws and trait association mechanisms of tilapia. In the field of genetic assessment, random regression analysis models (RRM) and multiple mixed effects models (MRRM) are widely used in the dynamic analysis of growth traits (He et al., 2017; He et al., 2018). These models
Animal Molecular Breeding, 2025, Vol.15, No.1, 9-18 http://animalscipublisher.com/index.php/amb 12 use the covariance matrix to quantify the time-cumulative effect of genetic effects and precisely describe the genetic regulatory characteristics of the growth process. Such methods significantly enhance the credibility of the integrated analysis results of aquatic genetics (He et al., 2017; He et al., 2018; Orzuna-Orzuna and Granados-Rivera, 2024). 3.3 Inter-study difference regulation and bias assessment Regulating the heterogeneity among studies is the core link to ensure the reliability of the conclusion. By using subgroup analysis, integrated regression model and sensitivity test method, the root cause of data variation can be effectively traced. This strategy has received empirical support in the study of the association between nutritional intervention and growth (Orzuna-Orzuna and Granos-Rivera, 2024). These methods can clearly distinguish the interference of biological essential differences and experimental operation errors on research conclusions. Publication bias assessment is of decisive significance for the objectivity of research, as positive results tend to be published first. Through the combination of funnel plot - Iger test techniques, such biases can be systematically identified and corrected to ensure that the conclusions cover all valid data (Orzuna-Orzuna and Granados-Rivera, 2024). By synergistically regulating data heterogeneity and reporting bias, the study can provide multi-dimensional theoretical support for the genetic improvement strategy of tilapia (Zhao and Jin, 2024). 4 Main Research Conclusions 4.1 Analysis of the heritability level of growth traits The main growth traits of tilapia (including body size specifications, body length indicators and growth rate) generally show moderate to high genetic characteristics in different aquaculture systems. Studies on freshwater and brackish water aquaculture systems have shown that the heritability estimates of harvest weight, standard body length and average daily growth rate are concentrated in the range of 0.35~0.50, confirming significant genetic regulatory effects and selective breeding responses (Setyawan et al., 2022). The evaluation data of different breeding models (recirculating water, ecological ponds, cages) indicate that the genetic capacity of body weight at 168 days of age can reach 0.62~0.84, further verifying the genetic gain potential of targeted breeding (Turra et al., 2016). This pattern is universal across different strains. Even taking into account the interaction between genes and environment, the weight heritability is steadily distributed within the range of 0.32~0.62 (Thỏa et al., 2016). These high heritability traits suggest that precision breeding can significantly increase the rate of genetic progression, making these traits core targets for optimizing breeding efficiency (Trọng et al., 2013; Thỏa et al., 2016). 4.2 Genetic correlation characteristics among traits The strong genetic correlation among growth traits indicates that the genetic improvement of a single trait may produce a synergistic effect. For instance, harvest weight showed a high genetic correlation of 0.89~0.98 with body length and height, suggesting that larger-sized breeding could simultaneously improve overall body structure (Trọng et al., 2013). The genetic correlation between body weight and trunk length (>0.85) provides theoretical support for the combined breeding of multiple traits (Mourão et al., 2023). However, some traits show a negative association. Studies have shown that under specific breeding conditions, growth indicators such as body weight have a negative genetic correlation with head size, suggesting that rapid growth may inhibit head development (Mourão et al., 2023). Although growth rate is positively correlated with body mass score, the pursuit of weight gain alone may not improve overall health, highlighting the necessity of multitrait balanced breeding (Trọng et al., 2013; LaFrentz et al., 2020). 4.3 The regulatory role of the environment on genetic expression The aquaculture environment significantly regulates the expression intensity of genes on growth traits and affects the evaluation results of genetic parameters. Analysis based on response norms indicates that the heritability of growth traits in different environmental systems can vary by up to 300%, and some genetic correlations even drop
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