Aeromonas hydrophila infection is one of the key factors limiting tilapia production, and antibiotics play important roles in the control of diseases. This study evaluated the effectiveness of florfenicol (FFC) when administered orally at the therapeutic dose of 15 mg/kg fish biomass/day for 10 days against A. hydrophila infection in Oreochromis niloticus in terms of survival, changes in haemato-biochemistry, erythrocyte morphology, and histoarchitecture of the vital organs. A. hydrophila was moderately virulent to tilapia with an LD50 of 1.15 × 107 cells/fish. When challenged, it caused systemic infection in fish. The challenged fish were lethargic, wandered around the corners, rested at the bottom, swam vertically, and darkly pigmented. The FFC therapy effectively reduced bacteria-induced mortalities and physiological stress as the measured haemato-biochemical parameters indicated. The histopathological findings suggested alterations in tissue architecture of the kidney and liver tissues, which improved in the treated fish. Erythrocytes of the challenged fish showed elongated, irregular-shaped, tear-drop-shaped, crenated, and hypochromic erythrocytes, ragged cytoplasmic membranes, vacuolation, hypertrophied nucleus, and eccentric nucleus. These morphological alterations were reduced with FFC therapy. Compared to the untreated group, the FFC treatment normalized the haemato-biochemical parameters, improved wound healing, and promoted fish recovery against bacterial infections. The results hinted at the effectiveness of FFC against A. hydrophila infection in O. niloticus juveniles at the therapeutic dose. However, care must be taken for its judicious aquacultural application to avoid its negative impacts on fish, the environment, and consumers.
{"title":"Haemato-biochemistry, erythromorphology, and histopathology of Oreochromis niloticus as influenced by Aeromonas hydrophila infection and florfenicol therapy","authors":"Joshi Sharon, Thangapalam Jawahar Abraham, Arya Sen, Ratnapriya Das, Priyanka Sinha, Satyanarayana Boda, Prasanna Kumar Patil","doi":"10.1002/aro2.100","DOIUrl":"https://doi.org/10.1002/aro2.100","url":null,"abstract":"<p><i>Aeromonas hydrophila</i> infection is one of the key factors limiting tilapia production, and antibiotics play important roles in the control of diseases. This study evaluated the effectiveness of florfenicol (FFC) when administered orally at the therapeutic dose of 15 mg/kg fish biomass/day for 10 days against <i>A. hydrophila</i> infection in <i>Oreochromis niloticus</i> in terms of survival, changes in haemato-biochemistry, erythrocyte morphology, and histoarchitecture of the vital organs. <i>A. hydrophila</i> was moderately virulent to tilapia with an LD<sub>50</sub> of 1.15 × 10<sup>7</sup> cells/fish. When challenged, it caused systemic infection in fish. The challenged fish were lethargic, wandered around the corners, rested at the bottom, swam vertically, and darkly pigmented. The FFC therapy effectively reduced bacteria-induced mortalities and physiological stress as the measured haemato-biochemical parameters indicated. The histopathological findings suggested alterations in tissue architecture of the kidney and liver tissues, which improved in the treated fish. Erythrocytes of the challenged fish showed elongated, irregular-shaped, tear-drop-shaped, crenated, and hypochromic erythrocytes, ragged cytoplasmic membranes, vacuolation, hypertrophied nucleus, and eccentric nucleus. These morphological alterations were reduced with FFC therapy. Compared to the untreated group, the FFC treatment normalized the haemato-biochemical parameters, improved wound healing, and promoted fish recovery against bacterial infections. The results hinted at the effectiveness of FFC against <i>A. hydrophila</i> infection in <i>O. niloticus</i> juveniles at the therapeutic dose. However, care must be taken for its judicious aquacultural application to avoid its negative impacts on fish, the environment, and consumers.</p>","PeriodicalId":100086,"journal":{"name":"Animal Research and One Health","volume":"3 1","pages":"54-70"},"PeriodicalIF":0.0,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aro2.100","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143489695","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
This review provides an in-depth analysis of vitamin E's multifaceted role in swine nutrition, incorporating both traditional insights and contemporary research. It begins with an exploration of vitamin E from an evolutionary perspective, followed by a detailed examination of its absorption, metabolism, and excretion in swine. The review emphasizes the micronutrient's critical functions in swine physiology, particularly its antioxidant properties and its emerging links to epigenetics, which include deoxyribonucleic acid methylation, histone modification, and noncoding ribonucleic acid regulation. The interactions of vitamin E with other dietary components are discussed, along with established nutritional requirements and current recommendations for supplementation. Additionally, the health benefits and performance improvements associated with vitamin E are presented, emphasizing its importance in immune function, growth, and meat quality. Despite extensive research, the review identifies gaps in understanding the bioavailability and long-term impacts of different vitamin E isoforms and supra-nutritional supplementation levels. It concludes with a discussion of research gaps and future directions, particularly the need for studies on the long-term effects of high-dose vitamin E supplementation and the influence of environmental factors on its metabolism. Through this comprehensive synthesis, this study aims to provide a holistic understanding of vitamin E's essential contributions to swine health and nutrition, with the goal of informing better dietary practices and enhancing swine productivity.
{"title":"The E-volution in swine nutrition: Current perspectives on vitamin E","authors":"Yauheni Shastak, Wolf Pelletier","doi":"10.1002/aro2.93","DOIUrl":"https://doi.org/10.1002/aro2.93","url":null,"abstract":"<p>This review provides an in-depth analysis of vitamin E's multifaceted role in swine nutrition, incorporating both traditional insights and contemporary research. It begins with an exploration of vitamin E from an evolutionary perspective, followed by a detailed examination of its absorption, metabolism, and excretion in swine. The review emphasizes the micronutrient's critical functions in swine physiology, particularly its antioxidant properties and its emerging links to epigenetics, which include deoxyribonucleic acid methylation, histone modification, and noncoding ribonucleic acid regulation. The interactions of vitamin E with other dietary components are discussed, along with established nutritional requirements and current recommendations for supplementation. Additionally, the health benefits and performance improvements associated with vitamin E are presented, emphasizing its importance in immune function, growth, and meat quality. Despite extensive research, the review identifies gaps in understanding the bioavailability and long-term impacts of different vitamin E isoforms and supra-nutritional supplementation levels. It concludes with a discussion of research gaps and future directions, particularly the need for studies on the long-term effects of high-dose vitamin E supplementation and the influence of environmental factors on its metabolism. Through this comprehensive synthesis, this study aims to provide a holistic understanding of vitamin E's essential contributions to swine health and nutrition, with the goal of informing better dietary practices and enhancing swine productivity.</p>","PeriodicalId":100086,"journal":{"name":"Animal Research and One Health","volume":"3 1","pages":"2-30"},"PeriodicalIF":0.0,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aro2.93","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143489844","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
<p>Animal-based products, such as meat, eggs, milk, and their by-products, serve as the predominant protein sources for humans and are vital for supporting physiological functions. Animal proteins align more closely with our nutritional requirements compared to plant-based proteins. With the ever-growing global population, the demand for these fundamental food sources is increasing. Globally, about 97.64 million tons of livestock products, including meat, eggs, and milk, are consumed annually, accounting for nearly 48% of all feed grain usage. Nevertheless, the livestock industry imposes a substantial environmental footprint, contributing to 57% of the total CO<sub>2</sub> emissions from food production. Amidst escalating resource limitations and evolving geopolitical dynamics, the security of our livestock food supply is in threat. To address these challenges, the livestock sector must prioritize high-quality growth through innovative scientific and technological breakthroughs.</p><p>Exceptional livestock and poultry breeds contribute over 40% to the advancement of the livestock industry and are instrumental in enhancing its productivity. The integration of biotechnology, information technology, and artificial intelligence is driving animal breeding into a more efficient and precise phase known as Animal Breeding 4.0. A new wave of high-efficiency breeding technologies, exemplified by genomic selection (GS), gene editing, and in vitro embryo production accelerates targeted animal breeding significantly by enhancing breeding efficiency and reducing the breeding cycle time. GS has been widely adopted for cattle, pig, and sheep breeding, cutting breeding costs by 90% and boosting the genetic progress of critical traits by 50%. The industrialization of genetically modified animals is gaining momentum and promises to offer competitive advantages over conventional breeding methods. Currently, several types of gene-edited animals have passed safety evaluations, including GalSafe, a gene-knockout pig approved by the U.S. FDA in 2020, gene-edited heat stress-resistant beef cattle approved by the U.S. FDA in 2022, and gene-edited tiger puffer-fish and red snapper approved by the Japanese Ministry of Health, Labor, and Welfare in 2021. With the progression of multi-omics technology, key trait-related functional genes in livestock and poultry are continually being uncovered. The application of novel biological breeding techniques is anticipated to generate more diverse livestock and poultry varieties with high-yield, high-quality, disease-resistant, and environmentally friendly phenotypes.</p><p>This special issue, entitled <i>Animal Biotech Breeding and Reproduction</i>, is designed to facilitate academic dialog in this special domain, fostering the convergence of significant insights, breakthroughs, technological advancements, and industrial growth in the areas of molecular breeding and reproduction. The scope is to accelerate the pace of scientific and t
{"title":"Animal biotech breeding and reproduction: A new engine for high-quality development of animal husbandry","authors":"Yong Zhang, Jun Liu","doi":"10.1002/aro2.84","DOIUrl":"https://doi.org/10.1002/aro2.84","url":null,"abstract":"<p>Animal-based products, such as meat, eggs, milk, and their by-products, serve as the predominant protein sources for humans and are vital for supporting physiological functions. Animal proteins align more closely with our nutritional requirements compared to plant-based proteins. With the ever-growing global population, the demand for these fundamental food sources is increasing. Globally, about 97.64 million tons of livestock products, including meat, eggs, and milk, are consumed annually, accounting for nearly 48% of all feed grain usage. Nevertheless, the livestock industry imposes a substantial environmental footprint, contributing to 57% of the total CO<sub>2</sub> emissions from food production. Amidst escalating resource limitations and evolving geopolitical dynamics, the security of our livestock food supply is in threat. To address these challenges, the livestock sector must prioritize high-quality growth through innovative scientific and technological breakthroughs.</p><p>Exceptional livestock and poultry breeds contribute over 40% to the advancement of the livestock industry and are instrumental in enhancing its productivity. The integration of biotechnology, information technology, and artificial intelligence is driving animal breeding into a more efficient and precise phase known as Animal Breeding 4.0. A new wave of high-efficiency breeding technologies, exemplified by genomic selection (GS), gene editing, and in vitro embryo production accelerates targeted animal breeding significantly by enhancing breeding efficiency and reducing the breeding cycle time. GS has been widely adopted for cattle, pig, and sheep breeding, cutting breeding costs by 90% and boosting the genetic progress of critical traits by 50%. The industrialization of genetically modified animals is gaining momentum and promises to offer competitive advantages over conventional breeding methods. Currently, several types of gene-edited animals have passed safety evaluations, including GalSafe, a gene-knockout pig approved by the U.S. FDA in 2020, gene-edited heat stress-resistant beef cattle approved by the U.S. FDA in 2022, and gene-edited tiger puffer-fish and red snapper approved by the Japanese Ministry of Health, Labor, and Welfare in 2021. With the progression of multi-omics technology, key trait-related functional genes in livestock and poultry are continually being uncovered. The application of novel biological breeding techniques is anticipated to generate more diverse livestock and poultry varieties with high-yield, high-quality, disease-resistant, and environmentally friendly phenotypes.</p><p>This special issue, entitled <i>Animal Biotech Breeding and Reproduction</i>, is designed to facilitate academic dialog in this special domain, fostering the convergence of significant insights, breakthroughs, technological advancements, and industrial growth in the areas of molecular breeding and reproduction. The scope is to accelerate the pace of scientific and t","PeriodicalId":100086,"journal":{"name":"Animal Research and One Health","volume":"2 4","pages":"354-355"},"PeriodicalIF":0.0,"publicationDate":"2024-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aro2.84","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142665105","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
To address the escalating challenge of food scarcity and the associated conflicts between human and animal consumption, it is imperative to seek alternative resources that can substitute for traditional feed. Non-grain feed (NGF) raw materials represent a category of biomass resources that are distinct from grains in their composition. These materials are characterized by their high nutritional content, cost-effectiveness, ample availability, and consistent supply, which contribute to their significant economic potential. Nonetheless, the extensive application of NGF is currently hindered by several limitations, including a high concentration of antinutritional factors, suboptimal palatability, and an offensive odor, among other shortcomings. The synergistic fermentation of probiotics and enzymes (SFPE) is an innovative approach that integrates the use of a diverse array of enzymes during the feed fermentation process, as well as various strains of probiotics throughout the feed digestion process. This method aims to enhance the nutritional value of the feed, diminish the presence of antinutritional factors, and improve the overall palatability, thereby facilitating the optimal utilization of NGF. This strategy holds the promise of not only replacing conventional feed options but also mitigating the pressing issue of grain scarcity. This paper delves into the practical applications of NGF and presents an overview of the latest research advancements in SFPE fermentation techniques, which can provide cutting-edge and valuable reference for researchers who devote themselves to research in this field in the future.
{"title":"Advancements in synergistic fermentation of probiotics and enzymes for non-grain feed raw materials","authors":"Xiangrong Deng, Kai Chen, Dahai Jiang, Liming Lu","doi":"10.1002/aro2.90","DOIUrl":"https://doi.org/10.1002/aro2.90","url":null,"abstract":"<p>To address the escalating challenge of food scarcity and the associated conflicts between human and animal consumption, it is imperative to seek alternative resources that can substitute for traditional feed. Non-grain feed (NGF) raw materials represent a category of biomass resources that are distinct from grains in their composition. These materials are characterized by their high nutritional content, cost-effectiveness, ample availability, and consistent supply, which contribute to their significant economic potential. Nonetheless, the extensive application of NGF is currently hindered by several limitations, including a high concentration of antinutritional factors, suboptimal palatability, and an offensive odor, among other shortcomings. The synergistic fermentation of probiotics and enzymes (SFPE) is an innovative approach that integrates the use of a diverse array of enzymes during the feed fermentation process, as well as various strains of probiotics throughout the feed digestion process. This method aims to enhance the nutritional value of the feed, diminish the presence of antinutritional factors, and improve the overall palatability, thereby facilitating the optimal utilization of NGF. This strategy holds the promise of not only replacing conventional feed options but also mitigating the pressing issue of grain scarcity. This paper delves into the practical applications of NGF and presents an overview of the latest research advancements in SFPE fermentation techniques, which can provide cutting-edge and valuable reference for researchers who devote themselves to research in this field in the future.</p>","PeriodicalId":100086,"journal":{"name":"Animal Research and One Health","volume":"3 1","pages":"31-42"},"PeriodicalIF":0.0,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aro2.90","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143489753","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The duck (Anas platyrhynchos) is not only a vital farm animal but also an excellent model for genetic dissection of economic traits. The integration of multiomics data provides a powerful approach to elucidate the genetic basis of domestication and phenotype variation. Since its inception in 2014, the Duck 1000 Genomes Project has aimed to uncover the genetic foundation of key economic traits in ducks by combining multiomics data including genomic, transcriptomic, and metabolomic from various natural and segregating populations. This paper summarizes the strategies and achievements of the Duck 1000 Genomes Project, highlighting the reference genome assembly, genome evolution analysis, and the identification of genes and causative mutations responsible for key economic traits in ducks. We also discuss perspectives and potential challenges in functional genomic studies that could further accelerate duck molecular breeding.
{"title":"The Duck 1000 Genomes Project: Achievements and perspectives","authors":"Wenlei Fan, Shuisheng Hou, Zhengkui Zhou","doi":"10.1002/aro2.89","DOIUrl":"https://doi.org/10.1002/aro2.89","url":null,"abstract":"<p>The duck (<i>Anas platyrhynchos</i>) is not only a vital farm animal but also an excellent model for genetic dissection of economic traits. The integration of multiomics data provides a powerful approach to elucidate the genetic basis of domestication and phenotype variation. Since its inception in 2014, the Duck 1000 Genomes Project has aimed to uncover the genetic foundation of key economic traits in ducks by combining multiomics data including genomic, transcriptomic, and metabolomic from various natural and segregating populations. This paper summarizes the strategies and achievements of the Duck 1000 Genomes Project, highlighting the reference genome assembly, genome evolution analysis, and the identification of genes and causative mutations responsible for key economic traits in ducks. We also discuss perspectives and potential challenges in functional genomic studies that could further accelerate duck molecular breeding.</p>","PeriodicalId":100086,"journal":{"name":"Animal Research and One Health","volume":"2 4","pages":"366-376"},"PeriodicalIF":0.0,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aro2.89","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142664987","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
<p>The genetics and genomics of livestock is, as for other species, a dynamic and successful field of research. It is divided into two clearly different, although closely interacting disciplines: the molecular and the quantitative genetics. Remarkably, this contrast has a close parallel in the opposing views during a short and fierce war (1904–1906) between Mendelians and biometricians. Although the accepted views soon became more balanced [<span>1, 2</span>], the 20th century saw the emergence of two distinct genetic disciplines.</p><p>The development of the molecular genetics is an amazing and unending series of pioneering success stories featuring a legion of Nobel prize winners [<span>3</span>]: from chromosomes to DNA and to the central dogma; from recombinant DNA to PCR, microsatellites and SNPs; the routine whole-genome sequencing (WGS) with telomere to telomere genomes and pangenomes as the newest toys; and now also the CRISPR/Cas9 gene editing, although not yet of primary relevance for livestock [<span>4, 5</span>]. This was all typical laboratory science, which now has become a lot cleaner by automation and a growing emphasis on bioinformatics.</p><p>It illustrates the hectic progress that the promises made after one breakthrough were fulfilled after the next. Southern blotting of restriction fragment length polymorphism (RFLP) markers in the 80s and a little later the PCR–RFLP did not deliver the intended dense genetic map of a genome, so the discovery at the end of the decade of the microsatellites was most timely. This allowed the genetic mapping of monogenic traits, but until 20 years ago most causative mutations in livestock species were found via the candidate gene approach [<span>1, 6</span>]. In the new millennium microsatellites were replaced by high-density genome-wide SNP arrays, which deliver accurate genetic localizations. At the same time, WGS became affordable and monogenic causative variants became sitting ducks. However, we did not unravel the molecular mechanisms of complex traits [<span>6, 7</span>], so now we accept a less than satisfactory infinitesimal model of countless small contributions [<span>4</span>].</p><p>Starting during the decade of WWII, the quantitative geneticists, who never touch a pipette, started to provide scientific support to the breeding industry and developed the concept of breeding values [<span>8</span>]. For a long time, this was solely based on phenotypes, but they did not hesitate to exploit the advances in the molecular field. During the last 2 decades of the millennium the concept or dream of master-assisted selection was an important source of inspiration [<span>9, 10</span>]. This led to genetic localizations of enough quantitative trait loci (QTL) to fill the Animal QTLdb, but these explain only a small part of the phenotypic variation [<span>4</span>].</p><p>Again, we needed another breakthrough to fulfill the promises already made. In a visionary paper, Meuwissen et al. proposed ge
{"title":"The paradigm of genomic selection: Does it need an update?","authors":"Johannes A. Lenstra","doi":"10.1002/aro2.88","DOIUrl":"https://doi.org/10.1002/aro2.88","url":null,"abstract":"<p>The genetics and genomics of livestock is, as for other species, a dynamic and successful field of research. It is divided into two clearly different, although closely interacting disciplines: the molecular and the quantitative genetics. Remarkably, this contrast has a close parallel in the opposing views during a short and fierce war (1904–1906) between Mendelians and biometricians. Although the accepted views soon became more balanced [<span>1, 2</span>], the 20th century saw the emergence of two distinct genetic disciplines.</p><p>The development of the molecular genetics is an amazing and unending series of pioneering success stories featuring a legion of Nobel prize winners [<span>3</span>]: from chromosomes to DNA and to the central dogma; from recombinant DNA to PCR, microsatellites and SNPs; the routine whole-genome sequencing (WGS) with telomere to telomere genomes and pangenomes as the newest toys; and now also the CRISPR/Cas9 gene editing, although not yet of primary relevance for livestock [<span>4, 5</span>]. This was all typical laboratory science, which now has become a lot cleaner by automation and a growing emphasis on bioinformatics.</p><p>It illustrates the hectic progress that the promises made after one breakthrough were fulfilled after the next. Southern blotting of restriction fragment length polymorphism (RFLP) markers in the 80s and a little later the PCR–RFLP did not deliver the intended dense genetic map of a genome, so the discovery at the end of the decade of the microsatellites was most timely. This allowed the genetic mapping of monogenic traits, but until 20 years ago most causative mutations in livestock species were found via the candidate gene approach [<span>1, 6</span>]. In the new millennium microsatellites were replaced by high-density genome-wide SNP arrays, which deliver accurate genetic localizations. At the same time, WGS became affordable and monogenic causative variants became sitting ducks. However, we did not unravel the molecular mechanisms of complex traits [<span>6, 7</span>], so now we accept a less than satisfactory infinitesimal model of countless small contributions [<span>4</span>].</p><p>Starting during the decade of WWII, the quantitative geneticists, who never touch a pipette, started to provide scientific support to the breeding industry and developed the concept of breeding values [<span>8</span>]. For a long time, this was solely based on phenotypes, but they did not hesitate to exploit the advances in the molecular field. During the last 2 decades of the millennium the concept or dream of master-assisted selection was an important source of inspiration [<span>9, 10</span>]. This led to genetic localizations of enough quantitative trait loci (QTL) to fill the Animal QTLdb, but these explain only a small part of the phenotypic variation [<span>4</span>].</p><p>Again, we needed another breakthrough to fulfill the promises already made. In a visionary paper, Meuwissen et al. proposed ge","PeriodicalId":100086,"journal":{"name":"Animal Research and One Health","volume":"2 4","pages":"360-362"},"PeriodicalIF":0.0,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aro2.88","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142664628","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chong Zhang, Yonghang Zhang, Cong Liu, Lingyu Wang, Yani Dong, Donglei Sun, Haishen Wen, Kaiqiang Zhang, Xin Qi, Yun Li
Spotted sea bass (Lateolabrax maculatus) is a species of significant economic importance in aquaculture. However, genetic degeneration, such as declining growth performance, has severely impeded industry development, necessitating urgent genetic improvement. Here, we conducted a genome-wide association study (GWAS) and genomic prediction for growth traits using insertion and deletion (InDel) markers, and systematically compared the results with our previous studies using single nucleotide polymorphism (SNP) markers. A total of 97 significant InDels including a 6 bp insertion in an exon region were identified. It is worth noting that only 5 and 1 candidate genes for DY and TS populations were also detected in previous GWAS using SNPs, and numerous novel genes including c4b, fgf4, and dnajb9 were identified as vital candidate genes. Moreover, several novel growth-related procedures, such as the growth and development of the bone and muscle, were also detected. These findings indicated that InDel-based GWAS can provide valuable complement to SNP-based studies. The comparison of genomic predictive performance for total length trait under different marker selection strategies and genomic selection models indicated that GWAS selection strategy exhibits more stable predictive performance compared to the evenly selection strategy. Additionally, support vector machine model demonstrated better predictive accuracy and efficiency than traditional best linear unbiased prediction and Bayes models. Furthermore, the superior predictive performance using InDel markers compared to SNP markers highlighted the potential of InDels to enhance genomic predictive accuracy and efficiency. Our results carry significant implications for dissecting genetic mechanisms and contributing genetic improvement of growth traits in spotted sea bass through genomic resources.
斑点叉尾鲈(Lateolabrax maculatus)是水产养殖业中具有重要经济意义的物种。然而,生长性能下降等遗传退化问题严重阻碍了产业发展,迫切需要进行遗传改良。在此,我们利用插入和缺失(InDel)标记物进行了生长性状的全基因组关联研究(GWAS)和基因组预测,并将结果与之前利用单核苷酸多态性(SNP)标记物进行的研究进行了系统比较。共鉴定出 97 个重要的 InDel,包括一个外显子区域的 6 bp 插入。值得注意的是,在之前使用 SNP 进行的 GWAS 研究中,DY 和 TS 群体的候选基因分别只有 5 个和 1 个,而包括 c4b、fgf4 和 dnajb9 在内的许多新基因被确定为重要的候选基因。此外,还发现了一些与生长相关的新程序,如骨骼和肌肉的生长发育。这些发现表明,基于 InDel 的 GWAS 可以为基于 SNP 的研究提供有价值的补充。在不同的标记选择策略和基因组选择模型下,总长度性状的基因组预测性能比较表明,与均匀选择策略相比,GWAS 选择策略表现出更稳定的预测性能。此外,与传统的最佳线性无偏预测和贝叶斯模型相比,支持向量机模型表现出更好的预测精度和效率。此外,与 SNP 标记相比,使用 InDel 标记的预测性能更优,这凸显了 InDel 在提高基因组预测准确性和效率方面的潜力。我们的研究结果对于通过基因组资源剖析遗传机制并促进斑点叉尾鲈生长性状的遗传改良具有重要意义。
{"title":"Genome-wide association study and genomic prediction for growth traits in spotted sea bass (Lateolabrax maculatus) using insertion and deletion markers","authors":"Chong Zhang, Yonghang Zhang, Cong Liu, Lingyu Wang, Yani Dong, Donglei Sun, Haishen Wen, Kaiqiang Zhang, Xin Qi, Yun Li","doi":"10.1002/aro2.87","DOIUrl":"https://doi.org/10.1002/aro2.87","url":null,"abstract":"<p>Spotted sea bass (<i>Lateolabrax maculatus</i>) is a species of significant economic importance in aquaculture. However, genetic degeneration, such as declining growth performance, has severely impeded industry development, necessitating urgent genetic improvement. Here, we conducted a genome-wide association study (GWAS) and genomic prediction for growth traits using insertion and deletion (InDel) markers, and systematically compared the results with our previous studies using single nucleotide polymorphism (SNP) markers. A total of 97 significant InDels including a 6 bp insertion in an exon region were identified. It is worth noting that only 5 and 1 candidate genes for DY and TS populations were also detected in previous GWAS using SNPs, and numerous novel genes including <i>c4b</i>, <i>fgf4</i>, and <i>dnajb9</i> were identified as vital candidate genes. Moreover, several novel growth-related procedures, such as the growth and development of the bone and muscle, were also detected. These findings indicated that InDel-based GWAS can provide valuable complement to SNP-based studies. The comparison of genomic predictive performance for total length trait under different marker selection strategies and genomic selection models indicated that GWAS selection strategy exhibits more stable predictive performance compared to the evenly selection strategy. Additionally, support vector machine model demonstrated better predictive accuracy and efficiency than traditional best linear unbiased prediction and Bayes models. Furthermore, the superior predictive performance using InDel markers compared to SNP markers highlighted the potential of InDels to enhance genomic predictive accuracy and efficiency. Our results carry significant implications for dissecting genetic mechanisms and contributing genetic improvement of growth traits in spotted sea bass through genomic resources.</p>","PeriodicalId":100086,"journal":{"name":"Animal Research and One Health","volume":"2 4","pages":"400-416"},"PeriodicalIF":0.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aro2.87","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142664505","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
<p>The single reference genome assembly approach has been shown to be insufficient for capturing the full spectrum of genetic variation. This inadequacy has been well-documented in human genomics [<span>1</span>] and the solution is to create a pangenome reference. A pangenome reference is a comprehensive genomic representation that captures the full genetic diversity within a species by incorporating multiple individual genomes. In agricultural genomics, the creation of a bovine pangenome is important for designing or selecting animal genomes that are better adapted to climate change, capable of reducing methane emissions, and conducive to producing healthy food for a growing global population. The Bovine Pangenome Consortium (BPC) [<span>2</span>], which has over 60 members spread across 20 countries, has been established to coordinate global efforts in this area. At present, the BPC has collected more than 100 long-read-based genome assemblies representing ∼60 unique breeds/species. The primary goal is to construct a pangenome to enable accurate detection of genetic variation, which includes single nucleotide polymorphisms (SNPs) and structural variants (SVs) in bovine species especially cattle.</p><p>The BPC uses collaborative open science model and requires samples and expertise from multiple laboratories worldwide. The project focuses on global cattle breeds, including both taurine and indicine subspecies. Beyond cattle, the BPC aims to include other members of the Bovini tribe, such as water buffalo, yak, and bison, in the pangenome. In the case of water buffalo, there is a plan for a pangenome specific for the species as part of the 1000 Buffalo Genomes Project [<span>17</span>]. The inclusion of bovine species other than cattle will facilitate comparative genomic analysis and enhance the understanding of evolutionary processes and potential introgression events [<span>3</span>].</p><p>Current genetic variant detection tools are highly sensitive to the quality and representation of reference genomes, often resulting in reference bias [<span>4</span>]. Identification of SVs and copy number variants is sensitive to the specific reference genome chosen [<span>5</span>]. Detection of epigenetic markers such as DNA methylation is also sensitive to the choice of reference genome [<span>6</span>]. It is expected that in highly polymorphic and repetitive sequences, such as the major histocompatibility complex region [<span>7</span>], a single linear reference is problematic to represent the genetic variants at this locus. These issues are some of the reasons why the BPC was formed to create bovine pangenome to improve the accuracy of genetic analyses.</p><p>Building pangenome graphs can be computationally challenging, especially when the number of genomes being included is high (e.g., >100), and hence determining the best way to construct these references is crucial. There are at least three main methods to build a pangenome: reference-guided
构建牛基因组的动机是提高 SNP 和 SV 调用的准确性。一个构建良好的牛基因组应能取代特定品种的基因组,并促进多品种比较,最终推动农业和进化基因组学研究。Wai Yee Low:构思;获取资金;写作-审稿&;编辑;写作-原稿。
{"title":"The case for bovine pangenome","authors":"Wai Yee Low","doi":"10.1002/aro2.86","DOIUrl":"https://doi.org/10.1002/aro2.86","url":null,"abstract":"<p>The single reference genome assembly approach has been shown to be insufficient for capturing the full spectrum of genetic variation. This inadequacy has been well-documented in human genomics [<span>1</span>] and the solution is to create a pangenome reference. A pangenome reference is a comprehensive genomic representation that captures the full genetic diversity within a species by incorporating multiple individual genomes. In agricultural genomics, the creation of a bovine pangenome is important for designing or selecting animal genomes that are better adapted to climate change, capable of reducing methane emissions, and conducive to producing healthy food for a growing global population. The Bovine Pangenome Consortium (BPC) [<span>2</span>], which has over 60 members spread across 20 countries, has been established to coordinate global efforts in this area. At present, the BPC has collected more than 100 long-read-based genome assemblies representing ∼60 unique breeds/species. The primary goal is to construct a pangenome to enable accurate detection of genetic variation, which includes single nucleotide polymorphisms (SNPs) and structural variants (SVs) in bovine species especially cattle.</p><p>The BPC uses collaborative open science model and requires samples and expertise from multiple laboratories worldwide. The project focuses on global cattle breeds, including both taurine and indicine subspecies. Beyond cattle, the BPC aims to include other members of the Bovini tribe, such as water buffalo, yak, and bison, in the pangenome. In the case of water buffalo, there is a plan for a pangenome specific for the species as part of the 1000 Buffalo Genomes Project [<span>17</span>]. The inclusion of bovine species other than cattle will facilitate comparative genomic analysis and enhance the understanding of evolutionary processes and potential introgression events [<span>3</span>].</p><p>Current genetic variant detection tools are highly sensitive to the quality and representation of reference genomes, often resulting in reference bias [<span>4</span>]. Identification of SVs and copy number variants is sensitive to the specific reference genome chosen [<span>5</span>]. Detection of epigenetic markers such as DNA methylation is also sensitive to the choice of reference genome [<span>6</span>]. It is expected that in highly polymorphic and repetitive sequences, such as the major histocompatibility complex region [<span>7</span>], a single linear reference is problematic to represent the genetic variants at this locus. These issues are some of the reasons why the BPC was formed to create bovine pangenome to improve the accuracy of genetic analyses.</p><p>Building pangenome graphs can be computationally challenging, especially when the number of genomes being included is high (e.g., >100), and hence determining the best way to construct these references is crucial. There are at least three main methods to build a pangenome: reference-guided ","PeriodicalId":100086,"journal":{"name":"Animal Research and One Health","volume":"2 4","pages":"363-365"},"PeriodicalIF":0.0,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aro2.86","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142665163","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
To meet the requirements of the modern chicken industry, high levels of productivity and efficient feed conversion are necessary. This can be partially accomplished by using particular feed additives. The prohibition of antibiotic usage has compelled researchers to explore alternative options to antibiotics. Organic acids and their salts are commonly employed in poultry farming as substitutes for antibiotic growth promoters. These compounds are distinguished by the presence of a carboxylic acid group and are classified as weak acids. They function as intermediates in the degradation of amino acids, sugars, and fatty acids. Organic acids encompass a wide range of chemical substances that are commonly found naturally as fundamental constituents of animal tissues, plants, and microorganisms. Organic acids decrease the pH of the intestinal tract, promoting the growth of beneficial microorganisms. This enhances the digestion of nutrients and increases immunity in chickens, eliminating the need for antibiotics. This review provides an overview of recent research findings regarding the antimicrobial effect of organic acids and the impact of organic acids on growth performance, intestinal health, and carcass and organ characteristics of broiler chickens.
{"title":"The effects of organic acids on broiler chicken nutrition: A review","authors":"Prosper Chukwudi, Paulinus Ikenna Umeugokwe, Nnanna Ephraim Ikeh, Bright Chigozie Amaefule","doi":"10.1002/aro2.85","DOIUrl":"https://doi.org/10.1002/aro2.85","url":null,"abstract":"<p>To meet the requirements of the modern chicken industry, high levels of productivity and efficient feed conversion are necessary. This can be partially accomplished by using particular feed additives. The prohibition of antibiotic usage has compelled researchers to explore alternative options to antibiotics. Organic acids and their salts are commonly employed in poultry farming as substitutes for antibiotic growth promoters. These compounds are distinguished by the presence of a carboxylic acid group and are classified as weak acids. They function as intermediates in the degradation of amino acids, sugars, and fatty acids. Organic acids encompass a wide range of chemical substances that are commonly found naturally as fundamental constituents of animal tissues, plants, and microorganisms. Organic acids decrease the pH of the intestinal tract, promoting the growth of beneficial microorganisms. This enhances the digestion of nutrients and increases immunity in chickens, eliminating the need for antibiotics. This review provides an overview of recent research findings regarding the antimicrobial effect of organic acids and the impact of organic acids on growth performance, intestinal health, and carcass and organ characteristics of broiler chickens.</p>","PeriodicalId":100086,"journal":{"name":"Animal Research and One Health","volume":"3 1","pages":"43-53"},"PeriodicalIF":0.0,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aro2.85","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143489749","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
<p>Reproductive efficiency is the cornerstone of all animal-based agricultural enterprises and is crucial for profitable, environmentally sustainable food systems. In livestock production systems, particularly cattle production, reproductive efficiency is the main driver of farm profitability. Pregnancy loss, rather than fertilization failure, is one of the major causes of reproductive failure in cattle [<span>1, 2</span>] and leads to extended calving intervals which, especially in a seasonal system, can have a major impact on profitability due to costs associated with increased calving intervals, increased culling, increased labor costs, and increased interventions of one form or another [<span>3</span>].</p><p>In cattle, most pregnancy failure occurs quite early after fertilization; ∼75% of conceptus loss occurs in the first 2–3 weeks of gestation, before maternal recognition of pregnancy (around day 16–17) and the start of placentation (around day 20) [<span>2, 4-7</span>]. Indeed, in some situations (e.g., metabolic stress associated with high milk production), as many as 50% of embryos may be lost in the first week after fertilization [<span>4, 6</span>]. Even when all of the biological and technical causes for pregnancy failure in the first week are avoided by transferring an embryo directly into the uterus (typically done on day 7 of the cycle), pregnancy success is not consistently improved compared to artificial insemination (AI) [<span>8</span>]. Thus, improving our understanding of the underlying physiological and molecular regulation of early embryo development leading to a successful pregnancy will significantly contribute to social and economic sustainability in agri-food production, a crucial objective in the face of an ever-increasing global population [<span>9</span>] and growing concerns about the impact of inefficient agricultural practices on the environment [<span>10</span>].</p><p>The development of AI in the 1950s has driven genetic improvement in dairy cattle and is now the main method of impregnating dairy females with semen from elite bulls [<span>11</span>]. Since then, considerable progress has been made in the development and application of a wide range of assisted reproductive technologies (ARTs) at farm level [<span>12</span>], including multiple ovulation embryo transfer (MOET, or ‘superovulation’), involving the generation of multiple embryos within the female (in vivo) [<span>13</span>], ovum pick-up/in vitro fertilization (in vitro embryo production), involving the generation of embryos in the laboratory [<span>14, 15</span>], and the use of sex-sorted semen to predetermine the offspring sex [<span>16-18</span>]. All these technologies facilitate accelerated genetic improvement and increase the economic value of the offspring generated [<span>19</span>].</p><p>In vitro embryo production (IVP) is now an established technology in the toolbox of ARTs available to farmers and breeding companies for genetic improvem
{"title":"The assisted reproductive technology of in vitro embryo production","authors":"Pat Lonergan","doi":"10.1002/aro2.81","DOIUrl":"https://doi.org/10.1002/aro2.81","url":null,"abstract":"<p>Reproductive efficiency is the cornerstone of all animal-based agricultural enterprises and is crucial for profitable, environmentally sustainable food systems. In livestock production systems, particularly cattle production, reproductive efficiency is the main driver of farm profitability. Pregnancy loss, rather than fertilization failure, is one of the major causes of reproductive failure in cattle [<span>1, 2</span>] and leads to extended calving intervals which, especially in a seasonal system, can have a major impact on profitability due to costs associated with increased calving intervals, increased culling, increased labor costs, and increased interventions of one form or another [<span>3</span>].</p><p>In cattle, most pregnancy failure occurs quite early after fertilization; ∼75% of conceptus loss occurs in the first 2–3 weeks of gestation, before maternal recognition of pregnancy (around day 16–17) and the start of placentation (around day 20) [<span>2, 4-7</span>]. Indeed, in some situations (e.g., metabolic stress associated with high milk production), as many as 50% of embryos may be lost in the first week after fertilization [<span>4, 6</span>]. Even when all of the biological and technical causes for pregnancy failure in the first week are avoided by transferring an embryo directly into the uterus (typically done on day 7 of the cycle), pregnancy success is not consistently improved compared to artificial insemination (AI) [<span>8</span>]. Thus, improving our understanding of the underlying physiological and molecular regulation of early embryo development leading to a successful pregnancy will significantly contribute to social and economic sustainability in agri-food production, a crucial objective in the face of an ever-increasing global population [<span>9</span>] and growing concerns about the impact of inefficient agricultural practices on the environment [<span>10</span>].</p><p>The development of AI in the 1950s has driven genetic improvement in dairy cattle and is now the main method of impregnating dairy females with semen from elite bulls [<span>11</span>]. Since then, considerable progress has been made in the development and application of a wide range of assisted reproductive technologies (ARTs) at farm level [<span>12</span>], including multiple ovulation embryo transfer (MOET, or ‘superovulation’), involving the generation of multiple embryos within the female (in vivo) [<span>13</span>], ovum pick-up/in vitro fertilization (in vitro embryo production), involving the generation of embryos in the laboratory [<span>14, 15</span>], and the use of sex-sorted semen to predetermine the offspring sex [<span>16-18</span>]. All these technologies facilitate accelerated genetic improvement and increase the economic value of the offspring generated [<span>19</span>].</p><p>In vitro embryo production (IVP) is now an established technology in the toolbox of ARTs available to farmers and breeding companies for genetic improvem","PeriodicalId":100086,"journal":{"name":"Animal Research and One Health","volume":"2 4","pages":"356-359"},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aro2.81","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142665061","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}