{"title":"高通量基因分型在水产养殖中估计遗传资源和检测病原体中的应用","authors":"Chenhong Li, Junlong Jiang","doi":"10.1111/jwas.12996","DOIUrl":null,"url":null,"abstract":"<p>Aquatic genetic resources (AqGR) include DNA, tissues, gametes, embryos, and other early life stages, wild and farmed individuals, and communities of organisms of actual or potential value for food and aquaculture. Monitoring the AqGR at national, regional, and global levels would not only help to improve production traits, enhance disease resistance, and ensure the long-term sustainability of aquatic species but also provide valuable information on the state of rare or endangered aquatic species. While the importance of monitoring and reporting of AqGR is becoming more and more apparent among different stakeholders, efforts to date are still insufficient (FAO, <span>2022</span>).</p><p>A common method to estimate the AqGR is genotyping, which is a process of determining the genotype at positions within the genome of an individual and comparing it to other individuals' sequences. It is often used to understand association between genotype and phenotype. Sequence variations like single-nucleotide polymorphisms (SNPs) or microsatellite loci are applied as markers in linkage and association studies to determine genes relevant to specific traits. SNPs are the most common sequence variant widely used in genome-wide association studies (GWAS). With more and more SNPs being discovered, SNP genotyping technologies have been greatly promoted and include low-throughput and high-throughput methods. Nowadays, demands of high-throughput SNP genotyping are increasing, especially for hybridization-based SNP arrays and various next-generation sequencing (NGS)-enabled genotyping methods, such as genotyping-by-sequencing (GBS).</p><p>Besides genotyping AqGR, related molecular methods have also been wildly used in pathogen diagnosis in aquaculture. For farmers, early detection of pathogens can help to prevent spread of disease and minimize economic losses due to disease outbreaks. Rapid, pond-side methods allow for quick and efficient diagnosis of diseases, which can lead to more timely and effective treatment options. Furthermore, effective disease management can help to minimize the use of antibiotics and other treatments, thus reducing the risk of antimicrobial resistance and promoting more sustainable aquaculture practices.</p><p>Both good management of AqGR and disease control are key elements of sustainable aquaculture. Here, we summarize the methods used for genotyping AqGR and detecting disease by molecular diagnosis with an emphasis on high-throughput and onsite solutions.</p><p>The common laboratory procedure for genotyping involves sample collection, DNA extraction, PCR, and subsequent detection of genetic variation. For example, tissue samples are collected from fish, usually by taking a small piece of tissue such as a fin clip. DNA is extracted from the tissue sample using standard laboratory techniques, such as phenol-chloroform extraction or commercial DNA extraction kits. Then, specific molecular markers may need to be designed for detecting any genetic variation; an example is the mitochondrial cytochrome oxidase subunit 1 (COI) gene. Microsatellite markers can be used for genotyping, but SNP markers are now more commonly used for genotyping since more loci and greater information can be extracted from genome-wise SNP data. SNP genotyping can be performed using various methods, such as restriction fragment length polymorphism (RFLP), single-strand conformation polymorphism (SSCP), or sequencing. RFLP and SSCP are based on differences in the size and/or shape of the DNA fragments resulting from SNP variation, while sequencing provides direct information on the nucleotide sequences.</p><p>Compared with high-throughput genotyping, traditional methods are generally less efficient and time consuming, and may require a larger amount of starting material. Traditional genotyping methods may also have a higher error rate and be less sensitive to low-frequency variants. Additionally, traditional methods may not be able to genotype as many loci simultaneously as high-throughput methods, and this can limit their utility in certain applications such as genome-wide association studies.</p><p>With the rapid development of next-generation sequencing (NGS), many high-throughput genotyping methods have been developed and are primarily divided into SNP arrays and genotyping by sequencing (GBS) methods (Scheben et al., <span>2017</span>). The latter has various related methods, such as whole genome resequencing (WGR) and reduced representation sequencing (RRS), including sequence capture, restriction-site-associated DNA sequencing (RAD-seq), genotyping-in-thousands by sequencing (GT-seq), etc.</p><p>Intensive aquaculture with high stocking density can lead to outbreaks of disease. The best way to control aquatic disease is by prevention, but detection of a problem and timely treatment can be equally important. A rapid, pond-side pathogen detection method would be essential and aid in the control of disease in aquaculture.</p>","PeriodicalId":17284,"journal":{"name":"Journal of The World Aquaculture Society","volume":null,"pages":null},"PeriodicalIF":2.3000,"publicationDate":"2023-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jwas.12996","citationCount":"0","resultStr":"{\"title\":\"High-throughput genotyping in estimating genetic resources and detecting pathogens in aquaculture\",\"authors\":\"Chenhong Li, Junlong Jiang\",\"doi\":\"10.1111/jwas.12996\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p>Aquatic genetic resources (AqGR) include DNA, tissues, gametes, embryos, and other early life stages, wild and farmed individuals, and communities of organisms of actual or potential value for food and aquaculture. Monitoring the AqGR at national, regional, and global levels would not only help to improve production traits, enhance disease resistance, and ensure the long-term sustainability of aquatic species but also provide valuable information on the state of rare or endangered aquatic species. While the importance of monitoring and reporting of AqGR is becoming more and more apparent among different stakeholders, efforts to date are still insufficient (FAO, <span>2022</span>).</p><p>A common method to estimate the AqGR is genotyping, which is a process of determining the genotype at positions within the genome of an individual and comparing it to other individuals' sequences. It is often used to understand association between genotype and phenotype. Sequence variations like single-nucleotide polymorphisms (SNPs) or microsatellite loci are applied as markers in linkage and association studies to determine genes relevant to specific traits. SNPs are the most common sequence variant widely used in genome-wide association studies (GWAS). With more and more SNPs being discovered, SNP genotyping technologies have been greatly promoted and include low-throughput and high-throughput methods. Nowadays, demands of high-throughput SNP genotyping are increasing, especially for hybridization-based SNP arrays and various next-generation sequencing (NGS)-enabled genotyping methods, such as genotyping-by-sequencing (GBS).</p><p>Besides genotyping AqGR, related molecular methods have also been wildly used in pathogen diagnosis in aquaculture. For farmers, early detection of pathogens can help to prevent spread of disease and minimize economic losses due to disease outbreaks. Rapid, pond-side methods allow for quick and efficient diagnosis of diseases, which can lead to more timely and effective treatment options. Furthermore, effective disease management can help to minimize the use of antibiotics and other treatments, thus reducing the risk of antimicrobial resistance and promoting more sustainable aquaculture practices.</p><p>Both good management of AqGR and disease control are key elements of sustainable aquaculture. Here, we summarize the methods used for genotyping AqGR and detecting disease by molecular diagnosis with an emphasis on high-throughput and onsite solutions.</p><p>The common laboratory procedure for genotyping involves sample collection, DNA extraction, PCR, and subsequent detection of genetic variation. For example, tissue samples are collected from fish, usually by taking a small piece of tissue such as a fin clip. DNA is extracted from the tissue sample using standard laboratory techniques, such as phenol-chloroform extraction or commercial DNA extraction kits. Then, specific molecular markers may need to be designed for detecting any genetic variation; an example is the mitochondrial cytochrome oxidase subunit 1 (COI) gene. Microsatellite markers can be used for genotyping, but SNP markers are now more commonly used for genotyping since more loci and greater information can be extracted from genome-wise SNP data. SNP genotyping can be performed using various methods, such as restriction fragment length polymorphism (RFLP), single-strand conformation polymorphism (SSCP), or sequencing. RFLP and SSCP are based on differences in the size and/or shape of the DNA fragments resulting from SNP variation, while sequencing provides direct information on the nucleotide sequences.</p><p>Compared with high-throughput genotyping, traditional methods are generally less efficient and time consuming, and may require a larger amount of starting material. Traditional genotyping methods may also have a higher error rate and be less sensitive to low-frequency variants. Additionally, traditional methods may not be able to genotype as many loci simultaneously as high-throughput methods, and this can limit their utility in certain applications such as genome-wide association studies.</p><p>With the rapid development of next-generation sequencing (NGS), many high-throughput genotyping methods have been developed and are primarily divided into SNP arrays and genotyping by sequencing (GBS) methods (Scheben et al., <span>2017</span>). The latter has various related methods, such as whole genome resequencing (WGR) and reduced representation sequencing (RRS), including sequence capture, restriction-site-associated DNA sequencing (RAD-seq), genotyping-in-thousands by sequencing (GT-seq), etc.</p><p>Intensive aquaculture with high stocking density can lead to outbreaks of disease. The best way to control aquatic disease is by prevention, but detection of a problem and timely treatment can be equally important. A rapid, pond-side pathogen detection method would be essential and aid in the control of disease in aquaculture.</p>\",\"PeriodicalId\":17284,\"journal\":{\"name\":\"Journal of The World Aquaculture Society\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":2.3000,\"publicationDate\":\"2023-06-20\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jwas.12996\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of The World Aquaculture Society\",\"FirstCategoryId\":\"97\",\"ListUrlMain\":\"https://onlinelibrary.wiley.com/doi/10.1111/jwas.12996\",\"RegionNum\":3,\"RegionCategory\":\"农林科学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"FISHERIES\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of The World Aquaculture Society","FirstCategoryId":"97","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1111/jwas.12996","RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"FISHERIES","Score":null,"Total":0}
引用次数: 0
摘要
水生遗传资源包括对食品和水产养殖具有实际或潜在价值的DNA、组织、配子、胚胎和其他早期生命阶段、野生和养殖个体以及生物群落。在国家、区域和全球各级监测水生遗传资源不仅有助于改善生产性状、增强抗病性和确保水生物种的长期可持续性,而且还可提供有关稀有或濒危水生物种状况的宝贵信息。虽然监测和报告水生遗传资源的重要性在不同利益攸关方之间变得越来越明显,但迄今为止的努力仍然不足(粮农组织,2022年)。估计AqGR的一种常用方法是基因分型,这是一个确定个体基因组中位置的基因型并将其与其他个体的序列进行比较的过程。它经常被用来理解基因型和表型之间的关系。序列变异如单核苷酸多态性(snp)或微卫星位点被用作连锁和关联研究中的标记,以确定与特定性状相关的基因。SNPs是全基因组关联研究(GWAS)中最常用的序列变异。随着越来越多的SNP被发现,SNP基因分型技术得到了极大的推广,包括低通量和高通量两种方法。目前,对高通量SNP基因分型的需求正在增加,特别是基于杂交的SNP阵列和各种支持下一代测序(NGS)的基因分型方法,如测序基因分型(GBS)。除AqGR基因分型外,相关分子方法也广泛应用于水产养殖病原体诊断。对农民来说,早期发现病原体有助于防止疾病传播,并最大限度地减少疾病爆发造成的经济损失。快速的池边方法允许快速和有效地诊断疾病,这可以导致更及时和有效的治疗方案。此外,有效的疾病管理有助于最大限度地减少抗生素和其他治疗方法的使用,从而减少抗微生物药物耐药性的风险,促进更可持续的水产养殖做法。良好的水生遗传资源管理和疾病控制都是可持续水产养殖的关键要素。本文综述了AqGR基因分型和分子诊断检测疾病的方法,重点介绍了高通量和现场解决方案。基因分型的常见实验室程序包括样本收集、DNA提取、PCR和随后的遗传变异检测。例如,从鱼身上收集组织样本,通常是取一小块组织,比如鱼鳍夹。使用标准实验室技术从组织样本中提取DNA,如苯酚-氯仿提取或商业DNA提取试剂盒。然后,可能需要设计特定的分子标记来检测任何遗传变异;一个例子是线粒体细胞色素氧化酶亚基1 (COI)基因。微卫星标记可用于基因分型,但SNP标记现在更常用于基因分型,因为可以从基因组SNP数据中提取更多的位点和更多的信息。SNP基因分型可以使用多种方法进行,如限制性片段长度多态性(RFLP)、单链构象多态性(SSCP)或测序。RFLP和SSCP基于SNP变异导致的DNA片段的大小和/或形状差异,而测序提供了核苷酸序列的直接信息。与高通量基因分型相比,传统方法通常效率较低,耗时较长,并且可能需要大量的起始材料。传统的基因分型方法也可能有较高的错误率,对低频变异不太敏感。此外,传统方法可能无法像高通量方法那样同时对许多位点进行基因分型,这限制了它们在某些应用中的实用性,例如全基因组关联研究。随着下一代测序(NGS)技术的快速发展,许多高通量基因分型方法被开发出来,主要分为SNP阵列和测序(GBS)方法的基因分型(Scheben et al., 2017)。后者有各种相关方法,如全基因组重测序(WGR)和减少代表性测序(RRS),包括序列捕获、限制性位点相关DNA测序(RAD-seq)、千位基因分型测序(GT-seq)等。控制水生疾病的最佳方法是预防,但发现问题和及时治疗同样重要。一种快速的池边病原体检测方法对水产养殖业的疾病控制至关重要。
High-throughput genotyping in estimating genetic resources and detecting pathogens in aquaculture
Aquatic genetic resources (AqGR) include DNA, tissues, gametes, embryos, and other early life stages, wild and farmed individuals, and communities of organisms of actual or potential value for food and aquaculture. Monitoring the AqGR at national, regional, and global levels would not only help to improve production traits, enhance disease resistance, and ensure the long-term sustainability of aquatic species but also provide valuable information on the state of rare or endangered aquatic species. While the importance of monitoring and reporting of AqGR is becoming more and more apparent among different stakeholders, efforts to date are still insufficient (FAO, 2022).
A common method to estimate the AqGR is genotyping, which is a process of determining the genotype at positions within the genome of an individual and comparing it to other individuals' sequences. It is often used to understand association between genotype and phenotype. Sequence variations like single-nucleotide polymorphisms (SNPs) or microsatellite loci are applied as markers in linkage and association studies to determine genes relevant to specific traits. SNPs are the most common sequence variant widely used in genome-wide association studies (GWAS). With more and more SNPs being discovered, SNP genotyping technologies have been greatly promoted and include low-throughput and high-throughput methods. Nowadays, demands of high-throughput SNP genotyping are increasing, especially for hybridization-based SNP arrays and various next-generation sequencing (NGS)-enabled genotyping methods, such as genotyping-by-sequencing (GBS).
Besides genotyping AqGR, related molecular methods have also been wildly used in pathogen diagnosis in aquaculture. For farmers, early detection of pathogens can help to prevent spread of disease and minimize economic losses due to disease outbreaks. Rapid, pond-side methods allow for quick and efficient diagnosis of diseases, which can lead to more timely and effective treatment options. Furthermore, effective disease management can help to minimize the use of antibiotics and other treatments, thus reducing the risk of antimicrobial resistance and promoting more sustainable aquaculture practices.
Both good management of AqGR and disease control are key elements of sustainable aquaculture. Here, we summarize the methods used for genotyping AqGR and detecting disease by molecular diagnosis with an emphasis on high-throughput and onsite solutions.
The common laboratory procedure for genotyping involves sample collection, DNA extraction, PCR, and subsequent detection of genetic variation. For example, tissue samples are collected from fish, usually by taking a small piece of tissue such as a fin clip. DNA is extracted from the tissue sample using standard laboratory techniques, such as phenol-chloroform extraction or commercial DNA extraction kits. Then, specific molecular markers may need to be designed for detecting any genetic variation; an example is the mitochondrial cytochrome oxidase subunit 1 (COI) gene. Microsatellite markers can be used for genotyping, but SNP markers are now more commonly used for genotyping since more loci and greater information can be extracted from genome-wise SNP data. SNP genotyping can be performed using various methods, such as restriction fragment length polymorphism (RFLP), single-strand conformation polymorphism (SSCP), or sequencing. RFLP and SSCP are based on differences in the size and/or shape of the DNA fragments resulting from SNP variation, while sequencing provides direct information on the nucleotide sequences.
Compared with high-throughput genotyping, traditional methods are generally less efficient and time consuming, and may require a larger amount of starting material. Traditional genotyping methods may also have a higher error rate and be less sensitive to low-frequency variants. Additionally, traditional methods may not be able to genotype as many loci simultaneously as high-throughput methods, and this can limit their utility in certain applications such as genome-wide association studies.
With the rapid development of next-generation sequencing (NGS), many high-throughput genotyping methods have been developed and are primarily divided into SNP arrays and genotyping by sequencing (GBS) methods (Scheben et al., 2017). The latter has various related methods, such as whole genome resequencing (WGR) and reduced representation sequencing (RRS), including sequence capture, restriction-site-associated DNA sequencing (RAD-seq), genotyping-in-thousands by sequencing (GT-seq), etc.
Intensive aquaculture with high stocking density can lead to outbreaks of disease. The best way to control aquatic disease is by prevention, but detection of a problem and timely treatment can be equally important. A rapid, pond-side pathogen detection method would be essential and aid in the control of disease in aquaculture.
期刊介绍:
The Journal of the World Aquaculture Society is an international scientific journal publishing original research on the culture of aquatic plants and animals including:
Nutrition;
Disease;
Genetics and breeding;
Physiology;
Environmental quality;
Culture systems engineering;
Husbandry practices;
Economics and marketing.