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全基因组重测序揭示了选择特征与鲑鱼对人工饲养的适应性之间的相关性
Whole genome resequencing reveals the correlation between selection signatures and adaptability of Micropterus salmoides to artificial fed
Nature 等信源发布 2024-12-03 19:55
可切换为仅中文
AbstractLargemouth bass (Micropterus salmoides, LMB) is an important aquaculture species due to its excellent flesh quality and environmental adaptability. It has been continuously introduced to many countries and cultured for decades. Here, an LMB population was used for selective breeding to improve growth rate and feed adaptability.
摘要大口黑鲈（Micropterus salmoides，LMB）因其优异的肉质和环境适应性而成为重要的水产养殖物种。几十年来，它不断被引入许多国家并被培养。在这里，LMB群体被用于选择性育种，以提高生长速度和饲料适应性。
After five generations of breeding, the growth rate improved by 38%, and feed adaptability improved by 22% compared to the non-breeding population. To study the underlying genetic mechanism, 100 LMB from the breeding population and 100 from the non-breeding population were sampled for whole-genome resequencing.
经过五代繁殖，与非繁殖种群相比，生长速度提高了38%，饲料适应性提高了22%。为了研究潜在的遗传机制，对来自育种群体的100个LMB和来自非育种群体的100个LMB进行了全基因组重测序。
The population genetics analysis shows that the breeding population has a higher inbreeding coefficient and linkage disequilibrium (LD) level, a lower nucleic acid diversity and effective population size (Ne). Using \(F_{ST}\) (fixation index), we found that the average \(F_{ST}\) value between the two populations was 0.07, with the highest \(F_{ST}\) value reaching 0.38, which overlaps with the trypsin gene.
群体遗传学分析表明，育种群体具有较高的近交系数和连锁不平衡（LD）水平，较低的核酸多样性和有效群体大小（Ne）。使用（F{ST}）（固定指数），我们发现两个种群之间的平均（F{ST}）值为0.07，最高的（F{ST}）值达到0.38，与胰蛋白酶基因重叠。
Additionally, other genes exhibiting high \(F_{ST}\) values are associated with functions such as neural development, glucose metabolism, and growth. Using \(F_{ST}\) and nucleic acid diversity as criteria, we identified 698 genes that are positively selected in the breeding population, and gene functional enrichment analysis shows that 36 genes are related to the olfactory receptor pathway.
此外，其他表现出高（F{ST}）值的基因与神经发育，葡萄糖代谢和生长等功能有关。以（F（ST）和核酸多样性为标准，我们鉴定了698个在育种群体中被正向选择的基因，基因功能富集分析表明36个基因与嗅觉受体途径有关。
Overall, our study found that multiple genes were selected in the LMB breeding population. These genes may be associated with adaptation and digestion of artificial feed in fish..
总体而言，我们的研究发现，在LMB育种群体中选择了多个基因。这些基因可能与鱼类对人工饲料的适应和消化有关。。
IntroductionDue to the depletion of biological resources, natural fishery resources are becoming increasingly scarce, and aquaculture has become the main source of fish supply1. To meet the demand for high-quality aquatic germplasm in aquaculture, selective breeding is used to improve growth rates. Through long-term breeding, the growth rate of selected fish has significantly improved2.
引言由于生物资源的枯竭，天然渔业资源越来越稀缺，水产养殖已成为鱼类供应的主要来源1。为了满足水产养殖对优质水生种质的需求，采用选择性育种来提高生长速度。通过长期繁殖，所选鱼类的生长速度显着提高2。
With the development of molecular biology, fish breeding has entered the era of molecular breeding, through genome-wide association analysis, \(F_{ST}\) (fixation index) and other algorithms, a large number of growth-related genes and molecular markers have been uncovered and applied in fish breeding3.
随着分子生物学的发展，鱼类育种已进入分子育种时代，通过全基因组关联分析，\（F{ST}\）（固定指数）等算法，发现了大量与生长相关的基因和分子标记，并将其应用于鱼类育种3。
Many studies have shown that growth is influenced by multiple genes, and even within the same species with different genetic backgrounds, growth-related genes can vary significantly. For example, in Nile tilapia (Oreochromis niloticus), researchers found that the growth rate is related to the feed conversion rate, while the genes ntrk3a, ghrh, and eif34e5 are associated with feed conversion efficiency4.
许多研究表明，生长受多个基因的影响，即使在具有不同遗传背景的同一物种中，生长相关基因也可能存在显着差异。。
In other studies, researchers found that the calcrl and gulp1 genes are significantly associated with harvest weight5.Figure 1The box plot of body weight of two populations, black dots represent the body weight of individuals.Full size imageLargemouth bass (Micropterus salmoides, LMB) is a freshwater fish belonging to the Centrarchidae family.
在其他研究中，研究人员发现calcrl和gulp1基因与收获重量显着相关。图1两个种群的体重箱形图，黑点代表个体的体重。全尺寸imageLargemouth bass（Micropterus salmoides，LMB）是属于Centrarchidae家族的淡水鱼。
Native to eastern North America, it inhabits various types of water, including swamps, ponds, lakes, reservoirs, creeks, and rivers6. LMB is one of the most widely distributed sport fish in the world7. Its current range includes the United States, South Africa, Japan, Europe, and China8,9,10. Meanwhile, LMB has been extensively cultured in China, with.
原产于北美东部，栖息于各种水域，包括沼泽、池塘、湖泊、水库、小溪和河流6。LMB是世界上分布最广泛的运动鱼之一7。它目前的范围包括美国、南非、日本、欧洲和中国8、9、10。同时，LMB在中国得到了广泛的培养。
Data availability
数据可用性
Sequencing data that support the findings of this study have been deposited in the NCBI with the accession code PRJNA940859.
支持这项研究结果的测序数据已保存在NCBI中，登录号为PRJNA940859。
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Download referencesAcknowledgementsThis project was supported by the Special-funds Project for Rural Revitalization Strategy of Guangdong Province (2024SPY00003); the Central Public-Interest Scientific Institution Basal Research Fund, CAFS (2022CG02 and 2023TD95).Author informationAuthors and AffiliationsKey Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, ChinaTao Zhu, Jinxing Du, Hongmei Song, Caixia Lei & Shengjie LiCollege of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, ChinaTao Zhu & Chenghui WangFoshan Jiyurunda Fishery Technology Co.
下载参考文献致谢本项目得到了广东省农村振兴战略专项资金项目（2024SPY00003）的支持；中央公共利益科学机构基础研究基金，CAFS（2022CG02和2023TD95）。作者信息作者和所属单位中国水产科学院珠江水产研究所农业和农村事务部热带和亚热带渔业资源应用与培育实验室，广州，510380，朱涛，杜金星，宋红梅，雷彩霞，上海海洋大学渔业与生命科学学院，上海，201306。
Ltd., Foshan, 528247, ChinaYingshen CenAuthorsTao ZhuView author publicationsYou can also search for this author in.
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PubMed Google ScholarContributionsConceptualization, S.L. and C.W.; Methodology, T.Z. and J.D.; Resources, Y.C., H.S and C.L.; Writing-original draft preparation, T.Z. All authors reviewed the manuscript.Corresponding authorCorrespondence to
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Reprints and permissionsAbout this articleCite this articleZhu, T., Du, J., Song, H. et al. Whole genome resequencing reveals the correlation between selection signatures and adaptability of Micropterus salmoides to artificial fed.
转载和许可本文引用本文Zhu，T.，Du，J.，Song，H。等人。全基因组重测序揭示了选择特征与鲑鱼对人工喂养的适应性之间的相关性。
Sci Rep 14, 30058 (2024). https://doi.org/10.1038/s41598-024-80904-2Download citationReceived: 15 July 2024Accepted: 22 November 2024Published: 03 December 2024DOI: https://doi.org/10.1038/s41598-024-80904-2Share this articleAnyone you share the following link with will be able to read this content:Get shareable linkSorry, a shareable link is not currently available for this article.Copy to clipboard.
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KeywordsFish domesticationLargemouth bassSelection signaturesTrypsin geneOlfactory receptor
关键词鱼类驯化大口贝斯选择特征酪氨酸基因嗅觉受体
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