57 InDel markers for spotted longbarbel catfish, Hemibagrus guttatus developed by whole genome resequencing

57 InDel markers for spotted longbarbel catfish, Hemibagrus guttatus developed by whole genome resequencing | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Method Article 57 InDel markers for spotted longbarbel catfish, Hemibagrus guttatus developed by whole genome resequencing Yuli Wu, Zhiyong Jiang, Zhichao He, Wanying Jiang This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-4727601/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 6 You are reading this latest preprint version Abstract Spotted longbarbel catfish, Hemibagrus guttatus (Lacepède, 1803), is benthic freshwater fish, mainly distributed in southern China, Laos, Thai, and Viet Nam. The wild population of H. guttatus is continuously decreasing, making it essential to protect this valuable fish resources. Understanding the genetic diversity and population structure of H. guttatus is critical to its protection. In the study, we therefore developed 57 InDel markers for H. guttatus by whole genome resequencing. The observed heterozygosity and expected heterozygosity ranged from 0.3333 to 0.5833 and 0.2778 to 0.5000, respectively. The value of polymorphism information content was between 0.2692 and 0.3750. One locus significantly deviated from the Hardy-Weinberg equilibrium ( p <0.05). These InDel markers are of great value for genetic diversity and conservation of H. guttatus . Hemibagrus guttatus InDel markers genetic diversity whole-genome resequencing Full Text Spotted longbarbel catfish, Hemibagrus guttatus (Lacepède, 1803), is a freshwater catfish with high economic value. It is primarily distributed in southern China, Laos, Thai, and Viet Nam (Yang and He 2008; Ha et al. 2017; My et al. 2018). It is carnivorous and feeds on crustaceans, aquatic insects, juvenile fish, and plant debris (Chu et al. 1999). H. guttatus is benthic fish inhabiting lotic environment with gravel substrates (Yang and He 2008). The wild population size of H. guttatus is gradually declining year by year because of overfishing and habitat loss. In 2012, H. guttatus was listed as "Population Decreasing" by IUCN (Zhao 2012). Recently, China has taken further measures to protect the valuable fish resources by designating the wild H. guttatus as a second-level National Key Protected Wildlife species in 2021. Hence, it is imperative to elucidate the genetic diversity and population structure of this species to facilitate its protection and offer guidance for governmental conservation management. However, the availability of molecular markers for H. guttatus is limited, posing challenges to assessing its genetic diversity. Recently, the genome of H. guttatus has sequenced and assembled (Yang et al. 2024). This genome provides a great amount of information, and we thus developed a series of molecular markers based on this genome. In this study, we reported 57 insertion/deletion (InDel) markers developed by whole-genome resequencing. InDels are widely distributed across the genomes, providing abundant information of genetic variation. With the development of next-generation sequencing (NGS), InDel markers have been extensively used as they are fast, stable, and accurate (Hechanova et al. 2021). While, to our knowledge, no InDel markers have been developed and used for genetic diversity assessment and molecular marker-assisted breeding in spotted longbarbel catfish. Muscle tissue samples of 32 individuals of H. guttatus were collected form Guangdong Hanyu Ecological Technology Co., LTD, Guangzhou city, Guangdong Province, China (113°30′45″N, 22°55′54″E). The TIANamp Genomic DNA Kit (TIANGEN, Beijing, China) was used to extract the genomic DNA. Afterwards, we employed 1% agarose gel electrophoresis and Qubit 2.0 fluorometer to assess the quality and concentration of DNA. The qualified DNA was then used for library construction and sequenced on an Illumina novaseq 6000 platform. A total of 2186140 InDels were identified using GATK v4.2.6.1 (DePristo et al. 2011), of which 57 InDels were randomly selected for primers design using primer3 web version 4.1.0 (https://primer3.ut.ee/) and evaluated polymorphisms by PCR. PCR amplification was performed using 25 µl of solution that contained 12.5 µL 2× PCR mix (Sangon, Shanghai, China), 0.25 µΜ of forward and reverse primers, 2 µL genomic DNA, and 10 µl ddH2O. Reaction cycles were set as follows: 95℃ for 5 min; 35 cycles of 95℃ for 30 s, 60℃ for 30 s, 72℃ for 1 min; and a final extension at 72℃ for 7 min. PCR products were sequenced using the ABI 3730 platform. We calculated observed heterozygosity (H O ) and expected heterozygosity (H E ) using PLINK v1.9 (Purcell et al. 2007), departures from Hardy-Weinberg equilibrium (HWE) was detected using PLINK v1.9 (Purcell et al. 2007). Polymorphism information content (PIC) was calculated using PIC_CALC v0.6 (Botstein et al. 1980). The observed heterozygosity (Ho) and expected heterozygosity (He) ranged from 0.3333 to 0.5833 and 0.2778 to 0.5000, respectively (Table 1). The range of polymorphism information content (PIC) varied from 0.2692 to 0.3750 (Table 1). Among 57 loci, one locus significantly deviated from the HWE (Table 1). These InDel markers are of great value for genetic and genomic studies of H. guttatus . Table 1. Characteristics of 57 InDel markers developed for Hemibagrus guttatus Declarations Acknowledgements This study was supported by Guangdong Agricultural Technology Service Light Cavalry Major Agricultural Technology Rural Tour Promotion Project (2130106). Author contributions Yuli Wu designed the study. Zhiyong Jiang wrote the manuscript. Zhichao He collected and identified the samples. Wanying Jiang analyzed the data. All authors reviewed and approved the final manuscript for publication Competing interests The authors declare no competing interests. Ethics statement In this study, all experiments were conducted in accordance with the recommendations outlined in the Guide for the Care and Use of Laboratory Animals issued by the Agro-Tech Extension Center of Guangdong Province. Additionally, this study received approval from the Committee on the Ethics of Animal Experiments of the Agro-Tech Extension Center of Guangdong Province. References Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32(3): 314-331 Chu XL, Zheng BS, Dai DY (1999) Fauna Sinica, Class Teleostei, Siluriformes (in Chinese). Scientific Press, Beijing. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, Del Angel G, Rivas MA, Hanna M, McKenna A (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43(5): 491-498 Ha NTH, Van Thang B, Vinh TV, Van TT (2017) Genetic diversity of Hemibagrus guttatus in Thai Nguyen Province by RAPD markers. Journal of forestry science and technology 5:11-17 Hechanova SL, Bhattarai K, Simon EV, Clave G, Karunarathne P, Ahn EK, Li CP, Lee JS, Kohli A, Hamilton NR, Hernandez JE (2021) Development of a genome-wide InDel marker set for allele discrimination between rice ( Oryza sativa ) and the other seven AA-genome Oryza species. Scientific reports 11(1):8962 My BH, Hương NT, Đức NH, Hà TT (2018) A study on genetic diversity of bagrid catfish ( Hemibagrus guttatus Lacepede, 1803) using microsatellite markers. Vietnam Journal of Biotechnology 16(1): 59-65 Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, De Bakker PI, Daly MJ, Sham PC (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81(3): 559-75 Yang L, He S (2008) Phylogeography of the freshwater catfish Hemibagrus guttatus (Siluriformes, Bagridae): implications for South China biogeography and influence of sea-level changes. Mol Phylogenet Evol 49(1): 393-398 Yang Y, Liu Y, Chen F, Wang Y, Wu Y, He Z, Liu C, Jiang Z, Mu X, Bian C (2024) Gap-free chromosome-level genomes of male and female spotted longbarbel catfish Hemibagrus guttatus . Sci. Data 11(1): 572 Zhao H (2012) Hemibagrus guttatus . The IUCN Red List of Threatened Species 2012 Table Table 1 is available in the Supplementary Files section Additional Declarations No competing interests reported. Supplementary Files Table1.docx Cite Share Download PDF Status: Under Review Version 1 posted Reviews received at journal 06 Dec, 2024 Reviewers agreed at journal 05 Dec, 2024 Reviewers invited by journal 21 Aug, 2024 Editor assigned by journal 12 Jul, 2024 Submission checks completed at journal 12 Jul, 2024 First submitted to journal 11 Jul, 2024 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-4727601","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Method Article","associatedPublications":[],"authors":[{"id":329433943,"identity":"32dea211-c22a-4ef2-a4ea-61e15ea1f528","order_by":0,"name":"Yuli Wu","email":"","orcid":"","institution":"Agro-Tech Extension Center of Guangdong Province","correspondingAuthor":false,"prefix":"","firstName":"Yuli","middleName":"","lastName":"Wu","suffix":""},{"id":329433944,"identity":"74857d93-f9a4-4bba-8773-530c0cef7ca0","order_by":1,"name":"Zhiyong Jiang","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA20lEQVRIie3PsQrCMBCA4UghXaJ1jKDtKxR8oQuuCo4dqiiV6yDuPoajY0qhXeLu2D6Ag5sOglEEt7SjYP7hpvu4hBCb7TcDqQejTmddQRS3J37PTZKwUkX7U2OflTioN07zarCHWt6PC4FcYCRWlHjpFoykswfIdqp8k7M4DglXp4OROBxAdrH4EEVJyGdmQjXJHh8yF+g0E6ZJ3sV4TFmGpBXhrIJ8hNKn7jrhoArW+JcgnU6uF1yyIHHr6y2KfS/dmQnpT0HP/PtS8/orr5R6LpsXbTab7X97AnsyT16Tpoi0AAAAAElFTkSuQmCC","orcid":"","institution":"Agro-Tech Extension Center of Guangdong Province","correspondingAuthor":true,"prefix":"","firstName":"Zhiyong","middleName":"","lastName":"Jiang","suffix":""},{"id":329433945,"identity":"3199b924-3d9c-4afa-ae7c-2c2578c9ab82","order_by":2,"name":"Zhichao He","email":"","orcid":"","institution":"Agro-Tech Extension Center of Guangdong Province","correspondingAuthor":false,"prefix":"","firstName":"Zhichao","middleName":"","lastName":"He","suffix":""},{"id":329433946,"identity":"0c109b48-bbee-466b-92a5-6abdb4c88b98","order_by":3,"name":"Wanying Jiang","email":"","orcid":"","institution":"Agro-Tech Extension Center of Guangdong Province","correspondingAuthor":false,"prefix":"","firstName":"Wanying","middleName":"","lastName":"Jiang","suffix":""}],"badges":[],"createdAt":"2024-07-12 03:17:52","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-4727601/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-4727601/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":61838346,"identity":"17bd8350-80fe-4243-b6cd-8f1ff2b4e511","added_by":"auto","created_at":"2024-08-06 06:09:05","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":189064,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-4727601/v1/e971d1a8-e4f6-404c-85a0-7b12c9617118.pdf"},{"id":61838342,"identity":"f5ea583b-860d-4a3b-8a15-7f54b7844957","added_by":"auto","created_at":"2024-08-06 06:09:01","extension":"docx","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":28097,"visible":true,"origin":"","legend":"","description":"","filename":"Table1.docx","url":"https://assets-eu.researchsquare.com/files/rs-4727601/v1/242178f3890d7d202ba765b8.docx"}],"financialInterests":"No competing interests reported.","formattedTitle":"57 InDel markers for spotted longbarbel catfish, Hemibagrus guttatus developed by whole genome resequencing","fulltext":[{"header":"Full Text","content":"\u003cp\u003eSpotted longbarbel catfish,\u003cem\u003e\u0026nbsp;Hemibagrus guttatus\u003c/em\u003e (Lacepède, 1803), is a freshwater catfish with high economic value. It is primarily distributed in southern China, Laos, Thai, and Viet Nam (Yang and He 2008; Ha et al. 2017; My et al. 2018). It is carnivorous and feeds on crustaceans, aquatic insects, juvenile fish, and plant debris (Chu et al. 1999). \u003cem\u003eH. guttatus\u003c/em\u003e is benthic fish inhabiting lotic environment with gravel substrates (Yang and He 2008). The wild population size of \u003cem\u003eH. guttatus\u003c/em\u003e is gradually declining year by year because of overfishing and habitat loss. In 2012, \u003cem\u003eH. guttatus\u003c/em\u003e was listed as \"Population Decreasing\" by IUCN (Zhao 2012). Recently, China has taken further measures to protect the valuable fish resources by designating the wild \u003cem\u003eH. guttatus\u003c/em\u003e as a second-level National Key Protected Wildlife species in 2021. Hence, it is imperative to elucidate the genetic diversity and population structure of this species to facilitate its protection and offer guidance for governmental conservation management. However, the availability of molecular markers for \u003cem\u003eH. guttatus\u003c/em\u003e is limited, posing challenges to assessing its genetic diversity.\u003c/p\u003e\n\u003cp\u003eRecently, the genome of \u003cem\u003eH. guttatus\u003c/em\u003e has sequenced and assembled (Yang et al. 2024). This genome provides a great amount of information, and we thus developed a series of molecular markers based on this genome. In this study, we reported 57 insertion/deletion (InDel) markers developed by whole-genome resequencing. InDels are widely distributed across the genomes, providing abundant information of genetic variation. With the development of next-generation sequencing (NGS), InDel markers have been extensively used as they are fast, stable, and accurate (Hechanova et al. 2021). While, to our knowledge, no InDel markers have been developed and used for genetic diversity assessment and molecular marker-assisted breeding in spotted longbarbel catfish.\u003c/p\u003e\n\u003cp\u003eMuscle tissue samples of 32 individuals of \u003cem\u003eH. guttatus\u003c/em\u003e were collected form Guangdong Hanyu Ecological Technology Co., LTD, Guangzhou city, Guangdong Province, China (113°30′45″N, 22°55′54″E). The TIANamp Genomic DNA Kit (TIANGEN, Beijing, China) was used to extract the genomic DNA. Afterwards, we employed 1% agarose gel electrophoresis and Qubit 2.0 fluorometer to assess the quality and concentration of DNA. The qualified DNA was then used for library construction and sequenced on an Illumina novaseq 6000 platform. A total of 2186140 InDels were identified using GATK v4.2.6.1 (DePristo et al. 2011), of which 57 InDels were randomly selected for primers design using primer3 web version 4.1.0 (https://primer3.ut.ee/) and evaluated polymorphisms by PCR.\u003c/p\u003e\n\u003cp\u003ePCR amplification was performed using 25 µl of solution that contained 12.5 µL 2× PCR mix (Sangon, Shanghai, China), 0.25 µΜ of forward and reverse primers, 2 µL genomic DNA, and 10 µl ddH2O. Reaction cycles were set as follows: 95℃ for 5 min; 35 cycles of 95℃ for 30 s, 60℃ for 30 s, 72℃ for 1 min; and a final extension at 72℃ for 7 min. PCR products were sequenced using the ABI 3730 platform. We calculated observed heterozygosity (H\u003csub\u003eO\u003c/sub\u003e) and expected heterozygosity (H\u003csub\u003eE\u003c/sub\u003e) using PLINK v1.9 (Purcell et al. 2007), departures from Hardy-Weinberg equilibrium (HWE) was detected using PLINK v1.9 (Purcell et al. 2007). Polymorphism information content (PIC) was calculated using PIC_CALC v0.6 (Botstein et al. 1980).\u003c/p\u003e\n\u003cp\u003eThe observed heterozygosity (Ho) and expected heterozygosity (He) ranged from 0.3333 to 0.5833 and 0.2778 to 0.5000, respectively (Table 1). The range of polymorphism information content (PIC) varied from 0.2692 to 0.3750 (Table 1). Among 57 loci, one locus significantly deviated from the HWE (Table 1). These InDel markers are of great value for genetic and genomic studies of \u003cem\u003eH. guttatus\u003c/em\u003e.\u003c/p\u003e\n\u003cp\u003eTable 1. Characteristics of 57 InDel markers developed for \u003cem\u003eHemibagrus guttatus\u003c/em\u003e\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eAcknowledgements\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis study was supported by Guangdong Agricultural Technology Service Light Cavalry Major Agricultural Technology Rural Tour Promotion Project (2130106).\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAuthor contributions\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eYuli Wu designed the study. Zhiyong Jiang wrote the manuscript. Zhichao He collected and identified the samples. Wanying Jiang analyzed the data. All authors reviewed and approved the final manuscript for publication\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eCompeting interests\u0026nbsp;\u003c/strong\u003eThe authors declare no competing interests.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eEthics statement\u003c/strong\u003e In this study, all experiments were conducted in accordance with the recommendations outlined in the Guide for the Care and Use of Laboratory Animals issued by the Agro-Tech Extension Center of Guangdong Province. Additionally, this study received approval from the Committee on the Ethics of Animal Experiments of the Agro-Tech Extension Center of Guangdong Province.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n \u003cli\u003eBotstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32(3): 314-331\u003c/li\u003e\n \u003cli\u003eChu XL, Zheng BS, Dai DY (1999) Fauna Sinica, Class Teleostei, Siluriformes (in Chinese). Scientific Press, Beijing.\u003c/li\u003e\n \u003cli\u003eDePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, Del Angel G, Rivas MA, Hanna M, McKenna A (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43(5): 491-498\u003c/li\u003e\n \u003cli\u003eHa NTH, Van Thang B, Vinh TV, Van TT (2017) Genetic diversity of \u003cem\u003eHemibagrus guttatus\u003c/em\u003e in Thai Nguyen Province by RAPD markers. Journal of forestry science and technology 5:11-17\u003c/li\u003e\n \u003cli\u003eHechanova SL, Bhattarai K, Simon EV, Clave G, Karunarathne P, Ahn EK, Li CP, Lee JS, Kohli A, Hamilton NR, Hernandez JE (2021) Development of a genome-wide InDel marker set for allele discrimination between rice (\u003cem\u003eOryza sativa\u003c/em\u003e) and the other seven AA-genome Oryza species. Scientific reports 11(1):8962\u003c/li\u003e\n \u003cli\u003eMy BH, Hương NT, Đức NH, H\u0026agrave; TT (2018) A study on genetic diversity of bagrid catfish (\u003cem\u003eHemibagrus guttatus\u003c/em\u003e Lacepede, 1803) using microsatellite markers. Vietnam Journal of Biotechnology 16(1): 59-65\u003c/li\u003e\n \u003cli\u003ePurcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, De Bakker PI, Daly MJ, Sham PC (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81(3): 559-75\u003c/li\u003e\n \u003cli\u003eYang L, He S (2008) Phylogeography of the freshwater catfish \u003cem\u003eHemibagrus guttatus\u003c/em\u003e (Siluriformes, Bagridae): implications for South China biogeography and influence of sea-level changes. Mol Phylogenet Evol 49(1): 393-398\u003c/li\u003e\n \u003cli\u003eYang Y, Liu Y, Chen F, Wang Y, Wu Y, He Z, Liu C, Jiang Z, Mu X, Bian C (2024) Gap-free chromosome-level genomes of male and female spotted longbarbel catfish \u003cem\u003eHemibagrus guttatus\u003c/em\u003e. Sci. Data 11(1): 572\u003c/li\u003e\n \u003cli\u003eZhao H (2012) \u003cem\u003eHemibagrus guttatus\u003c/em\u003e. The IUCN Red List of Threatened Species 2012\u003c/li\u003e\n\u003c/ol\u003e"},{"header":"Table","content":"\u003cp\u003eTable 1 is available in the Supplementary Files section\u003c/p\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"conservation-genetics-resources","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"cogr","sideBox":"Learn more about [Conservation Genetics Resources](https://www.springer.com/journal/12686)","snPcode":"12686","submissionUrl":"https://submission.nature.com/new-submission/12686/3","title":"Conservation Genetics Resources","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"Hemibagrus guttatus, InDel markers, genetic diversity, whole-genome resequencing","lastPublishedDoi":"10.21203/rs.3.rs-4727601/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-4727601/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eSpotted longbarbel catfish,\u003cem\u003e Hemibagrus guttatus\u003c/em\u003e (Lacepède, 1803), is benthic freshwater fish, mainly distributed in southern China, Laos, Thai, and Viet Nam. The wild population of \u003cem\u003eH. guttatus\u003c/em\u003e is continuously decreasing, making it essential to protect this valuable fish resources. Understanding the genetic diversity and population structure of \u003cem\u003eH. guttatus\u003c/em\u003e is critical to its protection. In the study, we therefore developed 57 InDel markers for \u003cem\u003eH. guttatus\u003c/em\u003e by whole genome resequencing. The observed heterozygosity and expected heterozygosity ranged from 0.3333 to 0.5833 and 0.2778 to 0.5000, respectively. The value of polymorphism information content was between 0.2692 and 0.3750. One locus significantly deviated from the Hardy-Weinberg equilibrium (\u003cem\u003ep\u003c/em\u003e\u0026lt;0.05). These InDel markers are of great value for genetic diversity and conservation of \u003cem\u003eH. guttatus\u003c/em\u003e.\u003c/p\u003e","manuscriptTitle":"57 InDel markers for spotted longbarbel catfish, Hemibagrus guttatus developed by whole genome resequencing","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2024-08-06 06:08:56","doi":"10.21203/rs.3.rs-4727601/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"editorInvitedReview","content":"","date":"2024-12-07T03:21:48+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"70036727591992523212179737091825666085","date":"2024-12-05T07:56:58+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2024-08-21T07:01:13+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2024-07-12T08:06:21+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2024-07-12T08:04:55+00:00","index":"","fulltext":""},{"type":"submitted","content":"Conservation Genetics Resources","date":"2024-07-12T03:16:23+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"conservation-genetics-resources","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"cogr","sideBox":"Learn more about [Conservation Genetics Resources](https://www.springer.com/journal/12686)","snPcode":"12686","submissionUrl":"https://submission.nature.com/new-submission/12686/3","title":"Conservation Genetics Resources","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"d7a101ff-9b87-4d85-9e92-fc0c339d3218","owner":[],"postedDate":"August 6th, 2024","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[],"tags":[],"updatedAt":"2025-01-16T10:08:55+00:00","versionOfRecord":[],"versionCreatedAt":"2024-08-06 06:08:56","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-4727601","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-4727601","identity":"rs-4727601","version":["v1"]},"buildId":"qtupq5eGEP_6zYnWcrvyt","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}