دورية أكاديمية
Mapping of a major QTL for increased robustness and detection of genome assembly errors in Asian seabass (Lates calcarifer).
العنوان: | Mapping of a major QTL for increased robustness and detection of genome assembly errors in Asian seabass (Lates calcarifer). |
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المؤلفون: | Shen X; Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore. xueyan.shen@jcu.eud.au.; Tropical Futures Institute, James Cook University Singapore, Singapore, Singapore. xueyan.shen@jcu.eud.au., Niu YC; Biozeron Shenzhen, Inc., Shenzhen, China., Uichanco JAV; Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore.; James Cook University Singapore, Singapore, Singapore., Phua N; Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore.; Present Address: School of Chemical & Life Sciences, Life Sciences Applied Research Group, Nanyang Polytechnic, Singapore, Singapore., Bhandare P; Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore.; Present address: Theodor Boven Institute (Biocenter), University of Würzburg, Würzburg, Germany., Thevasagayam NM; Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore.; Present address: Infectious Disease Research Laboratory, National Centre for Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore., Prakki SRS; Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore.; Present address: Infectious Disease Research Laboratory, National Centre for Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore., Orbán L; Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore. orban.laszlo@uni-mate.hu.; Frontline Fish Genomics Research Group, Department of Applied Fish Biology, Institute of Aquaculture and Environmental Safety, Georgikon Campus, Hungarian University of Agriculture and Life Sciences, Keszthely, Hungary. orban.laszlo@uni-mate.hu. |
المصدر: | BMC genomics [BMC Genomics] 2023 Aug 10; Vol. 24 (1), pp. 449. Date of Electronic Publication: 2023 Aug 10. |
نوع المنشور: | Journal Article |
اللغة: | English |
بيانات الدورية: | Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE |
أسماء مطبوعة: | Original Publication: London : BioMed Central, [2000- |
مواضيع طبية MeSH: | Quantitative Trait Loci* , Perciformes*/genetics, Animals ; Chromosome Mapping ; Chromosomes ; Genomics ; Polymorphism, Single Nucleotide ; Genetic Linkage |
مستخلص: | Background: For Asian seabass (Lates calcarifer, Bloch 1790) cultured at sea cages various aquatic pathogens, complex environmental and stress factors are considered as leading causes of disease, causing tens of millions of dollars of annual economic losses. Over the years, we conducted farm-based challenges by exposing Asian seabass juveniles to complex natural environmental conditions. In one of these challenges, we collected a total of 1,250 fish classified as either 'sensitive' or 'robust' individuals during the 28-day observation period. Results: We constructed a high-resolution linkage map with 3,089 SNPs for Asian seabass using the double digest Restriction-site Associated DNA (ddRAD) technology and a performed a search for Quantitative Trait Loci (QTL) associated with robustness. The search detected a major genome-wide significant QTL for increased robustness in pathogen-infected marine environment on linkage group 11 (ASB_LG11; 88.9 cM to 93.6 cM) with phenotypic variation explained of 81.0%. The QTL was positioned within a > 800 kb genomic region located at the tip of chromosome ASB_LG11 with two Single Nucleotide Polymorphism markers, R1-38468 and R1-61252, located near to the two ends of the QTL. When the R1-61252 marker was validated experimentally in a different mass cross population, it showed a statistically significant association with increased robustness. The majority of thirty-six potential candidate genes located within the QTL have known functions related to innate immunity, stress response or disease. By utilizing this ddRAD-based map, we detected five mis-assemblies corresponding to four chromosomes, namely ASB_LG8, ASB_LG9, ASB_LG15 and ASB_LG20, in the current Asian seabass reference genome assembly. Conclusion: According to our knowledge, the QTL associated with increased robustness is the first such finding from a tropical fish species. Depending on further validation in other stocks and populations, it might be potentially useful for selecting robust Asian seabass lines in selection programs. (© 2023. BioMed Central Ltd., part of Springer Nature.) |
References: | Jerry DR, editor. Biology and culture of Asian seabass, Lates calcarifer. Boca Raton: CRC Press; 2013. p. 1–326. Pierce CP. The next big fish. The Boston Globe Magazine. 2006;22:2008. Khang PV, Phuong TH, Dat NK, Knibb W, Nguyen NH. An 8-year breeding program for Asian seabass Lates calcarifer: Genetic evaluation, experiences, and challenges. Front Genet. 2018;9:191. (PMID: 298970555987403) Orbán L, Shen X, Phua N, Varga L. Toward genome-based selection in Asian seabass: what can we learn from other food fishes and farm animals? Front Genet. 2021;12:506754. (PMID: 339681258097054) Domingos JA, Shen X, Terence C, Senapin S, Dong HT, Tan MR, et al. Scale Drop Disease Virus (SDDV) and Lates calcarifer Herpes Virus (LCHV) coinfection downregulate immune-relevant pathways and cause splenic and kidney necrosis in barramundi under commercial farming conditions. Front Genet. 2021;12:983. Gibson-Kueh S, Chee D, Chen J, Wang Y, Tay S, Leong L, et al. The pathology of ‘scale drop syndrome’in Asian seabass, Lates calcarifer Bloch, a first description. J Fish Dis. 2012;35(1):19–27. (PMID: 22103767) Chang S, Ng K, Grisez L, De Groof A, Vogels W, Van Der Hoek L, Deijs M. Novel fish pathogenic virus. International patent No WO. 2018;29301:A1. Gibson-Kueh S, Crumlish M, Ferguson H. A novel “skinny pot-belly” disease in Asian seabass fry, Lates calcarifer (Bloch). J Fish Dis. 2004;27(12):731–5. (PMID: 15575881) Jiang J, Miyata M, Chan C, Ngoh SY, Liew WC, Saju JM, et al. Differential transcriptomic response in the spleen and head kidney following vaccination and infection of Asian seabass with Streptococcus iniae. PLoS ONE. 2014;9(7): e99128. (PMID: 249925874081116) Gibson-Kueh S. Diseases of Asian seabass (or barramundi), Lates calcarifer Bloch. Perth: PhD thesis, Murdoch University; p. 1–140. Retrieved from https://researchrepository.murdoch.edu.au/id/eprint/14817/ . Raman R, Prakash C, Makesh M, Pawar N. Environmental stress mediated diseases of fish: an overview. Adv Fish Res. 2013;5:141–58. Bly J, Quiniou S, Clem L. Environmental effects on fish immune mechanisms. Dev Biol Stand. 1997;90:33–43. (PMID: 9270832) Ødegård J, Baranski M, Gjerde B, Gjedrem T. Methodology for genetic evaluation of disease resistance in aquaculture species: challenges and future prospects. Aquacult Res. 2011;42(s1):103–14. Fraslin C, Quillet E, Rochat T, Dechamp N, Bernardet JF, Collet B, et al. Combining multiple approaches and models to dissect the genetic architecture of resistance to infections in fish. Front Genet. 2020;11:677. (PMID: 327541937365936) Barroso RM, Wheeler PA, LaPatra SE, Drew RE, Thorgaard GH. QTL for IHNV resistance and growth identified in a rainbow (Oncorhynchus mykiss) × Yellowstone cutthroat (Oncorhynchus clarki bouvieri) trout cross. Aquaculture. 2008;277(3):156–63. Johnson NA, Vallejo RL, Silverstein JT, Welch TJ, Wiens GD, Hallerman EM, et al. Suggestive association of major histocompatibility IB genetic markers with resistance to bacterial cold water disease in rainbow trout (Oncorhynchus mykiss). Mar Biotech. 2008;10(4):429–37. Palti Y, Vallejo RL, Gao G, Liu S, Hernandez AG, Rexroad CE III, Wiens GD. Detection and validation of QTL affecting bacterial cold water disease resistance in rainbow trout using restriction-site associated DNA sequencing. PLoS ONE. 2015;10(9):e0138435. (PMID: 263761824574402) Karami AM, Ødegård J, Marana MH, Zuo S, Jaafar R, Mathiessen H, et al. A major QTL for resistance to Vibrio anguillarum in rainbow trout. Front Genet. 2020;11:607558. (PMID: 334472547802751) Moen T, Torgersen J, Santi N, Davidson WS, Baranski M, Ødegård J, et al. Epithelial cadherin determines resistance to infectious pancreatic necrosis virus in Atlantic salmon. Genetics. 2015;200(4):1313–26. (PMID: 260412764574245) Houston RD, Haley CS, Hamilton A, Guy DR, Tinch AE, Taggart JB, et al. Major quantitative trait loci affect resistance to infectious pancreatic necrosis in Atlantic salmon (Salmo salar). Genetics. 2008;178(2):1109–15. (PMID: 182453412248365) Moen T, Baranski M, Sonesson AK, Kjøglum S. Confirmation and fine-mapping of a major QTL for resistance to infectious pancreatic necrosis in Atlantic salmon (Salmo salar): population-level associations between markers and trait. BMC Genomics. 2009;10(1):1–14. Fuji K, Kobayashi K, Hasegawa O, Coimbra MRM, Sakamoto T, Okamoto N. Identification of a single major genetic locus controlling the resistance to lymphocystis disease in Japanese flounder (Paralichthys olivaceus). Aquaculture. 2006;254(1–4):203–10. Liu P, Wang L, Wan ZY, Ye BQ, Huang S, Wong S-M, Yue GH. Mapping QTL for resistance against viral nervous necrosis disease in Asian seabass. Mar Biotech. 2016;18(1):107–16. Wang L, Liu P, Huang S, Ye B, Chua E, Wan ZY, Yue GH. Genome-wide association study identifies loci associated with resistance to viral nervous necrosis disease in Asian seabass. Mar Biotech. 2017;19(3):255–65. Liu P, Wang L, Wong S-M, Yue GH. Fine mapping QTL for resistance to VNN disease using a high-density linkage map in Asian seabass. Sci Rep. 2016;6(1):1–11. Wang L, Bai B, Huang S, Liu P, Wan ZY, Ye B, et al. QTL mapping for resistance to iridovirus in Asian seabass using genotyping-by-sequencing. Mar Biotech. 2017;19(5):517–27. Guerrero-Cózar I, Gomez-Garrido J, Berbel C, Martinez-Blanch JF, Alioto T, Claros MG, et al. Chromosome anchoring in Senegalese sole (Solea senegalensis) reveals sex-associated markers and genome rearrangements in flatfish. Sci Rep. 2021;11(1):1–16. Norrell AE, Jones KL, Saillant EA. Development and characterization of genomic resources for a non-model marine teleost, the red snapper (Lutjanus campechanus, Lutjanidae): Construction of a high-density linkage map, anchoring of genome contigs and comparative genomic analysis. PLoS One. 2020;15(4):e0232402. (PMID: 323483457190162) Bian C, Hu Y, Ravi V, Kuznetsova IS, Shen X, Mu X, Sun Y, et al. The Asian arowana (Scleropages formosus) genome provides new insights into the evolution of an early lineage of teleosts. Sci Rep. 2016;6(1):1–17. You X, Shan X, Shi Q. Research advances in the genomics and applications for molecular breeding of aquaculture animals. Aquaculture. 2020;526: 735357. Hedgecock D D, Shin G G, Gracey AY AY, van den Berg D, Samanta MP. Second-generation linkage maps for the pacific oyster Crassostrea gigas reveal errors in assembly of genome scaffolds. G3. 2015;5(10):2007–19. (PMID: 262489814592983) Conte MA, Gammerdinger WJ, Bartie KL, Penman DJ, Kocher TD. A high quality assembly of the Nile tilapia (Oreochromis niloticus) genome reveals the structure of two sex determination regions. BMC Genomics. 2017;18(1):1–19.32. Zeng Q, Fu Q, Li Y, Waldbieser G, Bosworth B, Liu S, et al. Development of a 690 K SNP array in catfish and its application for genetic mapping and validation of the reference genome sequence. Sci Rep. 2017;7(1):1–14. Peng W, Xu J, Zhang Y, Feng J, Dong C, Jiang L, et al. An ultra-high density linkage map and QTL mapping for sex and growth-related traits of common carp (Cyprinus carpio). Sci Rep. 2016;6(1):1–16. Vij S, Kuhl H, Kuznetsova IS, Komissarov A, Yurchenko AA, Van Heusden P, et al. Chromosomal-level assembly of the Asian seabass genome using long sequence reads and multi-layered scaffolding. PLoS Genet. 2016;12(4):e1005954. (PMID: 270822504833346) Hunt M, Kikuchi T, Sanders M, Newbold C, Berriman M, Otto TD. REAPR: a universal tool for genome assembly evaluation. Genome Biol. 2013;14(5):R47. (PMID: 237107273798757) Liu P, Wang L, Wong S-M, Yue GH. Fine mapping QTL for resistance to VNN disease using a high-density linkage map in Asian seabass. Sci Rep. 2016;6:32122. (PMID: 275550394995370) Baerwald M, Petersen J, Hedrick R, Schisler G, May B. A major effect quantitative trait locus for whirling disease resistance identified in rainbow trout (Oncorhynchus mykiss). Heredity. 2011;106(6):920–6. (PMID: 21048672) Uchino T, Tabata J, Yoshida K, Suzuki T, Noda T, Fujinami Y, et al. Novel Benedenia disease resistance QTLs in five F1 families of yellowtail (Seriola quinqueradiata). Aquaculture. 2020;529:735622. Houston RD, Haley CS, Hamilton A, Guy DR, Mota-Velasco JC, Gheyas AA, et al. The susceptibility of Atlantic salmon fry to freshwater infectious pancreatic necrosis is largely explained by a major QTL. Heredity. 2010;105(3):318–27. (PMID: 19935825) Fuji K, Hasegawa O, Honda K, Kumasaka K, Sakamoto T, Okamoto N. Marker-assisted breeding of a lymphocystis disease-resistant Japanese flounder (Paralichthys olivaceus). Aquaculture. 2007;272(1–4):291–5. Ting JPY, Lovering RC, Alnemri ESPD, Bertin J, Boss JM, Davis B, et al. The NLR gene family: an official nomenclature. Immunity. 2008;28(3):285. (PMID: 183419982630772) Unajak S, Santos MD, Hikima J, Jung TS, Kondo H, Hirono I, et al. Molecular characterization, expression and functional analysis of a nuclear oligomerization domain proteins subfamily C (NLRC) in Japanese flounder (Paralichthys olivaceus). Fish Shellfish Immunol. 2011;31(2):202–11. (PMID: 21642003) Zhou T, Liu S, Geng X, Jin Y, Jiang C, Bao L, et al. GWAS analysis of QTL for enteric septicemia of catfish and their involved genes suggest evolutionary conservation of a molecular mechanism of disease resistance. Mol Genet Genomics. 2017;292(1):231–42. (PMID: 27826737) Paria A, Deepika A, Sreedharan K, Makesh M, Chaudhari A, Purushothaman CS, et al. Identification of Nod like receptor C3 (NLRC3) in Asian seabass, Lates calcarifer: characterisation, ontogeny and expression analysis after experimental infection and ligand stimulation. Fish Shellfish Immunol. 2016;55:602–12. (PMID: 27346158) Sung YY. Heat shock proteins: An alternative to control disease in aquatic organism. Fish Shellfish Immunol. 2014;22:318–26. Sung YY, Pineda C, MacRae TH, Sorgeloos P, Bossier P. Exposure of gnotobiotic Artemia franciscana larvae to abiotic stress promotes heat shock protein 70 synthesis and enhances resistance to pathogenic Vibrio campbellii. Cell Stress Chaperon. 2008;13(1):59–66. de la Vega E, Hall MR, Degnan BM, Wilson KJ. Short-term hyperthermic treatment of Penaeus monodon increases expression of heat shock protein 70 (HSP70) and reduces replication of gill associated virus (GAV). Aquaculture. 2006;253(1):82–90. Jesus TF, Inácio Â, Coelho MM. Different levels of hsp70 and hsc70 mRNA expression in Iberian fish exposed to distinct river conditions. Gen Mol Biol. 2013;36(1):061–9. Yanuhar U, Arfiati D, Musa M, Junirahma NS, Caesar NR. The association between Hsp70 and TNF-α as immune response in groupers infected with Viral Nervous Necrosis. IOP Conf Ser Earth Environ Sci. 2021;860(1):012027. Liu P, Wang L, Kwang J, Yue GH, Wong S-M. Transcriptome analysis of genes responding to NNV infection in Asian seabass epithelial cells. Fish Shellfish Immunol. 2016;54:342–52. (PMID: 27109582) Michels MA, Volokhina EB, van de Kar NC, van den Heuvel LP. The role of properdin in complement-mediated renal diseases: a new player in complement-inhibiting therapy? Ped Nephrol. 2019;34(8):1349–67. Jiang C, Zhang J, Yao J, Liu S, Li Y, Song L, et al. Complement regulatory protein genes in channel catfish and their involvement in disease defense response. Dev Comp Immunol. 2015;53(1):33–41. (PMID: 26111998) Xia JH, Yue GH. Identification and analysis of immune-related transcriptome in Asian seabass (Lates calcarifer). BMC Genomics. 2010;11(1):1–12. Wang L, Bai B, Liu P, Huang SQ, Wan ZY, Chua E, Ye B, Yue GH. Construction of high-resolution recombination maps in Asian seabass. BMC Genomics. 2017;18(1):63. (PMID: 280689195223582) Zhu Z, Wang C, Lo L, Lin G, Feng F, Tan J, et al. A standard panel of microsatellites for Asian seabass (Lates calcarifer). Anim Genet. 2010;41(2):208–12. (PMID: 19793264) Aljanabi SM, Martinez I. Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques. Nucleic Acids Res. 1997;25(22):4692–3. (PMID: 9358185147078) Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE. Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS ONE. 2012;7(5): e37135. (PMID: 226754233365034) Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–20. Catchen J, Hohenlohe PA, Bassham S, Amores A, Cresko WA. Stacks: an analysis tool set for population genomics. Mol Ecol. 2013;22(11):3124–40. (PMID: 237013973936987) Van Ooijen J. Multipoint maximum likelihood mapping in a full-sib family of an outbreeding species. Genetics Res. 2011;93(05):343–9. Van Ooijen J. MapQTLÒ 6. Software for the mapping of quantitative trait loci in experimental populations of diploid species. Wageningen: Kyazma BV; 2009. Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 2016;44(D1):D457–62. (PMID: 26476454) Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754–60. (PMID: 194511682705234) |
معلومات مُعتمدة: | NRF-CRP7-2010-001 National Research Foundation, Prime Minister's Office, Singapore |
فهرسة مساهمة: | Keywords: Asian seabass; Genome; Linkage map; Quantitative trait loci; Robustness |
تواريخ الأحداث: | Date Created: 20230809 Date Completed: 20230811 Latest Revision: 20231118 |
رمز التحديث: | 20240628 |
مُعرف محوري في PubMed: | PMC10413685 |
DOI: | 10.1186/s12864-023-09513-z |
PMID: | 37558985 |
قاعدة البيانات: | MEDLINE |
تدمد: | 1471-2164 |
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DOI: | 10.1186/s12864-023-09513-z |