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Mapping of a major QTL for increased robustness and detection of genome assembly errors in Asian seabass (Lates calcarifer).

التفاصيل البيبلوغرافية
العنوان: Mapping of a major QTL for increased robustness and detection of genome assembly errors in Asian seabass (Lates calcarifer).
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.)
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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
الوصف
تدمد:1471-2164
DOI:10.1186/s12864-023-09513-z