title: Signatures of selection in tilapia revealed by whole genome resequencing.
abstract: Natural selection and selective breeding for genetic improvement have left detectable signatures within the genome of a species. Identification of selection signatures is important in evolutionary biology and for detecting genes that facilitate to accelerate genetic improvement. However, selection signatures, including artificial selection and natural selection, have only been identified at the whole genome level in several genetically improved fish species. Tilapia is one of the most important genetically improved fish species in the world. Using next-generation sequencing, we sequenced the genomes of 47 tilapia individuals. We identified a total of 1.43 million high-quality SNPs and found that the LD block sizes ranged from 10-100 kb in tilapia. We detected over a hundred putative selective sweep regions in each line of tilapia. Most selection signatures were located in non-coding regions of the tilapia genome. The Wnt signaling, gonadotropin-releasing hormone receptor and integrin signaling pathways were under positive selection in all improved tilapia lines. Our study provides a genome-wide map of genetic variation and selection footprints in tilapia, which could be important for genetic studies and accelerating genetic improvement of tilapia.
authors.affiliation: Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore.|State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China.
authors.forename: Jun Hong
authors.initials: JH
authors.lastname: Xia
authors.affiliation: Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, China.
authors.forename: Zhiyi
authors.initials: Z
authors.lastname: Bai
authors.affiliation: State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China.
authors.forename: Zining
authors.initials: Z
authors.lastname: Meng
authors.affiliation: State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore.
authors.forename: Le
authors.initials: L
authors.lastname: Wang
authors.affiliation: Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore.
authors.forename: Feng
authors.initials: F
authors.lastname: Liu
authors.affiliation: Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China.
authors.forename: Wu
authors.initials: W
authors.lastname: Jing
authors.affiliation: Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore.
authors.forename: Zi Yi
authors.initials: ZY
authors.lastname: Wan
authors.affiliation: Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, China.
authors.forename: Jiale
authors.initials: J
authors.lastname: Li
authors.affiliation: State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China.
authors.forename: Haoran
authors.initials: H
authors.lastname: Lin
authors.affiliation: Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore.|Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.|School of Biological Sciences Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
authors.forename: Gen Hua
authors.initials: GH
authors.lastname: Yue
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D019295:Computational Biology / Q000379:methods; D005828:Genetics, Population; D016678:Genome; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods; D006579:Heterozygote; D059014:High-Throughput Nucleotide Sequencing; D015810:Linkage Disequilibrium; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic; D017210:Tilapia / Q000235:genetics*