title: Genome-Wide Mapping of Growth-Related Quantitative Trait Loci in Orange-Spotted Grouper (Epinephelus coioides) Using Double Digest Restriction-Site Associated DNA Sequencing (ddRADseq).
abstract: Mapping of quantitative trait loci (QTL) is essential for the discovery of genetic structures that related to complex quantitative traits. In this study, we identified 264,072 raw SNPs (single-nucleotide polymorphisms) by double digest restriction site associated DNA sequencing (ddRADseq), and utilized 3029 of these SNPs to construct a genetic linkage map in orange-spotted grouper (Epinephelus coioides) using a regression mapping algorithm. The genetic map contained 24 linkage groups (LGs) spanning a total genetic distance of 1231.98 cM. Twenty-seven significant growth-related QTLs were identified. Furthermore, we identified 17 genes (fez2, alg3, ece2, arvcf, sla27a4, sgk223, camk2, prrc2b, mchr1, sardh, pappa, syk, tert, wdrcp91, ftz-f1, mate1 and notch1) including three (tert, ftz-f1 and notch1) that have been reported to be involved in fish growth. To summarize, we mapped growth-related QTLs in the orange-spotted grouper. These QTLs will be useful in marker-assisted selection (MAS) efforts to improve growth-related traits in this economically important fish.
authors.affiliation: BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China. yuhui@genomics.cn.|Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, State Key Laboratory of Agricultural Genomics, BGI, Shenzhen 518083, China. yuhui@genomics.cn.
authors.forename: Hui
authors.initials: H
authors.lastname: Yu
authors.affiliation: Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, State Key Laboratory of Agricultural Genomics, BGI, Shenzhen 518083, China. youxinxin@genomics.cn.|State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China. youxinxin@genomics.cn.
authors.forename: Xinxin
authors.initials: X
authors.lastname: You
authors.affiliation: BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China. lijia1@genomics.cn.|Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, State Key Laboratory of Agricultural Genomics, BGI, Shenzhen 518083, China. lijia1@genomics.cn.
authors.forename: Jia
authors.initials: J
authors.lastname: Li
authors.affiliation: Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, State Key Laboratory of Agricultural Genomics, BGI, Shenzhen 518083, China. liuhankui@genomics.cn.
authors.forename: Hankui
authors.initials: H
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China. mengzn@mail.sysu.edu.cn.
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, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China. xiaoling459@126.com.
authors.forename: Ling
authors.initials: L
authors.lastname: Xiao
authors.affiliation: Marine Fisheries Development Center of Guangdong Province, Huizhou 510610, China. zhhaifa812@hotmail.com.
authors.forename: Haifa
authors.initials: H
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China. lsslhr@mail.sysu.edu.cn.|South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou 510275, China. lsslhr@mail.sysu.edu.cn.
authors.forename: Hao-Ran
authors.initials: HR
authors.lastname: Lin
authors.affiliation: State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China. lsszy@mail.sysu.edu.cn.|Marine Fisheries Development Center of Guangdong Province, Huizhou 510610, China. lsszy@mail.sysu.edu.cn.|South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou 510275, China. lsszy@mail.sysu.edu.cn.
authors.forename: Yong
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China. shiqiong@genomics.cn.|Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, State Key Laboratory of Agricultural Genomics, BGI, Shenzhen 518083, China. shiqiong@genomics.cn.|College of Life Sciences, Shenzhen University, Shenzhen 518060, China. shiqiong@genomics.cn.
authors.forename: Qiong
authors.initials: Q
authors.lastname: Shi
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D010473:Perciformes / Q000235:genetics* / Q000254:growth & development*; D040641:Quantitative Trait Loci; D017422:Sequence Analysis, DNA / Q000379:methods
keywords: ddRADseq; genetic linkage map; growth-related genes; orange-spotted grouper (Epinephelus coioides); quantitative trait loci (QTL)