Genome-Wide Mapping of Growth-Related Quantitative Trait Loci in Orange-Spotted Grouper (Epinephelus coioides) Using Double Digest Restriction-Site Associated DNA Sequencing (ddRADseq)

Hui Yu; Xinxin You; Jia Li; Hankui Liu; Zining Meng; Ling Xiao; Haifa Zhang; Hao-Ran Lin; Yong Zhang; Qiong Shi

doi:10.3390/ijms17040501

Genome-Wide Mapping of Growth-Related Quantitative Trait Loci in Orange-Spotted Grouper (Epinephelus coioides) Using Double Digest Restriction-Site Associated DNA Sequencing (ddRADseq)

Int J Mol Sci. 2016 Apr 6;17(4):501. doi: 10.3390/ijms17040501.

Authors

Hui Yu^{1

2}, Xinxin You^{3

4}, Jia Li^{5

6}, Hankui Liu⁷, Zining Meng⁸, Ling Xiao⁹, Haifa Zhang¹⁰, Hao-Ran Lin^{11

12}, Yong Zhang^{13

14

15}, Qiong Shi^{16

17

18}

Affiliations

¹ BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China. yuhui@genomics.cn.
² 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.
³ 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.
⁴ 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.
⁵ BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China. lijia1@genomics.cn.
⁶ 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.
⁷ 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.
⁸ 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.
⁹ 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.
¹⁰ Marine Fisheries Development Center of Guangdong Province, Huizhou 510610, China. zhhaifa812@hotmail.com.
¹¹ 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.
¹² South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou 510275, China. lsslhr@mail.sysu.edu.cn.
¹³ 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.
¹⁴ Marine Fisheries Development Center of Guangdong Province, Huizhou 510610, China. lsszy@mail.sysu.edu.cn.
¹⁵ South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou 510275, China. lsszy@mail.sysu.edu.cn.
¹⁶ BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China. shiqiong@genomics.cn.
¹⁷ 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.
¹⁸ College of Life Sciences, Shenzhen University, Shenzhen 518060, China. shiqiong@genomics.cn.

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.

Keywords: ddRADseq; genetic linkage map; growth-related genes; orange-spotted grouper (Epinephelus coioides); quantitative trait loci (QTL).

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Chromosome Mapping
Perciformes / genetics*
Perciformes / growth & development*
Quantitative Trait Loci*
Sequence Analysis, DNA / methods