An SNP-Based Genetic Map and QTL Mapping for Growth Traits in the Red-Spotted Grouper (Epinephelus akaara)

Xiang Wang; Shoujia Jiang; Leyun Zheng; Ling Xiao; Xinhui Zhang; Dengdong Wang; Shuisheng Li; Qiong Shi; Shuiqing Wu; Haoran Lin; Xinxin You; Yong Zhang

doi:10.3390/genes10100793

An SNP-Based Genetic Map and QTL Mapping for Growth Traits in the Red-Spotted Grouper (Epinephelus akaara)

Genes (Basel). 2019 Oct 12;10(10):793. doi: 10.3390/genes10100793.

Authors

Xiang Wang^{1

2}, Shoujia Jiang³, Leyun Zheng⁴, Ling Xiao⁵, Xinhui Zhang⁶, Dengdong Wang⁷, Shuisheng Li^{8

9}, Qiong Shi¹⁰, Shuiqing Wu¹¹, Haoran Lin^{12

13

14}, Xinxin You¹⁵, Yong Zhang^{16

17

18}

Affiliations

¹ South China Sea Marine Survey and Technology Center, SOA, Guangzhou 510275, China. wangxiang@smst.gz.cn.
² Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266373, China. wangxiang@smst.gz.cn.
³ Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China. jiangshoujia@genomics.cn.
⁴ Fisheries Research Institute of Fujian, Xiamen 361012, China. lyzheng69@sina.com.
⁵ State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China. xiaoling459@126.com.
⁶ Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China. zhangxinhui@genomics.cn.
⁷ State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China. wangdengdong@hotmail.com.
⁸ State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China. Lshuish@mail.sysu.edu.cn.
⁹ Southern Marine Science and Engineering Guangdong Laboratory (ZhanJiang), Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China. Lshuish@mail.sysu.edu.cn.
¹⁰ Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China. shiqiong@genomics.cn.
¹¹ Fisheries Research Institute of Fujian, Xiamen 361012, China. wushuiqing90@163.com.
¹² Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266373, China. Lsslhr@mail.sysu.edu.cn.
¹³ State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China. Lsslhr@mail.sysu.edu.cn.
¹⁴ Southern Marine Science and Engineering Guangdong Laboratory (ZhanJiang), Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China. Lsslhr@mail.sysu.edu.cn.
¹⁵ Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China. youxinxin@genomics.cn.
¹⁶ Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266373, China. lsszy@mail.sysu.edu.cn.
¹⁷ State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China. lsszy@mail.sysu.edu.cn.
¹⁸ Southern Marine Science and Engineering Guangdong Laboratory (ZhanJiang), Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China. lsszy@mail.sysu.edu.cn.

Abstract

The red-spotted grouper (Epinephelus akaara) is one of the most commercially important aquatic species in China. However, its seedstock has low larval survival rates, and its stability is confronted with the danger of overexploitation. In this study, a high-density genetic map was constructed using 3435 single nucleotide polymorphisms (SNPs) from 142 first generation (F₁) full-sib offspring and two parents of a red-spotted grouper population. The total genetic length of the map was 2300.12 cM with an average intermarker distance of 0.67 cM. Seventeen genome-wide significant quantitative trait loci (QTLs) for growth-related traits were detected on 24 linkage groups, including 5 QTLs for full length, 7 QTLs for body length, and 5 QTLs for body weight. The contribution values of explained phenotypic variance ranged from 10.7% to 12.9%. Moreover, 13 potential candidate genes for growth-related traits were identified. Collectively, these findings will be useful for conducting marker-assisted selection of the red-spotted grouper in future studies.

Keywords: Epinephelus akaara; QTL; RAD; genetic map; growth-related traits; network analysis.

Publication types

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

MeSH terms

Animals
China
Chromosome Mapping
Gene Regulatory Networks
Genetic Linkage*
Genotype
Perciformes / genetics*
Perciformes / growth & development
Phenotype
Polymorphism, Single Nucleotide
Quantitative Trait Loci*
Sequence Analysis, DNA