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Int. J. Mol. Sci. 2016, 17(4), 501; 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)

1,2,†
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3,5,* , 3,4,5,* and 1,2,6,*
1
BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
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
3
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
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Marine Fisheries Development Center of Guangdong Province, Huizhou 510610, China
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South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou 510275, China
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College of Life Sciences, Shenzhen University, Shenzhen 518060, China
These authors contributed equally to this work.
*
Authors to whom correspondence should be addressed.
Academic Editors: Jun Li and Li Lin
Received: 1 March 2016 / Revised: 28 March 2016 / Accepted: 29 March 2016 / Published: 6 April 2016
(This article belongs to the Special Issue Fish Molecular Biology)
View Full-Text   |   Download PDF [418 KB, uploaded 6 April 2016]   |  

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. View Full-Text
Keywords: quantitative trait loci (QTL); genetic linkage map; growth-related genes; ddRADseq; orange-spotted grouper (Epinephelus coioides) quantitative trait loci (QTL); genetic linkage map; growth-related genes; ddRADseq; orange-spotted grouper (Epinephelus coioides)
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Yu, H.; You, X.; Li, J.; Liu, H.; Meng, Z.; Xiao, L.; Zhang, H.; Lin, H.-R.; Zhang, Y.; Shi, Q. 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, 17, 501.

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