Construction of high-density genetic linkage maps for orange-spotted grouper Epinephelus coioidesusing multiplexed shotgun genotyping

BMC Genetics

Research Article

Jian Luo¹  Guohua Chen¹  Haifa Zhang²  Jieming Chen³  Qian Mu³  Jun Lu⁴  Jie Bai⁵  Qiong Shi⁶  Shuisheng Li⁷  Yong Zhang⁷  Haoran Lin⁸  Xinxin You⁹  Qingchun Chen^1,10  Liping Shu^1,10  Yanjie Cai^1,10  Qiuju Xia^1,10 

[1] College of Ocean, Hainan University, 570228, Haikou, China;Guangdong Daya Bay Fishery Development Center, 510681, Huizhou, China;Marine and Fisheries Institute, BGI-Shenzhen, 518083, Shenzhen, China;Marine and Fisheries Institute, BGI-Shenzhen, 518083, Shenzhen, China;Guangdong Daya Bay Fishery Development Center, 510681, Huizhou, China;Marine and Fisheries Institute, BGI-Shenzhen, 518083, Shenzhen, China;State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, 518083, Shenzhen, China;Marine and Fisheries Institute, BGI-Shenzhen, 518083, Shenzhen, China;State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, 518083, Shenzhen, China;Shenzhen BGI Fisheries Sci & Tech Co. Ltd., BGI-Shenzhen, 518083, Shenzhen, China;School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China;School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China;College of Ocean, Hainan University, 570228, Haikou, China;School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China;Marine and Fisheries Institute, BGI-Shenzhen, 518083, Shenzhen, China;State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, 518083, Shenzhen, China;State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, 518083, Shenzhen, China;

关键词: Epinephelus coioides;    Genetic linkage map;    Next generation sequencing (NGS);    Multiplexed shotgun genotyping (MSG);   

DOI  :  10.1186/1471-2156-14-113

 received in 2013-06-23, accepted in 2013-11-25,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundOrange-spotted grouper, Epinephelus coioides, is one of the most valuable fish species in China. Commercial production of orange-spotted grouper could be increased by developing higher growth rates and improving commercially important traits. Information on genetic markers associated with quantitative trait loci (QTL) can be used in breeding programs to identify and select individuals carrying desired traits. A high-density genetic linkage map is the basis for QTL study, and multiplexed shotgun genotyping (MSG) facilitates the development of single nucleotide polymorphisms (SNPs) and genotyping. In this study, the first high-density genetic linkage maps for groupers were generated on the basis of the MSG method.ResultsThe sex-averaged map contained a total of 4,608 SNPs, which spanned 1581.7 cM, with a mean distance between SNPs of 0.34 cM. The 4,608 SNPs were located in 2,849 unique locations on the linkage map, with an average inter-location space at 0.56 cM. There were 2,516 SNPs on the female map, and the number of unique locus was 1,902. However, the male map contained more numbers of SNP (2,939) and unique locations (2,005). The total length of the female and male maps was 1,370.9 and 1,335.5 cM, respectively.ConclusionsThe high-resolution genetic linkage maps will be very useful for QTL analyses and marker-assisted selection (MAS) for economically important traits in molecular breeding of the orange-spotted grouper.

【 授权许可】

Unknown   
© You et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.