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

Xinxin You,Qian Mu,Yanjie Cai,Guohua Chen,Qingchun Chen,Jian Luo,Liping Shu,Jieming Chen,Qiong Shi,Yong Zhang,Haoran Lin,Haifa Zhang,Qiuju Xia,Jie Bai,Jun Lu,Shuisheng Li

doi:10.1186/1471-2156-14-113

Abstract

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.

Highlights

Orange-spotted grouper, Epinephelus coioides, is one of the most valuable fish species in China
18,256 single nucleotide polymorphisms (SNPs) were retained after discarding those with a deviation from a Mendelian segregation pattern, and they were passed forward into the linkage map construction
multiplexed shotgun genotyping (MSG) and linkage mapping In this study, 25,892 SNPs were informative and were scored for sufficient numbers of progeny, and a Chi-square goodness-of-fit test (χ2 test, P < 0.001) was used to assess these SNPs whether deviate from the Mendelian segregation patterns. 18,256 SNPs were retained after discarding those with a deviation from a Mendelian segregation pattern, suggesting non-monogenetic inheritance of those discarded SNP markers

Summary

Introduction

Orange-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. 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. The first high-density genetic linkage maps for groupers were generated on the basis of the MSG method. The orange-spotted grouper, Epinephelus coioides, is a valuable and popular seafood fish, and is one of the major mariculture species in China. The vast market demands for orange-spotted grouper have driven efforts to breed families and populations with higher growth rates and lower food coefficients. The application of marker-assisted selection (MAS) to the orange-spotted grouper will become a promising strategy for improving growth traits [3]

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Discussion

Conclusion