A high-density genetic linkage map for Chinese perch (Siniperca chuatsi) using genotyping-by-sequencing (GBS)

Abstract Background: Chinese perch, Siniperca chuatsi (Basilewsky), is one of the most commercially important cultured fishes in China. In the present study, a high-density genetic linkage map of Chinese perch was constructed by genotyping-by-sequencing (GBS) technique with an F1 mapping panel containing 190 progenies. Result: A total of 2328 SNPs were assigned to 24 linkage groups (LGs), agreeing with the chromosome haploid number in this species (n = 24). The sex-averaged map covered 97.9% of the Chinese perch genome, with the length of 1694.3 cM and a marker density of 0.7 cM/locus. The number of markers per LG ranged from 57 to 222, with a mean of 97. The length of LGs varied from 43.2 cM to 108.2 cM, with a mean size of 70.6 cM. The recombination rate of females was 1.50 : 1, which was higher than that of males. In order to better understand the distribution pattern of segregation distortion between the two sexes of Chinese perch, the skewed markers were retained and used to reconstruct the sex-specific maps. The 16 SDRs were identified on 10 LGs of the female map, while 12 SDRs on 8 LGs of the male map. Among these LGs, 6 LGs matched between the sex-specific maps. Conclusion: This high-density linkage map could provide a solid basis for identifying QTLs associated with economically important traits, and for implementing marker-assisted selection breeding of Chinese perch.