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Black carp, Mylopharyngodon piceus , is one of the major farmed fish in China, generating a considerable amount of economic value annually. To investigate the genetic variation of black carp germplasm resources in China, this study was the first to use the whole genome SNPs of black carp for analysis. A total of 139 samples of nine black carp populations in the Yangtze River and Pearl River Systems of China were collected, and 53,322 high-quality SNP loci were obtained after GBS sequencing and filtering. Genetic diversity parameters were calculated for nine populations of black carp based on these genetic data. All 7 populations from the Yangtze River system and 2 populations from the Pearl River system showed high level of genetic diversity. For each population, the nucleotide diversity (π) varied from 0.283 to 0.308, the observed heterozygosity (H o) from 0.271 to 0.317, the expected heterozygosity (He) from 0.273 to 0.292，the number of effective alleles (Ne) from 1.440 to 1.475, and the polymorphism information content (PIC) from 0.224 to 0.239. The fixation index (F st) between populations ranged from 0.036 to 0.133, remaining at low and medium differentiation. Phylogenetic tree analysis, principal component analysis (PCA) and population genetic structure analysis revealed that the nine populations could be divided into three ancestral populations. The seven populations of the Yangtze River system comprised two primary ancestral groups, with a small amount of gene flow between populations. The internal genetic structure of populations within the Pearl River system was homogeneous, with one common ancestral source as the dominant component. In conclusion, the data and results generated from this study will provide a useful addition to the genetic resources of black carp and will provide reference information for further germplasm conservation and genetic improvement of black carp. • 53,322 high-quality SNP loci were obtained using Genotyping-by-sequencing technology. • High level of genetic diversity was in selected black carp populations. • Selected populations of black carp have low or medium genetic differentiation. • These black carp populations can be divided into three ancestral populations. [ABSTRACT FROM AUTHOR]

Growth related traits controlled by quantitative trait loci (QTL) are important economic traits in aquaculture fish species. In order to dissect these QTL, a high-density genetic linkage map is particularly important. In this study, the first high-density genetic linkage map of black carp (Mylopharyngodon piceus) was constructed using one F 1 family comprising of 128 progenies, based on genotyping-by-sequencing (GBS). A total of 10,390 single nucleotide polymorphisms (SNPs) were discovered and genotyped. A number of 4108 high-quality SNPs were assigned to 24 linkage groups (LGs) and the total length of the map was 1708.53 cM with a resolution of 0.51 cM. Conserved syntenic relationship between the high-density linkage map and the zebrafish chromosomes was detected. Relying on this high-density linkage map, 17 suggestive QTL: one for body weight, four for body length, six for body height, and six for body wide, were identified on three linkage groups (LG10, LG17, LG20). The phenotypic variance explained (PVE) by these QTL ranged from 10.9 to 15.5%. The high-density genetic linkage map serves as valuable genomic resources not only for understanding the genomic basis of economically important traits in this fish species, but also for comparative genomics and evolutionary studies of black carp. The identified QTL provide important value for ongoing marker assisted selection (MAS) in this fish. • The first genetic linkage map for black carp with an average resolution of 0.51 cM per locus was constructed using 4197 SNPs • 17 QTL related to body weight, body length, body width and body height were identified on three linkage groups • The LG1 in black carp corresponding to Chr10 and Chr22 in zebrafish genome. [ABSTRACT FROM AUTHOR]