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. 2015 Nov 3;16(11):26237-48.
doi: 10.3390/ijms161125951.

Construction of the High-Density Genetic Linkage Map and Chromosome Map of Large Yellow Croaker (Larimichthys crocea)

Jingqun Ao  1   2 , Jia Li  3 , Xinxin You  4 , Yinnan Mu  5   6 , Yang Ding  7   8 , Kaiqiong Mao  9   10 , Chao Bian  11 , Pengfei Mu  12   13 , Qiong Shi  14 , Xinhua Chen  15   16
Affiliations

Construction of the High-Density Genetic Linkage Map and Chromosome Map of Large Yellow Croaker (Larimichthys crocea)

Jingqun Ao et al. Int J Mol Sci. .

Abstract

High-density genetic maps are essential for genome assembly, comparative genomic analysis and fine mapping of complex traits. In this study, 31,191 single nucleotide polymorphisms (SNPs) evenly distributed across the large yellow croaker (Larimichthys crocea) genome were identified using restriction-site associated DNA sequencing (RAD-seq). Among them, 10,150 high-confidence SNPs were assigned to 24 consensus linkage groups (LGs). The total length of the genetic linkage map was 5451.3 cM with an average distance of 0.54 cM between loci. This represents the densest genetic map currently reported for large yellow croaker. Using 2889 SNPs to target specific scaffolds, we assigned 533 scaffolds, comprising 421.44 Mb (62.04%) of the large yellow croaker assembled sequence, to the 24 linkage groups. The mapped assembly scaffolds in large yellow croaker were used for genome synteny analyses against the stickleback (Gasterosteus aculeatus) and medaka (Oryzias latipes). Greater synteny was observed between large yellow croaker and stickleback. This supports the hypothesis that large yellow croaker is more closely related to stickleback than to medaka. Moreover, 1274 immunity-related genes and 195 hypoxia-related genes were mapped to the 24 chromosomes of large yellow croaker. The integration of the high-resolution genetic map and the assembled sequence provides a valuable resource for fine mapping and positional cloning of quantitative trait loci associated with economically important traits in large yellow croaker.

Keywords: SNP; chromosome map; genetic linkage map; hypoxia-related genes; immunity-related genes; large yellow croaker (Larimichthys crocea).

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Figures

Figure 1
Figure 1
Linkage group lengths, genes involved in immunity and hypoxia adaptation, and marker distribution of the high-density SNP genetic map of large yellow croaker. NOTE: in each group, black lines represent SNPs, red lines represent genes involved in immunity and green lines represent genes involved in hypoxia adaptation. Genetic map details were given in Table S2.
Figure 2
Figure 2
Circos atlas representation of the chromosome scaffold assembly information. The most external circle represents the length of each pseudo-chromosome. From inside to the outside ring: (I) GC content of 100-kb genomic interval. Each colored line represents a colinear match between two chromosomes; (II) Density of SNP distribution of 100-kb genomic interval; (III) Density of gene distribution of 100-kb genomic interval; (IV) Distribution of genes involved in immunity and hypoxia adaptation. The line colors of this ring were similar to those of Figure 1.
Figure 3
Figure 3
Circos atlas represents the collinear relationships between large yellow croaker and (a) stickleback and (b) medaka. The circle represents the length of each chromosome. Each colored line presents an orthologous match between two species. Ol: Oryzias latipes; Gs: Gasterosteus aculeatus; Lc; Larimichthys crocea.
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