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.
Highlights
Large yellow croaker (Larimichthys crocea (Richardson, 1846)) is a temperate-water migratory fish that is mainly distributed in the coastal areas of East China and Southeast China [1]
10,150 single nucleotide polymorphisms (SNPs) that were consistent with Mendelian segregation pattern were retained
All putative SNPs were successfully grouped into 24 linkage groups (LGs) (Table 1 and Figure 1), which mamtcahtcehsews iwthiththtehehahpalpoliodidchchrorommoososommeennuummbbeerr ooff tthhee llaarrggee yyeellllooww ccrrooaakkeerr[1[188].].ThTehteottaoltaglegneentiectic disdtaisntacnecwe awsa5s455415.13.3cMcMananddththeeaavveerraaggee iinntteer-marker ddiissttaanncceewwaass00.5.544cMcM. .FoFrordedteatilasi,lse,aechacLhGLG concotanitnaeinde4d2432S3NSNPsPsanadndththeeaavveerraaggeelleennggtthh wwas 227.144 ccMM..TThheelolonnggeeststLLGGwwasasLGLG3 3wwithitah gaegnentiectic lenlgenthgtohfo4f1421.426.4c6McM, c,ocnotnatianininingg551177SSNNPPss
Summary
Large yellow croaker (Larimichthys crocea (Richardson, 1846)) is a temperate-water migratory fish that is mainly distributed in the coastal areas of East China and Southeast China [1]. A genetic linkage map of large yellow croaker was constructed using type II microsatellites and expressed sequence tag (EST)-derived microsatellites in two half-sib families (two females and one male), and seven quantitative trait loci (QTLs) were identified for growth traits on five linkage groups [8]. These genetic maps of large yellow croaker can only be applied to map a limited number of QTLs for a few economic traits. Construction of a high-resolution genetic linkage map is necessary for fine-scale mapping of important traits such as stress resistance and growth rate in large yellow croaker. The immunity- and hypoxia-related genes were mapped to the pseudo-chromosomes in order to better understand the economically important traits of large yellow croaker
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