Construction of the High-Density Genetic Linkage Map and Chromosome Map of Large Yellow Croaker (Larimichthys crocea).
Construction of the High-Density Genetic Linkage Map and Chromosome Map of Large Yellow Croaker (Larimichthys crocea).
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DOI：
10.3390/ijms161125951
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发表时间：
2015-11-03
影响因子：
5.6
通讯作者：
Chen X
中科院分区：
文献类型：
--
作者：
Ao J;Li J;You X;Mu Y;Ding Y;Mao K;Bian C;Mu P;Shi Q;Chen X
高密度遗传图谱对于基因组组装、比较基因组分析和复杂性状的精细定位至关重要。本研究利用限制性限制位点相关DNA测序（RAD-seq）技术，鉴定了分布在大黄鱼（Larimichthys crocea）基因组中的31,191个单核苷酸多态性（SNPs）。其中，10,150个高置信度snp被分配给24个共识连锁组（LGs）。遗传连锁图谱总长度为5451.3 cM，位点间平均距离为0.54 cM。这是目前报道的大黄鱼最密集的基因图谱。利用2889个snp靶向特异性支架，我们将533个支架分配到24个连锁组中，占大黄鱼组装序列的421.44 Mb（62.04%）。绘制的大黄鱼组装支架用于棘鱼（Gasterosteus aculeatus）和medaka （Oryzias latipes）的基因组合成分析。大黄鱼和棘鱼的同步性更强。这支持了大黄鱼与棘鱼的关系比与medaka的关系更密切的假设。在大黄鱼的24条染色体上，共定位到1274个免疫相关基因和195个缺氧相关基因。高分辨率遗传图谱与组装序列的结合，为大黄鱼经济性状相关数量性状位点的精细定位和定位克隆提供了宝贵的资源。
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.