Molecular Population Genetics Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore.
PLoS One. 2010 Aug 5;5(8):e11974. doi: 10.1371/journal.pone.0011974.
The Asian seabass (Lates calcarifer) is an important marine foodfish species in Southeast Asia and Australia. Genetic improvement of this species has been achieved to some extent through selective breeding programs since 1990s. Several genomic tools such as DNA markers, a linkage map, cDNA and BAC libraries have been developed to assist selective breeding. A physical map is still lacking, although it is essential for positional cloning of genes located in quantitative trait loci (QTL) and assembly of whole genome sequences.
METHODOLOGY/PRINCIPAL FINDINGS: A genome-wide physical map of the Asian seabass was constructed by restriction fingerprinting of 38,208 BAC clones with SNaPshot HICF FPC technique. A total of 30,454 were assembled into 2,865 contigs. The physical length of the assembled contigs summed up to 665 Mb. Analyses of some contigs using different methods demonstrated the reliability of the assembly.
CONCLUSIONS/SIGNIFICANCE: The present physical map is the first physical map for Asian seabass. This physical map will facilitate the fine mapping of QTL for economically important traits and the positional cloning of genes located in QTL. It will also be useful for the whole genome sequencing and assembly. Detailed information about BAC-contigs and BAC clones are available upon request.
亚洲羊头鱼（Lates calcarifer）是东南亚和澳大利亚重要的海水食用鱼类。自 20 世纪 90 年代以来，通过选择性育种计划，该物种在一定程度上实现了遗传改良。已经开发了几种基因组工具，如 DNA 标记、连锁图谱、cDNA 和 BAC 文库，以辅助选择育种。尽管物理图谱对于位于数量性状基因座（QTL）的基因的定位克隆和整个基因组序列的组装至关重要，但仍缺乏物理图谱。
方法/主要发现：通过 SNaPshot HICF FPC 技术对 38,208 个 BAC 克隆进行限制性指纹图谱分析，构建了亚洲羊头鱼的全基因组物理图谱。总共组装了 30,454 个 BAC 克隆到 2,865 个 contigs 中。组装 contigs 的总物理长度总计为 665 Mb。使用不同方法对一些 contigs 进行分析证明了组装的可靠性。
结论/意义：本研究构建的物理图谱是亚洲羊头鱼的第一张物理图谱。该物理图谱将有助于对经济重要性状的 QTL 进行精细定位以及 QTL 中基因的定位克隆。它还将有助于全基因组测序和组装。有关 BAC-contigs 和 BAC 克隆的详细信息可应要求提供。
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