Abstract
Sea urchins have long been used as research model organisms for developmental biology and evolutionary studies. Some of them are also important aquaculture species in East Asia. In this work, we report the construction of RAD-tag based high-density genetic maps by genotyping F1 interspecific hybrids derived from a crossing between a female sea urchin Strongylocentrotus nudus and a male Strongylocentrotus intermedius. With polymorphisms present in these two wild individuals, we constructed a female meiotic map containing 3,080 markers for S. nudus, and a male meiotic map for S. intermedius which contains 1,577 markers. Using the linkage maps, we were able to anchor a total of 1,591 scaffolds (495.9 Mb) accounting for 60.8% of the genome assembly of Strongylocentrotus purpuratus. A genome-wide scan resulted in the identification of one putative QTL for body size which spanned from 25.3 cM to 30.3 cM. This study showed the efficiency of RAD-Seq based high-density genetic map construction using F1 progenies for species with no prior genomic information. The genetic maps are essential for QTL mapping and are useful as framework to order and orientate contiguous scaffolds from sea urchin genome assembly. The integration of the genetic map with genome assembly would provide an unprecedented opportunity to conduct QTL analysis, comparative genomics, and population genetics studies.
Highlights
Sea urchins have been popularly used as research model organisms to address questions in many aspects of biological sciences [1], including developmental biology, biochemistry, cellPLOS ONE | DOI:10.1371/journal.pone.0138585 September 23, 2015High-Density Genetic Mapping of Sea Urchin and molecular biology, as well as evolutionary biology
0.80 0.25 0.88 0.28 0.95 0.43 0.05 0.66 0.37 0.47 0.27 0.32 0.49 0.37 0.46 0.57 0.70 0.47 0.51 0.41 0.08 0.48 linkage maps, we were able to anchor a total of 1,591 scaffolds of the S. purpuratus genome assembly onto chromosomes, which accounted for 60.8% of the whole genome assembly
The genetic maps provided in this study will be essential for quantitative trait locus (QTL) mapping and integration with genome assembly of related sea urchin species
Summary
Sea urchins have been popularly used as research model organisms to address questions in many aspects of biological sciences [1], including developmental biology, biochemistry, cell. High-Density Genetic Mapping of Sea Urchin and molecular biology, as well as evolutionary biology. Some sea urchins are important aquaculture species in East Asia, including China, Japan and Korea. The sea urchin industry has been expanded rapidly since 1990s. Two main sea urchin species, Strongylocentrotus nudus and Strongylocentrotus intermedius, are widely cultured in China. The S. nudus is a native species in China, which is mainly cultured in the northern areas, while S. intermedius, introduced from Japan in 1989, is cultured more extensively along the coast of northern China. The heterosis resulting from interspecific hybridization of other sea urchins has been observed [4]
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