Abstract
Genetic linkage maps are indispensable tools in a wide range of genetic and genomic research. With the advancement of genotyping-by-sequencing (GBS) methods, the construction of a high-density linkage maps has become achievable in marine organisms lacking sufficient genomic resources, such as mollusks. In this study, high-density linkage map was constructed for an ecologically and commercially important clam species, Ruditapes philippinarum. For the consensus linkage map, a total of 9658 markers spanning 1926.98 cM were mapped to 18 sex-averaged linkage groups, with an average marker distance of 0.42 cM. Based on the high-density linkage map, ten QTLs for growth-related traits and shell color were detected. The coverage and density of the current map are sufficient for us to effectively detect QTL for segregating traits, and two QTL positions were all coincident with the closest markers. This high-density genetic linkage map reveals basic genomic architecture and will be useful for comparative genomics research, genome assembly and genetic improvement of R. philippinarum and other bivalve molluscan species.
Highlights
Genetic linkage maps are indispensable tools in a wide range of genetic and genomic research
A genetic linkage map is a critical and indispensable tool for genetic and genomic research[9], which can provide a foundation for identification of genomic loci linked to phenotypic variants, mapping of quantitative trait loci (QTL) and even anchoring genomic sequence scaffolds[10,11]
Recent advances in next-generation sequencing (NGS) technologies have enabled the identification of sufficient genetic molecular markers at a reasonable price, thereby promoting the development of several high-throughput single-nucleotide polymorphisms (SNPs) genotyping methods
Summary
Genetic linkage maps are indispensable tools in a wide range of genetic and genomic research. With the advancement of genotyping-by-sequencing (GBS) methods, the construction of a high-density linkage maps has become achievable in marine organisms lacking sufficient genomic resources, such as mollusks. The coverage and density of the current map are sufficient for us to effectively detect QTL for segregating traits, and two QTL positions were all coincident with the closest markers This high-density genetic linkage map reveals basic genomic architecture and will be useful for comparative genomics research, genome assembly and genetic improvement of R. philippinarum and other bivalve molluscan species. One of the major methods used to construct high-density linkage maps, called genotyping by sequencing (GBS) technology, has been widely used in non-model species[20]. We adapted this technology to construct a high-density linkage map for genomic and genetic studies in the marine bivalve R. philippinarum
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