title: Second-Generation Linkage Maps for the Pacific Oyster Crassostrea gigas Reveal Errors in Assembly of Genome Scaffolds.
abstract: The Pacific oyster Crassostrea gigas, a widely cultivated marine bivalve mollusc, is becoming a genetically and genomically enabled model for highly fecund marine metazoans with complex life-histories. A genome sequence is available for the Pacific oyster, as are first-generation, low-density, linkage and gene-centromere maps mostly constructed from microsatellite DNA makers. Here, higher density, second-generation, linkage maps are constructed from more than 1100 coding (exonic) single-nucleotide polymorphisms (SNPs), as well as 66 previously mapped microsatellite DNA markers, all typed in five families of Pacific oysters (nearly 172,000 genotypes). The map comprises 10 linkage groups, as expected, has an average total length of 588 cM, an average marker-spacing of 1.0 cM, and covers 86% of a genome estimated to be 616 cM. All but seven of the mapped SNPs map to 618 genome scaffolds; 260 scaffolds contain two or more mapped SNPs, but for 100 of these scaffolds (38.5%), the contained SNPs map to different linkage groups, suggesting widespread errors in scaffold assemblies. The 100 misassembled scaffolds are significantly longer than those that map to a single linkage group. On the genetic maps, marker orders and intermarker distances vary across families and mapping methods, owing to an abundance of markers segregating from only one parent, to widespread distortions of segregation ratios caused by early mortality, as previously observed for oysters, and to genotyping errors. Maps made from framework markers provide stronger support for marker orders and reasonable map lengths and are used to produce a consensus high-density linkage map containing 656 markers.
authors.affiliation: Department of Biological Sciences, University of Southern California, Los Angeles, California 90089-0371 dhedge@usc.edu.
authors.forename: Dennis
authors.identifier: http://orcid.org/0000-0002-3995-646X
authors.initials: D
authors.lastname: Hedgecock
authors.affiliation: Department of Biological Sciences, University of Southern California, Los Angeles, California 90089-0371.
authors.forename: Grace
authors.initials: G
authors.lastname: Shin
authors.affiliation: Department of Biological Sciences, University of Southern California, Los Angeles, California 90089-0371.
authors.forename: Andrew Y
authors.initials: AY
authors.lastname: Gracey
authors.affiliation: Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California 90089-9601.
authors.forename: David Van
authors.identifier: http://orcid.org/0000-0002-5404-5218
authors.initials: DV
authors.lastname: Den Berg
authors.affiliation: Systemix Institute, Redmond, Washington 98053.
authors.forename: Manoj P
authors.initials: MP
authors.lastname: Samanta
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D049896:Crassostrea / Q000235:genetics*; D005260:Female; D008040:Genetic Linkage; D005819:Genetic Markers; D023281:Genomics / Q000379:methods; D008297:Male; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic
chemical_list: D005819:Genetic Markers
keywords: Illumina GoldenGate bead assays; distortion of segregation ratios; genotyping error; maximum likelihood maps; regression maps