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Genes 2018, 9(3), 120; https://doi.org/10.3390/genes9030120

Ultrahigh-Density Linkage Map Construction Using Low-Coverage Whole-Genome Sequencing of a Doubled Haploid Population: Case Study of Torafugu (Takifugu rubripes)

1
Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
2
Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
3
Akita Prefectural Fisheries Promotion Center, Oga, Akita 010-0531, Japan
4
School of Marine Bioscience, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan
*
Author to whom correspondence should be addressed.
Received: 20 December 2017 / Revised: 15 February 2018 / Accepted: 20 February 2018 / Published: 26 February 2018
(This article belongs to the Section Animal Genetics and Genomics)
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Abstract

Next-generation sequencing enables genome-wide genotyping of a large population and further facilitates the construction of a genetic linkage map. Low-coverage whole-genome sequencing has been employed for genetic linkage map construction in several species. However, this strategy generally requires available high-quality reference genomes and/or designed inbred pedigree lines, which restrict the scope of application for non-model and unsequenced species. Here, using torafugu (Takifugu rubripes) as a test model, we propose a new strategy for ultrahigh-density genetic linkage map construction using low-coverage whole-genome sequencing of a haploid/doubled haploid (H/DH) population without above requirements. Low-coverage (≈1×) whole-genome sequencing data of 165 DH individuals were used for de novo assembly and further performed single nucleotide polymorphisms (SNPs) calling, resulting in the identification of 1,070,601 SNPs. Based on SNP genotypes and de novo assembly, genotypes were associated with short DNA segments and an ultrahigh-density linkage map was constructed containing information of 802,277 SNPs in 3090 unique positions. Comparative analyses showed near-perfect concordance between the present linkage map and the latest published torafugu genome (FUGU5). This strategy would facilitate ultrahigh-density linkage map construction in various sexually reproducing organisms for which H/DH populations can be generated. View Full-Text
Keywords: genetic linkage map; low-coverage whole-genome sequencing; doubled haploid population; Takifugu rubripes; linkage phase unknown genetic linkage map; low-coverage whole-genome sequencing; doubled haploid population; Takifugu rubripes; linkage phase unknown
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Zhang, X.; Mizukoshi, M.; Zhang, H.; Tan, E.; Igarashi, Y.; Suzuki, Y.; Mitsuyama, S.; Kinoshita, S.; Saito, K.; Watabe, S.; Asakawa, S. Ultrahigh-Density Linkage Map Construction Using Low-Coverage Whole-Genome Sequencing of a Doubled Haploid Population: Case Study of Torafugu (Takifugu rubripes). Genes 2018, 9, 120.

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