Ultrahigh-Density Linkage Map Construction Using Low-Coverage Whole-Genome Sequencing of a Doubled Haploid Population: Case Study of Torafugu (Takifugu rubripes).
Ultrahigh-Density Linkage Map Construction Using Low-Coverage Whole-Genome Sequencing of a Doubled Haploid Population: Case Study of Torafugu (Takifugu rubripes).
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DOI：
10.3390/genes9030120
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发表时间：
2018-02-26
期刊：
影响因子：
3.5
通讯作者：
Asakawa S
中科院分区：
文献类型：
--
作者：
Zhang X;Mizukoshi M;Zhang H;Tan E;Igarashi Y;Suzuki Y;Mitsuyama S;Kinoshita S;Saito K;Watabe S;Asakawa S
下一代测序技术能够对大量人群进行全基因组基因分型，并进一步促进遗传连锁图谱的构建。低覆盖率全基因组测序已被用于几个物种的遗传连锁图谱构建。然而，这种策略通常需要可用的高质量参考基因组和/或设计的近交系，这限制了非模式和未测序物种的应用范围。在这里，使用torafugu（红鳍东方鲀）作为测试模型，我们提出了一种新的策略超高密度遗传连锁图谱的构建使用低覆盖率的全基因组测序的单倍体/双单倍体（H/DH）人口没有上述要求。利用165个DH个体的低覆盖度（101 ×）全基因组测序数据进行从头组装，并进一步进行单核苷酸多态性（SNP）调用，结果鉴定出1，070，601个SNP。基于SNP基因型和从头组装，基因型与短DNA片段相关联，构建了包含3090个独特位置中802，277个SNP信息的超高密度连锁图。比较分析表明，本连锁图和最新公布的torafugu基因组（FUGU 5）之间的接近完美的一致性。这种策略将有助于超高密度连锁图谱的建设，在各种有性生殖的生物，H/DH人口可以产生。
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.
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影响因子：
4.4
作者：
Delourme R;Falentin C;Fomeju BF;Boillot M;Lassalle G;André I;Duarte J;Gauthier V;Lucante N;Marty A;Pauchon M;Pichon JP;Ribière N;Trotoux G;Blanchard P;Rivière N;Martinant JP;Pauquet J
通讯作者：
Pauquet J
影响因子：
3.7
作者：
Baird NA;Etter PD;Atwood TS;Currey MC;Shiver AL;Lewis ZA;Selker EU;Cresko WA;Johnson EA
通讯作者：
Johnson EA
DOI：
10.1073/pnas.0402251101
发表时间：
2004-10-26
影响因子：
11.1
作者：
Choi, HK;Mun, JH;Cook, DR
通讯作者：
Cook, DR
影响因子：
64.8
作者：
BRENNER, S;ELGAR, G;APARICIO, S
通讯作者：
APARICIO, S
影响因子：
4.5
作者：
Hollenbeck, Christopher M.;Portnoy, David S.;Gold, John R.
通讯作者：
Gold, John R.