Applications of genotyping by sequencing in aquaculture breeding and genetics.
Applications of genotyping by sequencing in aquaculture breeding and genetics.
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DOI：
10.1111/raq.12193
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发表时间：
2018-08
影响因子：
10.4
通讯作者：
Houston R
中科院分区：
文献类型：
--
作者：
Robledo D;Palaiokostas C;Bargelloni L;Martínez P;Houston R
选择性育种越来越被认为是水产养殖物种可持续生产的关键组成部分。基因组技术在水产养殖育种中的应用传统上落后于陆生动物。然而，测序技术的快速发展和应用使水产养殖缩小了差距，为所有主要水产养殖物种带来了大量的基因组资源。虽然最近开发了一些物种的高密度单核苷酸多态性（SNP）阵列，但直接测序基因分型（GBS）技术支撑了迄今为止水产养殖遗传学和育种领域的许多进展。特别是，限制性位点相关 DNA 测序 (RAD-Seq) 和后续变异已被广泛应用于生成群体水平的 SNP 基因型数据。这些 GBS 技术不依赖于先前的基因组信息，例如感兴趣物种的参考基因组组装。因此，它们已被专注于研究群体相对较小的非模式水产养殖物种的研究人员和公司广泛使用。 RAD-Seq 技术的应用包括生成遗传连锁图、进行全基因组关联研究、参考基因组组装的改进，以及最近对水产养殖感兴趣的性状（如生长、性别决定或抗病性）的基因组选择。在这篇综述中，我们简要讨论了 GBS 的历史、各种 GBS 技术的细微差别、生物信息学方法以及这些技术在各种水产养殖物种中的应用。
Selective breeding is increasingly recognized as a key component of sustainable production of aquaculture species. The uptake of genomic technology in aquaculture breeding has traditionally lagged behind terrestrial farmed animals. However, the rapid development and application of sequencing technologies has allowed aquaculture to narrow the gap, leading to substantial genomic resources for all major aquaculture species. While high‐density single‐nucleotide polymorphism (SNP) arrays for some species have been developed recently, direct genotyping by sequencing (GBS) techniques have underpinned many of the advances in aquaculture genetics and breeding to date. In particular, restriction‐site associated DNA sequencing (RAD‐Seq) and subsequent variations have been extensively applied to generate population‐level SNP genotype data. These GBS techniques are not dependent on prior genomic information such as a reference genome assembly for the species of interest. As such, they have been widely utilized by researchers and companies focussing on nonmodel aquaculture species with relatively small research communities. Applications of RAD‐Seq techniques have included generation of genetic linkage maps, performing genome‐wide association studies, improvements of reference genome assemblies and, more recently, genomic selection for traits of interest to aquaculture like growth, sex determination or disease resistance. In this review, we briefly discuss the history of GBS, the nuances of the various GBS techniques, bioinformatics approaches and application of these techniques to various aquaculture species.
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影响因子：
9.2
作者：
Chen X;Zhong L;Bian C;Xu P;Qiu Y;You X;Zhang S;Huang Y;Li J;Wang M;Qin Q;Zhu X;Peng C;Wong A;Zhu Z;Wang M;Gu R;Xu J;Shi Q;Bian W
通讯作者：
Bian W
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
影响因子：
16.6
作者：
Berthelot, Camille;Brunet, Frederic;Chalopin, Domitille;Juanchich, Amelie;Bernard, Maria;Noel, Benjamin;Bento, Pascal;Da Silva, Corinne;Labadie, Karine;Alberti, Adriana;Aury, Jean-Marc;Louis, Alexandra;Dehais, Patrice;Bardou, Philippe;Montfort, Jerome;Klopp, Christophe;Cabau, Cedric;Gaspin, Christine;Thorgaard, Gary H.;Boussaha, Mekki;Quillet, Edwige;Guyomard, Rene;Galiana, Delphine;Bobe, Julien;Volff, Jean-Nicolas;Genet, Carine;Wincker, Patrick;Jaillon, Olivier;Roest Crollius, Hugues;Guiguen, Yann
通讯作者：
Guiguen, Yann
影响因子：
7.7
作者：
Campbell, Nathan R.;Harmon, Stephanie A.;Narum, Shawn R.
通讯作者：
Narum, Shawn R.
影响因子：
4.9
作者：
Gautier, Mathieu;Gharbi, Karim;Estoup, Arnaud
通讯作者：
Estoup, Arnaud