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《工程(英文)》 >> 2021年 第7卷 第3期 doi: 10.1016/j.eng.2020.06.017

牙鲆50K SNP芯片的研制及其在抗病性状基因组选择中的应用

a Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
b Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266373, China

# These authors contributed equally to this work.

收稿日期: 2020-01-17 修回日期: 2020-05-12 录用日期: 2020-06-10 发布日期: 2020-08-01

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摘要

单核苷酸多态性(SNP)芯片是一种强大的基因分型工具,用于遗传学研究和基因组选择(GS)育种。牙鲆是许多国家重要的经济养殖比目鱼品种。然而,高效基因分型工具的缺乏,严重阻碍了牙鲆基因组育种的进程。在本文中,我们研发了一款牙鲆50K“鱼芯1号”SNP芯片,并将其应用于抗病基因组选择。利用Affymetrix Axiom基因分型技术,我们从1099个个体的全基因组重测序数据中获得了超过4220万个SNP,从中选择了在基因组中均匀分布的48 697个SNP,研制成“鱼芯1号”SNP芯片。利用168个牙鲆个体对“鱼芯1号”芯片的分型效果进行了评价,结果表明,检出率(call rate, CR)高于98%的SNP位点占74.7%,多态性SNP位点具有较好的等位基因分离效果,并且85%以上的SNP与基于全基因组重测序数据获得的SNP一致。为了验证“鱼芯1号”芯片在基因组选择方面的应用效果,利用候选群体的27个个体和参考群体的931个个体的基因分型数据,计算了抗迟缓爱德华氏菌病性状的基因组估计育种值(GEBV)。与传统的基于系谱的最佳线性无偏预测(ABLUP)相比,加权基因组最佳线性无偏预测(wGBLUP)的预测准确性提高了21.2%,说明“鱼芯1号”芯片在基因组选择中的应用效果良好。综上所述,本文研制的牙鲆50K“鱼芯1号”芯片,为高质量的基因分型提供了一个有效的工具,推动了基于基因组选择的牙鲆抗病良种选育进程。

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