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

Qian Zhou; Ya-dong Chen; Sheng Lu; Yang Liu; Wen-teng Xu; Yang-zhen Li; Lei Wang; Na Wang; Ying-ming Yang; Song-lin Chen

doi:10.1016/j.eng.2020.06.017

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工程（英文） ›› 2021, Vol. 7 ›› Issue (3) : 406-411. DOI: 10.1016/j.eng.2020.06.017

研究论文

Article

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

Qian Zhou ^a^,^b^,^* ,
Ya-dong Chen ^a^,^* ,
Sheng Lu ^a ,
Yang Liu ^a ,
Wen-teng Xu ^a^,^b ,
Yang-zhen Li ^a ,
Lei Wang ^a ,
Na Wang ^a^,^b ,
Ying-ming Yang ^a ,
Song-lin Chen ^a^,^b

作者信息 +

Development of a 50K SNP Array for Japanese Flounder and Its Application in Genomic Selection for Disease Resistance

Qian Zhou ^a^,^b^,^* ,
Ya-dong Chen ^a^,^* ,
Sheng Lu ^a ,
Yang Liu ^a ,
Wen-teng Xu ^a^,^b ,
Yang-zhen Li ^a ,
Lei Wang ^a ,
Na Wang ^a^,^b ,
Ying-ming Yang ^a ,
Song-lin Chen ^a^,^b

Author information +

History +

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。

Abstract

Single nucleotide polymorphism (SNP) arrays are a powerful genotyping tool used in genetic research and genomic breeding programs. Japanese flounder (Paralichthys olivaceus) is an economically-important aquaculture flatfish in many countries. However, the lack of high-efficient genotyping tools has impeded the genomic breeding programs for Japanese flounder. We developed a 50K Japanese flounder SNP array, ″Yuxin No. 1,″ and report its utility in genomic selection (GS) for disease resistance to bacterial pathogens. We screened more than 42.2 million SNPs from the whole-genome resequencing data of 1099 individuals and selected 48 697 SNPs that were evenly distributed across the genome to anchor the array with Affymetrix Axiom genotyping technology. Evaluation of the array performance with 168 fish showed that 74.7% of the loci were successfully genotyped with high call rates (> 98%) and that the polymorphic SNPs had good cluster separations. More than 85% of the SNPs were concordant with SNPs obtained from the whole-genome resequencing data. To validate ″Yuxin No. 1″ for GS, the arrayed genotyping data of 27 individuals from a candidate population and 931 individuals from a reference population were used to calculate the genomic estimated breeding values (GEBVs) for disease resistance to Edwardsiella tarda. There was a 21.2% relative increase in the accuracy of GEBV using the weighted genomic best linear unbiased prediction (wGBLUP), compared to traditional pedigree-based best linear unbiased prediction (ABLUP), suggesting good performance of the ″Yuxin No. 1″ SNP array for GS. In summary, we developed the ″Yuxin No. 1″ 50K SNP array, which provides a useful platform for high-quality genotyping that may be beneficial to the genomic selective breeding of Japanese flounder.

关键词

牙鲆 / 单核苷酸多态性 / SNP芯片 / 抗病性 / 基因组选择 /

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Qian Zhou, Ya-dong Chen, Sheng Lu. 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. Engineering. 2021, 7(3): 406-411 https://doi.org/10.1016/j.eng.2020.06.017

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