Prediction of genomic breeding values based on pre-selected SNPs using ssGBLUP, WssGBLUP and BayesB for Edwardsiellosis resistance in Japanese flounder

文献类型： 外文期刊

第一作者： Lu, Sheng

作者： Lu, Sheng;Chen, Songlin;Lu, Sheng;Liu, Yang;Yu, Xijiang;Li, Yangzhen;Yang, Yingming;Wei, Min;Zhou, Qian;Wang, Jie;Zhang, Yingping;Zheng, Weiwei;Chen, Songlin;Lu, Sheng;Liu, Yang;Li, Yangzhen;Yang, Yingming;Wei, Min;Zhou, Qian;Wang, Jie;Zhang, Yingping;Zheng, Weiwei;Chen, Songlin;Yu, Xijiang

作者机构：

期刊名称：GENETICS SELECTION EVOLUTION （ 影响因子：4.297； 五年影响因子：4.925 ）

ISSN： 0999-193X

年卷期： 2020 年 52 卷 1 期

页码：

收录情况： SCI

摘要： Background Edwardsiella tardacauses acute symptoms with ascites in Japanese flounder (Paralichthys olivaceus) and is a major problem for China's aquaculture sector. Genomic selection (GS) has been widely adopted in breeding industries because it shortens generation intervals and results in the selection of individuals that have great breeding potential with high accuracy. Based on an artificial challenge test and re-sequenced data of 1099 flounders, the aims of this study were to estimate the genetic parameters of resistance toE. tardain Japanese flounder and to evaluate the accuracy of single-step GBLUP (ssGBLUP), weighted ssGBLUP (WssGBLUP), and BayesB for improving resistance toE. tardaby using three subsets of pre-selected single nucleotide polymorphisms (SNPs). In addition, SNPs that are associated with this trait were identified using a single-SNP genome-wide association study (GWAS) and WssGBLUP. Results We estimated a heritability of 0.13 +/- 0.02 for resistance toE. tardain Japanese flounder. One million SNPs at fixed intervals were selected from 4,978,724 SNPs that passed quality controls. GWAS identified significant SNPs on chromosomes 14 and 24. WssGBLUP revealed that the putative quantitative trait loci on chromosomes 1 and 14 contained SNPs that explained more than 1% of the genetic variance. Three 50 k-SNP subsets were pre-selected based on different criteria. Compared with pedigree-based prediction (ABLUP), the three genomic methods evaluated resulted in at least 7.7% greater accuracy of predictions. The accuracy of these genomic prediction methods was almost unchanged when pre-selected trait-related SNPs were used for prediction. Conclusions Resistance toE. tardain Japanese flounder has a low heritability. GWAS and WssGBLUP revealed that the genetic architecture of this trait is polygenic. Genomic prediction of breeding values performed better than ABLUP. It is feasible to implement genomic selection to increase resistance toE. tardain Japanese flounder with 50 k SNPs. Based on the criteria used here, pre-selection of SNPs was not beneficial and other criteria for pre-selection should be considered.

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