Accurate genomic selection using low-density SNP panels preselected by maximum likelihood estimation
文献类型: 外文期刊
作者: Qu, Shiyu 1 ; Lu, Sheng 1 ; Liu, Yang 1 ; Li, Ming 1 ; Chen, Songlin 1 ;
作者机构: 1.Chinese Acad Fishery Sci, Yellow Sea Fisheries Res Inst, State Key Lab Mariculture Biobreeding & Sustainabl, Qingdao 266071, Shandong, Peoples R China
2.Chinese Acad Fishery Sci, Yellow Sea Fisheries Res Inst, Key Lab Sustainable Dev Marine Fisheries, Minist Agr & Rural Affairs, Qingdao 266071, Shandong, Peoples R China
3.Laoshan Lab, Lab Marine Fisheries Sci & Food Prod Proc, Qingdao 266237, Shandong, Peoples R China
4.Yellow Sea Fisheries Res Inst, 106 Nanjing Rd, Qingdao 266071, Peoples R China
关键词: Maximum likelihood estimation; Genomic selection; SNP pre-selection; MLE-rank
期刊名称:AQUACULTURE ( 影响因子:4.5; 五年影响因子:4.6 )
ISSN: 0044-8486
年卷期: 2024 年 579 卷
页码:
收录情况: SCI
摘要: Genomic selection (GS) poses a challenge for the prediction of the genomic estimated breeding value (GEBV) using a low-density SNP panel. Several methods have been proposed for SNP preselection. However, these methods often suffer from either significant computational complexity or erratic accuracy in GS. In this study, we developed an approach called MLE-rank based on maximum likelihood estimation to preselect a set of SNPs for GS. First, we generated 90 simulated datasets and compared the performance of MLE-rank with uniform dis-tribution and preselection based on a genome-wide association study (GWAS). For simulated datasets, compared to uniform distribution, both MLE-rank and GWAS preselection reduced the SNP density by a factor of 10 while maintaining prediction accuracy. Additionally, compared to the other two methods, MLE-rank's prediction ac-curacy was significantly improved with the medium-and high-heritability datasets. Then, we further evaluated these three preselection approaches using real disease-resistant phenotypes of leopard coral grouper (Plec-tropomus leopardus) and Japanese flounder (Paralichthys olivaceus). We found that the 3 k SNPs preselected by MLE-rank had a stable and effective prediction effect. The uniform distribution requires 70 k, while the GWAS preselection method requires 3 k (P. leopardus) and 50 k (P. olivaceus) to achieve similar prediction accuracy. Finally, we evaluated the prediction accuracy of MLE-rank using candidate populations of flounders and their progeny survival rates, with uniform distribution and GWAS preselection as benchmarks. In the results for this dataset, MLE-rank was found to have the same predictive effect for low-density SNP panels as it did for high-density SNPs, regardless of whether GWAS preselection or uniform distribution was used. Taken together, the results we have observed indicate that we have ensured that MLE-rank does not reduce prediction accuracy for any of the datasets. MLE-rank showed superior performance in reducing the number of SNPs. Moreover, we observed a relative standard deviation in prediction accuracy when using a low density of SNPs selected by MLE-rank compared to a high density determined through a uniform distribution strategy. In conclusion, MLE-rank not only reduces the number of SNPs used for GS but also exhibits high predictive accuracy. This could potentially lead to a decrease in genotyping costs and promote the wider application of GS in fish breeding.
- 相关文献
作者其他论文 更多>>
-
Development of a 20 K SNP array for the leopard coral grouper, Plectropomus leopardus
作者:Zhou, Qian;Lu, Sheng;Liu, Yang;Chen, Songlin;Zhou, Qian;Lu, Sheng;Liu, Yang;Chen, Songlin;Zhou, Bo;Zhou, Qian;Chen, Songlin
关键词:Leopard coral grouper; Plectropomus leopardus; SNP array; Aquaculture
-
Evaluation of regulatory capacity of three lactic acid bacteria on the growth performance, non-specific immunity, and intestinal microbiota of the sea cucumber Apostichopus japonicus
作者:Liu, Longzhen;Liu, Yang;Qin, Guangcai;Wei, Cong;Li, Yongmei;Cui, Liang;Tian, Xiangli;Liu, Longzhen
关键词:Growth performance; Non-specific immunity; Intestinal microbiota; Probiotics; Apostichopus japonicus
-
Comparative transcriptome analysis of hybrid Jinhu grouper (Epinephelus fuscoguttatus ♀ x Epinephelus tukula ♂) and Epinephelus fuscoguttatus under temperature stress
作者:Duan, Pengfei;Tian, Yongsheng;Li, Zhentong;Chen, Shuai;Li, Linlin;Wang, Xinyi;Wang, Linna;Liu, Yang;Tian, Yongsheng;Li, Zhentong;Li, Linlin;Wang, Linna;Liu, Yang;Duan, Pengfei;Chen, Shuai;Wang, Xinyi;Zhai, Jieming;Li, Wensheng;Wang, Qingbin;Ma, Wenhui;Pang, Zunfang;Tian, Yongsheng
关键词:Epinephelus fuscoguttatus; Jinhu grouper ( Epinephelus fuscoguttatus female x Epinephelus tukula male); Temperature stress; Transcriptome
-
Characterization and potential function of 7-dehydrocholesterol reductase (dhcr7) and lathosterol 5-desaturase (sc5d) in Cynoglossus semilaevis sexual size dimorphism
作者:Wang, Jialin;Shi, Rui;Yang, Qian;Chen, Zhangfan;Wang, Jiacheng;Gong, Zhihong;Chen, Songlin;Wang, Na;Wang, Jialin;Shi, Rui;Yang, Qian;Wang, Jiacheng;Gong, Zhihong;Chen, Zhangfan;Chen, Songlin;Wang, Na;Chen, Zhangfan;Chen, Songlin;Wang, Na
关键词:Chinese tongue sole ( Cynoglossus semilaevis ); 7-dehydrocholesterol reductase ( dhcr7 ); lathosterol 5-desaturase ( sc5d ); Promoter activity; siRNA; Protein subcellular localization
-
Development of a prey-predator species distribution model for a large piscivorous fish: A case study for Japanese Spanish mackerel Scomberomorus niphonius and Japanese anchovy Engraulis japonicus
作者:Liu, Shuhao;Tian, Yongjun;Liu, Yang;Liu, Shuhao;Tian, Yongjun;Liu, Yang;Tian, Yongjun;Liu, Yang;Alabia, Irene D.;Cheng, Jiahua;Ito, Shin-ichi;Liu, Yang
关键词:Species distribution model; Climate change; Machine learning; Fisheries oceanography; Western North Pacific
-
Genome-wide DNA methylation mediates the resistance to vibriosis in Cynoglossus semilaevis
作者:Ma, Xinran;Chen, Quanchao;Chen, Zhangfan;Chen, Songlin;Zhou, Qian;Ma, Xinran;Chen, Quanchao;Chen, Zhangfan;Chen, Songlin;Zhou, Qian;Ma, Xinran
关键词:Cynoglossus semilaevis; Kidney; Vibriosis resistance; Transcriptome; DNA methylation
-
Phosphoproteomics Reveal New Candidates in Abnormal Spermatogenesis of Pseudomales in Cynoglossus semilaevis
作者:Li, Xihong;Li, Lu;Cui, Zhongkai;Li, Ming;Xu, Wenteng;Li, Lu
关键词:Cynoglossus semilaevis; phosphoproteome; spermatogenesis; RanBP2; Mapk