Cost-effective genomic prediction of critical economic traits in sturgeons through low-coverage sequencing
文献类型： 外文期刊
作者： Song, Hailiang 1 ; Dong, Tian 1 ; Wang, Wei 1 ; Jiang, Boyun 3 ; Yan, Xiaoyu 1 ; Geng, Chenfan 1 ; Bai, Song 1 ; Xu, Shijian 3 ; Hu, Hongxia 1 ;
作者机构： 1.Beijing Acad Agr & Forestry Sci, Fisheries Sci Inst, Beijing 100068, Peoples R China
2.Beijing Key Lab Fisheries Biotechnol, Beijing 100068, Peoples R China
3.Minist Agr & Rural Affairs, Key Lab Sturgeon Genet & Breeding, Hangzhou 311799, Peoples R China
4.Hangzhou Qiandaohu Xunlong Scitech Co Ltd, Hangzhou 311799, Peoples R China
5.Natl Innovat Ctr Digital Seed Ind, Beijing 100097, Peoples R China
关键词： Sturgeon; Low-coverage whole-genome sequencing; Imputation; Genomic prediction; Linkage disequilibrium pruning; Incremental feature selection
期刊名称：GENOMICS （ 影响因子：3.4； 五年影响因子：3.5 ）
ISSN： 0888-7543
年卷期： 2024 年 116 卷 4 期
页码：
收录情况： SCI
摘要： Low-coverage whole-genome sequencing (LCS) offers a cost-effective alternative for sturgeon breeding, especially given the lack of SNP chips and the high costs associated with whole-genome sequencing. In this study, the efficiency of LCS for genotype imputation and genomic prediction was assessed in 643 sequenced Russian sturgeons (similar to 13.68x). The results showed that using BaseVar+STITCH at a sequencing depth of 2x with a sample size larger than 300 resulted in the highest genotyping accuracy. In addition, when the sequencing depth reached 0.5x and SNP density was reduced to 50 K through linkage disequilibrium pruning, the prediction accuracy was comparable to that of whole sequencing depth. Furthermore, an incremental feature selection method has the potential to improve prediction accuracy. This study suggests that the combination of LCS and imputation can be a cost-effective strategy, contributing to the genetic improvement of economic traits and promoting genetic gains in aquaculture species.
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