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Genomic selection strategies to overcome genotype by environment interactions in biosecurity-based aquaculture breeding programs

文献类型： 外文期刊

作者： Kang, Ziyi 1 ; Kong, Jie 1 ; Li, Qi 3 ; Sui, Juan 1 ; Dai, Ping 1 ; Luo, Kun 1 ; Meng, Xianhong 1 ; Chen, Baolong 1 ; Cao, Jiawang 1 ; Tan, Jian 1 ; Fu, Qiang 1 ; Xing, Qun 4 ; Luan, Sheng 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.Qingdao Marine Sci & Technol Ctr, Lab Marine Fisheries Sci & Food Prod Proc, Qingdao 266237, Shandong, Peoples R China

3.Ocean Univ China, Fisheries Coll, Qingdao 266003, Peoples R China

4.BLUP Aquabreed Co Ltd, Weifang 261312, Peoples R China

期刊名称：GENETICS SELECTION EVOLUTION （ 影响因子：3.1； 五年影响因子：4.2 ）

ISSN： 0999-193X

年卷期： 2025 年 57 卷 1 期

页码：

收录情况： SCI

摘要： BackgroundFamily-based selective breeding programs typically employ both between-family and within-family selection in aquaculture. However, these programs may exhibit a reduced genetic gain in the presence of a genotype by environment interactions (G x E) when employing biosecurity-based breeding schemes (BS), compared to non-biosecurity-based breeding schemes (NBS). Fortunately, genomic selection shows promise in improving genetic gain by taking within-family variance into account. Stochastic simulation was employed to evaluate genetic gain and G x E trends in BS for improving the body weight of L. vannamei, considering selective genotyping strategies for test group (TG) at a commercial farm environment (CE), the number individuals of the selection group (SG) genotyped at nucleus breeding center (NE), and varying levels of G x E.ResultsThe loss of genetic gain in BS ranged from 9.4 to 38.9% in pedigree-based selection and was more pronounced when G x E was stronger, as quantified by a lower genetic correlation for body weight between NE and CE. Genomic selection, particularly with selective genotyping of TG individuals with extreme performance, effectively offset the loss of genetic gain. With a genetic correlation of 0.8, genotyping 20 SG individuals in each candidate family achieved 93.2% of the genetic gain observed for NBS. However, when the genetic correlation fell below 0.5, the number of genotyped SG individuals per family had to be increased to 50 or more. Genetic gain improved by on average 9.4% when the number of genotyped SG individuals rose from 20 to 50, but the increase in genetic gain averaged only 2.4% when expanding from 50 to 80 individuals genotyped. In addition, the genetic correlation decreased by on average 0.13 over 30 generations of selection when performing BS and the genetic correlation fluctuated across generations.ConclusionsGenomic selection can effectively compensate for the loss of genetic gain in BS due to G x E. However, the number of genotyped SG individuals and the level of G x E significantly affected the extra genetic gain from genomic selection. A family-based BS selective breeding program should monitor the level of G x E and genotyping 50 SG individuals per candidate family to minimize the loss of genetic gain due to G x E, unless the level of G x E is confirmed to be low.

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