The theory on and software simulating large-scale genomic data for genotype-by-environment interactions

BMC Genomics

Zhe Zhang¹  Xiujin Li²  Yunmao Huang²  Xiangdong Ding³  Hailiang Song³  Qin Zhang⁴ 

[1] Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, 510642, Guangzhou, People’s Republic of China;Guangdong Provincial Key Laboratory of Waterfowl Healthy Breeding, College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, 510225, Guangzhou, Guangdong, People’s Republic of China;Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China;Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, 271001, Taian, China;

关键词: Data simulation;    Genotype-by-environment interaction;    Threshold trait;    GPOPSIM2.0;   

DOI  :  10.1186/s12864-021-08191-z

来源: Springer

【 摘 要 】

BackgroundWith the emphasis on analysing genotype-by-environment interactions within the framework of genomic selection and genome-wide association analysis, there is an increasing demand for reliable tools that can be used to simulate large-scale genomic data in order to assess related approaches.ResultsWe proposed a theory to simulate large-scale genomic data on genotype-by-environment interactions and added this new function to our developed tool GPOPSIM. Additionally, a simulated threshold trait with large-scale genomic data was also added. The validation of the simulated data indicated that GPOSPIM2.0 is an efficient tool for mimicking the phenotypic data of quantitative traits, threshold traits, and genetically correlated traits with large-scale genomic data while taking genotype-by-environment interactions into account.ConclusionsThis tool is useful for assessing genotype-by-environment interactions and threshold traits methods.

【 授权许可】

CC BY