Genomic mating is a technology unionizing all available SNPs to predict the expected genetic performance of progeny for all combinations between males and females (Tang, et al. 2023). To implement genomic mating, genotype of all individuals and additive or dominant effects of all SNPs should be provided. The format of SNP effect file can be found at here. The command to do genomic mating by HIBLUP is as following:
./hiblup --mating
--bfile demo
--score demo.snpeff
--thread 32
--out demo
Mating results are saved in file demo.mating, brief view of this file:
sir dam g Ind704 Ind710 -0.0675817 Ind704 Ind711 1.06056 Ind704 Ind712 2.00997 Ind704 Ind713 -0.0879987 Ind704 Ind714 -0.492576
The last column is the expected genetic performance of progeny for different combinations.
IMPORTANT
(1) The SNP with the same name between demo.bim and demo.snpeff should have the consistent reference (A1) and alternative (A2) allele.
(2) All the individuals in demo.fam should be clearly marked with gender (located at the 5th column, 1=male; 2=female; other=unknown), any individual with unknown gender will be deleted in analysis.