Improving the accuracy of genomic predictions in an outcrossing species with hybrid cultivars between heterozygote parents: a case study of oil palm (Elaeis guineensis Jacq.)

Genomic selection (GS) is a method of marker-assisted selection revolutionizing crop improvement, but it can still be optimized. For hybrid breeding between heterozygote parents of different populations or species, specific aspects can be considered to increase GS accuracy: (1) training population genotyping, i.e., only genotyping the hybrid parents or also a sample of hybrid individuals, and (2) marker effects modeling, i.e., using population-specific effects of single nucleotide polymorphism alleles model (PSAM) or across-population SNP genotype model (ASGM). Here, this was investigated empirically for the prediction of the performances of oil palm hybrids for yield traits. The GS model was trained on 352 hybrid crosses and validated on 213 independent hybrid crosses. The training and validation hybrid parents and 399 training hybrid individuals were genotyping by sequencing. Despite the small proportion of hybrid individuals genotyped and low parental heterozygosity, GS prediction accuracy increased on average by 5% (range 1.4–31.3%, depending on trait and model) when training was done using genomic data on hybrids and parents compared with only parental genomic data. With ASGM, GS prediction accuracy increased on average by 3% (− 10.2 to 40%, depending on trait and genotyping strategy) compared with PSAM. We conclude that the best GS strategy for oil palm is to aggregate genomic data of parents and hybrid individuals and to ignore the parental origin of marker alleles (ASGM). To gain a better insight into these results, future studies should examine the respective effect of capturing genetic variability within crosses and taking segregation distortion into account when genotyping hybrid individuals, and investigate the factors controlling the relative performances of ASGM and PSAM in hybrid crops.