Genomic selection prediction accuracy in a perennial crop: case study of oil palm (Elaeis guineensis Jacq.)

Abstract

Key message

Genomic selection empirically appeared valuable for reciprocal recurrent selection in oil palm as it could account for family effects and Mendelian sampling terms, despite small populations and low marker density.

Abstract

Genomic selection (GS) can increase the genetic gain in plants. In perennial crops, this is expected mainly through shortened breeding cycles and increased selection intensity, which requires sufficient GS accuracy in selection candidates, despite often small training populations. Our objective was to obtain the first empirical estimate of GS accuracy in oil palm (Elaeis guineensis), the major world oil crop. We used two parental populations involved in conventional reciprocal recurrent selection (Deli and Group B) with 131 individuals each, genotyped with 265 SSR. We estimated within-population GS accuracies when predicting breeding values of non-progeny-tested individuals for eight yield traits. We used three methods to sample training sets and five statistical methods to estimate genomic breeding values. The results showed that GS could account for family effects and Mendelian sampling terms in Group B but only for family effects in Deli. Presumably, this difference between populations originated from their contrasting breeding history. The GS accuracy ranged from −0.41 to 0.94 and was positively correlated with the relationship between training and test sets. Training sets optimized with the so-called CDmean criterion gave the highest accuracies, ranging from 0.49 (pulp to fruit ratio in Group B) to 0.94 (fruit weight in Group B). The statistical methods did not affect the accuracy. Finally, Group B could be preselected for progeny tests by applying GS to key yield traits, therefore increasing the selection intensity. Our results should be valuable for breeding programs with small populations, long breeding cycles, or reduced effective size.

Appendix: Estimation of parental breeding values

The mating design of the progeny tests consisted of 445 Deli × Group B crosses made according to an incomplete factorial design. The crosses were evaluated in 26 trials planted between 1995 and 2000. The experimental designs of the trials were RCBD with five or six blocks and balanced lattices of rank four or five. The bunch production was measured on 30,872 palms and bunch quality on 21,525 palms. Eight traits were studied. The bunch number (BN) and average bunch weight (ABW) were measured every ten days on palms from ages 6 to 11. The annual cumulative BN and mean annual ABW were used in analysis. The median number of progenies with bunch production data was 169 per Deli parent (ranging from 25 to 743) and 141 (23–859) per Group B parent. The fruit-to-bunch (F/B), pulp-to-fruit (P/F), kernel-to-fruit (K/F), and oil-to-pulp (O/P) ratios, the number of fruits per bunch (NF), and the average fruit weight (FW) were measured on two bunches at ages five and six on a sample of at least 24 palms per cross. The median number of bunches analyzed was 327 per Deli parent (ranging from 69 to 1,358) and 309 per Group B parent (73–1,149).

EBV were computed as traditional pedigree-based BLUP (T-BLUP) predictors of the random effects a _A and a _B , using a mixed model of the form:

$$y \, = \, {\varvec{X\beta}} + \, {\varvec{Z}}_{{\mathbf{1}}} {\varvec{a}}_{\text{Deli}} + \, {\varvec{Z}}_{{\mathbf{2}}} {\varvec{a}}_{B} + \, {\varvec{Z}}_{{\mathbf{3}}} {\varvec{b}} \, + \, {\varvec{Z}}_{{\mathbf{4}}} {\varvec{c}} \, + \, {\varvec{Z}}_{{\mathbf{5}}} {\varvec{p}} \, + \, {\varvec{Z}}_{{\mathbf{6}}} k \, + \, {\varvec{e}},$$

where y is the vector of data records for the trait being analyzed, β the vector of fixed effects (general mean, trial and block within trial), a _Deli and a _B vectors of general combining ability of Deli ~N(0, 0.5A _Deli $\sigma_{\rm{Deli}}^{2}$) and Group B individuals ~N(0, 0.5A _B $\sigma_{B}^{2}$), respectively, b the vector of the incomplete block within block and trial effects ~N(0, I $\sigma_{b}^{2}$), c the vector of specific combining ability of single crosses ~N(0, D $\sigma_{c}^{2}$), p the vector of permanent environmental effects used to take repeated measures into account ~N(0, I $\sigma_{p}^{2}$), k the vector of elementary plot effects ~N(0, I $\sigma_{k}^{2}$) and e the vector of residual effects ~N(0, I $\sigma_{e}^{2}$). X, Z ₁  − Z ₆ are incidence matrices. A _Deli and A _B are matrices of additive relationships among Deli and Group B individuals, respectively, computed from pedigrees. D is the matrix of dominance relationships among crosses computed from the pedigree, with value between crosses Deli × B and Deli′ × B′ equal to f _Deli,_Deli′ × f _B,B′ , where f _Deli,_Deli′ and f _B,B′ are the coefficient of coancestry between the Deli and Group B parents. I is an identity matrix. For BN and ABW, the model also included a fixed age effect and a random age within cross effect a ~N(0, D $\otimes$ I $\sigma_{a}^{2}$). This model was based on the model of Stuber and Cockerham (1966) for hybrids between unrelated populations, as previously used in oil palm by Purba et al. (2001). The R-ASReml package (Butler et al. 2009) for R (R Core Team 2013) was used to obtain variance component estimates and EBV of all individuals.

The accuracy of the general combining ability a _i of an individual i (actually $a_{{{\text{Deli}}_{\text{i}} }}$ or $a_{{B_{i} }}$ depending on the population of origin of i) is given by $r_{{a,\hat{a}_{i} }} = \sqrt {\frac{{1 - PEV_{{a_{i} }} }}{{0.5(1 + F_{i} )\sigma_{a}^{2} }}},$ where PEV _ai is the prediction error variance associated with a _i , 0.5(1 + F _i ) is the diagonal of the relationship matrix used in the mixed model (i.e., 0.5A _Deli or 0.5A _B , depending on the population of origin of i), F _i is the inbreeding coefficient and $\sigma_{a}^{2}$ is the additive variance (i.e., $\sigma_{\text{Deli}}^{2}$ or $\sigma_{B}^{2}$, depending on the population). This formula was used to compute the mean accuracy of the general combining ability of the 131 Deli and 131 Group B parents used in the GS analysis, which was 0.89, ranging from 0.83 ± 0.06 (SD) for O/P in Deli to 0.93 ± 0.04 for K/F in Group B.