Predicting the performance of untested single crosses: Trait and marker data

Predicting the performance of untested single crosses is an important objective in hybrid breeding programs. The effectiveness of best linear unbiased prediction (BLUP) of grain yield, moisture, stalk lodging, and root lodging of untested maize (Zea mays L.) single crosses was investigated. Multilocation data, from 1990 to 1995, for 4775 single crosses were obtained from the hybrid testing program of Limagrain Genetics. For each of 16 heterotic patterns, the performance of m untested single crosses was predicted from the trait phenotypes (T-BLUP) of n tested single crosses as Y_M = C_MP C_pp ^-1 Y_P, where Y_M = m × 1 vector of predicted performance of untested single crosses; C_MP = m × n matrix of genetic covariances between untested single crosses and tested single crosses; C_pp = n × n phenotypic covariance matrix among tested single crosses; and y_p = n × 1 vector of average performance of tested single crosses, corrected for yield trial effects. For one heterotic pattern with available parental RFLP data, performance also was predicted from (i) marker genotypes (M-BLUP) at loci with significant general combining ability effects and (ii) both trait phenotypes and marker genotypes (TM-BLUP). Correlations between predicted and observed performance were obtained by a delete-one cross-validation procedure. Across heterotic patterns, the correlations for T-BLUP ranged from 0.463 to 0.770 for yield, 0.868 to 0.936 for moisture, 0.466 to 0.685 for stalk lodging, and 0.164 to 0.518 for root lodging. Out of 74 RFLP loci, 9 had significant (P = 0.1) effects on yield, 14 on moisture, and 22 on stalk lodging. Correlations between predicted and observed yield were 0.764 for T-BLUP, 0.765 for TM-BLUP, and 0.341 for M-BLUP. Simplifying assumptions regarding marker effects and variances were used in TM-BLUP and M-BLUP, and whether a more complex model would lead to better TM-BLUP and M-BLUP predictions is yet to be determined. The results indicated that BLUP based on trait data alone is useful for routine identification of superior single crosses prior to field testing.