Novel strategies for genomic prediction of untested single-cross maize hybrids using unbalanced historical data.

KEY MESSAGE: Weighted outperformed unweighted genomic prediction using an unbalanced dataset representative of a commercial breeding program. Moreover, the use of the two cycles preceding predictions as training set achieved optimal prediction ability. Predicting the performance of untested single-cross hybrids through genomic prediction (GP) is highly desirable to increase genetic gain. Here, we evaluate the predictive ability (PA) of novel genomic strategies to predict single-cross maize hybrids using an unbalanced historical dataset of a tropical breeding program. Field data comprised 949 single-cross hybrids evaluated from 2006 to 2013, representing eight breeding cycles. Hybrid genotypes were inferred based on their parents' genotypes (inbred lines) using single-nucleotide polymorphism markers obtained via genotyping-by-sequencing. GP analyses were fitted using genomic best linear unbiased prediction via a stage-wise approach, considering two distinct cross-validation schemes. Results highlight the importance of taking into account the uncertainty regarding the adjusted means at each step of a stage-wise analysis, due to the highly unbalanced data structure and the expected heterogeneity of variances across years and locations of a commercial breeding program. Further, an increase in the size of the training set was not always advantageous even in the same breeding program. The use of the two cycles preceding predictions achieved optimal PA of untested single-cross hybrids in a forward prediction scenario, which could be used to replace the first step of field screening. Finally, in addition to the practical and theoretical results applied to maize hybrid breeding programs, the stage-wise analysis performed in this study may be applied to any crop historical unbalanced data.

Estimate of genetic gain in popcorn after cycles of phenotypic recurrent selection.

Popcorn is widely consumed in Brazil, yet there are few breeding programs for this crop. Recurrent selection (RS) is a viable breeding alternative for popcorn; however, the gains achieved must be frequently checked. The aim of this study was to assess the effect of selection for grain type (round and pointed) after four cycles of phenotypic RS on the main agronomic traits of popcorn, to estimate the genetic gain achieved for the trait of expansion volume (EV), and to obtain estimates of phenotypic correlations for the main traits of the crop in the UFLA E and UFLA R populations. The zero, one, two, and three cycles of the UFLA E and UFLA R populations, the fourth cycle, and the controls IAC-112 and IAC-125 were used. The experiments were conducted at the experimental farm of Universidade Federal de Lavras (UFLA; Environment 1) and at the experimental area of the Genetics and Plant Breeding Sector of the Department of Biology at UFLA (Environment 2) in the 2010/11 crop season. Nine agronomic traits were evaluated, including EV and grain yield (GY). The UFLA R and UFLA E populations showed similar behavior for all evaluated traits. The type of grain did not affect the genetic gain for EV, which was 5 and 3.7% in each cycle carried out in the UFLA E and UFLA R population, respectively. Phenotypic selection carried out during recombination for EV is an effective method for increasing expression of the trait. EV and GY did not show a linear association.

Evaluation of progenies from the fifth reciprocal recurrent selection cycle in maize.

The objective of this study was to evaluate the performance of 119 full sib progenies of the fifth cycle of reciprocal recurrent selection (RRS) derived from of Universidade Federal de Lavras maize breeding program. The experiment was carried out in an 11 x 11 triple lattice design at two locations (Lavras, Lambari). The plots consisted of two rows of 3 m, with four plants per 1 m and 0.60 meters of spacing between lines. The grain yield was obtained as kg/plot through weighing of husked ears. The contrast between progenies and controls was not significant, indicating there were no significant differences among the average grain yields of the progenies and controls. When considering the joint analysis, heritability was 64.2%; however, this estimate did not differ from the values estimated for each location separately. Estimates of genetic and phenotypic variance among progenies ranged from 0.21 to 0.28 and 0.30 to 0.47, respectively. Estimates of selection gain, for 10% selection intensity, indicated gains of 16% in the joint analysis of the two locations. The progenies of the fifth cycle of RRS had high average grain yield, associated with high variability. In comparison to the average grain yields exhibited by the controls, it was concluded that the progenies have the potential to be commercially exploited.

Genetic control of the number of leaves above the ear in maize.

In this study, we examined the genetic control of the number of leaves above the first ear in maize. The F2 generations and the backcrosses were obtained from 2 contrasting lines for this trait. All generations were assessed in a completely randomized block design with 2 replications. The number of leaves above the ear was counted when the plants were in the tasseling stage at the level of plants per plot. Mean and variance components were estimated using the weighted least square method. We observed a predominance of non-additive effects in the genetic control of number of leaves above the ear. These results indicate that this trait shows high heritability.