Genome-wide identification of genes enabling accurate prediction of hybrid performance from parents across environments and populations for gene-based breeding in maize.

Accurate prediction of hybrid offspring complex trait phenotype from parents is paramount to enhanced plant breeding, animal breeding, and human medicine. Here we report genome-wide identification of genes enabling accurate prediction of hybrid offspring complex traits from parents using maize grain yield as the target trait. We identified 181 ZmF1GY genes enabling prediction of maize (Zea mays L.) F1 hybrid grain yield from parents and tested their utility and efficiency for predicting F1 hybrid grain yields from parents using their expressions, genic SNPs, and number of favorable alleles (NFAs), respectively. The ZmF1GY genes predicted hybrid grain yields from parents at an accuracy of 0.86, presented by correlation coefficient between predicted and observed phenotypes, within an environment, 0.74 across environments, and 0.64 across populations, outperforming genomic prediction by 27-406%, 23%, and 40%, respectively. Furthermore, we identified nine of the ZmF1GY genes containing SNPs or InDels in parents that increased or decreased hybrid grain yields by 14-46%. When the NFAs of these nine ZmF1GY genes were used for hybrid grain yield prediction from parents, they predicted hybrid grain yields at an accuracy of 0.79, outperforming genomic prediction by 21% that was based on up to tens of thousands of genome-wide SNPs. These results demonstrate the feasibility of developing a gene toolkit for a species enabling gene-based breeding across environments and populations that is much more powerful and efficient than current breeding, thereby helping secure the world's food production. The methodology is applicable to all crops, livestock, and humans.

Yield, Insect-Derived Ear Injury, and Aflatoxin Among Developmental and Commercial Maize Hybrids Adapted to the North American Subtropics.

The development of maize (Zea mays L.) hybrids that are adapted to subtropical areas of North America should consider yield potential under heat and moisture stress, and reduced susceptibility to insect herbivory and disease. To aid in this process, maize hybrids (43 developmental and seven non-Bt commercial hybrids) were evaluated for severity of ear injury to Helicoverpa zea (Boddie) and Spodoptera frugiperda (J. E. Smith) (Lepidoptera: Noctuidae), susceptibility to Aspergillus flavus (Link) (Deuteromycetes: Moniliales), and yield. In subtropical Corpus Christi and College Station, TX, field experiments conducted over three years revealed significant differences among maize hybrids with the rank of the selected measurements differing across the two locations. When the location by maize hybrid interaction was not significant, variation across the main factors of maize hybrid genetics (in all cases) and location (in some cases) was detected. In 2014, a significant location by maize hybrid interaction in yield but not aflatoxin and ear injury were likely associated with differences in weather between locations. In Corpus Christi in 2015, a location by maize hybrid interaction was detected for ear injury only. Overall, experimental maize hybrids, containing the inbred line Tx777, displayed partial resistance to insect derived ear injury in both locations, and some hybrid testcrosses exhibited low rates of aflatoxin accumulation while maintaining relatively high yields. Tx777 was selected from populations originating in Bolivia and adapted to subtropical climates. The most promising hybrid testcrosses had lower ear injury and aflatoxin accumulation, and good yield under varying heat and moisture stress at the two subtropical maize growing areas in this study.