Gene-based Breeding in Maize: A New Method Powerful and Efficient for Enhanced Grain Yield Breeding

We previously cloned 1,501 ZmINGY (Zea mays Inbred Grain Yield) and 137 ZmF1GY (Zea mays F1 hybrid Grain Yield) genes using the gExpress technology (U.S. Patent Serial No.: 62/298,606). Here we report a gene-based breeding (GBB) method developed using these cloned genes. GBB designs and breeds superior cultivars based on alleles and expression profiles of the genes controlling the targeted trait. We identified 63 SNPs/InDels from 27 of the ZmINGY genes that increased or decreased inbred grain yield by 14.1% - 54.2%. Using these SNPs/InDels, we developed a gene allele selection chip that allows designing and developing superior F₁ hybrids. Furthermore, we predicted the grain yields of inbreds and hybrids with nine genomic selection models using 27 of the ZmINGY SNPs/InDels and the ZmINGY or ZmF1GY expression profiles, respectively. The 27 ZmINGY SNPs/InDels predicted inbred grain yield at a correlation coefficient between predicted and observed grain yield of r = 0.36 – 0.46 (P = 2.50E-07 – 0.00E+00) and the ZmINGY expression profiles predicted inbred grain yield at r = 0.59 – 0.84 (P = 0.00E+00), which was higher than those of DNA marker-based genomic selection by 14% - 73%. We also predicted the F₁ hybrid grain yield using the 137 ZmF1GY genes (r = 0.43 – 0.70, P = 0.00E+00). In comparison, none of the randomly-selected maize gene sets could predict the grain yield. These results provide a new line of evidence on the efficiency of the gExpress technology in genome-wide high-throughput gene cloning and an efficient method for enhanced maize yield breeding.