Pyramiding of favorable haplotypes of major QTLs for yield-related traits to improve maize (Zea mays L.) productivity

Although numerous genetic loci related to maize ( Zea mays L.) yield have been identified, their variability across germplasms shows challenges to apply them in breeding. Here, we aimed to utilized yield-related genetic loci to breed high-yielding maize varieties. We developed a recombinant inbred line (RIL) population comprising 320 lines and investigated seven ear-related and two kernel-related phenotypes in two environments. Using a linkage map (length, 2193.38 ​cM) with 2154 genetic bins, we identified 79 unique quantitative trait loci (QTLs), 37 (46.83 ​%) of which had been reported previously. Additionally, nine major QTLs and 13 pleiotropic QTLs were detected, with additive effects showed in traits of ear row number and ear length. We further analyzed lines containing one to six major QTLs associated with ear-related traits. The phenotypic values of all seven ear traits were significantly positively correlated with the number of favorable haplotypes of major QTLs (FHMQs). Materials containing multiple FHMQs exhibited higher yield, which was indicative of a high breeding value. We crossed the RIL materials with three tester lines, and the yield of the hybrids with parents containing three to four FHMQs were significantly higher than those of the hybrids with parents containing two or fewer FHMQs. This result confirmed a positive correlation between hybrid yield and the number of FHMQs in the parents. Finally, we successfully generated three new hybrid varieties by crossing three lines pyramiding three, four, and four FHMQs with the tester line Jing724. The materials generated in this study exhibit excellent breeding potential for enhancing maize yield. • QTLs associated with ear- and kernel-related traits in maize were identified. • Favorable haplotypes of major QTLs (FHMQs) were characterized. • Inbred lines' yields increased with more FHMQs for yield-related traits. • Hybrids' yields increased with more FHMQs for yield-related traits in the parents. • High-yielding hybrids were bred using recombinant inbred lines with more FHMQs.