Dissecting the genetic architecture of important traits that enhance wild germplasm resource usage in modern maize breeding

Domestication and improvement of maize (Zea mays L.) from 10,000 years ago has produced remarkable alterations from its wild ancestor, teosinte. To investigate the genetic basis of changes in plant and inflorescence traits, we developed a teosinte-maize intermated population. More than 200 common quantitative trait loci (QTLs) and 44 QTL clusters were identified underlying 13 vegetative and reproductive traits. Among them, few common QTLs with major effects were observed, which supported previous hypotheses that a small number of major loci can explain a large portion of phenotypic changes during domestication. Additionally, we found many moderate or minor QTLs that might have critical roles in shaping plant architecture and enhancing grain yield of modern maize. Although maize has better performance for the traits studied here, teosinte still harbored desirable alleles in some of the common QTLs. Furthermore, we integrated multiple datasets and predicted candidate genes underlying these QTLs. This study elucidates the genetic basis of these vegetative and reproductive traits in maize and teosinte, and suggests the possibility of improving maize by teosinte re-domestication using a small number of loci.