Gene expression and eQTL analyses uncover natural variations underlying improvement of important agronomic traits during modern maize breeding.

Maize is a major staple crop worldwide, and during modern maize breeding, cultivars with increased tolerance to high-density planting and higher yield per plant contributed significantly to the increased yield per unit land area. Systematically identifying the key agronomic traits and the associated genomic changes during modern maize breeding remains a significant challenge due to the complexity of genetic regulation and interaction of the various agronomic traits, and most of them are often controlled by numerous small-effect quantitative trait loci (QTLs). Here, we performed phenotypic and gene expression analyses for a set of 137 maize elite inbred lines from different breeding eras in China. We found 4 yield-related traits are significantly improved during modern maize breeding. Through gene clustering analyses, we identified four groups of expressed genes with distinct trends of expression pattern change across the historical breeding eras. In combination with weighted gene coexpression network analysis, we identified several new candidate genes regulating various plant architecture- and yield-related agronomic traits, such as ZmARF16, ZmARF34, ZmTCP40, ZmPIN7, ZmPYL10, ZmJMJ10, ZmARF1, ZmSWEET15b, ZmGLN6 and Zm00001d019150. Further, by combining cis-eQTL analyses, correlation coefficient analyses, and population genetics, we identified a set of candidate genes that might have been under selection and contributed to the genetic improvement of various agronomic traits during modern maize breeding, including a number of known key regulators of plant architecture, flowering time and yield-related traits, such as ZmPIF3.3, ZAG1, ZFL2 and ZmBES1. Lastly, we validated the functional variations in GL15, ZmPHYB2, and ZmPYL10 for regulation of kernel row number, flowering time, plant height and ear height, respectively. Our results demonstrates the effectiveness of our combined approaches for uncovering key candidate regulatory genes and functional variation underlying improvement of important agronomic traits during modern maize breeding, and provide a valuable genetic resource for molecular breeding of high-density tolerant maize cultivars.