Genetic architecture of embryo size and related traits in maize

The embryo in maize has a critical role in controlling kernel nutrition components and grain yield. We measured five embryo weight and size traits, six kernel weight and size traits, and five embryo-to-kernel ratio traits in a nested association mapping (NAM) population of 611 recombinant inbred lines (RILs) derived from four inbred lines including the high-oil, giant-embryo line BY815 as the common parent. Using three statistical methods, we identified 5–22 quantitative trait loci (QTL) for each trait, explaining 4.7%–46.7% of the phenotypic variation. The genetic architecture of maize embryo size and its related traits appeared to be dominated by multiple small-effect loci with little epistasis, and the genetic control underlying embryo size appeared to be distinct from that underlying kernel size. A trait–QTL association network included 205 nodes and 439 edges and revealed 28 key loci associated with at least three traits. Cloned maize genes including ZmUrb2, Emp12 and ZmBAM1d, maize orthologs of known rice genes that control seed size including BG1, XIAO and GS9, and 11 maize orthologs of Arabidopsis EMBRYO-DEFECTIVE (EMB) genes were identified as underlying these key loci. Further, the phenotypic and genetic relationships between embryo size and kernel size were evaluated, and genetic patterns for identified loci that control embryo size and its related traits were proposed. Our findings reveal distinct genetic architectures for embryo size, kernel size, and embryo-to-kernel ratio traits and establish a foundation for the improvement of embryo-size-mediated kernel nutrition and grain yield.