Phenotypic and genetic analysis of the seed pedicel of Zea mays

The maize seed pedicel, an important tissue connecting the seed to the cob, plays a crucial role in seed development. However, surprisingly little is known about the genetic basis of the maize seed pedicel-placenta (SP) and its impact on seed germination. Here, we established a biomechanical model of maize seed water absorption and dehydration using 50 maize cultivars, and conducted a comparative analysis of SP and its related traits, as well as their effects on seed germination and vigor. The results revealed that SP size is closely related to seed size and that there are differences in SP traits among various cultivars. Removal of the SP can improve seed germination and enhance seed vigor in maize. Additionally, the genetic basis of four SP traits—pedicel-placenta length (PL), pedicel-placenta width (PW), pedicel-placenta thickness (PT), and pedicel-placenta cross-sectional area (PC)—was investigated in a population of recombinant inbred lines (RILs) derived from Xinzi517 × B73 and an association panel comprising 368 inbred lines. A total of nine quantitative trait loci (QTLs) controlling these traits were detected: one for PL, three for PW, three for PT, and two for PC. Furthermore, 58 single nucleotide polymorphisms (SNPs) significantly associated with these four traits were identified in the association panel across four environments: 16 for PL, 18 for PW, 19 for PT, and 5 for PC. A total of 61 candidate genes were identified via association analysis and linkage mapping: 18 for PL, 18 for PW, 13 for PT, and 12 for PC. These findings provide insights into the mechanism of seed germination and support the improvement of molecular marker assisted selection (MAS) for high-vigor maize breeding.