The use of UAS phenotyping can provide functional information about the phenotypic effect of single nucleotide polymorphisms (SNP) on complex trait (e.g. plant height) using advanced breeding populations, Two SNPs affecting plant height (PHT) and grain yield in maize (Zea mays L.) where previously discovered using diversity panel of maize hybrids in GWAS study in Texas and have been implemented into Kompetitive Allele Specific PCR (KASP) assays. Backcross-based heterogeneous inbred families (HIFs) were advanced using four different linkage mapping populations during 2016 to 2019 using the two SNPs to (i) advance the HIF populations and (ii) validate allelic effect sizes of the SNPs on PHT during multiple growth stages via UAS surveys. Weekly PHT measurements were estimated from UAS survey images from emergence to harvest (5/17/19 to 7/12/19). Manual PHT measurements were collected at a single time point nearing harvest (7/02/2019), as typically done. Manual PHT measurements results showed that the best linear unbiased estimations (BLUEs) of the dominant allele (XX calls) contributed by NC356 and LH82 were consistently 2 to 12 cm taller, depending on thegenetic background of each HIF. UAS PHT estimates confirmed hand measurements (r=0.85), and for the first time, demonstrated a temporal dimension to these SNP’s allelic effects size. In early growing stages the allelic effect sizes of each SNPs varied from 10 to 14 cm narrowing to 4 cm as populations reached termination of terminal growth stages, when manual PHT measurements are typically taken. Our results demonstrated that allelic effect sizes of quantitative traits can be dynamic in temporal growth resulting in informative phenotypic variability is being overlooked following traditional phenotyping methods.