Methods for evaluating effects of transgenes for quantitative traits

Transgenes that improve quantitative traits have traditionally been evaluated in one or a few genetic backgrounds across multiple environments. However, testing across multiple genetic backgrounds can be equally important to accurately quantify the value of a transgene for breeding objectives. Creating near‐isogenic lines across a wide germplasm space is costly and time consuming, which renders it impractical during early stages of testing. In this experiment, we evaluate three approaches to sample the genetic space while concurrently testing across environments. We created both transgenic and non‐transgenic doubled haploid maize (Zea mays L.) lines, F2:3 lines, and bulk F3 families to determine if all methods resulted in similar estimation of transgene value and to identify the number of yield trial plots from each method necessary to obtain a stable estimate of the transgene value. With one exception, the three methods consistently estimated a similar effect of the transgene. We suggest that bulked F3 lines topcrossed to a tester inbred is the most effective method to estimate the value of a transgene across both genetic space and environments. Core Ideas Transgenes affecting quantitative traits should be tested widely in a breeding program's germplasm. Developing and testing many isogenic line pairs will show the value of the transgene, but it is costly. Using bulked F3 lines streamlines the evaluation of a wide germplasm base. Bulked F3 lines are equivalent to doubled haploids or F2:3 lines in estimating the value of a transgene.