Spectral Phenotyping Reveals Time-Specific QTLs in Field-Grown Lettuce

Lettuce (Lactuca sativa) is an important field crop, but our understanding of its phenotypic variation and underlying genetics under natural field conditions remains limited, posing challenges for identifying effective crop breeding targets. Longitudinal hyperspectral phenotyping allows for non-invasive monitoring of crop performance under diverse agricultural conditions. In this study, we used hyperspectral imaging to assess the phenotypic variation of almost 200 different field-grown lettuce varieties, following the same plants from just after seedling- to flowering-stage. With automated image processing, we extracted a wide range of spectral phenotypes related to metabolite content, growth efficiency, and environmental stress responses, creating a multi-dimensional time-resolved data set. Principal component analysis (PCA) revealed the major axes of spectral variation over time, and highlighted differences in spectral patterns among lettuce genotypes. Integrating on-site weather data, we modelled GxE interactions of reflectance, revealing regions of the lettuce vegetation spectrum that are primarily shaped by genotype and/or environment. We estimated phenotypic plasticity in response to time, temperature and rainfall using best linear unbiased predictions (BLUPs), capturing genotype-specific developmental trajectories and responses to the environment. We used genome-wide association studies (GWAS) to identify quantitative trait loci (QTLs) of PC-based, single and BLUP-based phenotypes, disentangling the genetic architecture of spectral lettuce phenotypes from major axes of variation down to single wavelength spectral plasticity. These findings provide new insights into the genome-wide genetic regulation and dynamics of spectral phenotypes in field grown lettuce.