Phenotypic associations at individual loci
Although 50 maternal families were initially selected for the greenhouse experiment, only 42 had sufficient germination for measurements to be included in analyses. Six out of the eight measured phenotypic traits were significantly different in the drought treatment versus the wet treatment. Height growth (GR) and shoot weight (SW) decreased, while root length (RL), the root-shoot dry mass ratio (R2S), stomata density on the adaxial side (SD_AD), and the number of stomatal rows on the abaxial side (NR_AB) increased. We therefore focused on these traits for the G2P association. We measure the association of SNPs to either the average measurement of control treatment family for each trait or the average change in the trait from wet to dry conditions (drought responsiveness). Heritabilities of trait responses to drought ranged from 0.15 to 0.65, and are discussed further in (Wu et al. 2023), with variation in shoot growth in response to drought being particularly variable.
More SNPs were associated with the trait drought responses (1,154) than with the control traits (817). While control R2S had the most associations and SW the least (Table 2), the opposite was the case for drought responsiveness (Table 3). The number of SNPs associated with more than one trait was low in both G2P analyses. The highest degree of overlap was in control traits of RL and R2S (12 SNPs) and of R2S and NR_AB (9 SNPs) (Fig. 3). The proportion of associated upstream SNPs was similar across control traits (32-40%), but proportions of other categories varied widely, with the proportion of missense SNPs ranging from 8-25%. For drought response, the distribution of SNPs in all categories differed, with the proportion of upstream being 19-34% and the proportion of missense being 7-16% for traits other than R2S. R2S was only associated with 6 SNPs, five upstream and one downstream.