Hypocotyl length and associated genetic variants are important for seedling emergence in Arabidopsis thaliana populations from beaches
Because beach plants face burial by shifting sand, elongated hypocotyls are hypothesized to be an important trait promoting emergence of seedlings. Natural populations of Arabidopsis thaliana exhibit fixed and plastic differences in hypocotyl length. Long hypocotyls were observed in the greenhouse in A. thaliana lines sampled from gravel beaches. To explore this phenotype and test for a positive effect on seedling emergence, I used focal populations from gravel beaches in Sweden, as well as conspecific populations from fine sand beaches and inland sites. I grew a 298 line Swedish mapping panel on soil, fine sand, and pebbles. Hypocotyl length was measured, from the bottom of the petioles to the root-shoot junction, at day 10. I performed a genome wide association test to search for the genetic basis of the phenotype in R, using EMMAx (Kang et al. 2010) and the 250k SNP set (Atwell et al. 2010). To test for a possible fitness effect, I assayed the relationship of the phenotype and related genetic variants to emergence by planting seeds on fine sand and burying them to a depth of ~1 cm with coarse pebbles. Emergence of germinants was recorded daily for two weeks.
Lines from gravel beaches had significantly longer hypocotyls than fine sand beach or inland accessions (5.4 mm compared to 3.67 mm; Student’s t-test p-value < 0.0001). In the GWA, a peak on chromosome 4 was strongly associated with the hypocotyl length phenotype. This peak lies near the gene SPA2 (suppressor of phytochrome A 2), which has been implicated in growth in darkness. Variation at the top scoring SNP in the peak was also associated with a long hypocotyl phenotype in populations other than the Swedish mapping panel. In a 161 line sample from across Europe, lines with the T allele had longer hypocotyls (mean = 4.96 mm) than lines with the G allele (mean = 4.51; student’s t-test p value = 0.0001). Bay x Sha RIL lines with the T allele also had longer hypocotyls (mean = 3.78) than lines with the G allele (mean = 3.28; student’s t-test p-value = 0.025). Overall, lines with the T allele at the SNP of interest emerged from burial more frequently than lines with the G allele (chi-square test of independence; p-value = 0.001), suggesting that this genetic region is related to seedling fitness when plants are subject to burial.