Many plants undergo adaptation to fire. Yet, as global change is increasing fire frequency worldwide, our understanding of the genetics of adaptation to fire is still limited. We studied the genetic basis of serotiny (the ability to disseminate seed exclusively after fire) in the widespread, pioneer Mediterranean conifer Pinus halepensis Mill., by linking individual variation in serotiny presence and level to fire frequency and to genetic polymorphism in natural populations.

After filtering steps, 885 Single Nucleotide Polymorphisms (SNPs) out of 8,000 SNPs used for genotyping were implemented to perform an in situ association study between genotypes and serotiny presence and level. To identify serotiny-associated loci, we performed random forest analyses of the effect of SNPs on serotiny levels, while controlling for tree size, frequency of wildfires, and background environmental parameters.

Serotiny showed a bimodal distribution, with serotinous trees more frequent in populations exposed to fire in their recent history. Twenty-two SNPs found in genes involved in stress tolerance were associated with presence-absence of serotiny while thirty-seven found in genes controlling for flowering were associated with continuous serotiny variation.

This study shows the high potential of P. halepensis to adapt to changing fire regimes, benefiting from a large and flexible genetic basis of trait variation.

Overall, 10 populations of P. halepensis were selected according to two fire modalities, half located in areas that were fire-free from 1959 until 2018 (“No-Fire” modality populations, PHNF) and the other half in areas having suffered at least one fire (“Fire” modality populations, PHF) during the same time period. The pairs “Fire” - “No-Fire” were located between 5 and 25 kilometers apart in order to minimize genetic divergence caused solely by drift (Lotterhos & Whitlock, 2015). The populations were sampled in sites where the past land use was the same in order to mitigate the impact of soil conditions on trait variation (See Romero & Ganteaume 2020). In the current work, the sampling occurred in recent forests (as opposed to ancient forests that could have already been mapped in the 18th–19th centuries), mostly resulting from land abandonment that can provide adequate conditions for regeneration in the absence of fire. In each population, 19 to 20 mature and dominant trees, between 15 and 30 years old (on average 22.03 ± 3.1 years old), were sampled. In areas undergoing fires during the past 60 years, we only sampled populations when at least 10 years had elapsed since the last fire event in order to be sure of the sexual maturity of the trees that have grown post-fire (Santos del Blanco et al., 2010). Furthermore, in order to reduce environmental differences between populations, we selected sample sites with as homogeneous environmental conditions as possible (slope, exposure, elevation, and past land use; see Table S1). However, Romero & Ganteaume (2020) found a significant effect on trait variation, working on the same database as the one used in the current study. This effect has therefore to be accounted for in the analyses (see below). 

Serotiny measurements were carried out following Budde et al. (2014). Using binoculars, we counted, on each tree, 20 mature cones (older than three years) on healthy branches, avoiding dominated trees and those with a diameter smaller than 10 cm. Measurements were performed during the summer (June – July 2018), at least 48 h after a rain event occurred to avoid counting cones closed due to high relative humidity. Tree serotiny level was calculated as the number of closed cones divided by the total number of cones (on 192 trees).