Integrative linkage mapping and transcriptomic profiling uncover ozone-response modules in a peri-urban forest tree

The genus Abies Mill. (Pinaceae) comprises a group of conifers distributed across boreal and temperate regions, including eight species with disjunct distributions across Mexico's highest mountain chains. Abies religiosa (Kunth) Schltdl. & Cham. is a dominant species of the Trans-Mexican Volcanic Belt in central Mexico, forming forests crucial for water retention, carbon sequestration, and soil stabilization. Despite its ecological importance, peri-urban forests dominated by this species around Mexico City are exposed to high levels of tropospheric ozone, which cause premature senescence and forest decline. Here, we report a saturated linkage map for A. religiosa generated by genotyping 182 megagametophytes from two mother trees for 9,702 single nucleotide polymorphisms. The linkage map is composed of 12 linkage groups (LGs) containing between 518 and 1,207 markers and spanning 1,567.88 cM (114 to 208 cM per LG). Annotation of reads containing SNPs allowed us to locate 5,881 coding genes on the map, of which 1,952 had known functions in conifers. Differential expression analyses of these genes in symptomatic and asymptomatic trees growing in a peri-urban forest heavily affected by ozone pollution revealed eight genes that were differentially expressed when ozone levels increased. Co-expression analyses further showed that neighboring genes tended to co-express more often in symptomatic than in asymptomatic trees, especially in clusters within LGs 5, 8, and 10. Gene pairs within co-expression clusters coded for similar proteins, suggesting functional co-localization. Our integrated approach reveals previously uncharacterized metabolic and defense pathways associated with ozone tolerance in conifers and lays the groundwork for developing molecular-based management programs accounting for ozone resistance in peri-urban forests.