Genetic architecture underlying response to the fungal pathogen Dothistroma septosporum in lodgepole pine, jack pine, and their hybrids

In recent decades, Dothistroma needle blight (DNB), a pine tree disease caused by the fungal pathogen Dothistroma septosporum, has severely damaged lodgepole pine (Pinus contorta Dougl. ex. Loud.) in British Columbia, Canada, and raised health concerns for jack pine (Pinus banksiana Lamb.). The pathogen has already shown signs of host shift eastward to the hybrid populations between lodgepole pine and jack pine (Pinus contorta ´ P. banksiana), and possibly into pure jack pine. However, we have little knowledge about mechanisms of resistance to D. septosporum, especially the underlying genetic basis of variation in pines. In this study, we conducted controlled inoculations to induce infection by D. septosporum and performed a genome-wide case-control association study with pooled sequencing (pool-seq) data to dissect the genetic architecture underlying response in lodgepole pine, jack pine, and their hybrids. We identified candidate genes associated with D. septosporum response in lodgep..., Plant materials
Seeds were obtained from 40 natural seedlots across Western Canada (Figure 1, seedlot numbers and locations can be found in Table S1, seed contributors http://adaptree.forestry.ubc.ca/seed-contributors/), including 25 LP seedlots from British Columbia (BC_LP) and three from Alberta (AB_LP), seven LP ´ JP seedlots from Alberta (AB_LPxJP), and five JP seedlots from Alberta (AB_JP). The range maps were downloaded from https://sites.ualberta.ca/~ahamann/data/rangemaps.html (Hamann et al., 2005). When the seeds were collected in the wild, they were assigned to pure LP, pure JP, or LP ´ JP, based on their location and morphological traits such as cone and branch characteristics, microfibril angle, and cell area (Wheeler & Guries, 1987; Wood et al., 2009; Yeatman & Teich, 1969). The proportion of LP and JP ancestry of the collected seeds were genotyped using 11 microsatellite loci by Cullingham et al. (2012). Briefly, seeds were germinated to obtain seedlings, then DNA ..., , # **Genetic architecture underlying response to the fungal pathogen *Dothistroma septosporum* in lodgepole pine, jack pine, and their hybrids**

## Description of the data and file structure

The datasets here were used for analyses in the manuscript. The codes can be found in

DOI:   [https://zenodo.org/records/14756909](https://zenodo.org/records/14756909)

### 1) For generating genetic structure

`fil_mask_MAD_rnd.input` is the input including “randomly chosen” major allele depth for adegenet.

`majorAF_rnd.input` is the input including major allele frequencies for corrplot.

`long_key.txt` includes the index to re-order the populations based on longitude.

`popool_fst_rnd.txt` is the final input for calculating pairwise Fst using randomly chosen loci.

`all_info.txt` includes the population IDs and ploidy, which are necessary for running pairwise Fst.

### 2) For pool-GWAS using CMH

**Abbreviations:**

* LPp -- pine tree seedlot;
* 1R -- resistant trees inoculated with *Dothistroma...