DOI: 10.5061/dryad.4xgxd25mj
title: Data from: Genomic approaches to accelerate American chestnut restoration

description: Over a century after two introduced pathogens killed billions of American
 chestnuts, introgression of pre-adapted resistance alleles from Chinese
 chestnuts has contributed to recovering of self-sustaining populations.
 However, progress has been slow because of the complex genetic
 architecture of resistance. To better understand blight resistance, we
 compared reference genomes, gene expression responses, and stem metabolite
 profiles of the resistant Chinese and susceptible American chestnut
 species. To accelerate resistance breeding, we conducted large-scale
 phenotyping and genotyping in hybrids of these species. Simulation and
 inoculation experiments suggest that significant resistance gains are
 possible through selectively breeding trees with an average of 70% to 85%
 American chestnut ancestry. The resources developed here are foundational
 for breeding to create diverse restoration populations with sufficient
 disease resistance and competitive growth.  
description: # Data from: Genomic approaches to accelerate American chestnut
 restoration
 [https://doi.org/10.5061/dryad.4xgxd25mj](https://doi.org/10.5061/dryad.4xgxd25mj) ## Description of the data and file structure **Supplementary Data 1** | Blight and growth phenotypes for 5.5k trees  **Supplementary Data 2** | Genotyping data at ~93k SNPs from 5,003 trees in variant calling format (VCF) **Supplementary Data 3** | Hybrid ancestry estimates for ~5k genotyped trees  **Supplementary Data 4** | Genetic maps for the ‘GMBig x Horn’ *C. dentata* full sib family **Supplementary Data 5** | Genome (‘Ellis-1’) coordinates for *C. dentata* and *C. mollissima* ancestry in hybrids **Supplementary Data 6** | Pedigree for trees phenotyped in this study **Supplementary Data 7** | Seedling blight resistance data for ~1k backcross progeny **Supplementary Data 8** | Seedling blight resistance data for LSAC progeny **Supplementary Data 9** | Blight resistance and height data for ~500 ‘Darling 54’ progeny **Supplementary Data 10** | A bed file with orthogroup and tandem array information for each gene **Supplementary Data 11** | Pan-genome sets for C. dentata and C. mollissima genomes in ‘Ellis’ coordinates **Supplementary Data 12** | Syntenic block breakpoints  **Supplementary Data 13** | Chestnut blight timecourse RNA-seq metadata **Supplementary Data 14** | Chestnut blight timecourse RNA-seq count matrix for *C. dentata * **Supplementary Data 15** | Chestnut blight RNA-seq count matrix for *C. mollissima* **Supplementary Data 16** | Species- and allele-specific gene expression responses to *Cr. parasitica*.  **Supplementary Data 17** | Blight-responsive orthogroups with higher copy number and expression upregulation in resistant *C. mollissima* v. susceptible *C. dentata*  **Supplementary Data 18** | KEGG pathway enrichment among single copy orthologs with species-specific and common expression responses to chestnut blight fungal inoculation **Supplementary Data 19** | Secondary metabolites present at higher concentrations in the stems of resistant *C. mollissima* v. susceptible *C. dentata* **Supplementary Data 20** | *Cryphonectria parasitica* fungal growth in the presence of metabolites that are at higher concentrations in resistant *C. mollissima* stems v. susceptible *C. dentata* stems **Supplementary Data 21** | Root rot resistance phenotypes for ~27 k open-pollinated progeny of *C. dentata* backcross hybrids, resistant *C. mollissima,* and susceptible *C. dentata* controls **Supplementary Data 22** | Family means for root resistance used for genetic analyses **Supplementary Data 23** | *C. dentata* v. *C. mollissima* ancestry calls used for QTL mapping **Supplementary Data 24** | Genetic map used for QTL mapping **Supplementary Data 25** | Effect of inheriting a *C. mollissima* allele on blight resistance and root rot survival across 641 loci used in QTL analysis **Supplementary Data 26** | Coordinates and effect sizes for blight and root rot QTL intervals and GWAS peaks **Supplementary Data 27** | *P*-values from genome wide associations studies of blight and root rot resistance **Supplementary Data 28** | Breeding values for blight and root rot resistance estimated with single-step GBLUP **Supplementary Data 29** | Genomic estimated breeding values for blight resistance, root rot resistance, and height growth from simulation of progeny genotypes ### Files and variables #### File: SIData1.blight.phenotypes.all.oct2025.v4.txt **Description:** Blight and growth phenotypes. Blight presence/absence phenotypes were coded into 0 (susceptible) and 1 (resistant) phenotypic classes.  ##### Variables * shortcode: tree id * mom: mother of tree * dad: father of tree * mainstemalive: is the main stem alive? (1 = yes, 0 = no) * largecankers: are large cankers present? (1 = no, 0 = yes) * blightcontained: are the cankers expanded beyond initial margins? (1 = no, 0 = yes) * exposedwood: are most cankers &gt; 15 cm in length? (1 = no, 0 = yes) * sunkenswollen: are cankers generally sunken (0), swollen (1), or flat (2)? * sporulation: are cankers forming fruiting bodies? (1 = no, 0 = yes) * stumpsprouts: are stump sprouts present (1 = no, 0 = yes) * propcanopyalive: proportion of canopy that is alive * dbhlargest_cm: diameter at breast height of the largest living stem in cm * height_m: height of the tallest living stem in meters * chapter: chapter of the American Chestnut Foundation that grew the tree * parcel: property name where the tree is growing  * orchard: orchard name where the tree is growing   * inoculated: inoculated with C. parasitica (1 = yes, 0 = no) * plantdate: date that the tree was planted * obsdate: date that the tree was phenotyped * age: age in years that the tree was phenotyped * tmax_c: average maximum monthly temperate in degrees celsius  * tmin_c: average minimum monthly temperature in degrees celcius * prec_mm: average monthly precipitation in mm * ph: average soil pH down to 30 m depth interpolated from USGS soil survey data * sand: average % sand in soil down to 30 m depth interpolated from USGS soil survey data * height_m_adj: residual variation in tree height after adjusting for the effects of age, inoculated, tmax_c, prec_mm, sand, ph,  * blightresistanceindex: sum of mainstemalive, largecankers, blightcontained, exposedwood, sunkenswollen, sporulation, & stump sprouts after correcting phenotypes for average effects of inoculated, age, tmax_c, prec_mm, ph, & sand (see methods) * dentata_ahmm: C. dentata ancestry estimated from ancestry hmm (if NA, tree was not genotyped) * mollissima_ahmm: C. mollissima ancestry estimated from ancestry hmm * crenata_ahmm: C. crenata ancestry estimated from ancestry hmm * pumila_ahmm: C. pumila ancestry estimated from ancestry hmm * resistance source: C. mollissima or parent from other species (e.g. C. crenata or LSAC) that contributed resistance to progeny * generation: hybrid or backcross generation * gwas: TRUE = included in blight resistance genome wide association study * clapper_blight_qtl: TRUE = included in ancestry based QTL analysis for Clapper descendants * graves_blight_qtl: TRUE = included in ancestry based QTL analysis for Graves descendants * dentataparent: last known wild type C. dentata parent * h2: TRUE = included in estimation of heritability * gblup.xval: TRUE = included in cross validations to estimate genomic selection accuracy * ssgblup: TRUE = included in estimation of breeding values using the single step GBLUP method * survival: whether or not tree was alive or dead at time of study * survival.obs.year: last year that survival was observed #### File: SIData2.tacf.gbs.genotypes.imputed.filtered.vcf.gz **Description:** Genotyping-by-sequencing data for 93,333 SNPs in 5,003 trees in variant calling format (VCF). After filtering to sites with &lt; 20% missing genotypes, missing genotypes were imputed in Beagle.  #### File: SIData3.tacf.castanea.hybrid.species.ancestry.txt **Description:** Hybrid species ancestry inferences for ~5 k trees from Ancestry_HMM ##### Variables * shortcode: tree id  * dentata_ahmm: C. dentata ancestry proportion * mollissima_ahmm: C. mollissima ancestry proportion * crenata_ahmm: C. crenata ancestry proportion * sativa_ahmm: C. sativa ancestry proportion * pumila_ahmm: C. pumila ancestry proportion * henryi_ahmm: C. henryi ancestry proportion * contributor: chapter that contributed the sample * new_generation: backcross generation that was corrected for samples with ancestry that deviated from original pedigree expectations. * resistancesource: source of resistance  * vcf.header.gbs: original sample id in the vcf (ignore) #### File: SIData4.gmbigxhorn.genetic.map.txt **Description:** Genetic maps for the ‘GMBig x Horn’ *C. dentata* full sib family. Contains genetic map positions in centiMorgans and physical coordinates in the ‘Ellis’ genome for each parent from this cross.  ##### Variables * map: separate maps were created for marker sets that were segregating in the GMBig or Horn parents  * chr: chromosome * mb: physical position in the 'Ellis' genome in megabases  * cm: genetic position in centiMorgans #### File: SIData5.blockCoords.qtl.gwas.oct25.txt **Description:** Ellis-1 genome coordinates of ancestry tracts estimated with Ancestry_HMM for C. dentata hybrids ##### Variables * shortcode: tree id  * chr: chromosome * block.id: id of the ancestry block * call: A - homozygous C. dentata ancestry, H - heterozygous C. mollissima and C. dentata ancestry, C - homozygous for C. mollissima ancestry * start: start coordinate for ancestry block * end: end coordinate for ancestry block * n.markers: number of markers contained in ancestry block 
 
 #### File: SIData6.tacf.pedigree.2024.txt
 **Description:** Multi-generation pedigree for all trees phenotyped in
 this study. Includes maternal and paternal parents for multiple
 generations of hybrid trees in The American Chestnut Foundation breeding
 program. ##### Variables * shortcode: name of tree  * mom: mother of tree
 * dad: father of tree * generation: hybrid or backcross generation  *
 genorder: variable to order the pedigree such that early generations are
 first * source: name of the original source of resistance * resparent:
 whether mother, father, both, or neither parent contributed resistance to
 progeny * dentataparent: id of the last known C. dentata parent #### File:
 SIData7.progeny.blight.resistance.data.txt **Description:** Progeny blight
 resistance phenotypic data. Seedling blight resistance phenotypes for ~1 K
 progeny from 30 full or half sib families ##### Variables * treeid:
 individual tree * cross: cross from which tree was derived * mom: id of
 tree's mother * dad: id of tree's father * cross.type: BC x F1 =
 backcross tree crossed with C. dentata x C. mollissima F1 hybrid, BC x BC
 = intercross between two backcross trees, BC x op = open pollinated
 progeny of a backcross tree, LSA x LSA = intercross between large
 surviving American chestnuts, mollissima = resistant C. mollissima
 controls, F1 = C. dentata x C. mollissima, dentata = susceptible C.
 dentata controls.   * site: site where trees were inoculated (University
 of Tennessee Chattanooga or Berry College, GA) * orangezone_mm: length of
 orange zone of the canker in mm * oz.bins: canker length quartile  *
 spores: whether or not canker was sporulating (0 = no, 1 = yes) * rating:
 canker length quartile + 1 if spores present  * ht_cm: height of the
 seedling before inoculation in cm * scaled.orange.zone: orange zone scaled
 from 0 = C. dentata mean to 100 = C. mollissima mean. * scaled.rating:
 rating scaled from 0 = C. dentata mean to 100 = C. mollissima mean.  
 
 #### File: SIData8.scrivener.ssa.2025.csv **Description:** Blight
 resistance data from open pollination progeny from large surviving
 American chestnuts planted in the Scrivener orchard in Maryland #####
 Variables * cross: description of cross (op = open pollinated) * letter:
 shortcode for cross * tag: greenhouse id for tree * inoculated: 1 = tree
 was inoculated with the highly virulent EP155 strain of Cr. parasitica.  *
 height_mm: height of tree in mm at time of inoculation * site: site where
 trees were inoculated (University of Tennessee Chattanooga or Berry
 College, GA) * survival: Y = main inoculated stem alive at 60 days post
 inoculation * full_zone_mm: full length (in millimeters) of the necrotic
 tissue around the Cr. parasitica inoculation site * orange_zone_mm: length
 of the orange coloration within the canker * sunken: whether canker was
 sunken, swollen, or flat * rating: cankers were rated on a scale of 1
 (inoculation failure), 2 (minimal canker expansion within 5 mm of
 inoculation site), 3 (large canker with no sporulation), 4 (large, sunken,
 sporulating canker), and 5 (tree dead with large cankers). * basal_canker:
 presence of natural blight infection  * spores: whether or not canker was
 sporulating (0 = no, 1 = yes) * rating: canker length quartile + 1 if
 spores present  * ht_cm: height of the seedling before inoculation in cm *
 scaled.orange.zone: orange zone scaled from 0 = C. dentata mean to 100 =
 C. mollissima mean. * scaled.rating: rating scaled from 0 = C. dentata
 mean to 100 = C. mollissima mean.  ### #### File:
 SIData9.darling54.blight.height.phenotypes.purdue.txt
 **Description:** Canker length, canker severity ratings, and height on
 ~500 3 year old T3 OxO+ and OxO- full sibling progeny of 'Darling
 54' from a field trial near Purdue University  ##### Variables * mom:
 female (wild type) C. dentata parent * dad: male T2 'Darling 54'
 parent * family: mom x dad * year: year trees were inoculated  * oxo: 1 =
 OxO+ and 0 = OxO- * row: row within plot * tree: tree number within row *
 select: 1 = high resistance and vigor * ht: total tree height in cm * gld:
 ground line diamter in mm * inoc: 1 = inoculated, 0 = uninoculated * len:
 canker length in mm * width: canker width in mm * rating: canker severity
 rating (5 = large, sunken, and sporulating to 1 = canker contained and
 superficial) * sporulation: 1 = Cryphonectria parasitica fruiting bodies
 present or 0 = absent * natcanker: 1 = presence on natural canker in
 additional to the canker from inoculation * dead: 1 = tree dead   ####
 File: SIData10.comb.bed.txt **Description:** Combined bed-like annotation
 file. This contains syntenic orthogroup information, as produced by
 GENESPACE. The standard bed file with a set of additional fields
 presenting orthogroup and tandem array information for each gene.  #####
 Variables * chr: chromosome where the gene is located * start: Start
 position of the gene on the chromosome * end: fnd position of the gene on
 the chromosome * id: Unique gene name * ofID: orthofinder ID, a unique
 identifier for orthologous groups. * pepLen: length of the peptide
 sequence associated with the feature * ord: order of the genome within the
 pangenome * genome: name of the genome to which the gene belongs *
 arrayID: identifier for the array or cluster of related genes *
 isArrayRep: Boolean indicating whether the feature is a representative of
 its array * globOG: Global ortholog group identifier, representing
 orthologs across multiple genomes * globHOG: Global hierarchical ortholog
 group identifier, representing a higher-level grouping of orthologs *
 noAnchor: boolean indicating whether the feature lacks an anchor point in
 synteny analysis * og: ortholog group identifier, representing a set of
 orthologous genes #### File: SIData11.dentata.pangenes.txt
 **Description:** GENESPACE pan-gene sets against the Ellis coordinate
 system. Pangenes file presenting the interpolated syntenic position of
 each syntenic phylogenetically hierarchical orthogroup.  ##### Variables *
 ofID: refers to OrthoFinder ID, which is assigned to genes and proteins by
 OrthoFinder * pgID: pan-genome ID, a unique identifier for each entry in
 the pan-genome annotation * interpChr: interpolated chromosome, referring
 to the inferred chromosomal location of a gene based on syntenic
 relationships * interpOrd: the inferred gene order within a chromosome *
 pgRepID: pan-genome representative ID, identifying the representative gene
 for a group of related genes in the pan-genome * genome: the specific
 genome to which a gene belongs * og: orthogroup, a group of genes
 descended from a single gene in the last common ancestor of all the
 species being considered * flag: a marker indicating specific attributes
 of a gene, such as syntenic relationships or array membership * id: gene
 identifier, unique within each genome * chr: chromosome on which the gene
 is located * start: start position of the gene on the chromosome * end:
 end position of the gene on the chromosome * ord: refers to the ordinal
 position or rank of the gene within its genome or chromosome #### File:
 SIData12.combinedWindowedBlockCoordinates.txt **Description:** Syntenic
 block breakpoints. Syntenic blocks were inferred with DEEPSPACE using
 default parameters except as noted in the methods. This is a standard .paf
 file except that the first field contains the DEEPSPACE file identifier
 and the last two fields contain the identifier for the query (windows) and
 target genomes.   ##### Variables * file: names of pairwise mApping Format
 (PAF) file * qname: query sequence name * qlen: query length * qstart:
 query start * qend: query end * strand: + or - * tname: target sequence
 name * tlen: target length * tstart: target start * tend: target end *
 nmatch: number of matching bases * alen: alignment length * mapq: a score
 that indicates the confidence level of a read's alignment to a
 reference genome * windows: query genome * target: target genome ####
 File: SIData13.chestnut.rnaseq.metadata.v2.txt **Description:** RNA-seq
 metadata. Contains species, tissue, and treatment information for samples
 used for genome annotation and *C. parasitica *gene expression responses. 
 ##### Variables * lib: id of RNA seq library (libraries sequenced across
 two flow cells are denoted with 1 and 2) * species: indicated whether
 sequences came from *Castanea mollissima*, *Castanea dentata*, or *C.
 mollissima* x *C. dentata* F1 hybrids  * genotype: name of tree sequenced
 * tissue: tissue type sequenced * timepoint: days post inoculation (dpi)
 for stem samples that were inoculated with *C. parasitica* * treatment:
 denotes whether samples were uninocuated, wounded only, or inoculated with
 *C. parastica* *  R1R2.size(GB): Gibabases of sequence obtained for each
 library * read_1: id of library for read 1 of paired end sequences  *
 read_2: id of library for read 2 of paired end sequence #### File:
 SIData14.dentata.blight.rnaseq.count.matrix.txt
 **Description:** transcript count matrix for *C. parasitica* inoculation
 timecourse aligned to the *C. dentata* Ellis genome.  ##### Variables *
 rows - transcript IDs from Ellis genome. Genomic features format files and
 annotation information for these transcripts can be downloaded from
 Phytozome * columns - library IDs - genotype, treatment, and timepoint
 information associated with library IDs can be accessed from SIData1. ####
 File: SIData15.mollissima.blight.rnaseq.count.matrix.txt
 **Description:** transcript count matrix for*C. parasitica* inoculation
 timecourse aligned to the *C. mollissima* Mahogany Hap1 genome.  #####
 Variables * rows - transcript IDs from Mahogany Hap1 genome. Genomic
 features format files and annotation information for these transcripts can
 be downloaded from Phytozome * columns - library IDs - genotype,
 treatment, and timepoint information associated with library IDs can be
 accessed from SIData1. #### File:
 SIData16.blight.rnaseq.within.between.species.allele.contrasts.3d.10d.txt
 **Description:** Species and allele specific expression responses to *C.
 parasitica*. Log2fold change and P-values for species- and allele-specific
 expression responses to *C. parasitica* inoculation. ##### Variables *
 gene.id: unique gene identifier * baseMean: The average of the normalized
 count values across all samples. It represents the overall expression
 level of a gene, accounting for sequencing depth but not gene length. *
 log2FoldChange: The logarithm (base 2) of the fold change in expression
 between the comparison and control groups. It indicates the magnitude and
 direction of differential expression. * lfcSE: Standard error of the
 log2FoldChange estimate * stat: Wald statistic, which is the
 log2FoldChange divided by its standard error. It measures the significance
 of the fold change * pvalue: raw p-value from the Wald test, indicating
 the probability of observing such an extreme fold change by chance *
 padj: The adjusted p-value, corrected for multiple testing using the
 Benjamini-Hochberg method to control the false discovery rate. This value
 should be used to determine statistically significant differential
 expression. * species: indicates whether contrast is within C. dentata
 (dentata), C. mollissima (mollissima), between C. mollissima and C.
 dentata (mollissima - dentata), within C. dentata alleles in F1s (dentata
 ase), within C. mollissima alleles in F1s (mollissima ase), or between C.
 mollissima and C. dentata alleles in F1s (mollissima - dentata ase)  *
 timepoint: indicates whether contrast was made at 3 or 10 days post
 inoculation (dpi)  - contrast: type of expression contrast including
 inoculation - wound only treatment (within species), inoculation - wound
 only treatment (between species),  inoculation - wound only treatment
 (within allele) in F1s, and inoculation - wound only treatment (between
 alleles) in F1s #### File:
 SIData17.mol.v.den.copy.number.expansion.gene.expression.txt
 **Description:** Comparison of gene expression responses between C.
 mollissima and C. dentata among orthogroups that with greater copy number
 in C. mollissima ##### Variables * og: orthogroup from C. mollissima
 Mahogany Hap1 pangenome * mol.copy.n: average copy number among all four
 C. mollissima genome assemblies * den.copy.n: copy number in the Ellis C.
 dentata genome * tpm.den.3d: transcripts per million for the orthogroup in
 the C. parasitica-inoculated C. dentata samples  3 days post inoculation *
 tpm.den.3d: transcripts per million for the orthogroup in the C.
 parasitica-inoculated C. mollissima samples  3 days post inoculation *
 tpm.diff.3d: differences (Cmol - Cden) in orthogroup TPM at 3 dpi *
 p.adj.3d: P-value for the t-test between Cmol - Cden tpm contrast adjusted
 with the Benjamini-Hochberg false discovery rate. *  tpm.den.10d:
 transcripts per million for the orthogroup in the C. parasitica-inoculated
 C. dentata samples  3 days post inoculation * tpm.den.10d: transcripts per
 million for the orthogroup in the C. parasitica-inoculated C. mollissima
 samples  3 days post inoculation * tpm.diff.10d: differences (Cmol - Cden)
 in orthogroup TPM at 3 dpi * p.adj.10d: P-value for the t-test between
 Cmol - Cden tpm contrast adjusted with the Benjamini-Hochberg false
 discovery rate. * id: C. mollissima mahogany hap1 genes from orthogroup
 that were significantly upregulated in response to C. parasitica.   *
 Best-hit-arabi-defline: annotation of ortholog in Arabidopsis thaliana *
 Best-hit-rice-defline: annotation of ortholog in rice (Oryza sativa) ####
 File: SIData18.mollissima.dentata.degs.kegg.enrichment.txt
 **Description:** Enrichment of KEGG (Kyoto Encyclopedia of Genes and
 Genomes) pathways among genes specifically upregulated in C. mollissima 3
 or 10 days post inoculation with C. parasitica  ##### Variables *
 pathway.code: KEGG pathway in Arabidopsis * pathway.name: name of pathway
 * Annotated: number of orthologs in pathway that were specifically
 upregulated C. mollissima * TotalGenes: total number of genes in pathway *
 arabidopsis_genes: Arabidopsis orthologs to genes specifically upregulated
 C. mollissima * mollissima_genes: C. mollissima Mahogany Hap1 genes in
 pathway that were uniquely upregulated * timepoint: 3 or 10 days post
 inoculation (dpi) * p.adjust: Benjamini-Hochberg false discovery rate to
 control for false positives from multiple testing #### File:
 SIData19.chestnut.metabolite.summary.oct25.txt
 **Description:** Metabolites at higher concentrations in the stems of
 resistant C. mollissima (n = 8) v. susceptible C. dentata (n = 11) #####
 Variables * Metabolite: name of metabolite. Unknowns are designated by
 their retention times and key mass-to-charge ratios. * cden_avg: mean
 concentration in ug/g dry weight in C. dentata stems * cden_sem: standard
 error on cden_avg * cmol_avg: mean concentration in ug/g dry weight in C.
 mollissima stems * cmol_sem: standard error on mollissima_mean *
 cmol_cden_fc: cmol_avg/cden_avg * cmol_cden_p: t-test P-value for cmol_avg
 - cden_avg * hyb_avg: mean concentration in ug/g dry weight in C.
 mollissima x C. dentata F1 stems * hyb_sem: standard error on hyb_avg *
 hyb_cden_fc: hyb_avg/den_avg * hyb_cden_p: t-test P-value for hyb_avg -
 cden_avg * cden_wsw1_26 ..... hyb_vso_88: concentration (ug/g dry weight)
 of metabolite in a specific sample where sample ID = species.tree.sample
 number. Species include Castanea dentata ("cden"), Castanea
 mollissima ("cmol"), or C. dentata x C. mollissima F1 hybrid
 ("hyb").  * cmol: **C** = Cropper, **Q** = Qing (both provided
 by Greg Miller/Empire Chestnut ~2006-2009) * hyb: **K** = KL-BC1, **G** =
 GR68-B1 (both backcross-1 generation, I believe both were provided by
 TACF/Sara via Chuck Maynard ~2006-2009) * hyb: **V** = Luvall's
 Monster (complex commercial hybrid) * cden: **W** = WB275-27, **Z** =
 Zoar, **L** = Lasdon all three origins/sources described
 in [https://apsjournals.apsnet.org/doi/abs/10.1094/PDIS-01-13-0047-RE](https://apsjournals.apsnet.org/doi/abs/10.1094/PDIS-01-13-0047-RE) * Other parts of the sample names indicate the tissue type, site, and replicate number.  Thus, sample WSO1 is **W**B275, **S**tem, **O**pen field, Replicate **1**.  All trees were grown in Syracuse NY, and ranged in age from 2-7 years at the time of sample collection. Samples were collected in July-August 2013 with sterilized hand pruners.   Tissue was woody stem segments from the previous year's growth (not fresh green tissue), approx 3-7mm diameter. #### File: SIData20.fungal.growth.metabolites.rawdata.txt **Description:** growth of C. parasitica in the presence of metabolites present at higher concentrations in C. mollissima v. C. dentata bark ##### Variables * treatment: metabolite in PDA growth medium * concentration: concentration of metabolite * solvent: solvent used for metabolite * rep: replicate number for each metabolite treatment * area_2d: fungal area 2 days after culture initiation * area_4d: fungal area 4 days after culture initiation * area_6d: fungal area 6 days after culture initiation * area_8d: fungal area 8 days after culture initiation * area_10d: fungal area 8 days after culture initiation #### File: SIData21.tacf.root.rot.phenotypic.rawdata.2024.txt **Description:** Root rot resistance phenotypes. Survival and root lesion severity data after *Phytophthora cinnamomi* inoculation for ~27 k open pollinated progeny of *C. dentata* backcross hybrids, resistant *C. mollissima,* & susceptible *C. dentata* controls.  ##### Variables * mother: mother of progeny screened for root rot resistance * father: father of progeny screened for root rot resistance * source: founder tree that potentially contributed root rot resistance to the progeny * id: seedling id * mom_generation: generation of mother * progeny_generation: generation of progeny * rating: 0 = no lesions on roots, plant healthy; 1 = minimal lesions limited to secondary roots; 2 = any lesions on the tap root or extensive lesions on secondary roots; 3 = severe root rot, plant dead * mortality: 1 = dead, 0 = alive at end of trial * site: site of screening * year: year of screening * tub: tub where trees were screened (relevant for Chestnut Return Farm, where families were screened in a randomized complete block)  * isolate: *P. cinnamomi* isolate used for inoculation #### File: SIData22.root.rot.phenotypic.summary.oct2025.txt **Description:** family means for root rot resistance among 662 open pollinated families  ##### Variables * mother: mother of progeny screened for root rot resistance * nmort: number of progeny phenotyped for mortality after P. cinnamomi inoculation * mort.adj: mortality proportion after adjusting for average effect of year, site, and strain of P. cinnamomi * nrate: number of progeny phenotyped for lesion severity rating * rate.adj: average lesion severity rating after accounting for the average effect of year, site, and strain of P. cinnamomi * subjectpargen: generation of mother tree * progenygeneration: generation of progeny that were inoculated with P. cinnamomi * source: source of resistance for the progeny * nphenotyped: number of progeny phenotyped * survprop: raw survival proportion (with no adjustment for covariates) * avglesion rating: family average lesion rating (with no adjustment for covariates) * ssgblup: TRUE - breeding value estimated with single step GBLUP * dentata_ahmm: C. dentata ancestry proportion of the mother tree * mollissima_ahmm: C. mollissima ancestry proportion of the mother tree * crentata_ahmm: C. crenata ancestry proportion of the mother tree * h2: TRUE- tree included in heritability estimation * gwas: TRUE - tree included in genome wide association study of root rot survival * gblup.xval: TRUE- tree included in cross validations to estimate genomic prediction accuracy * graves_rootrot_qtl: TRUE- tree included in QTL analysis for the Graves source of resistance #### File: SIData23.ahmm.genotypes.qtl.nov2024.csv **Description:** genotype matrix of ancestry calls from Ancestry HMM that was subset to perform QTL analyses. Individuals are in rows, markers (Chr_position in Ellis coordinates) are in columns. Genotype calls are AA- homozygous for C. dentata ancestry, AC- heterozygous C. dentata and C. mollissima ancestry, and CC-homozygous for C. mollissima ancestry. #### File: SIData24.ahmm.qtl.gmap.nov2024.csv **Description:** genetic map used for ancestry-based QTL analysis ##### Variables * marker: chromosome and physical position in Ellis-1 genome * chr: chromosome * pos: genetic position in centimorgans #### File: SIData25.qtl.effects.all.oct25.v4.csv **Description:** Effect of inheriting a C. mollissima allele at 641 markers used in ancestry-based blight and and root rot resistance QTL mapping  ##### Variables * marker: chromosome and physical position in the 'Ellis-1' genome * chr: chromosome * gpos: physical position in the 'Ellis-1' genome.  * source: donor parent for resistance including the 'Clapper' BC1 tree and the 'Graves' F1 tree * mol.effect: average effect of inheriting a C. mollissima allele compared to inheriting a two alleles from C. dentata (i.e. AC - AA) * trait: trait used in QTL analysis including the blight resistance index or root rot survival 
 
 #### File: SIData26.blight.prr.qtl.gwas.intervals.metadata.oct2025.v4.csv
 **Description:** Blight and root rot resistance quantitative trait locus
 (QTL) and interval and genomewide association study (GWAS) metadata. Peak
 and border coordinates and effect sizes for blight and phytophthora root
 rot (PRR) QTL intervals across the *C. dentata* and *C. mollissima*
 genomes.   ##### Variables * disease: disease for which resistance QTL was
 discovered (blight or root rot) * trait: trait for which QTL was
 discovered * qtl: identifier for QTL * source: source of resistance *
 generation: generation of QTL mapping population * pop: identifier of
 population used for QTL mapping * study: study in which QTLs were reported
 (current study, Fan et al. 2024 or Zhebentyayeva et al. 2019) * n: number
 of progeny phenotyped for QTL discovery * chr: chromosome identifier *
 peak.dentata: position of QTL peak in the 'Ellis-1' genome *
 start.dentata: position of QTL left border in 'Ellis-1' genome.
 For GWAS, estimated as distance at which linkage disequilibrium r2 values
 between peak and surrounding markers decayed to &lt; .2 * end.dentata:
 position of QTL right border in the 'Ellis-1' genome. For GWAS,
 estimated as distance at which linkage disequilibrium r2 values between
 peak and surrounding markers decayed to &lt; .2  * widthMb: width of the
 QTL (right - left border) in megabases * lod.or.P: logarithm of the odds
 that QTL position has zero effect or P-value for association * PVE:
 percent of phenotypic variance explained by the QTL calculated
 as** **100*[1 - 10^(-2/N LOD)] * effect: effect of inheriting a C.
 mollissima allele (QTL) or alternative allele (GWAS) on the phenotype *
 chfreq.or.maf: frequency of C. mollissima alleles across the mapping
 population (QTL) or minor allele frequency (GWAS) *
 moll.mah.hap1.peak: position of QTL peak in the 'Mahogany' hap1
 genome * moll.mah.hap1.start: position of QTL left border in the
 'Mahogany' hap1 genome. For GWAS it was assumed peak - 73 kb
 corresponding rate of LD decay to r2 &lt; 0.2 *
 moll.mah.hap1.end: position of QTL right border in the
 'Mahogany' hap1 genome. For GWAS it was assumed peak + 73 kb
 corresponding rate of LD decay to r2 &lt; 0.2 *
 moll.mah.hap2.peak: position of QTL peak in the 'Mahogany' hap2
 genome.  * moll.mah.hap2.start: position of QTL left border in the
 'Mahogany' hap2 genome. For GWAS it was assumed peak - 73 kb
 corresponding rate of LD decay to r2 &lt; 0.2 *
 moll.mah.hap2.end: position of QTL right border in the
 'Mahogany' hap2 genome. For GWAS it was assumed peak + 73 kb
 corresponding rate of LD decay to r2 &lt; 0.2 *
 moll.nan.hap1.peak: position of QTL peak in the 'Nanking' hap1
 genome * moll.nan.hap1.start: position of QTL left border in the
 'Nanking' hap1 genome. For GWAS it was assumed peak - 73 kb
 corresponding rate of LD decay to r2 &lt; 0.2 *
 moll.nan.hap1.end: position of QTL right border in the 'Nanking'
 hap1 genome. For GWAS it was assumed peak + 73 kb corresponding rate of LD
 decay to r2 &lt; 0.2 * moll.nan.hap2.peak: position of QTL peak in the
 'Nanking' hap2 genome * moll.nan.hap2.start: position of QTL
 left border in the 'Nanking' hap2 genome. For GWAS it was
 assumed peak - 73 kb corresponding rate of LD decay to r2 &lt; 0.2 *
 moll.nan.hap2.end: position of QTL right border in the 'Nanking'
 hap2 genome. For GWAS it was assumed peak + 73 kb corresponding rate of LD
 decay to r2 &lt; 0.2 * analysis: QTL or GWAS #### File:
 SIData27.blight.root.rot.gwas.pvalues.effects.oct25.txt
 **Description:** P-values and effect sizes from genome wide association
 studies of blight and root rot resistance. ##### Variables * SNP: Marker
 identifier (chromosome_position)​ * Chromosome: Chromosome number​ *
 Position: Physical position of the SNP on the chromosome (base pairs,
 1-based coordinates)​ * P.value: Raw association P-value from BLINK GWAS
 linear model for marker-trait test​ * maf: Minor allele frequency for the
 SNP in the analyzed population​ * nobs: number of individuals including in
 the GWAS analysis​ * effect: estimated allelic substitution effect for
 inheriting the alternative allele​ * Example: 2.10116386 * P.adj:
 Benjamini-Hochberg adjusted P-value for multiple-testing correction *
 trait: Trait measured for association (e.g., blight resistance index)​ 
 
 #### File:
 SIData28.tacf.blight.root.rot.height.blups.inoculated.11.1.2025.txt
 **Description:** Estimated breeding values for blight resistance, root rot
 resistance, and tree height. Breeding values for blight and root rot
 resistance indices were scaled from 0 (*C. dentata* mean) to 100 (*C.
 mollissima* mean). Resistance data were merged with hybrid species
 ancestry estimates from Ancestry_HMM ##### Variables * shortcode: tree id
 * blightindex: breeding value for the blight resistance index scaled from
 0 = C. dentata mean to 100 = C. mollissima mean.  To create the blight
 resistance index, phenotypes were adjusted for fixed effects, residuals
 were weighted by trait heritability, and the following variables  were
 summed: ‘mainstemalive’, ‘largecankers’, ‘blightcontained’, ‘exposedwood’,
 ‘sporulation’, ‘sunkenswollen’, and ‘stumpsprouts’. *
 blightindex_accuracy: estimated accuracy of breeding value for breeding
 values for the blight resistance index. Accuracy was calculated from
 standard errors (SE) of breeding values as sqrt(1- [SE^2]/var(g)), where
 var(g) is the estimated genetic variance.   * phenotyped.blight: boolean
 indicating whether tree was phenotyped for blight resistance. *
 heightblup: breeding values for tree height in meters *
 heightblup_accuracy: estimated accuracy of breeding value for breeding
 values for tree height index. Accuracy was calculated from standard errors
 (SE) of breeding values as sqrt(1- [SE^2]/var(g)), where var(g) is the
 estimated genetic variance.   * phenotyped.height: boolean indicating
 whether tree was phenotyped for height *
 prr.survival.blup.scaled: breeding value for root rot survival scaled from
 0 = C. dentata mean to 100 = C. mollissima mean *
 prr.survival.blup.accuracy: estimated accuracy of breeding values for prr
 survival * prr.phenotyped: boolean indicating whether tree was phenotyped
 for prr resistance. * dentata ahmm: C. dentata ancestry proportions
 estimated in Ancestry_HMM * mollissima_ahmm: C. mollissima ancestry
 proportions estimated in Ancestry_HMM * crenata_ahmm: C. crenata ancestry
 proportions estimated in Ancestry_HMM * sativa_ahmm: C. sativa ancestry
 proportions estimated in Ancestry_HMM * pumila_ahmm: C. pumila ancestry
 proportions estimated in Ancestry_HMM * mom: mother of tree * dad: father
 of tree * generation: backcross generation * dentataparent: last known *C.
 dentata* parent * latitude: latitude of last known *C. dentata* parent *
 longitude: longitude of last known *C. dentata* parent * source: original
 source of resistance * chapter: chapter where tree originated * parcel:
 parcel where tree was grown * inoculated: whether tree was inoculated (1)
 or not (0) * plantdate: date that tree was planted * obsdate: date that
 tree was phenotyped * age: age in years that tree was phenotyped *
 seedzone: breeding zone from Sandercock et al. 2024. * survival: last
 observation of whether the tree was alive or dead * survival.obs.year:
 year when survival was last recorded on tree #### File:
 SIData29.chestnut.genomic.selection.simulation.outputs.txt
 **Description:** Predicted blight resistance, root rot resistance, height
 growth, and C. dentata ancestry after one generation of controlled
 pollinations and genomic selection ##### Variables * shortcode: tree id *
 generation: unselected - not selection, first selected - selected
 progeny,  current unselected: trees from current generation * type:
 selection type (blightheight - selection for blight resistance and height
 growth, blightheightrootrot - selection for blight resistance, root rot
 resistance, and height growth.  * replicate: simulation replicate where
 different parents that met selection criteria were randomly selected for
 controlled pollinations (inoculated reps - both parents were inoculated
 with Cr. parasitica, inoculated + naturally infected - parents either
 inoculated or naturally infected) * variable - blight resistance, height
 growth, root rot resistance, C. dentata ancestry * value - genomic
 estimated breeding values or C. dentata ancestry for tree  #### Files:
 Original photos of 'Darling 54' progeny * OxO_pos_2024_R2T57.jpg
 * OxO_pos_2024_R2T5.jpg * OxO_pos_2024_R1T53.jpg * OxO_pos_2024_R1T45.jpg
 * OxO_pos_2024_R1T29.jpg * OxO_pos_2023_R10T10.jpg *
 OxO_pos_2023_R7T13.jpg * OxO_pos_2023_R1T8.jpg * OxO_neg_2024_R1T14.jpg *
 OxO_neg_2024_R1T6.jpg **Description:** Original photos of Darling 54
 progeny from Fig S5. ID (OxO_pos = inherited the oxalate oxidase
 gene, OxO_neg = did not inherit the oxalate oxidase gene, 2023 or 2024 -
 year that three year old cohorts were inoculated with *Cr. parasitica,*
 RxTx = row and tree number of the tree. Raw canker data can be accessed in
 SIData9.  ## Access information Other publicly accessible locations of the
 data: * Raw PacBio and Illumina sequence data + RNA seq data for reference
 genomes can be accessed via NCBI bioproject PRJNA1147634 * Ellis,
 Mahogany, and Nanking genomes can be accessed on Phytozome * Raw fastq
 from files from genotyping-by-sequencing can be accessed through NCBI
 under bioproject PRJNA507748