Improving American chestnut resistance to two invasive pathogens through genome-enabled breeding

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.  
, , , # Data from: Improving American chestnut resistance to two invasive pathogens through genome-enabled breeding

[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 d...,

两种外来病原菌致使数十亿株美洲栗死亡一个多世纪后，通过从中国栗中导入预适应的抗性等位基因，已助力恢复能够自我维持的美洲栗种群。然而，由于抗性的遗传结构极为复杂，相关育种进展始终缓慢。为深入解析栗疫菌抗性机制，本研究对具有抗性的中国栗与易感病的美洲栗的参考基因组、基因表达响应以及茎部代谢物谱开展了比较分析。为加速抗性育种进程，我们对这两个物种的杂交后代进行了大规模表型组与基因型组鉴定。模拟与接种实验表明，通过选育平均美洲栗血统占比70%至85%的个体，可实现抗性的显著提升。本研究开发的各类资源，可为培育兼具充足抗病性与竞争生长能力的多样化恢复种群奠定核心基础。

# 数据来源：通过基因组辅助育种提升美洲栗对两种入侵病原菌的抗性

[https://doi.org/10.5061/dryad.4xgxd25mj](https://doi.org/10.5061/dryad.4xgxd25mj)

## 数据与文件结构说明

**补充数据1** | 5500株树木的栗疫菌抗性与生长表型数据

**补充数据2** | 5003株树木的约93k个单核苷酸多态性（SNP）基因型数据，格式为变异调用格式（VCF）

**补充数据3** | 约5000株基因分型树木的杂交祖先血统估计值

**补充数据4** | "GMBig × Horn"美洲栗（*Castanea dentata*）全同胞家系的遗传图谱

**补充数据5** | 杂交后代中美洲栗（*C. dentata*）与中国栗（*C. mollissima*）血统的基因组（"Ellis-1"）坐标信息

**补充数据6** | 本研究中进行表型分析的树木的系谱信息

**补充数据7** | 约1000株回交后代的实生苗栗疫菌抗性数据

**补充数据8** | LSAC后代的实生苗栗疫菌抗性数据

**补充数据9** | 栗疫菌抗性与株高数据……