Optimizing genomic selection for blight resistance in American chestnut backcross populations: a tradeoff with American chestnut ancestry implies resistance is polygenic

American chestnut was once a foundation species of eastern North American forests, but was rendered functionally extinct in the early 20th century by an exotic fungal blight (Cryphonectria parasitica). Over the past 30 years, The American Chestnut Foundation (TACF) has pursued backcross breeding to generate hybrids that combine the timber-type form of American chestnut with the blight resistance of Chinese chestnut based on a hypothesis of major gene resistance. To accelerate selection within two backcross populations that descended from two Chinese chestnuts, we developed genomic prediction models for five presence/absence blight phenotypes of 1,230 BC3F2 selection candidates and average canker severity of their BC3F3 progeny. We also genotyped pure Chinese and American chestnut reference panels to estimate the proportion of BC3F2 genomes inherited from parent species. We found that genomic prediction from a method that assumes an infinitesimal model of inheritance (HBLUP) has similar ...美洲栗（American chestnut）曾是北美东部森林的建群种，但在20世纪早期因外来真菌性疫病——栗疫病菌（Cryphonectria parasitica）的侵染而功能性灭绝。近30年来，美国栗树基金会（The American Chestnut Foundation, TACF）基于主基因抗性（major gene resistance）假说，开展回交育种工作以培育兼具美洲栗用材型形态与中国板栗（Chinese chestnut）疫病抗性的杂交品种。为加速源自两个中国板栗的两个回交群体内的选择进程，本研究为1230个BC3F2代选择候选株系的5种疫病有无表型，以及其BC3F3代后代的平均溃疡严重程度构建了基因组预测模型（genomic prediction models）。此外，我们对纯合中国板栗和美洲栗参考面板进行基因分型，以估算BC3F2代基因组来自亲本物种的遗传比例。研究发现，采用假定无穷小遗传模型（infinitesimal model of inheritance）的HBLUP方法进行基因组预测，其效果与……