Haplotypes provide useful information for genomics-based approaches, genomic prediction, and genome-wide association study. As a small number of superior founders have contributed largely to the breeding history of fruit trees, the information of founder haplotypes may be relevant for performing the genomics-based approaches in these plants. In this study, we proposed a method to estimate 14 haplotypes from 7 founders and automatically trace the haplotypes forward to apple parental (185 varieties) and breeding (659 F1 individuals from 16 full-sib families) populations based on 11,786 single-nucleotide polymorphisms, by combining multiple algorithms. Overall, 92% of the single-nucleotide polymorphisms information in the parental and breeding populations was characterized by the 14 founder haplotypes. The use of founder haplotype information improved the accuracy of genomic prediction in 7 traits and the resolution of genome-wide association study in 13 out of 27 fruit quality traits analyzed in this study. We also visualized the significant propagation of the founder haplotype with the largest genetic effect in genome-wide association study over the pedigree tree of the parental population. These results suggest that the information of founder haplotypes can be useful for not only genetic improvement of fruit quality traits in apples but also for understanding the selection history of founder haplotypes in the breeding program of Japanese apple varieties.

中文翻译：

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追踪日本苹果品种的创始人单倍型：在基因组预测和全基因组关联研究中的应用

单倍型为基于基因组学的方法、基因组预测和全基因组关联研究提供有用的信息。由于少数优秀的创始人对果树的育种历史做出了很大贡献，因此创始人单倍型的信息可能与在这些植物中执行基于基因组学的方法相关。在这项研究中，我们提出了一种方法来估计来自 7 个创始人的 14 个单倍型，并自动将单倍型向前追踪到苹果亲本（185 个品种）和育种（659 F1通过结合多种算法，基于 11,786 个单核苷酸多态性（来自 16 个全同胞家族的个体）群体。总体而言，亲本和育种群体中 92% 的单核苷酸多态性信息由 14 个创始人单倍型表征。使用创始人单倍型信息提高了 7 个性状的基因组预测的准确性，以及本研究分析的 27 个水果品质性状中的 13 个性状的全基因组关联研究的分辨率。我们还可视化了在亲代群体谱系树上的全基因组关联研究中具有最大遗传效应的创始人单倍型的显着传播。这些结果表明，创始人单倍型的信息不仅可用于苹果果实品质性状的遗传改良，而且还可用于了解日本苹果品种育种计划中创始人单倍型的选择历史。