Datasets of "On the usefulness of mock genomes to define heterotic pools, testers, and hybrid predictions in orphan crops"

The advances in genomics in recent years have increased the accuracy and efficiency of breeding programs for many crops. Nevertheless, the adoption of genomic enhancement for several other crops essential in developing countries is still limited, especially for those that do not have a reference genome. These crops are more often called orphans. This is the first report to show how the results provided by different platforms, including the use of a simulated genome called the mock genome, can generate in population structure and genetic diversity studies, especially when the intention is to use this information to support the formation of heterotic groups, choice of testers and genomic prediction of single-crosses. For that, we used a method to assemble a reference genome to perform the SNP calling without needing an external genome. Thus, we compared the analysis results using the mock genome with the standard approaches (Array and GBS). The results showed that the GBS-Mock presented similar results to the standard methods of genetic diversity studies, division of heterotic groups, the definition of testers, and genomic prediction. These results showed that a mock genome constructed from the population's intrinsic polymorphisms to perform the SNP calling is an effective alternative for conducting genomic studies of this nature in orphan crops, especially those that do not have a reference genome.

近年来基因组学领域的技术进展，显著提升了诸多作物育种项目的精准性与实施效率。尽管如此，发展中国家至关重要的多种其他作物，其基因组辅助改良技术的应用仍存在较大局限，尤以尚未拥有参考基因组（reference genome）的作物为甚，这类作物常被称为孤儿作物（orphan crops）。本研究首次报道，包括模拟基因组（mock genome）在内的不同分析平台所生成的结果，可有效应用于群体结构与遗传多样性研究，尤其当研究目标为依托相关信息支撑杂种优势群划分、测验种选择以及单交种的基因组预测（genomic prediction）时。为此，我们构建了一种无需依赖外部参考基因组即可完成单核苷酸多态性检测（SNP calling）的参考基因组组装方法。随后，我们将基于模拟基因组的分析结果与标准研究方法（基因芯片Array、基因组简化测序GBS）的分析结果进行了对比。结果显示，结合基因组简化测序与模拟基因组的分析策略，其在遗传多样性分析、杂种优势群划分、测验种确定以及基因组预测等场景下的结果，与标准方法表现出高度相似性。上述研究结果证实，依托群体自身固有多态性构建模拟基因组以开展SNP检测，是在孤儿作物中开展此类基因组学研究的有效替代方案，尤其适用于尚未拥有参考基因组的作物。