Successful management and utilization of increasingly large genomic datasets is essential for breeding programs to accelerate cultivar development. To help with this, we developed a Sorghum bicolor Practical Haplotype Graph (PHG) pangenome database that stores haplotypes and variant information. We developed two PHGs in sorghum that were used to identify genome‐wide variants for 24 founders of the Chibas sorghum breeding program from 0.01x sequence coverage. The PHG called single nucleotide polymorphisms (SNPs) with 5.9% error at 0.01x coverage—only 3% higher than PHG error when calling SNPs from 8x coverage sequence. Additionally, 207 progenies from the Chibas genomic selection (GS) training population were sequenced and processed through the PHG. Missing genotypes were imputed from PHG parental haplotypes and used for genomic prediction. Mean prediction accuracies with PHG SNP calls range from .57–.73 and are similar to prediction accuracies obtained with genotyping‐by‐sequencing or targeted amplicon sequencing (rhAmpSeq) markers. This study demonstrates the use of a sorghum PHG to impute SNPs from low‐coverage sequence data and shows that the PHG can unify genotype calls across multiple sequencing platforms. By reducing input sequence requirements, the PHG can decrease the cost of genotyping, make GS more feasible, and facilitate larger breeding populations. Our results demonstrate that the PHG is a useful research and breeding tool that maintains variant information from a diverse group of taxa, stores sequence data in a condensed but readily accessible format, unifies genotypes across genotyping platforms, and provides a cost‐effective option for genomic selection.

中文翻译：

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高粱实用的单倍型图有助于全基因组估算和具有成本效益的基因组预测

成功地管理和利用日益庞大的基因组数据集对于育种计划以加速品种发展至关重要。为了解决这个问题，我们开发了一种双色高粱实用单倍型图（PHG）全景基因组数据库，用于存储单倍型和变异信息。我们在高粱中开发了两种PHG，用于从0.01x序列覆盖率识别Chibas高粱育种计划的24位创始人的全基因组变异。PHG称为单核苷酸多态性（SNP），在0.01x覆盖率下错误率为5.9％，仅比从8x覆盖率序列调用SNP时的PHG错误高3％。此外，对来自Chibas基因组选择（GS）训练种群的207个后代进行了测序，并通过PHG进行了处理。从PHG亲本单倍型推算缺失的基因型，并将其用于基因组预测。PHG SNP调用的平均预测准确度范围为.57-.73，与通过测序进行基因分型或靶向扩增子测序（rhAmpSeq）标记获得的预测准确度相似。这项研究证明了使用高粱PHG从低覆盖率序列数据推算SNP，并表明PHG可以在多个测序平台上统一基因型调用。通过减少输入序列要求，PHG可以降低基因分型的成本，使GS更可行，并有利于更大的繁殖群体。我们的结果表明，PHG是一种有用的研究和育种工具，可以维护来自不同类群的变异信息，以浓缩但易于访问的格式存储序列数据，统一跨基因分型平台的基因型，并为基因组学提供经济高效的选择选择。通过减少输入序列要求，PHG可以降低基因分型的成本，使GS更可行，并有利于更大的繁殖群体。我们的结果表明，PHG是一种有用的研究和育种工具，可以维护来自不同类群的变异信息，以浓缩但易于访问的格式存储序列数据，统一跨基因分型平台的基因型，并为基因组学提供经济高效的选择选择。通过减少输入序列要求，PHG可以降低基因分型的成本，使GS更可行，并有利于更大的繁殖群体。我们的结果表明，PHG是一种有用的研究和育种工具，可以维护来自不同类群的变异信息，以浓缩但易于访问的格式存储序列数据，统一跨基因分型平台的基因型，并为基因组学提供经济高效的选择选择。