The use of molecular markers in plant breeding has become a routine practice, but the cost per accession can be a hindrance to the routine use of Quantitative Trait Loci (QTL) identification in breeding programs. In this study, we demonstrate the use of targeted re-sequencing as a proof of concept of a cost-effective approach to retrieve highly informative allele information, as well as develop a bioinformatics strategy to capture the genome-specific information of a polyploid species. SNPs were identified from alignment of raw transcriptome reads (2 × 50 bp) to a synthetic tetraploid genome using BWA followed by a GATK pipeline. Regions containing high polymorphic SNPs in both A genome and B genomes were selected as targets for the resequencing study. Targets were amplified using multiplex PCR followed by sequencing on an Illumina HiSeq. Eighty-one percent of the SNP calls in diploids and 68% of the SNP calls in tetraploids were confirmed. These results were also confirmed by KASP validation. Based on this study, we find that targeted resequencing technologies have potential for obtaining maximum allele information in allopolyploids at reduced cost.

中文翻译：

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在花生中使用靶向扩增子测序来生成异源四倍体亚基因组的等位基因信息

在植物育种中使用分子标记已成为常规做法，但每次种质的成本可能会阻碍定量性状位点 (QTL) 鉴定在育种计划中的常规使用。在这项研究中，我们展示了使用靶向重测序作为检索高信息等位基因信息的经济有效方法概念的证明，并开发了一种生物信息学策略来捕获多倍体物种的基因组特异性信息。使用 BWA 和 GATK 管道，从原始转录组读数（2 × 50 bp）与合成四倍体基因组的比对中鉴定 SNP。选择在 A 基因组和 B 基因组中都含有高多态性 SNP 的区域作为重测序研究的目标。使用多重 PCR 扩增目标，然后在 Illumina HiSeq 上测序。确认了二倍体中 81% 的 SNP 调用和四倍体中 68% 的 SNP 调用。这些结果也得到了 KASP 验证的证实。基于这项研究，我们发现靶向重测序技术具有以更低的成本获得异源多倍体中最大等位基因信息的潜力。