High-throughput genotyping tools can effectively promote molecular breeding in crops. In this study, genotyping by target sequencing (GBTS) system was utilized to develop a genome-wide liquid SNP chip for facilitating genetics and breeding in melon ( L.), a globally cultivated economically important horticultural crop. Based on over eight million SNPs derived from 823 representative melon accessions, 16K, 8K, 4K, 2K, 1K, 500, 250 and 125 informative SNPs were screened and evaluated for their polymorphisms, conservation of flanking sequences, and distributions. The set of 2K SNPs was found to be optimal for representing the maximum diversity with the lowest number of SNPs, and it was selected to develop the liquid chip, named “Melon2K”. Using Melon2K, more than 1500 SNPs were detected across 17 samples of five melon cultivars, and the phylogenetic relationships were clearly constructed. Within the same cultivar, genetic differences were also assessed between different samples. We evaluated the performance of Melon2K in genetic background selection during the breeding process, obtaining the introgression lines of interested trait with more than 97% genetic background of elite variety by only two rounds of backcrossing. These results suggest that Melon2K provides a cost-effective, efficient and reliable platform for genetic analysis and molecular breeding in melon.

中文翻译：

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Melon2K 阵列：用于甜瓜遗传和育种的多功能 2K 液体 SNP 芯片


高通量基因分型工具可以有效促进作物分子育种。在这项研究中，利用目标测序基因分型（GBTS）系统开发了全基因组液体SNP芯片，以促进甜瓜（L.）的遗传和育种，甜瓜是全球种植的重要经济园艺作物。基于来自823个代表性甜瓜种质的超过800万个SNP，筛选并评估了16K、8K、4K、2K、1K、500、250和125个信息丰富的SNP，并评估了它们的多态性、侧翼序列的保守性和分布。发现这组 2K SNP 是用最少数量的 SNP 代表最大多样性的最佳选择，并选择它来开发液体芯片，命名为“Melon2K”。使用 Melon2K，在 5 个甜瓜品种的 17 个样本中检测到了 1500 多个 SNP，并清晰地构建了系统发育关系。在同一品种内，还评估了不同样本之间的遗传差异。我们在育种过程中评估了Melon2K在遗传背景选择方面的表现，仅通过两轮回交就获得了具有97%以上优良品种遗传背景的感兴趣性状渗入系。这些结果表明，Melon2K 为甜瓜遗传分析和分子育种提供了一个经济有效、高效且可靠的平台。