马MASH是一种基于短读单元型的马基因组预测的具有成本效益的标记系统
Lea Vexler1,2,3, Agnieszka Konkolewska1,4, Stephen Byrne1
1Teagasc, Crop Science Department, Oak Park, Carlow, R93 XE12, Ireland.
概括
马MASH是一种具有成本效益的片测序方法,可以在马繁殖中进行基因组预测. 它使用单核酸多态 (SNPs) 和单核酸类型 (haplotags),其性能与高密度基因型定型相美,支持可扩展的应用.
科学领域:
- * 植物遗传学和育种
- * 基因组学和生物信息学
- * 农业科学 农业科学
背景情况:
- *基因组预测 (GP) 加快了植物育种中的遗传改进.
- * 密集基因造型的高成本限制了常规育种应用.
- *对于可扩展的土豆育种,需要具有成本效益的基因型化解决方案.
研究的目的:
- * 评估 PotatoMASH,一个低密度的安普利康测序平台,用于马的基因组预测.
- *比较PotatoMASH中的SNP和哈普罗标签的预测能力与测序 (GBS) 的高密度基因型定型.
- * 评估 PotatoMASH 在预测 23 个农学,质量和形态特征方面的表现.
主要方法:
- * 利用 PotatoMASH 平台进行安普利康测序,从 339 个位置生成了 2,236 个 SNP 和 2,000-3,390 个 haplotag.
- *比较预测能力 (PA) 与以前报告的数据,来自43.6k SNP GBS数据集.
- * 将平台应用于双胞胎土豆面板,用于预测23个特征.
主要成果:
- *与GBS相比,PotatoMASH显示了PA的适度降低 (SNP为14%,Haplotag为9%).
- * 在23个特征中,SNP和哈普罗标签都实现了中高的PA (0.29-0.81).
- *哈普洛标记在11个特征中胜过SNP,在6个特征中胜过SNP,在6个特征中没有差异.
结论:
- * PotatoMASH为土豆的基因组预测提供了一个可扩展和具有成本效益的GBS替代方案.
- * 该平台可以同时检测SNP和单种类型,支持集成的育种管道.
- * PotatoMASH适用于标记器辅助选择 (MAS) 和GP,提高了土豆育种效率.
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