针对性基因型测序的土豆和数据分析与R/polyBreedR
Jeffrey B Endelman1, Moctar Kante2, Hannele Lindqvist-Kreuze2
1Department of Plant & Agroecosystem Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA.
The plant genome
|June 18, 2024
概括
一种新的土豆基因型定型试验 (DArTag) 为遗传分析提供了一种具有成本效益的方法,提高了用于育种的标记精度. 这项技术有助于选择优质的土豆品种,以提高农业成果.
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:
- 中密度向基因型测序 (GBS) 为植物育种提供了成本和基因组信息的平衡.
- 开发高效准确的基因型定型工具对于加速作物改进至关重要.
研究的目的:
- 使用DArTag技术开发和验证一种针对土豆 (Solanum tuberosum L.) 的基因型测序 (GBS) 试验.
- 评估DArTag测定与现有SNP阵列的性能,并评估其在多倍体种群中对基因组选择和归算的有用性.
主要方法:
- 使用DArTag技术开发了一种2.5K和后来的4K针对土豆的GBS试验.
- 从土豆Infinium SNP阵列中选择标记物,以最大限度地提高基因组覆盖率和多态性.
- 使用树状图和定量协议指标 (RMSE) 的DArTag和SNP阵列平台的比较.
- 使用R包polyBreedR与链接分析和随机森林方法对标记器归算准确性的评估.
主要成果:
- DArTag和SNP阵列平台产生了同等的树突图,其中83%的共同标记物显示出良好的定量一致性 (RMSE<0.5).
- 在多体种群中使用链接分析对标记物的归算,与随机森林 (0.42) 相比,实现了显著较低的RMSE (0.15).
- DArTag标记器成功地追踪了土豆关键特征的目标,包括抗病性 (土豆病毒Y,黄金囊线虫,土豆) 和农学特征 (成熟度,形状).
结论:
- 马DArTag测定是一种具有成本效益和变革性的技术,用于马育种和遗传学.
- 该试验适用于克隆评估试验中的基因组选择,并且可以与训练人群的归算相结合.
- 该DArTag技术是公开可用的,促进其在世界各地的土豆研究和育种计划的采用.
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