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Zachary James Winn¹, Emily Hudson-Arns¹, Mikayla Hammers¹

¹Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA.

The plant genome

|November 16, 2023

概括

一个R包的HaploCatcher准确地预测小麦茎固度哈普洛类型,以提高害虫抵抗力. 这种工具有助于小麦育种计划高效地选择耐药品种.

科学领域:

植物遗传学植物遗传学
农业科学农业科学
生物信息学是一种生物信息学.

背景情况:

小麦 (Triticum aestivum L.) 对全球粮食安全至关重要,但面临着像小麦茎虫 (Cephus cinctus Norton) 这样的害虫的威胁.
对小麦茎虫的遗传耐药性主要存在于携带茎结实部位 (Sst1) 的固体茎小麦品种中.
标记器辅助选择 (MAS) 是一种关键技术,用于识别育种计划中可取的遗传特征.

研究的目的:

开发一个R包,HaploCatcher,用于预测小麦系中特定的单质类型,特别是Sst1位点.
为了评估HaploCatcher的预测准确性,使用已建立的培训群体和全基因组标记物.
为小麦种植者提供一个工具,以有效地选择茎的坚固性和虫耐药性.

主要方法:

策划了1056个小麦系的培训群体,这些小麦系的基因型为Sst1位点和全基因组标记物.
从科罗拉多州立大学的小麦育种计划开发了HaploCatcher R包,用于预测Sst1单元型在292条线上.
使用k-最近邻居和随机森林模型,比较预测的Sst1类型与标记器衍生的类型.

主要成果:

训练组表现出相当大的预测能力,kappa得分为0.83 (k-最近邻居) 和0.88 (随机森林).
前期验证证实了随机森林模型在新繁殖线上的准确性,显示了与交叉验证相似的结果.
通过PCR衍生标记分类的线的估计组平均值和预测建模之间没有发现显著差异.

结论:

该HaploCatcher R包准确地预测Sst1的哈普洛类型,有助于选择耐虫的小麦茎品种.
该工具是免费提供的,可以通过使用他们自己的培训数据进行全基因组测序材料的育种计划进行调整.
HaploCatcher促进了高效的标记器辅助选择,以增强小麦育种计划中的遗传耐药性.

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