PidTools:用于作物谱系识别分析的算法和网络工具
Yunlong Zhang1, Yikun Zhao1, Shipeng Ma1
1Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Key Laboratory of Crop DNA Fingerprinting Innovation and Utilization (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shuguang Garden Middle Road No. 9, Beijing 100097, China.
Computational and structural biotechnology journal
|August 7, 2024
概括
PidTools使用基因组数据准确识别作物谱系,帮助育种者进行遗传改进. 这个工具重建和可视化植物谱系,对于理解作物进化和最大化异构至关重要.
科学领域:
- 植物遗传学和育种.
- 生物信息学是一种生物信息学.
- 基因组分析 基因组分析
背景情况:
- 准确的作物谱系对于基因改进和异种利用至关重要.
- 缺少家谱信息阻碍了有效的生殖质选择和繁殖策略.
研究的目的:
- 开发一种算法 (PidTools),用于在作物中准确地识别和重建血统.
- 使用玉米基因组数据验证PidTools算法.
- 为分析和可视化植物育种材料谱系提供用户友好的工具.
主要方法:
- 开发PidTools,这是一个由五个算法组成的套件,跨越三个核心模块.
- 使用Maise6H-60K阵列数据,从5791个玉米杂交系中构建基因型数据库.
- 验证PidTools用于识别单个线条 (Jing72464,Zheng58) 和组 (双形,Dan340衍生线条) 的血统.
主要成果:
- 在没有先前的父母信息的情况下,成功地确定了玉米杂交系的全基因组血统.
- 通过基因定型数据确定双倍状组的父母.
- 可视化了21个Dan340衍生品种的血统.
结论:
- PidTools为所有作物提供准确的血统识别和重建.
- 开发的在线平台 (PidTools-WS) 和工具包 (PidTools-CLI) 为玉米育种提供了宝贵的资源.
- 这项技术有助于更好地了解作物亲属关系和进化历史,从而改善育种计划.
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