遗传 ›› 2020, Vol. 42 ›› Issue (5): 506-518.doi: 10.16288/j.yczz.20-070

• 研究报告 • 上一篇    

水稻典型品种日本晴和IR24根系微生物组的解析

胡雅丽1,2,3, 戴睿2,3,4,5, 刘永鑫2,3,4, 张婧赢2,3,4, 胡斌2, 储成才2, 袁怀波1(), 白洋2,3,4,5()   

  1. 1. 合肥工业大学,食品与生物工程学院,合肥 230009
    2. 中国科学院遗传与发育生物学研究所,植物基因组学国家重点实验室,北京 100101
    3. 中国科学院大学,生物互作卓越创新中心,北京 100049
    4. 中国科学院遗传与发育生物学研究所,中国科学院-英国约翰英纳斯中心植物和微生物科学联合研究中心,北京 100101
    5. 中国科学院大学现代农学院,北京 100049
  • 收稿日期:2020-03-15 修回日期:2020-04-16 出版日期:2020-05-20 发布日期:2020-04-26
  • 通讯作者: 袁怀波,白洋 E-mail:yuanhuaibo001@163.com;ybai@genetics.ac.cn
  • 作者简介:胡雅丽,在读硕士研究生,专业方向:根系微生物组。E-mail:2017111262@mail.hfut.edu.cn|戴睿,在读博士研究生,专业方向:根系微生物组,生物信息学。E-mail: raydai@genetics.ac.cn; 胡雅丽和戴睿为并列第一作者。
  • 基金资助:
    中国科学院前沿科学重点研究项目编号(QYZDB-SSW-SMC021);国家自然科学基金面上项目资助编号(31772400)

Analysis of rice root bacterial microbiota of Nipponbare and IR24

Hu Yali1,2,3, Dai Rui2,3,4,5, Liu Yongxin2,3,4, Zhang Jingying2,3,4, Hu Bin2, Chu Chengcai2, Yuan Huaibo1(), Bai Yang2,3,4,5()   

  1. 1. School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
    2. State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
    3. CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
    4. CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
    5. College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100101, China
  • Received:2020-03-15 Revised:2020-04-16 Online:2020-05-20 Published:2020-04-26
  • Contact: Yuan Huaibo,Bai Yang E-mail:yuanhuaibo001@163.com;ybai@genetics.ac.cn
  • Supported by:
    Supported by the Key Research Program of Frontier Sciences of the Chinese Academy of Science No(QYZDB-SSW-SMC021);the National Natural Science Foundation of China No(31772400)

摘要:

植物的各项生命活动与其根系微生物组密不可分,且根系微生物组的组成易受到植物生长环境和基因型的影响。为进一步探究中国北方地区种植的不同品种水稻根系微生物组的差异及其相互作用机制,本研究以种植于北京昌平和上庄农场的水稻典型品种日本晴(Nipponbare)和IR24为研究对象,基于16S rRNA基因扩增子测序技术获得根系微生物组序列,利用多样性分析、组成型分析、机器学习的随机森林和网络分析等方法,对旺盛生长期的两种不同品种的水稻根系微生物组进行详细比较。研究发现,种植地点和水稻基因型显著影响了水稻根系微生物组的群落结构,不同基因型导致了根系微生物组在物种分类组成上以及细菌间相互关系的差异,而且根系微生物组能作为生物标记跨地点区分宿主的基因型。本研究结果为深入理解我国北方种植的水稻根系微生物组的组成规律以及从根系微生物与植物互作的角度对品种进行改良提供了数据和理论基础。

关键词: 水稻根系生物组, 多样性分析, 组成型分析, 机器学习, 网络分析

Abstract:

The root-associated bacterial microbiota is closely related to life activities of land plants, and its composition is affected by geographic locations and plant genotypes. However, the influence of plant genotypes on root microbiota in rice grown in northern China remains to be explained. In this study, we performed 16S rRNA gene amplicon sequencing to generate bacterial community profiles of two representative rice cultivars, Nipponbare and IR24. They are planted in Changping and Shangzhuang farms in Beijing and have reached the reproductive stage. We compared their root microbiota in details by Random Forest machine learning algorithm and network analysis. We found that the diversity of rice root microbiota was significantly affected by geographic locations and rice genotypes. Nipponbare and IR24 showed distinct taxonomic composition of the root microbiota and the interactions between different bacteria. Moreover, the root bacteria could be used as biomarkers to distinguish Nipponbare from IR24 across regions. Our study provides a theoretical basis for the in-depth understanding of rice root microbiota in Northern China and the improvement of rice breeding from the perspective of the interaction between root microorganisms and plants.

Key words: rice root microbiota, diversity analysis, taxonomic composition, machine learning, network analysis