Network mapping of root–microbe interactions in Arabidopsis thaliana

Abstract Understanding how plants interact with their colonizing microbiota to determine plant phenotypes is a fundamental question in modern plant science. Existing approaches for genome-wide association studies (GWAS) are often focused on the association analysis between host genes and the abundan...

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Autores principales:	Xiaoqing He, Qi Zhang, Beibei Li, Yi Jin, Libo Jiang, Rongling Wu
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Microbial ecology QR100-130
Acceso en línea:	https://doaj.org/article/fb3f76463743455286087061a076e40c
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spelling	oai:doaj.org-article:fb3f76463743455286087061a076e40c2021-12-02T19:13:54ZNetwork mapping of root–microbe interactions in Arabidopsis thaliana10.1038/s41522-021-00241-42055-5008https://doaj.org/article/fb3f76463743455286087061a076e40c2021-09-01T00:00:00Zhttps://doi.org/10.1038/s41522-021-00241-4https://doaj.org/toc/2055-5008Abstract Understanding how plants interact with their colonizing microbiota to determine plant phenotypes is a fundamental question in modern plant science. Existing approaches for genome-wide association studies (GWAS) are often focused on the association analysis between host genes and the abundance of individual microbes, failing to characterize the genetic bases of microbial interactions that are thought to be important for microbiota structure, organization, and function. Here, we implement a behavioral model to quantify various patterns of microbe-microbe interactions, i.e., mutualism, antagonism, aggression, and altruism, and map host genes that modulate microbial networks constituted by these interaction types. We reanalyze a root-microbiome data involving 179 accessions of Arabidopsis thaliana and find that the four networks differ structurally in the pattern of bacterial-fungal interactions and microbiome complexity. We identify several fungus and bacterial hubs that play a central role in mediating microbial community assembly surrounding A. thaliana root systems. We detect 1142 significant host genetic variants throughout the plant genome and then implement Bayesian networks (BN) to reconstruct epistatic networks involving all significant SNPs, of which 91 are identified as hub QTLs. Results from gene annotation analysis suggest that most of the hub QTLs detected are in proximity to candidate genes, executing a variety of biological functions in plant growth and development, resilience against pathogens, root development, and abiotic stress resistance. This study provides a new gateway to understand how genetic variation in host plants influences microbial communities and our results could help improve crops by harnessing soil microbes.Xiaoqing HeQi ZhangBeibei LiYi JinLibo JiangRongling WuNature PortfolioarticleMicrobial ecologyQR100-130ENnpj Biofilms and Microbiomes, Vol 7, Iss 1, Pp 1-10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbial ecology QR100-130
spellingShingle	Microbial ecology QR100-130 Xiaoqing He Qi Zhang Beibei Li Yi Jin Libo Jiang Rongling Wu Network mapping of root–microbe interactions in Arabidopsis thaliana
description	Abstract Understanding how plants interact with their colonizing microbiota to determine plant phenotypes is a fundamental question in modern plant science. Existing approaches for genome-wide association studies (GWAS) are often focused on the association analysis between host genes and the abundance of individual microbes, failing to characterize the genetic bases of microbial interactions that are thought to be important for microbiota structure, organization, and function. Here, we implement a behavioral model to quantify various patterns of microbe-microbe interactions, i.e., mutualism, antagonism, aggression, and altruism, and map host genes that modulate microbial networks constituted by these interaction types. We reanalyze a root-microbiome data involving 179 accessions of Arabidopsis thaliana and find that the four networks differ structurally in the pattern of bacterial-fungal interactions and microbiome complexity. We identify several fungus and bacterial hubs that play a central role in mediating microbial community assembly surrounding A. thaliana root systems. We detect 1142 significant host genetic variants throughout the plant genome and then implement Bayesian networks (BN) to reconstruct epistatic networks involving all significant SNPs, of which 91 are identified as hub QTLs. Results from gene annotation analysis suggest that most of the hub QTLs detected are in proximity to candidate genes, executing a variety of biological functions in plant growth and development, resilience against pathogens, root development, and abiotic stress resistance. This study provides a new gateway to understand how genetic variation in host plants influences microbial communities and our results could help improve crops by harnessing soil microbes.
format	article
author	Xiaoqing He Qi Zhang Beibei Li Yi Jin Libo Jiang Rongling Wu
author_facet	Xiaoqing He Qi Zhang Beibei Li Yi Jin Libo Jiang Rongling Wu
author_sort	Xiaoqing He
title	Network mapping of root–microbe interactions in Arabidopsis thaliana
title_short	Network mapping of root–microbe interactions in Arabidopsis thaliana
title_full	Network mapping of root–microbe interactions in Arabidopsis thaliana
title_fullStr	Network mapping of root–microbe interactions in Arabidopsis thaliana
title_full_unstemmed	Network mapping of root–microbe interactions in Arabidopsis thaliana
title_sort	network mapping of root–microbe interactions in arabidopsis thaliana
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/fb3f76463743455286087061a076e40c
work_keys_str_mv	AT xiaoqinghe networkmappingofrootmicrobeinteractionsinarabidopsisthaliana AT qizhang networkmappingofrootmicrobeinteractionsinarabidopsisthaliana AT beibeili networkmappingofrootmicrobeinteractionsinarabidopsisthaliana AT yijin networkmappingofrootmicrobeinteractionsinarabidopsisthaliana AT libojiang networkmappingofrootmicrobeinteractionsinarabidopsisthaliana AT ronglingwu networkmappingofrootmicrobeinteractionsinarabidopsisthaliana
_version_	1718377008913711104

Network mapping of root–microbe interactions in Arabidopsis thaliana

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