全基因组关联分析研究植物与微生物组的互作遗传机制

doi:10.13560/j.cnki.biotech.bull.1985.2022-0557

摘要/Abstract

摘要：

所有栖息在植物宿主上的微生物被称为植物微生物组。随着高通量测序的发展，植物微生物组作为一个复杂的生态系统已经被广泛关注。植物微生物组群落的结构和功能等方面已得到了深入细致的研究，而植物与微生物组的互作机制仍有待探索。全基因组关联分析（Genome-Wide Association Analysis Study, GWAS）作为一种有效的手段已经被用来研究宿主和微生物组之间的关系。本文基于国内外最新研究进展，从以下方面进行综述，包括植物对微生物组的调控，以及如何应用GWAS研究植物与微生物组互作遗传机制，重点阐述了植物与微生物组关联分析中微生物组作为“拓展表型”数据的选择，并且总结了植物宿主影响微生物组的遗传机制，旨在阐明宿主遗传因素对微生物组的调控，增进对植物与微生物组互作的理解。

关键词: 植物微生物组, 互作遗传机制, GWAS, 网络作图, 遗传力

Abstract:

All the microorganisms that inhabit the plant host are called the plant microbiome. With the development of high-throughput sequencing, the plant microbiome as a complex ecosystem has been widely concerned. Despite increasing recognition of the structure and function of plant microbiome the interaction mechanism of plants and microbiomes remains largely elusive. As an effective method, the recent application of genome-wide association analysis study（GWAS）is instrumental in unravelling this issue.This review focuses on the latest research progresses by the following two aspects: the effect of plant on microbiome, and the genetic mechanism of plant-microbiome interaction. The selection of phenotypic data in plant-microbiome association analysis is elaborated, and genetic mechanisms by different hosts are summarized, aiming to elucidate the host regulation of the microbiome and enhance the understanding of plant-microbiome interactions.

Key words: plant-microbiome, interaction genetic mechanisms, GWAS, network mapping, heritability

李凯航, 王浩臣, 程可心, 杨艳, 金一, 何晓青. 全基因组关联分析研究植物与微生物组的互作遗传机制[J]. 生物技术通报, 2023, 39(2): 24-34.

LI Kai-hang, WANG Hao-chen, CHENG Ke-xin, YANG Yan, JIN Yi, HE Xiao-qing. Genetic Mechanisms of Plant-microbiome Interaction by Genome-wide Association Analysis Study[J]. Biotechnology Bulletin, 2023, 39(2): 24-34.

图/表 3

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物种 Species	基因 Gene	功能 Function	生态位 Niche	参考 Reference
拟南芥Arabidopsis thaliana	CAD1, MIN7 FLS2 ERF CERK1（mfec）	维持叶际微生物组稳定	叶际Phyllosphere	[34]
拟南芥Arabidopsis thaliana	AT2G3671，AT4G13210，AT5G26810,TERPENE SYNTHASE 10	负责防御和细胞壁完整性的植物位点	叶际Phyllosphere	[10]
拟南芥Arabidopsis thaliana	RPM1，RPS5，RPS2，AtABCG36	抗丁香假单胞菌	叶际Phyllosphere	[64]
拟南芥Arabidopsis thaliana	RRS1/RPS4，SSL4	抗青枯病菌	叶际Phyllosphere	[64]
拟南芥Arabidopsis thaliana	MYB72，BGLU42	诱导系统抗性	叶际Phyllosphere	[74] [75]
拟南芥Arabidopsis thaliana	ADA2B, HAL3A等	促进植物生长、抗病	叶际Phyllosphere	[59]
拟南芥Arabidopsis thaliana	PHR1	维持体内磷酸平衡	根际Rhizosphere	[76]
拟南芥Arabidopsis thaliana	TMK3，IBR1B等	促进拟南芥根系发育、抵抗生物与非生物胁迫	根际Rhizosphere	[14]
拟南芥Arabidopsis thaliana	BGLU42	诱导系统抗性和铁吸收重要调节因子	根际Rhizosphere	[77]
拟南芥Arabidopsis thaliana	F6’H1, PDR9	用于合成香豆素并转运到根际中来召集微生物组	根际Rhizosphere	[77]
拟南芥Arabidopsis thaliana	FERONIA	通过调节活性氧来控制根际微生物中的假单胞菌	根际Rhizosphere	[78]
拟南芥Arabidopsis thaliana	FERONIA	召集有益微生物	根际Rhizosphere	[79]
拟南芥Arabidopsis thaliana	CYP71A27	编码细胞色素P450，缺失会导致根际硫酸盐酶活性降低，假单胞菌对植物促生作用减弱	根际Rhizosphere	[73]
玉米Zea mays L.	AGPv3, GRMZM2G031545	作为管家基因参与蛋白表达，并普遍出现在所有组织中	叶际Phyllosphere	[11]
水稻 Oryza sativa L.	NRT1.1B	与根系微生物组成和氮素利用有关	根际Rhizosphere	[29]
番茄Lycopersicon esculentum Miller	HY5	调节菌根共生	根际Rhizosphere	[80]
高粱 Sorghum bicolor（Linn.）Moench	RGA2，CHAF1A，SAD5，EXO70B1，ANKRD52，UBA5，IDD16，NHL6，GCAL2	它们表现出很强的根特异性活性，包括γ碳酸酐酶样2、假定性β-1,4木聚糖内切酶和抗病蛋白RGA2	根际Rhizosphere	[12]
大麦 Hordeum vulgare Linn.	QRMC-3HS，NLR	植物特异性免疫系统的受体，激活植物的第二层免疫系统，抵御病原菌的侵染。	根际Rhizosphere	[81]

物种 Species	基因 Gene	功能 Function	生态位 Niche	参考 Reference
拟南芥Arabidopsis thaliana	CAD1, MIN7 FLS2 ERF CERK1（mfec）	维持叶际微生物组稳定	叶际Phyllosphere	[34]
拟南芥Arabidopsis thaliana	AT2G3671，AT4G13210，AT5G26810,TERPENE SYNTHASE 10	负责防御和细胞壁完整性的植物位点	叶际Phyllosphere	[10]
拟南芥Arabidopsis thaliana	RPM1，RPS5，RPS2，AtABCG36	抗丁香假单胞菌	叶际Phyllosphere	[64]
拟南芥Arabidopsis thaliana	RRS1/RPS4，SSL4	抗青枯病菌	叶际Phyllosphere	[64]
拟南芥Arabidopsis thaliana	MYB72，BGLU42	诱导系统抗性	叶际Phyllosphere	[74] [75]
拟南芥Arabidopsis thaliana	ADA2B, HAL3A等	促进植物生长、抗病	叶际Phyllosphere	[59]
拟南芥Arabidopsis thaliana	PHR1	维持体内磷酸平衡	根际Rhizosphere	[76]
拟南芥Arabidopsis thaliana	TMK3，IBR1B等	促进拟南芥根系发育、抵抗生物与非生物胁迫	根际Rhizosphere	[14]
拟南芥Arabidopsis thaliana	BGLU42	诱导系统抗性和铁吸收重要调节因子	根际Rhizosphere	[77]
拟南芥Arabidopsis thaliana	F6’H1, PDR9	用于合成香豆素并转运到根际中来召集微生物组	根际Rhizosphere	[77]
拟南芥Arabidopsis thaliana	FERONIA	通过调节活性氧来控制根际微生物中的假单胞菌	根际Rhizosphere	[78]
拟南芥Arabidopsis thaliana	FERONIA	召集有益微生物	根际Rhizosphere	[79]
拟南芥Arabidopsis thaliana	CYP71A27	编码细胞色素P450，缺失会导致根际硫酸盐酶活性降低，假单胞菌对植物促生作用减弱	根际Rhizosphere	[73]
玉米Zea mays L.	AGPv3, GRMZM2G031545	作为管家基因参与蛋白表达，并普遍出现在所有组织中	叶际Phyllosphere	[11]
水稻 Oryza sativa L.	NRT1.1B	与根系微生物组成和氮素利用有关	根际Rhizosphere	[29]
番茄Lycopersicon esculentum Miller	HY5	调节菌根共生	根际Rhizosphere	[80]
高粱 Sorghum bicolor（Linn.）Moench	RGA2，CHAF1A，SAD5，EXO70B1，ANKRD52，UBA5，IDD16，NHL6，GCAL2	它们表现出很强的根特异性活性，包括γ碳酸酐酶样2、假定性β-1,4木聚糖内切酶和抗病蛋白RGA2	根际Rhizosphere	[12]
大麦 Hordeum vulgare Linn.	QRMC-3HS，NLR	植物特异性免疫系统的受体，激活植物的第二层免疫系统，抵御病原菌的侵染。	根际Rhizosphere	[81]