基于遗传多样性和选择消除分析挖掘禾谷镰孢致病相关基因
Exploring key pathogenic genes in Fusarium graminearum based on genetic diver-sity and selection elimination analysis
甄金鹏 1柳健虎 1曹宏哲 1邢继红 1董金皋 1石承民 1张康1
作者信息
- 1. 华北作物改良与调控国家重点实验室,河北省植物生理与分子病理学重点实验室,河北农业大学,保定 071000
- 折叠
摘要
近年来,由禾谷镰孢(Fusarium graminearum)侵染引起的小麦赤霉病、玉米茎腐病和穗腐病频繁发生,造成严重的农作物产量损失.为了解禾谷镰孢的遗传多样性以及挖掘其致病相关基因,本研究利用单核苷酸多态性(Single nucleotide polymorphism,SNP)技术,对93份来自世界不同地区的禾谷镰孢进行群体遗传分析和选择消除分析.利用基因组分析工具箱(Genome Analysis Toolkit 4,GATK4)对这些禾谷镰孢的全基因组重测序数据进行处理,获得了 3,817,652个SNP标记.基于SNP获得的系统发育树、主成分分析(PCA)及群体遗传结构分析结果,将这些禾谷镰孢分为3个类群.基于选择性降低,对类群1和类群2进行选择消除分析,结果发现类群1受到的选择压力更大.在群体多态性(θπ)和群体分化指数(Fst)两者交集的前5％区域确定了 70个受选择区域,依据基因组位置信息获得了 76个蛋白编码基因.进一步通过KEGG通路富集分析,以及候选基因在禾谷镰孢.寄主植物互作过程中的转录水平分析,初步确定了其中8个基因(FGSG_05447、FGSG_05610、FGSG_10272、FGSG_10313、FGSG_01353、FGSG_05545、FGSG_10858 和 FGSG_12745)与禾谷镰孢的致病性密切相关.研究结果为揭示禾谷镰孢致病机理以及小麦和玉米相应抗性品种的选育奠定了基础.
Abstract
In recent years,wheat scab,corn stalk rot and ear rot caused by Fusarium graminearum have led to substantial losses in crop yields.To investigate the genetic diversity and identify pathogenicity-related genes of F.graminearum,we performed population genetic diversity analysis and selective elimination analysis on 93 F.gra-minearum strains with released genome-wide resequencing data,using single nucleotide polymorphism(SNP)technology.The resequencing data of these F.graminearum strains were meticulously processed by using the Ge-nome Analysis Toolkit 4(GATK4),yielding a collection of 3,817,652 SNP markers.Based on these markers,a phylogenetic tree was constructed,and principal component analysis(PCA)and population structure analysis were conducted,effectively partitioning the 93 F.graminearum into 3 distinct groups.The selection elimination analysis of group 1 and group 2 revealed that group 1 exhibited a more pronounced response to selection pressure.A total of 70 regions were identified as candidate sites within the top 5％intersection region of population poly-morphism(θπ)and population differentiation index(Fst).Furthermore,76 protein-coding genes were identi-fied in F.graminearum by leveraging the genomic location information.The results of Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analysis showed that these 76 candidate genes are mainly in-volved in metabolic pathways.Among them,eight genes(FGSG_05447,FGSG_05610,FGSG_10272,FGSG_10313,FGSG_01353,FGSG_05545,FGSG_10858 and FGSG_12745)are closely related to the pathogenicity of F.graminearum through further gene expression analysis.The result lays a basis for clarifying the pathogenic mechanism of F.graminearum and breeding F.graminearum-resistant wheat and maize varieties.
关键词
禾谷镰孢/单核苷酸多态性/进化树/主成分分析/遗传结构/选择消除Key words
Fusarium graminearum/SNP/evolutionary tree/PCA/genetic structure/selection elimination引用本文复制引用
基金项目
国家自然科学基金(31972217)
国家自然科学基金(32072369)
河北省中央引导地方科技发展专项(216Z6502G)
国家玉米产业技术体系建设项目(CARS-02)
河北省高等学校科研项目(BJK2022006)
出版年
2024
NETL
NSTL
万方数据