作物学报2024，Vol.50Issue(9)：2279-2296,18.DOI:10.3724/SP.J.1006.2024.33049
联合全基因组关联和转录组分析筛选玉米拟轮枝镰孢穗腐病的抗性候选基因
Screening candidate resistance genes to ear rot caused by Fusarium vertici-llioides in maize by combined GWAS and transcriptome analysis
摘要
Abstract
Maize,as the largest grain crop in China,holds great significance for food security and agricultural stability,making it crucial to achieve high and stable yields.Ear rot,a fungal disease,poses a serious threat to global corn production,resulting in significant yield reduction and quality deterioration.This study focused on the dominant pathogen Fusarium verticillioides and aimed to identify resistance in 241 maize inbred lines from diverse sources through two years of artificial inoculation in the field.Additionally,a genome-wide association study(GWAS)was conducted using 20,586 high-quality SNP markers to identify SNP loci significantly associated with ear rot resistance.Based on this research,one maize inbred line with high resistance and one with high susceptibility to F.verticillioides-induced ear rot were selected.The young kernels of these lines were subjected to RNA transcriptome sequencing(RNA-seq)at three different infection stages,and differentially expressied genes(DEGs)and enrich-ment analysis were conducted.The results of GWAS and RNA-seq were combined to identify candidate resistant genes.The main findings were as followed:(1)Four inbred lines resistant to F.verticillioides-induced ear rot were selected based on two years of field resistance identification.Maize germplasm with tropical consanguinity exhibited higher resistance.(2)A total of 26 SNP loci associated with ear rot resistance were detected through two years of GWAS analysis,with 18 loci located within previously iden-tified QTL regions.(3)RNA-seq analysis revealed differential response genes between resistant and susceptible lines upon F.verticillioides infection.The resistant line exhibited a greater number of DEGs and up-regulated genes.In the co-enriched GO entries and KEGG pathways specific to the DEGs of resistant and susceptible lines,the proportion of DEGs enriched in the resis-tant line was significantly higher.Moreover,some entries and pathways related to plant defense against pathogens were specifi-cally enriched in the resistant line.(4)Sixteen genes,detected by both GWAS and RNA-seq,were identified as candidate genes by screening those co-located with transcriptome DEGs within a range of 100 kb upstream and downstream of significant association loci.Based on protein function and relevant literature reports,six candidate genes related to ear rot resistance were predicted.In summary,this study identified four maize lines resistant to F.verticillioides-induced ear rot.Maize germplasm from tropical and subtropical regions holds promise for stress-tolerant variety breeding.The preliminary analysis of DEGs and related resistance mechanisms of maize in response to F.verticillioides infection was conducted.Furthermore,six candidate genes associated with ear rot resistance were identified through the integration of GWAS and RNA-seq.These findings provide a theoretical basis for the cloning and validation of maize ear rot resistance genes,as well as the breeding of resistant varieties.关键词
玉米穗腐病/拟轮枝镰孢/关联分析/转录组分析/抗性种质/候选基因Key words
maize ear rot/Fusarium verticillioides/association analysis/transcriptome analysis/resistant germplasm/candidate genes引用本文复制引用
叶靓,朱叶琳,裴琳婧,张思颖,左雪倩,李正真,刘芳,谭静..联合全基因组关联和转录组分析筛选玉米拟轮枝镰孢穗腐病的抗性候选基因[J].作物学报,2024,50(9):2279-2296,18.基金项目
本研究由国家自然科学基金项目(32260516)资助.This study was supported by the National Natural Science Foundation of China(32260516). （32260516）
