广西水稻地方品种核心种质稻瘟病抗性位点全基因组关联分析

稻瘟病是水稻重要病害之一,严重影响水稻的产量与品质。培育抗性品种是防治稻瘟病最经济、环保的方式。稻瘟病抗性基因的鉴定与挖掘是开展抗病育种的基础与前提。本课题组前期对419份广西水稻地方品种核心种质进行简化基因组测序,获得208,993个高质量SNP标记。本研究采用苗期喷雾接种方法,研究了该419份核心种质对7个稻瘟病生理小种的抗性,并根据表型和基因型数据,利用一般线性模型(general linear model,GLM)和混合线性模型(mixed linear model,MLM)进行全基因组关联分析。2种模型下共检测到20个位点,其中GLM检测到20个位点,MLM检测到1个位点,Chr12_10803913位点在2种模型下都检测到。17个位点与前人定位的基因/QTLs重叠,其余3个是新位点,分别为Chr3_18302718、Chr3_18302744及Chr5_10379127位点。在20个显著关联位点上下游各150 kb的基因组区域中共筛选出候选基因323个,初步确定8个候选基因与抗病相关,其中LOC_Os12g18360(Pita)、LOC_Os12g18729(Ptr)为已知克隆的基因,LOC_Os03g32100、LOC_Os03g32180和LOC_Os05g18090为新位点附近筛选到的候选基因。本研究结果为稻瘟病抗性位点挖掘与稻瘟病相关基因克隆提供了科学依据。

Genome-wide association study of blast resistance loci in the core germplasm of rice landraces from Guangxi

Blast disease is one of the most important rice diseases,which seriously affects the yield and quality in rice.In general,breeding resistant varieties is the most economical,environmental,and friendly way to control rice blast.Identification and mining of blast resistance genes are the basis and premise of disease resistance breeding.In our previous study,419 core germplasms from Guangxi rice landraces were sequenced using specific-locus amplified fragment sequencing(SLAF-seq)technology,and 208,993 high-quality SNPs were identified.Spray inoculation at seedling stage was used to evaluate the resistance of the 419 germplasms to 7 strains.According to phenotype and genotype data,genome-wide association study(GWAS)for rice blast was performed using general linear model(GLM)and mixed linear model(MLM).A total of 20 loci were detected under the two models,including 20 loci detected by GLM and 1 locus detected by MLM.Chr12_10803913 locus was detected in both models.There were 17 loci,overlapping with previously reported genes/QTLs,while the remaining three loci were the first reported,including Chr3_18302718,Chr3_18302744,and Chr5_10379127.A total of 323 candidate genes were screened out in the genomic regions of 150 kb upstream and downstream of 20 significantly associated loci.Eight candidate genes were preliminarily determined to be related to disease resistance.Among them,both LOC_Os12g18360(Pita)and LOC_Os12g18729(Ptr)were known cloned genes,LOC_Os03g32100,LOC_Os03g32180,and LOC_Os05g18090 were selected as candidate genes near the three loci.The results provided the scientific basis for the mining of rice blast resistance loci and gene cloning.