杨梅种质资源InDel标记开发及与熟期的关联分析  

Development of Insertion and Deletion(InDel)Markers in Germplasm Resources of Chinese Bayberry and Correlation Analysis with Mature Stage

作　　者：焦云 高中山[3] 汪国云 陈方永 姚小映 周超超 JIAO Yun;GAO Zhongshan;WANG Guoyun;CHEN Fangyong;YAO Xiaoying;ZHOU Chaochao(Ningbo Key Laboratory of Characteristic Horticultural Crops in Quality Adjustment and Resistance Breeding,Ningbo 315040,Zhejiang;Institute of Forestry,Ningbo Academy of Agricultural Sciences,Ningbo 315040,Zhejiang;Institute of Fruit Science,Zhejiang University,Hangzhou 310058;Yuyao Agricultural Technology Extension Service Station,Yuyao 315400,Zhejiang;Zhejiang Citrus Research Institute,Huangyan 318026;Ningbo Jiangbei Nanzhen Fruit Professional Cooperative,Ningbo 315037,Zhejiang)

机构地区：[1]宁波市特色园艺作物品质调控与抗性育种重点实验室,浙江宁波315040 [2]宁波市农业科学研究院林业研究所,浙江宁波315040 [3]浙江大学果树科学研究所,杭州310058 [4]余姚市农业技术推广服务总站,浙江余姚315400 [5]浙江省柑桔研究所,黄岩318026 [6]宁波市江北南珍水果专业合作社,浙江宁波315037

出　　处：《植物遗传资源学报》2025年第3期575-588,共14页Journal of Plant Genetic Resources

基　　金：宁波市现代种业专项(2021Z008);宁波市特色园艺作物品质调控与抗性育种重点实验室开放课题基金(NBYYL2023002)。

摘　　要：InDel标记已广泛用于果树分子标记辅助育种等研究领域,然而针对我国传统特色果树杨梅的相关研究报道甚少。本研究通过103份杨梅核心种质全基因组重测序及生物信息学分析,共获得了大小分布在1~50 bp范围内的25831个InDel。不同染色体上的InDel变异频率介于1/11297~1/8903;其中,CM025856.1染色体上发生InDel变异频率最高。通过注释分析发现有1312个InDel分布在基因外显子区域,另有21055和6659个InDel分别分布在基因间区和内含子区域。经GO注释,上述InDel生物过程主要涉及细胞过程(Cellular process)和代谢过程(Metabolic process);分子功能主要包括结合(Binding)和催化活性(Catalyticactivity)。经KEGG通路分析发现,InDel所在的基因区域的功能主要为次生代谢、碳代谢和核质运输等。通过全基因组关联分析,获得20个与杨梅果实成熟期性状显著关联的InDel,其功能注释主要涉及线粒体、质体结构基因,三磷酸核苷水解酶和细胞分裂素信号蛋白等。进一步验证显示InDelEP-18标记对杨梅果实成熟期性状鉴定准确率较高,达89.25%;通过基因预测结果发现该位点注释为早期结瘤素家族(Early nodulin)基因。本研究筛选获得的InDel EP-18标记将为杨梅分子辅助育种提供重要的理论依据。The InDel markers have been extensively used in molecular marker-assisted breeding for fruit trees.However,limited studies have been conducted on their application in Chinese bayberry(Morella rubra),a traditional Chinese fruit tree.This study identified 25831 InDels,ranging from 1 to 50 bp in size,through whole-genome resequencing and bioinformatics analysis of 103 Chinese bayberry core germplasm accessions.The frequency of InDel variation across different chromosomes ranged from 1/11297 to 1/8903,with chromosome CM025856.1 exhibiting the highese frequency of InDel mutation.Annotation analysis showed that 1312 InDels were located in gene exon regions,while 21055 and 6659 InDels were distributed in the intergenic and intron regions,respectively.Gene Ontology(GO)analysis indicated that these InDels were primarily associated with for cellular processes and metabolic processes in biological processes,and with binding and catalytic activity in molecular functions.KEGG pathway analysis demonstrated that the InDel-containing genes were predominantly involved in secondary metabolism,carbon metabolism and nucleocytoplasmic transport.Genome-wide association analysis identified 20 InDels significantly associated with fruit maturity traits.Functional annotations of these InDels revealed associations with mitochondrial and plastid structural genes,riboside triphosphate hydrolase,and cytokinin signaling proteins.Further validation and analysis identified the InDel EP-18 marker as having the highest accuracy(89.25%)for identifying fruit maturity traits.Gene prediction analysis indicated that this locus encodes an early nodulin family gene.In conclusion,the InDel EP-18 marker identified in this study provides an important theoretical basis for molecular assisted breeding of Chinese bayberry.

关 键 词：杨梅 INDEL 重测序 关联分析 成熟期 

分 类 号：S667.6[农业科学—果树学]