赣南野生山金柑全基因组InDel标记开发及应用  

Development and Application of Insertion-Deletion(InDel)Markers in Gannan wild Fortunella hindsii Based on Whole Genome Re-sequencing Data

作　　者：罗嗣芳 严翔 谢丽芳 孙静贤 郭紫晶 张祖铭 陈兆星 LUO Sifang;YAN Xiang;XIE Lifang;SUN Jingxian;GUO Zijing;ZHANG Zuming;CHEN Zhaoxing(Institute of Citrus Science Research of Ganzhou,Gannan Academy of Sciences,Ganzhou,Jiangxi 341000,China)

机构地区：[1]赣南科学院赣州市柑桔科学研究所,江西赣州341000

出　　处：《园艺学报》2025年第2期267-278,共12页Acta Horticulturae Sinica

基　　金：现代农业产业技术体系建设专项资助(CARS-26);赣州市重点研发计划重点项目(2022XM061209)。

摘　　要：为探究赣南野生山金柑InDel特征,选取99份赣南野生山金柑进行全基因组重测序,进而筛选InDel变异位点以开发InDel标记。获得590.58 Mb有效片段数据,共检测到211470个InDel,包括98043个插入和113427个缺失。从8760条插入/缺少碱基数大于10的InDel标记中选择出180条在染色体上均匀分布的多态性标记,并开发了58对扩增条带良好的InDel引物。InDel标记聚类与全基因组重测序聚类结果一致,99份赣南野生山金柑分为既存在关联性又具有特异性的4个分支;根据每份种质含有的核心InDel标记位点数和等位基因数,确定了29份赣南野生山金柑为核心种质,基因组覆盖度达99.7%,其中夹湖、余坑和蔡坊是种质核心区域;结合全基因组重测序数据和核心InDel标记构建了种质的DNA指纹图谱,图谱信息包含植株编号、基因型、变异位点和农艺性状数据。研究明确了赣南野生山金柑InDel特征,筛选的InDel标记能够应用在群体结构分析、核心种质筛选以及DNA指纹图谱构建等方面。To clarify the InDel characteristics of Gannan(Southern Jiangxi Province)wild Fortunella hindsii,99 Gannan wild F.hindsii were selected for whole genome resequencing,and then InDel variant sites were screened to develop InDel markers.A total of 590.58 Mb valid fragment data was obtained,and 211470 InDels were detected,including 98043 insertions and 113427 deletions.From 8760 InDel markers with Insertion or Deletion base numbers greater than 10180 polymorphic markers with uniform distribution on chromosomes were selected,and 58 pairs of InDel primers with good amplification bands were developed.The findings of 58 pairs of InDel markers demonstrated a similar grouping pattern with the clustering results obtained from whole genome resequencing.Additionally,the 99 Gannan wild F.count of core InDel marker sites and alleles present in each germplasm,a total of 29 Gannan wild F.hindsii were selected as the core germplasm.These germplasm samples had a genome coverage of 99.7%.Among them,Jiahu,Yukeng,and Caifang were recognised as the core germplasm regions.The DNA fingerprint was created by integrating the entire genome resequencing data with the core InDel marker sites.This fingerprint contains coding information such as plant number,genotype,mutation locus,and agronomic trait data.This study aimed to elucidate the InDel characteristics of Gannan wild F.hindsii.The identified InDel markers have potential applications in population structure analysis,core germplasm screening,and DNA fingerprint construction.

关 键 词：山金柑 INDEL标记 遗传多样性 核心种质 DNA指纹图谱 

分 类 号：S666[农业科学—果树学]