基于56K SNP芯片的云南高原粳稻群体结构分析  

Population Genetic Structure Analysis of Japonica Rice in Yunnan Plateau Based on 56K SNP Chip

作　　者：王天杰 李娟[1,2,3] 罗迪 朱骞[1,2,3] 王春丽 刘福根 李欣飞 李俊杰 苏鹏 何玉 陈丽娟[1,2,3] 李东宣[1,2,3] Wang Tianjie;Li Juan;Luo Di;Zhu Qian;Wang Chunli;Liu Fugen;Li Xinfei;Li Junjie;Su Peng;He Yu;Chen Lijuan;Lee Dongsun(Rice Research Institute,Yunnan Agricultural University,Kunming,650201;Key Laboratory for Crop Production and Smart Agriculture in Yunnan,Yunnan Agricultural University,Kunming,650201;State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan,Yunnan Agricultural University,Kunming,650201)

机构地区：[1]云南农业大学稻作研究所,昆明650201 [2]云南农业大学,云南省作物生产与智慧农业重点实验室,昆明650201 [3]云南农业大学,省部共建云南生物资源保护与利用国家重点实验室,昆明650201

出　　处：《分子植物育种》2024年第17期5630-5639,共10页Molecular Plant Breeding

基　　金：国家自然科学基金项目(31860108);云南省重大科技专项(2018ZG005)共同资助。

摘　　要：为了保存和合理利用云南宝贵的稻种资源,明晰云南高原粳稻资源间的遗传关系,本研究收集了云南不同稻区的代表性粳稻主栽品种及其骨干亲本,利用水稻56K SNP芯片检测鉴定,基于鉴定到的SNP进行了系统进化树构建、主成分分析以及遗传结构分析。246份供试材料共获得40207个高质量SNP,结合SNP变异类型注释,最终筛选获得均匀分布在12条染色体上的30939个核心多态性SNP位点,并成功构建了云南高原粳稻群体的特征分子指纹图谱数据库。云南高原粳稻群体群体结构分析(系统进化树,主成分分析以及遗传结构分析)结果高度保持一致趋势,结果表明同一系列类型稻区内的材料间亲缘关系较近;稻区间均有不同程度亲缘交融。群体遗传多态性与结构分析明确表明,云南高原粳稻品种资源以“滇杂”“滇禾优”“楚粳”“云粳”“合系”“凤稻”“丽粳”“剑粳”等系列育成品种为主导。研究阐明了云南高原粳稻品种资源的遗传结构及其亲缘关系,结果将为云南高原粳稻群体分子鉴定及其优良特性的研究奠定基础,为高原粳稻分子设计育种提供理论依据。To preserve and rational utilization of valuable rice resources,clear the genetic relationship between plateau japonica rice resources in Yunnan,this study collected the different typical japonica rice planting areas of Yunnan introduced cultivation variety and its backbone parent,using rice 56K SNP chip testing,based on the appraisal to the SNP has carried on the system construction of the evolutionary tree,principal component analysis and the analysis of the genetic structure.A total of 40207 high-quality SNPs were obtained from 246 materials,and these SNPs were annotated for their variation types:30939 core polymorphic SNPs were selected and distributed uniformly on 12 chromosomes,and the characteristic molecular fingerprint database of japonica rice population in Yunnan Plateau was successfully constructed.The results of phylogenetic tree,principal component analysis and genetic structure analysis were highly consistent,and the results showed that the materials in the same region were closely related.The resources in each region may have different degree of consanguinity and origin blending between japonica rice.The analysis of population genetic polymorphism and structure clearly indicated that the japonica rice variety resources in Yunnan Plateau were dominated by"Dian Za""Dian He You""Chu Geng""Yun Geng""He Xi""Feng Dao""Li Geng""Jian Geng"series varieties.This study clarified the genetic structure and genetic relationship of japonica rice variety resources in Yunnan Plateau.The results will lay a foundation for the study of molecular identification and excellent characteristics of japonica rice population in Yunnan Plateau,and provide theoretical basis for the molecular design and breeding of japonica rice in plateau.

关 键 词：云南粳稻资源 56K SNP 群体遗传进化 

分 类 号：S511.22[农业科学—作物学]