Chinese Journal OF Rice Science ›› 2021, Vol. 35 ›› Issue (2): 130-140.DOI: 10.16819/j.1001-7216.2021.0513

• Research Papers • Previous Articles     Next Articles

Analysis on Genetic Diversity, Population Structure, and Linkage Disequilibrium of 273 Rice Germplasms

Junjie DONG, Yuxiang ZENG, Zhijuan JI, Yan LIANG*(), Changdeng YANG*()   

  1. State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
  • Received:2020-05-19 Revised:2020-06-14 Online:2021-03-10 Published:2021-03-10
  • Contact: Yan LIANG, Changdeng YANG

273份水稻种质资源的遗传多样性、群体结构与连锁不平衡 分析

董俊杰, 曾宇翔, 季芝娟, 梁燕*(), 杨长登*()   

  1. 中国水稻研究所 水稻生物学国家重点实验室,杭州 310006
  • 通讯作者: 梁燕,杨长登

Abstract:

【Objective】The assessment of genetic diversity and population structure of 273 rice germplasms would provide important references for breeding as well as association mapping. 【Method】In this study, genetic diversity, population structure, and linkage disequilibrium for 273 rice landraces and breeding materials from 14 countries were assayed based on genotyping with 214 markers. 【Result】The test population were classified into two subgroups (SG1 and SG2) and one mixed group(AD) through population structure analysis, and the results of UMPGA clustering analysis and principal component analysis were consistent with the results of population structure analysis. Genetic diversity analysis showed that a total of 524 alleles were detected with 214 markers, the number of alleles detected on each locus ranged from 2 to 5 with the average genetic diversity of 0.44 and the average polymorphism information content (PIC) of 0.355. The genetic diversity and PIC were higher in SG2 than those in SG1. Analysis of molecular variance showed that 34 percent of variation was attributed to the genetic variation among groups and 66 percent to the genetic variation within groups. There was significant genetic differentiation between SG1 and SG2 (Fst=0.725, P<0.01). Linkage disequilibrium analysis showed that there were linkage disequilibrium loci in each linkage group, and the minimum distances extended when linkage disequilibrium was attenuated to below 75% in SG1 and SG2 were 13.7 Mb and 90.5 kb, respectively. 【Conclusion】Given rich genetic variation, the population consisting of 273 rice germplasm resources is suitable for excellent alleles mining through association mapping.

Key words: rice germplasms, genetic diversity, population structure, linkage disequilibrium

摘要:

【目的】评估273份水稻种质资源的遗传多样性和群体结构,为今后利用这些水稻种质资源进行遗传育种和关联分析提供参考。【方法】利用214个分子标记对来自14个国家的273份水稻地方品种和育种材料进行基因型检测,分析其遗传多样性、群体结构、连锁不平衡程度。【结果】群体结构分析将供试群体划分为2个亚群(SG1、SG2)以及1个混合群(AD),聚类分析和主成分分析结果与群体结构分析结果一致;遗传多样性分析结果显示,214个标记共检测到524个等位变异,变幅为2~5个,平均遗传多样性指数为0.44,平均多态性信息含量(PIC)为0.355,SG2群遗传多样性指数和PIC高于SG1群;分子方差分析表明34%的变异来源于种群内,66%的变异来源于种群间,SG1与SG2群体间存在显著的遗传分化(Fst=0.725,P<0.01);连锁不平衡分析结果显示,整个群体中存在较高程度连锁不平衡,平均r2为0.33,SG1和SG2中连锁不平衡衰减到75%以下所延伸的最小距离分别为13.7 Mb和90.5 kb。【结论】273份水稻种质资源群体内具有丰富的遗传变异,该群体适合通过关联作图来挖掘优异等位基因。

关键词: 水稻种质资源, 遗传多样性, 群体结构, 连锁不平衡