Chinese Journal OF Rice Science >
Analysis on Genetic Diversity, Population Structure, and Linkage Disequilibrium of 273 Rice Germplasms
Received date: 2020-05-19
Revised date: 2020-06-14
Online published: 2021-03-10
【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.
Junjie DONG, Yuxiang ZENG, Zhijuan JI, Yan LIANG, Changdeng YANG . Analysis on Genetic Diversity, Population Structure, and Linkage Disequilibrium of 273 Rice Germplasms[J]. Chinese Journal OF Rice Science, 2021 , 35(2) : 130 -140 . DOI: 10.16819/j.1001-7216.2021.0513
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