Journal of Applied Genetics

, Volume 60, Issue 1, pp 27–31 | Cite as

Genetic diversity, linkage disequilibrium, and population structure in a panel of Brazilian rice accessions

  • Eduardo Venske
  • Cássia Fernanda Stafen
  • Victoria Freitas de Oliveira
  • Luciano Carlos da Maia
  • Ariano Martins de Magalhães Junior
  • Kenneth L. McNally
  • Antonio Costa de OliveiraEmail author
  • Camila Pegoraro
Plant Genetics • Short Communication


Narrowing of genetic diversity and the quantitative nature of most agronomic traits is a challenge for rice breeding. Genome-wide association studies have a great potential to identify important variation in loci underlying quantitative and complex traits; however, before performing the analysis, it is important to assess parameters of the genotypic data and population under study, to improve the accuracy of the genotype-phenotype associations. The aim of this study was to access the genetic diversity, linkage disequilibrium, and population structure of a working panel of Brazilian and several introduced rice accessions, which are currently being phenotyped for a vast number of traits to undergo association mapping. Ninety-four accessions were genotyped with 7098 SNPs, and after filtering for higher call rates and removing rare variants, 93 accessions and 4973 high-quality SNPs remained for subsequent analyses and association studies. The overall mean of the polymorphic information content, heterozygosity, and gene diversity of the SNPs was comparable to other rice panels. The r2 measure of linkage disequilibrium decayed to 0.25 in approximately 150 kb, a slow decay, explained by the autogamous nature of rice and the small size of the panel. Regarding population structure, eight groups were formed according to Bayesian clustering. Principle components and neighbor-joining analyses were able to distinguish part of the groups formed, mainly regarding the sub-species indica and japonica. Our results demonstrate that the population and SNPs are of high quality for association mapping.


Genomic tools Association mapping Genotypic parameters 


Author contributions

Camila Pegoraro designed the study and wrote parts of the manuscript. Eduardo Venske performed the data analysis and wrote parts of the manuscript. Cássia Fernanda Stafen and Victoria Freitas de Oliveira obtained the accessions and isolated DNA. Ariano Martins de Magalhães Júnior was responsible for the germplasm. Kenneth L. McNally and Antonio Costa de Oliveira were responsible for the genotyping. Luciano Carlos da Maia performed analysis on the data. Camila Pegoraro and Eduardo Venske proofread the manuscript.

Funding information

This study was supported by the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) - Brazil, under grant No. 401902/2016-1. CNPq, CAPES, and FAPERGS also provided the fellowships for the investigators and students.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

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Copyright information

© Institute of Plant Genetics, Polish Academy of Sciences, Poznan 2018

Authors and Affiliations

  • Eduardo Venske
    • 1
  • Cássia Fernanda Stafen
    • 1
  • Victoria Freitas de Oliveira
    • 1
  • Luciano Carlos da Maia
    • 1
  • Ariano Martins de Magalhães Junior
    • 2
  • Kenneth L. McNally
    • 3
  • Antonio Costa de Oliveira
    • 1
    Email author
  • Camila Pegoraro
    • 1
  1. 1.Plant Genomics and Breeding Center, Crop Science Department, Eliseu Maciel College of AgronomyUniversidade Federal de Pelotas, Campus Universitário do Capão do LeãoPelotasBrazil
  2. 2.Embrapa Temperate Climate CenterPelotasBrazil
  3. 3.International Rice Research Institute, Te-Tzu Chang Genetic Resources CenterLos BañosPhilippines

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