Biallelic and Genome Wide Association Mapping of Germanium Tolerant Loci in Rice (Oryza sativa L.)

Partha Talukdar, Alex Douglas, Adam H. Price, Gareth J. Norton*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

6 Citations (Scopus)
6 Downloads (Pure)


Rice plants accumulate high concentrations of silicon. Silicon has been shown to be involved in plant growth, high yield, and mitigating biotic and abiotic stresses. However, it has been demonstrated that inorganic arsenic is taken up by rice through silicon transporters under anaerobic conditions, thus the ability to efficiently take up silicon may be considered either a positive or a negative trait in rice. Germanium is an analogue of silicon that produces brown lesions in shoots and leaves, and germanium toxicity has been used to identify mutants in silicon and arsenic transport. In this study, two different genetic mapping methods were performed to determine the loci involved in germanium sensitivity in rice. Genetic mapping in the biparental cross of Bala x Azucena (an F-6 population) and a genome wide association (GWA) study with 350 accessions from the Rice Diversity Panel 1 were conducted using 15 mu M of germanic acid. This identified a number of germanium sensitive loci: some co-localised with previously identified quantitative trait loci (QTL) for tissue silicon or arsenic concentration, none co-localised with Lsi1 or Lsi6, while one single nucleotide polymorphism (SNP) was detected within 200 kb of Lsi2 (these are genes known to transport silicon, whose identity was discovered using germanium toxicity). However, examining candidate genes that are within the genomic region of the loci detected above reveals genes homologous to both Lsi1 and Lsi2, as well as a number of other candidate genes, which are discussed.

Original languageEnglish
Article number0137577
Number of pages15
JournalPloS ONE
Issue number9
Early online date10 Sep 2015
Publication statusPublished - 10 Sep 2015


  • quantitative trait loci
  • arsenic accumulation
  • silicon uptake
  • genetic dissectin
  • root morphology
  • grain
  • transporter
  • soil
  • metabolism
  • plants


Dive into the research topics of 'Biallelic and Genome Wide Association Mapping of Germanium Tolerant Loci in Rice (Oryza sativa L.)'. Together they form a unique fingerprint.

Cite this