title: Biallelic and Genome Wide Association Mapping of Germanium Tolerant Loci in Rice (Oryza sativa L.).
abstract: 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 × Azucena (an F6 population) and a genome wide association (GWA) study with 350 accessions from the Rice Diversity Panel 1 were conducted using 15 μM 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.
authors.affiliation: Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, United Kingdom.
authors.forename: Partha
authors.initials: P
authors.lastname: Talukdar
authors.affiliation: Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, United Kingdom.
authors.forename: Alex
authors.initials: A
authors.lastname: Douglas
authors.affiliation: Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, United Kingdom.
authors.forename: Adam H
authors.initials: AH
authors.lastname: Price
authors.affiliation: Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, United Kingdom.
authors.forename: Gareth J
authors.initials: GJ
authors.lastname: Norton
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics*; D000483:Alleles; D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D003433:Crosses, Genetic; D017343:Genes, Plant; D056726:Genetic Association Studies; D055106:Genome-Wide Association Study; D005838:Genotype; D005857:Germanium / Q000378:metabolism*; D007178:Inbreeding; D012275:Oryza / Q000235:genetics* / Q000378:metabolism*; D040641:Quantitative Trait Loci; D013312:Stress, Physiological
chemical_list: D005857:Germanium