Identification of novel mutations in genes involved in silicon and arsenic uptake and accumulation in rice

Authors: KIM, HYUNJUNG - University Of California; Tai, Thomas

Submitted to: Euphytica
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/5/2019
Publication Date: 3/13/2019
Citation: Kim, H., Tai, T. 2019. Identification of novel mutations in genes involved in silicon and arsenic uptake and accumulation in rice. Euphytica. 215:72. https://doi.org/10.1007/s10681-019-2393-6.
DOI: https://doi.org/10.1007/s10681-019-2393-6

Interpretive Summary: Mutations in two genes encoding transporter proteins involved in the uptake and accumulation of silicon and arsenic by rice roots (Low silicon 1 and Low silicon 2) and one gene encoding a transporter involved in vacuolar sequestration of arsenic (OsABCC1) were identified using a reverse genetics method called Targeting of Local Lesions in Genomes by sequencing (TBS). DNA samples from a population of 2,048 rice mutants were screened for mutations by sequencing, resulting in the identification of 61 putative mutations in total. Of these mutations, 13 were confirmed and corresponding rice mutants carrying homozygous alleles of these mutations were isolated for trait analysis. Initial analysis of these mutants was conducted for sensitivity to germanium, an element which is taken up through the same pathway as silicon due to similar chemical attributes but is phytotoxic. Two of the mutants (NM-E1746 and NM-3403), which were both in Low silicon 1, exhibited greater tolerance to germanium. Preliminary evaluation of field grown mutants revealed altered uptake and accumulation of silicon and arsenic in the straw. NM-E1746 and NM-3403 showed large reductions in silicon which were consistent with the germanium tolerance they exhibited, but they also had very high arsenic. Most of the Low silicon 2 mutants showed increased silicon in the straw, but no changes in arsenic. The one mutant in OsABCC1 identified in this study (NM-4903) exhibited increased silicon, but a reduction in arsenic. This mutant was also the only one to show a significant reduction in grain total As. Although all three elements (silicon, arsenic, and germanium) are transported by the Low silicon 1 and 2 transporters, this study suggests that the mutations identified here may affect uptake of these elements differently (i.e., increasing one while not affecting or decreasing another). More work is needed to establish the relationship of the mutations and the phenotypes observed, but the current results indicate that these mutants will be useful for studying uptake of silicon and arsenic in rice and other species.

Technical Abstract: Novel mutations in rice genes involved in silicon (Si) and arsenic (As) transport (Lsi1, Lsi2) and vacuolar sequestration of As (OsABCC1) were identified using reverse genetics. TILLING by sequencing of a population of chemically-induced mutants (n = 2,048) detected 61 putative mutations. Following removal of mutations predicted to be synonymous or residing in introns, Sanger sequencing confirmed 21 of 23 nonsynonymous mutations and 13 M3 lines harboring homozygous mutant alleles (three lsi1, nine lsi2, and one Osabcc1) were identified for phenotyping. Altered sensitivity to germanium (Ge), a phytotoxic analog of Si, was observed in three lines. NM-E1746 and NM-3403 (both lsi1) had increased tolerance whereas NM-3036 (lsi2) was more sensitive, however, this appears unrelated to the mutation. Analysis of the straw from field grown plants revealed that NM-E1746 and NM-3403 were the only lines with significant reductions in total Si. Both mutants also had significant increases in total As and NM-3403 exhibited higher grain total As. The third lsi1 mutant (NM-3380) and two lsi2 mutants (NM-2902 and NM-2249) had increased straw total As. Increased grain total As was observed in NM-2902, NM-2249, and a third lsi2 mutant NM-E2244. Interestingly, NM-4903 (Osabcc1) had the highest total Si and was also the only line to have significantly less straw and grain total As. These novel mutant alleles represent useful genetic resources for further dissection of Si, As, and Ge transport in rice and the corresponding germplasm has potential for enhancing rice productivity and quality.