Genome wide association studies and candidate gene mining for understanding the genetic basis of straw silica content in a set of Oryza nivara (Sharma et Shastry) accessions

Rice is a high-silica (SiO₂·nH₂O) accumulator. Silicon (Si) is designated as a beneficial element associated with multiple positive effects on crops. However, the presence of high silica content is detrimental to rice straw management, hampering its use as animal feed and as raw material in multiple industries. Rice straw management is a serious concern in north-western India, and it is eventually burned in situ by farmers, contributing to air pollution. A practical solution could lie in reducing the silica content in rice while also attaining sound plant growth. A set of 258 Oryza nivara accessions along with 25 cultivated varieties of Oryza sativa was used to assess the variation in straw silica content using the molybdenum blue colorimetry method. A large continuous variation was observed for straw silica content in O. nivara accessions, ranging from 5.08% to 16%, while it varied from 6.18% to 15.81% in the cultivated varieties. The O. nivara accessions containing 43%-54% lower straw silica content than the currently prominent cultivated varieties in the region were identified. A set of 22,528 high-quality single nucleotide polymorphisms (SNPs) among 258 O. nivara accessions was used for estimating population structure and genome-wide association studies (GWAS). A weak population structure with 59% admixtures was identified among O. nivara accessions. Further, multi-locus GWAS revealed the presence of 14 marker-trait associations (MTAs) for straw silica content, with six of them co-localizing with previously reported quantitative trait loci (QTL). Twelve out of 14 MTAs showed statistically significant allelic differences. Thorough candidate gene analyses revealed the presence of promising candidate genes, including those encoding the ATP-binding cassette (ABC) transporter, Casparian thickening, multi-drug and toxin extrusion (MATE) protein, F-box, and MYB-transcription factors. Besides, ortho-QTLs among rice and maize genomes were identified, which could open ways for further genetic analysis of this trait. The findings of the study could aid in further understanding and characterizing genes for Si transport and regulation in the plant body. The donors carrying the alleles for lower straw silica content can be used in further marker-assisted breeding programs to develop rice varieties with lower silica content and higher yield potential.

Germanium in the soil-plant system-a review

Germanium (Ge) is widespread in the Earth's crust. As a cognate element to silicon (Si), Ge shows very similar chemical characteristics. Recent use of Ge/Si to trace Si cycles and changes in weathering over time, growing demand for Ge as raw material, and consequently an increasing interest in Ge phytomining have contributed to a growing interest in this previously rather scarcely considered element in geochemical studies. This review deals with the distribution of Ge in primary minerals and surface soils as well as the factors influencing the mobility of Ge in soils including the sequestration of Ge in secondary mineral phases and soil organic matter. Furthermore, the uptake and accumulation of Ge in plants and effects of plant-soil relationships on the availability of Ge in soils and the biogeochemical cycling of Ge are discussed. The formation of secondary soil minerals and soil organic matter are of particular importance for the concentration of Ge in plant-available forms. The transfer from soil to plant is usually low and shows clear differences between species belonging to the functional groups of grasses and forbs. Possible uptake mechanisms in the rhizosphere are discussed. However, the processes that are involved in the formation of plant-available Ge pools in soils and consequently its biogeochemical cycling are not yet well understood. There is, therefore, a need for future studies on the uptake mechanisms and stoichiometry of Ge uptake under field conditions and plant-soil-microbe interactions in the rhizosphere as well as the chemical speciation in different plant parts.

A model for the effects of germanium on silica biomineralization in choanoflagellates

Silica biomineralization is a widespread phenomenon of major biotechnological interest. Modifying biosilica with substances like germanium (Ge) can confer useful new properties, although exposure to high levels of Ge disrupts normal biosilicification. No clear mechanism explains why this disruption occurs. Here, we study the effect of Ge on loricate choanoflagellates, a group of protists that construct a species-specific extracellular lorica from multiple siliceous costal strips. High Ge exposures were toxic, whereas lower Ge exposures produced cells with incomplete or absent loricae. These effects can be ameliorated by restoring the germanium : silicon ratio, as observed in other biosilicifying organisms. We developed simulations of how Ge interacts with polymerizing silica. In our models, Ge is readily incorporated at the ends of silica forming from silicic acid condensation, but this prevents further silica polymerization. Our 'Ge-capping' model is supported by observations from loricate choanoflagellates. Ge exposure terminates costal strip synthesis and lorica formation, resulting in disruption to cytokinesis and fatal build-up of silicic acid. Applying the Ge-capping model to other siliceous organisms explains the general toxicity of Ge and identifies potential protective responses in metalloid uptake and sensing. This can improve the design of new silica biomaterials, and further our understanding of silicon metabolism.