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

Abstract Background Rice is a high silicon-accumulator. Silicon (Si) is designated as a beneficial element associated with multiple positive effects on crop plants. However, presence of high silica content is detrimental in rice straw and its 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 the farmers contributing to air pollution. A practical solution to the said issue could lie in reducing the silica content in rice, while also attaining sound plant growth. Results A set of 258 Oryza nivara accessions along with 25 cultivated varieties were used to assess the variation for straw silica content using molybdenum blue colorimetry method. Large and continuous variation was observed for straw silica content in O. nivara accessions, ranging from 5.08-16%, while it varied from 7.95–15.81% 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 polymorphism (SNP) among the 258 O. nivara accessions were 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 QTLs. Twelve out of the 14 MTAs showed statistically significant allelic differences. Thorough candidate gene analyses among the QTL regions revealed the presence of promising candidate genes, including ABC transporter, Casparian thickening genes, multi-drug and toxin extrusion (MATE) protein, F-box domains, and MYB-transcription factor domains. Besides ortho-QTLs among rice and maize genomes were also identified which could open up ways for further genetic analysis of this trait. Conclusion 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 programmes in order to develop rice varieties with lower silica content along with higher yield potential.