Dissecting the genetic basis of rice husk silica content and morphology using GWAS

Our findings reveal a complex genetic architecture underlying rice husk silica traits, identifying key QTLs, candidate genes, and epistatic interactions with potential applications in rice breeding and silica valorization. Rice contains large amounts of amorphous silica in its tissues. Rice husk (RH) contains 17-30% silica that can be recycled for use in a variety of industries. A genome-wide association study (GWAS) was performed to pinpoint the genetic determinants of five RH features: silica content, silica block length and width, thorn (cone-shaped protrusions on the surface of the husk) height, and base length. A data set of 44,100 SNPs from rice genotypes was used for genomic analysis. In total, 48 significant SNPs were identified, corresponding to 23 unique QTLs across nine rice chromosomes. The most significant SNPs and QTLs associated with silica traits are located on chromosomes 2, 6, and 9. The candidate genes in the definition of RH silica-related traits are involved in growth and development (zinc finger protein, esterase SGNH hydrolase-type domain-containing protein, glycosyltransferase), heavy metal detoxifying and transporting (ABC transporter, BTB domain-containing protein, heavy metal transport/detoxification protein domain-containing protein, ankyrin repeat domain-containing), stress response (genes coding for chitinase, peroxidases, polyphenoloxidases, β-1,3-glucanase, phenylalanine ammonia-lyase, superoxide dismutase, ascorbate peroxidase, glutathione reductase, catalase, lipoxygenase, glucanase, F-box protein, NB-ARC domain-containing protein, thylakoid membrane phosphoprotein), and transcription regulation (MYB transcription factor, TCP domain-containing protein). Haplotype analysis identified haplogroups qSBL91 and qTH31 for two traits of SBL (length of silica blocks) and TH (height of the silica thorns). An analysis of epistatic interactions among candidate SNPs identified 18 significant SNP-SNP interactions between cytochrome P450, glycosyl hydrolases, laccases, zinc finger, and bHLH.