Unravelling the genetics and genomics of pigmented rice variety using omics technology and bioinformatics approach)

Pigmented rice varieties (black and red) are rich in antioxidants and folate compared to white rice due to secondary metabolites such as anthocyanins and proanthocyanidins. Understanding the genetic and genomic variations underlying nutrient content differences is crucial for rice breeding programs. However, genetic and genomic data for Malaysian pigmented rice varieties remain limited in public databases.Objective: To unravel the genetics and genomics of Malaysian pigmented rice varieties using omics technologies and bioinformatics approaches, and to develop molecular markers and a comprehensive database for rice breeding applications.Methods: Six Malaysian rice varieties were studied: two black rice (Bali, Pulut Hitam 9), two red rice (MRM 16, MRQ 100), and two white rice (MR 297, MRQ 76). Genome and transcriptome sequencing was performed using Illumina HiSeq 4000 platform. Multiple omics platforms were employed including transcriptomics (RNA-seq, qPCR), metabolomics (GC-MS/MS, LC-MS/MS), proteomics (SWATH-MS), and nutrient profiling (ICP-MS, ICP-OES). SNP genotyping was conducted using Agena Mass ARRAY platform on 40 rice varieties.Integration of omics technologies successfully characterized genetic variations and biosynthetic pathways in Malaysian pigmented rice, providing valuable resources for marker-assisted selection (MAS), and marker-assisted breeding (MAB) programme.