Multi-omics resources for targeted agronomic improvement of pigmented rice

Abstract

Pigmented rice (Oryza sativa L.) is a rich source of nutrients, but pigmented lines typically have long life cycles and limited productivity. Here we generated genome assemblies of 5 pigmented rice varieties and evaluated the genetic variation among 51 pigmented rice varieties by resequencing an additional 46 varieties. Phylogenetic analyses divided the pigmented varieties into four varietal groups: Geng-japonica, Xian-indica, circum-Aus and circum-Basmati. Metabolomics and ionomics profiling revealed that black rice varieties are rich in aromatic secondary metabolites. We established a regeneration and transformation system and used CRISPR-Cas9 to knock out three flowering time repressors (Hd2, Hd4 and Hd5) in the black Indonesian rice Cempo Ireng, resulting in an early maturing variety with shorter stature. Our study thus provides a multi-omics resource for understanding and improving Asian pigmented rice.

Fig. 1. Population genomic analysis of pigmented rice.

a, Neighbour-joining tree for K = 15 subpopulations and one admixture group. The phenogram shows the clustering of the 474 accessions selected from the 3K-RG dataset (clockwise: GJ-temperate (okra), GJ-subtropical (orange), GJ-tropical2 (dark magenta), GJ-tropical1 (magenta), cB (goldenrod), cA1 (dark green), cA2 (light green), XI-2B (brown), XI-2A (pink), XI-adm (dark grey), XI-3A (light grey), XI-3B1 (brick red), XI-3B2 (turquoise), XI-1A (cyan), XI-1B2 (yellow) and XI-1B1 (sky blue)) and the 51 pigmented varieties (the red and black branches represent red- or black-pigmented varieties, respectively). O. sativa subpopulations are defined as described by Zhou et al.. b, Principal component analysis plot showing the clustering of the pigmented varieties into the four main groups of O. sativa. The analysis was performed on 51 pigmented varieties and 474 accessions selected from the 3K-RG dataset, but only the 51 pigmented varieties are shown. Red and black names represent red and black pigmented varieties, respectively.

Fig. 2. Global non-targeted metabolic screening of pigmented rice.

Heat map visualization of differences in the median-scaled relative abundance of the identified metabolites in pigmented rice. Each cell represents a specific metabolite. Red cells indicate abundances higher than the median value, while blue cells indicate abundances below the median; white cells are abundances similar to the median. IN, India; IO, Indonesia; MA, Malaysia; PH, Philippines; TH, Thailand; BD, Bangladesh; CH, China; SA, Saudi Arabia; SL, Sri Lanka; JA, Japan; PK, Pakistan.