TY - JOUR
T1 - Multi-omics resources for targeted agronomic improvement of pigmented rice
AU - Sedeek, Khalid
AU - Zuccolo, Andrea
AU - Fornasiero, Alice
AU - Weber, Annika M.
AU - Sanikommu, Krishnaveni
AU - Sampathkumar, Sangeetha
AU - Rivera, Luis F.
AU - Butt, Haroon
AU - Mussurova, Saule
AU - Alhabsi, Abdulrahman
AU - Nurmansyah, Nurmansyah
AU - Ryan, Elizabeth P.
AU - Wing, Rod A.
AU - Mahfouz, Magdy M.
N1 - Funding Information:
We thank the International Rice Research Institute for providing many of the pigmented rice grains. We thank N. Hassan and all members of the Laboratory for Genome Engineering and Synthetic Biology at King Abdullah University of Science and Technology (KAUST) for critical discussion and technical help in this work. This work is funded by KAUST-baseline funding to M.M.M.
Funding Information:
We thank the International Rice Research Institute for providing many of the pigmented rice grains. We thank N. Hassan and all members of the Laboratory for Genome Engineering and Synthetic Biology at King Abdullah University of Science and Technology (KAUST) for critical discussion and technical help in this work. This work is funded by KAUST-baseline funding to M.M.M.
Publisher Copyright:
© 2023, The Author(s).
PY - 2023/5
Y1 - 2023/5
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85159042902&partnerID=8YFLogxK
U2 - 10.1038/s43016-023-00742-9
DO - 10.1038/s43016-023-00742-9
M3 - Article
C2 - 37169820
AN - SCOPUS:85159042902
SN - 2662-1355
VL - 4
SP - 366
EP - 371
JO - Nature Food
JF - Nature Food
IS - 5
ER -