Oryza sativa (Geng/Japonica-trop2 var. Ketan Nangka) Assembly and Gene Annotation

About Oryza sativa (Geng/Japonica-trop2 var. Ketan Nangka)

Asian cultivated rice is a staple food for half of the world population. With a genome size of ~390 Mb (n=12), rice has the smallest genome among the domesticated cereals, making it particularly amenable to genomic studies. In 2020, a reanalysis of the population structure analysis showed that rice could be subdivided into a total of 15 subpopulations (XI-1A, XI-1B1, XI-1B2, XI-2B, XI-2A, XI-3B1, XI-3A, XI-3B2, GJ-trop1, GJ-trop2, GJ-subtrp, GJ-tmp, cA2, cA1 and cB) and 4 admixed populations (GJ-adm, XI-adm, admixed and cA-adm). Then 16 rice cultivar varieties were selected based on genetic diversity and origin that could represent the 15 subpopulations and the largest admixed population, i.e. XI-adm. The collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice. Oryza sativa cv. IRGC 128077 (variety cv. KETAN_NANGKA::IRGC_19961-2) (collected from: Indonesia) is selected as the representative of GJ-trop2 subpopulation, in which the accessions are mostly collected from Indonesia.

Notes of Subpopulations: cA = circum-Aus; cB = circum-Basmati; GJ= Geng-japonica where trop = tropical, subtrp = subtropical; XI = Xian-indica

More information can be found on the IRRI website.

Picture credit: Keerthana Manickam, Rod Wing, Yong Zhou, KAUST, 2023.