Rice feeds Indonesia, but local varieties hold genetic diversity that is disappearing in industrial lines. These varieties may carry genes for drought resistance, distinctive flavor, or nutritional value. Yet until now they have been poorly studied at the genome level. This work fills that gap and lays a foundation for future breeding.
The scientists grew seven varieties in a greenhouse and extracted DNA from the leaves. Sequencing was done on a PacBio Revio instrument, yielding long, accurate reads. The reads were aligned to the reference genome AGIS1.0, and consensus sequences were built for each variety. Then they predicted genes, compared them with one another, and checked 40 candidate genes linked to pigments, protein, and starch.
All seven genomes turned out to be nearly complete: BUSCO showed 98.3–98.5% completeness. Orthogroups revealed 27 514 gene groups shared by all varieties. Of the 280 variety–gene combinations tested, 278 were recovered. Differences were found in proteins: five varieties had the substitutions L94V and H196R in the SBE2b gene, five varieties had M730V in SSIIa, and four varieties had Y224S in Wx. The promoters of the genes ANS1, SBE2b, SSIIa, OsAAP6, and SSI passed quality control in all varieties, but in Wx two varieties dropped to 50% identity because of boundary problems.
The work shows that even when genomes are broadly similar, local varieties carry pinpoint differences in genes that affect grain quality. This means breeders can look for useful variants in local material, not only in international collections. The resource will serve as a starting point for testing the functions of the genes found.
The next step will be to assemble full genomes of each variety without relying on a reference. This will reveal large rearrangements and regions missing from the reference. Then it will be possible to build a pangenome of Indonesian rice and link genetic variants to real traits.
The results will be useful to rice breeders, agronomists, and food security specialists. They will also help preserve Indonesia's genetic heritage.
Perform local assembly and structural analysis at the sites of divergence. Then measure amylose, protein, and anthocyanin content in the grain to validate the candidates.
For plant genomics, the question remains open: how do you tell real differences between varieties from assembly and annotation artifacts? This work shows that even with a reference-based approach you can identify reliable candidates, but definitive proof requires independent assembly and functional tests.
The Cempo Ireng variety is a black rice that in Indonesia is considered ceremonial and is used in traditional medicine. Its dark color comes from anthocyanins, the same pigments that color blueberries.
Not published on arXiv. Here are its page, the PDF and the formalization: you can check it yourself, not only read our account.