Seven books with the same text but different notes in the margins. That's one way to picture the genomes of seven rice varieties from Indonesia. Scientists read these books and compared where the notes diverge.
Each variety was grown in a greenhouse, and DNA was extracted from the leaves. Long stretches of DNA were read on a special instrument and then aligned against a reference, the way you check a rough draft against a clean original. The result was seven nearly complete versions of the same genetic book: more than 98% of the pages are in place.
Next, the scientists focused on 40 genes responsible for grain color, protein, and starch. In these genes they found pinpoint substitutions, like typos in important paragraphs. For example, in a gene that affects starch, five varieties have one amino acid swapped for another. This may explain why one variety is dark while another tolerates drought better.
Until now it was unclear exactly where in the genomes of local varieties the useful variants were hidden. Now breeders have a list of 40 genes they can test further. This will help preserve the diversity of Indonesian rice and improve it for farmers.
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.