Seven books in one language, each with different notes in the margins. That is what the genomes of seven Indonesian rice varieties look like after scientists read them letter by letter. Every variety is a separate translation of the same book, and the task was to find the places where the translations diverge.
First, the researchers grew the rice in a greenhouse and extracted DNA from the leaves. Then they read long DNA fragments on a PacBio Revio machine, which produces stretches several thousand letters long, so the meaning does not get lost. The resulting reads were aligned against the reference genome AGIS1.0, the way a draft is checked against a clean original. For each variety, they assembled its own version of the text.
Then came the most interesting part. The scientists did not read all 27,514 gene groups shared by every variety. Instead, they focused on 40 preselected ones responsible for grain color, protein content and starch content. In these genes they found single-letter substitutions: for example, in the SBE2b gene, five varieties have the amino acid leucine replaced by valine, and in the SSIIa gene, five varieties have methionine replaced by valine. Think of them as typos in important paragraphs that change the meaning without destroying the book.
Until now it was unclear how strongly local varieties differ in their genomes and exactly where the variants useful for breeding lie. Now it is clear: despite the overall similarity, there are single-letter differences in the genes for starch, protein and pigments that can be tested further. A breeder can take this list of candidates and check them in their own programs, while a geneticist can use the data for functional studies.
Seven translations of one book have been read. What remains is to figure out which marginal notes actually change taste, color and drought tolerance, and which are just ink blots.
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.