August 17, 2025

Rice feeds over half the world, but before we dig in, it needs polishing! The outer husk and sometimes the bran get removed to make the rice white and ready to eat. Traditionally, pounding and winnowing did this job, but now machines roll over grains, sometimes breaking them. This breakage happens more when rice has a trait called chalkiness. Chalky rice grains look dull and brittle after milling because big patches turn opaque instead of see-through. But don’t worry — chalkiness doesn't change the taste or smell once cooked. Scientists measure chalkiness by two things: how many grains are chalky (chalky grain rate) and how much of each grain is chalky (degree of chalkiness). Many genes and weather factors like heat affect chalkiness, making it tough to fight. Enter a brilliant team at Yangzhou University in China! They found a gene named Chalk9 that controls chalkiness in many rice varieties. Their discovery, published in Nature Communications, holds hope for snack lovers and farmers alike. By studying 175 rice types, the researchers noticed a tiny bit of DNA on chromosome 9 was linked to low or high chalkiness. Varieties with this DNA piece had more Chalk9 activity in the endosperm — the starchy heart of the rice grain. A special protein called OsB3 binds to this DNA part and switches on Chalk9. But if the DNA is missing, Chalk9 stays silent. Chalk9 itself belongs to a group of enzymes, E3 ubiquitin ligases, that tag other proteins for destruction, like putting a “delete” sticker on them. Chalk9 targets a protein named OsEBP89, tagging it so the cell throws it away. OsEBP89 usually flips on genes that make amylose (starch) and proteins to store starch. Without OsEBP89, these production lines slow down, and less chalk forms in the rice. When OsEBP89 hangs around too long, rice turns chalkier. The team tested this in the lab, showing that even tiny changes in Chalk9 affect OsEBP89’s fate. Interestingly, all 4,726 cultivated rice varieties share the same OsEBP89 gene version. The big difference is how Chalk9 handles it, making Chalk9 the real star in controlling chalkiness. Looking back, the researchers found that before 1990, most rice had the Chalk9-H (high chalkiness) version. Since then, chalkiness has been dropping because breeders unknowingly chose the low chalkiness version Chalk9-L. Now, with this knowledge, breeding better rice is easier and faster by simply adding Chalk9-L into varieties missing it. The study beautifully explains that “by promoting the degradation of OsEBP89, Chalk9 functions as a ‘brake’ to limit starch accumulation and storage.” This ‘brake’ helps create clearer grains that break less, making rice both yummy and tough enough to handle. Thanks to D.P. Kasbekar for sharing this breakthrough from the world of grains!

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Tags: Rice chalkiness, Chalk9 gene, Rice quality, Starch synthesis, Rice breeding, Genetic research,