Loss of function is involved in the unique grain shape of "Tanpo", a Japanese landrace rice.

"Tanpo", a Japanese rice landrace widely cultivated approximately 120 years ago in Akita Prefecture, exhibits a shorter, wider, thicker, and heavier grain compared to Akitakomachi. Microscopic analysis has revealed that the epidermal cells of Tanpo spikelet hulls are narrower and shorter, with an increased number of cells in the grain width direction, thus resulting in a distinctive grain shape. In a genetic analysis of an F population derived from a cross between Tanpo and Akitakomachi, the Tanpo allele was found to determine the grain shape in a recessive manner. The allele in Tanpo is a loss-of-function allele because it generates a stop codon immediately after the start codon with a 100-bp deletion within the first exon. Because the GW5 protein suppresses glycogen synthase kinase 2 (GSK2), a negative regulator of brassinosteroid (BR) signaling, GW5 deficiency in Tanpo results in reduced BR signaling. As a result, the expansion of epidermal cells was suppressed, while the radial cell division was promoted, which led to thicker and shorter spikelet hulls and, ultimately, the characteristic grain shape of Tanpo. The identification of this unique allele in the Tanpo landrace provides a valuable resource for breeding new rice varieties with unique grain characteristics.