Pleiotropic effects of the rice qLTG3-1 allele: enhancing low-temperature germinability while reducing brown rice appearance quality

Rice quality has a major impact on its economic value, necessitating the breeding of high-quality grain varieties. In addition, varieties with superior germination and growth at low temperatures are required for direct sowing, which enables the low-cost production of rice. We developed Akikei770, a near-isogenic line from the high-quality, good-tasting cultivar Akitakomachi, carrying the qLTG3-1 gene from the Maratelli cultivar, which enhances low-temperature germinability. Although Akikei770 exhibited improved low-temperature germinability, it was inferior to Akitakomachi in appearance quality of brown rice and in eating quality of cooked rice. In Akikei770, a short arm region of up to 222 kb on chromosome 3 from Maratelli was introgressed, and only the qLTG3-1 gene exhibited polymorphisms within the coding region compared to Akitakomachi. The qLTG3-1 genotype was significantly associated with brown rice quality in the F₂ population, which indicates that the qLTG3-1 gene was involved in this trait with no involvement of other chromosomal regions of Akikei770. The functional qLTG3-1 allele in Akikei770, encoding a hybrid glycine-rich protein (HyGRP) that is localized on the cell wall or membrane, enhanced the low-temperature germinability. Because a loss-of-function allele of qLTG3-1 increased the appearance quality of brown rice in a recessive manner, it was concluded that HyGRP, which enhances low-temperature germinability, has a pleiotropic effect that reduces the appearance quality of brown rice.