Genome-wide association study identifies a gene responsible for temperature-dependent rice germination

Hideki Yoshida (), Ko Hirano, Kenji Yano, Fanmiao Wang, Masaki Mori, Mayuko Kawamura, Eriko Koketsu, Masako Hattori, Reynante Lacsamana Ordonio, Peng Huang, Eiji Yamamoto and Makoto Matsuoka ()
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Hideki Yoshida: Fukushima University
Ko Hirano: Nagoya University
Kenji Yano: Nagoya University
Fanmiao Wang: Nagoya University
Masaki Mori: Nagoya University
Mayuko Kawamura: Nagoya University
Eriko Koketsu: Nagoya University
Masako Hattori: Nagoya University
Reynante Lacsamana Ordonio: Nagoya University
Peng Huang: Nagoya University
Eiji Yamamoto: Graduate School of Agriculture, Meiji University 1-1-1 Higashi-Mita, Tama-ku
Makoto Matsuoka: Fukushima University

Nature Communications, 2022, vol. 13, issue 1, 1-13

Abstract: Abstract Environment is an important determinant of agricultural productivity; therefore, crops have been bred with traits adapted to their environment. It is assumed that the physiology of seed germination is optimised for various climatic conditions. Here, to understand the genetic basis underlying seed germination, we conduct a genome-wide association study considering genotype-by-environment interactions on the germination rate of Japanese rice cultivars under different temperature conditions. We find that a 4 bp InDel in one of the 14-3-3 family genes, GF14h, preferentially changes the germination rate of rice under optimum temperature conditions. The GF14h protein constitutes a transcriptional regulatory module with a bZIP-type transcription factor, OREB1, and a florigen-like protein, MOTHER OF FT AND TFL 2, to control the germination rate by regulating abscisic acid (ABA)-responsive genes. The GF14h loss-of-function allele enhances ABA signalling and reduces the germination rate. This allele is found in rice varieties grown in the northern area and in modern cultivars of Japan and China, suggesting that it contributes to the geographical adaptation of rice. This study demonstrates the complicated molecular system involved in the regulation of seed germination in response to temperature, which has allowed rice to be grown in various geographical locations.

Date: 2022
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DOI: 10.1038/s41467-022-33318-5

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