Impact of riceGENERAL REGULATORY FACTOR14h(GF14h) on low-temperature seed germination and its application to breeding

Abstract

AbstractDirect seeding is employed to circumvent the labor-intensive process of rice (Oryza sativa) transplantation, but this approach requires varieties with vigorous low-temperature germination (LTG) when sown in cold climates. To investigate the genetic basis of LTG, we identified the quantitative trait locus (QTL)qLTG11from rice variety Arroz da Terra, which shows rapid seed germination at lower temperatures, using QTL-seq. We delineated the candidate region to a 52-kb interval containingGENERAL REGULATORY FACTOR14h(GF14h) gene, which is expressed during seed germination. The Arroz da TerraGF14hallele encodes functional GF14h, whereas Japanese rice variety Hitomebore harbors a 4-bp deletion in the coding region. Knocking out functionalGF14hin a near-isogenic line (NIL) carrying the Arroz da Terra allele decreased LTG, whereas overexpressing functionalGF14hin Hitomebore increased LTG, indicating thatGF14his the causal gene behindqLTG11. Analysis of numerous Japanese rice accessions revealed that the functionalGF14hallele was lost from popular varieties during modern breeding. We generated a NIL in the Hitomebore background carrying a 172-kb genomic fragment from Arroz da Terra includingGF14h. The NIL showed superior LTG compared to Hitomebore, with otherwise comparable agronomic traits. The functionalGF14hallele from Arroz da Terra represents a valuable resource for direct seeding in cold regions.Author SummaryRice serves as a fundamental crop sustaining over half of the global population. With the rapid growth of the world’s population, it will become increasingly important to improve rice productivity. On the other hand, the aging of rice farmers in Japan has resulted in a constant labor shortage. To address this, direct seeding, in which seeds are sown directly in rice fields without going through the most labor-intensive part of the rice cultivation process, i.e., seedling production and transplanting, has been recommended. However, prevalent elite rice varieties are known to be unsuitable for direct seeding due to their poor seed germination ability under low-temperature conditions. In this study, we show for the first time thatGF14hgene from the Portuguese variety Arroz da Terra improves seed germination at low temperatures (LTG). In addition, a novel cross-bred line was generated by introducing theGF14h-containing genomic segment from Arroz da Terra into Hitomebore, a widely cultivated variety in northern Japan. This line is expected to be used as a pre-breeding material to enhance LTG. This study will provide a genetic basis for LTG and contribute to basic and applied research progress.