QTL Mapping Reveals OsSUT1 and OsNRT1 as Putative Genetic Regulators of Methane Emissions in Rice (Oryza sativa)

Climate change is a critical global issue fueled by greenhouse gas (GHG) emissions. Rice cultivation, especially under anaerobic conditions, significantly contributes to methane (CH₄) emissions, a potent GHG. In this study, we investigated CH₄ emissions in rice using a custom chamber with a sensitive methane sensor and a graphical user interface (GUI) for tracking emissions. Here, we examined the 120 Cheongcheong/Nagdong double haploid (CNDH) population, with methane measurements conducted at the fourth leaf stage. Using Windows QTL Cartographer 2.5 and a genetic map, we identified QTLs associated with CH₄ emission on chromosome 1, 3, and 6. Gene expression analysis highlighted significant differences in the expression of LOC_Os03g07480 (OsSUT1q3), a sucrose transporter, and LOC_Os03g13274 (OsNRTq3), a nitrate transporter on chromosome 3 between RM14330-RM7197. In rice plants, sucrose transporter genes release sugars, including sucrose, which are becoming a carbon source for methanogens in the soil. Nitrate transporter genes in rice plants influence nitrogen availability in paddy soil. Gene variations directly affect microbial nitrogen metabolism, enhanced carbon release and modified nitrogen availability in the rhizosphere, potentially changing methane emissions from rice paddies. Validation across 65 Korean rice cultivars confirmed a strong association between methane emission levels and the expression patterns of these two genes. Our findings shed light on the genetic factors influencing methane production in rice and offer hope for creating climate-resilient rice varieties that reduce methane emissions.