Evaluation of anaerobic germinability in various rice subpopulations: identifying genotypes suitable for direct-seeded rice cultivation

Anaerobic conditions in waterlogged soil lead to low germination rates, which significantly reduce crop yields. Good seed germination is prerequisite for direct-seeded cultivation of rice to obtain optimal yields not only in irrigated lowland but most importantly in rain-fed and waterlogged areas where water supply could be more than needed. Due to the limited availability of rice genotypes suitable for anaerobic germination, there is an urgent need to select diverse rice germplasm with enhanced anaerobic germinability. In this study, we evaluated 185 rice accessions from six subpopulations for germination rate (AGR) and coleoptile length (ACL) under anaerobic conditions. The highest average AGR (60%) and longest average ACL (2.13 cm) were observed in tropical japonica (TRJ) and temperate japonica (TEJ) germplasm, respectively. Meanwhile, the highest proportion of accessions with “very long” ACL was in the TEJ subpopulation, whereas those with the “highest” AGR were in the aus subpopulation based on our criteria. We selected seven strong accessions for anaerobic germinability (AG) based on AGR and ACL and analyzed the relative expression patterns of four AG-related genes in strong and weak accessions via qRT-PCR. In general, proton pyrophosphatase locus (OVP3) was expressed at the highest levels in strong accessions, whereas the expression level of rice ethylene response element binding protein locus (EREBP1) did not significantly differ among accessions under normal and anaerobic conditions. The relative expression results of rice alpha amylase locus (RAmy3D) and OVP3 showed distinct patterns and divided all strong accessions into two groups, suggesting that major genes involved in AG may vary depending on the germplasm. These findings could be helpful for breeders and lay the foundation for further genetic analysis.