Identification and substitution mapping of QTLs for anaerobic germination in rice

Hypoxia is a key limiting factor for seedling emergence and establishment of direct-seeded rice (DSR) under submergence. The anaerobic germination (AG) tolerance, therefore, is one of the most critical traits in DSR breeding programs. However, the genetic basis of AG is still unclear. In this study, 229 single segment substitution lines (SSSLs) were arranged in an augmented design in field planting. We evaluated the anaerobic germinability by measuring the SSSLs’ coleoptile length (CL) under submergence, and then identified AG QTLs. AG was a typical quantitative trait based on the results of five cropping seasons. We repeatedly detected 19 SSSLs with putative AG QTLs in at least two cropping seasons. Moreover, substitution mapping identified 11 integrated AG QTLs on nine chromosomes, including six positive and five negative QTLs with additive effect contributions ranging from 6.8 to 18.5%. Among the 11 QTLs, qAG4 and qAG11 were novel ones, qAG9 was cloned in a previous study, and the remaining eight QTLs overlapped with reported AG QTLs. Overall, we identified some genetic loci controlling AG in multiple environments, which may be useful for developing varieties suitable for DSR.