QTL mapping for tolerance of anaerobic germination from IR64 and the aus landrace Nanhi using SNP genotyping

Direct seeding is becoming more popular mainly due to its labor-saving nature. However, flooding during germination caused by unleveled fields and unpredicted heavy rain can prevent crop establishment. On the other hand, flooding just after sowing protects the seeds from rats and birds and is also a viable means of weed control. Thus, the development of varieties able to tolerate flooding during germination, referred to as anaerobic germination (AG), is essential. A study was conducted to identify QTLs associated with tolerance of flooding during germination from an F-2:3 mapping population derived from the cross of IR64 and the tolerant aus landrace Nanhi. Phenotyping was performed by counting the rate of seedling survival of 300 lines under the stress. Selective genotyping was employed by genotyping the 48 most tolerant and 48 most susceptible lines using a 384-plex SNP Indica/Indica set on the Illumina BeadXpress Reader, resulting in 234 polymorphic markers for the study. A major QTL for AG derived from Nanhi, named qAG7, was detected on chromosome 7 with an LOD of 13.93 and 22.3 % of the phenotypic variance explained. A second QTL of smaller effect, qAG11, was also derived from Nanhi, while one QTL with an increased effect from IR64 was detected on chromosome 2 (qAG2.1). The QTLs detected in this study can be used to further elucidate the mechanisms underlying AG tolerance in rice, and can also be used in marker-assisted selection and QTL pyramiding to provide higher AG tolerance to enable improved crop establishment in direct-seeded systems.