Mapping for the Quantitative Trait Loci (QTL) for Tolerance of Anaerobic Germination in Rice (Oryza sativa L.) Using SNP Genotyping

The adoption of direct-seeding is gaining prominence among rice farmers of both rainfed and irrigated fields due to lower labor input requirements than transplanting. However, flooding during germination caused by unleveled fields and unpredicted heavy rain results to poor crop establishment. Furthermore, flooding just after sowing protects the seeds from rats and birds and is also a practical means of controling weeds. Thus, the development of varieties able to tolerate flooding during germination, (referred to as anaerobic germination, AG), is necessary.

This 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 variety Nanhi. Genotyping of the 48 most tolerant and 48 most susceptible F₂ lines was done by using a 384-plex SNP Indica/Indica set on Illumina BeadXpress Reader, resulting in 234 polymorphic markers. Phenotyping was performed by counting the rate of seedling survival of 300 lines under the stress. A major QTL derived from Nanhi, 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 on chromosome 2 (qAG2.1).  The QTLs identified can be used to further elucidate the genetic basis and mechanisms of AG tolerance in rice and can be used in marker- assisted selection and QTL pyramiding to provide increased AG tolerance  for improved crop establishment in direct-seeded systems.