Mapping of QTL for anaerobic germination using the donor AC39416A in the genetic background of variety Swarna Sub-1 of rice (Oryza sativa L.)

Climate change is causing a decline in rice productivity and sustainability in coastal irrigated areas due to abiotic stresses. Flooding during germination, triggered by unexpected and heavy rainfall, poses a significant threat to the growth and survival of rice plants. Anaerobic germination (AG) is an important trait in particular circumstances for cultivation under the direct seeding method in kharif season. To identify QTLs responsible for AG, phenotypic screening was carried out using the 188 F₂₃ population of Swarna Sub1/AC39416A in the present investigation. The mean anaerobic germination percent recorded after the 2 weeks of submergence ranged from 0 to 95%, with an overall mean of 47.51%, whereas, for 3 weeks of submergence, the mean anaerobic germination percent recorded between 0 and 95%, with an overall mean of 37.66%. Parental polymorphism studies revealed that 134 out of 687 SSR markers were polymorphic. Linkage analysis with 83 polymorphic SSR markers was done using the QTL IciMapping software version 4.1.1. The length of the linkage map constructed across the whole genome was 3600.8 cM. Four QTLs were identified viz., qAG7-1, qAG7-2, qAG10 and qAG12 with the ICIM method. All these 4 QTLs explained a phenotypic variance of about 18.81% collectively for AG trait, with their individual contributions ranging from 2.99 to 8.67% of phenotypic variation and LOD scores of 5.05 to 5.86. The LOD score and phenotypic variance is 5.86 and 8.67% respectively for qAG10 a novel QTL identified in the present study using ICIM method.