Molecular marker-assisted introgression of submergence tolerance gene sub1 into popular rice varieties

Abstract:

Submergence tolerance defined as the ability to survive complete submersion for 10-14 days is controlled primarily by the Sub1 locus on chromosome 9 of rice. This research used marker-assisted backcrossing to introgress the Sub1A gene from donor line FR13A into four popular rice varieties (IR64, Swarna, BR11, Samba Mahsuri) at Sri Konda Laxman Telangana Agricultural University, Warangal, during 2020-2023. Foreground selection was performed using Sub1A-specific markers RM8300 and RM23869, while background selection employed 72 genome-wide SSR markers. After three backcross generations, recurrent parent genome recovery ranged from 91.8% (Samba Mahsuri-Sub1) to 93.6% (IR64-Sub1). Submergence screening confirmed that all four introgressed lines survived 14-17 days of complete submersion, compared to 6-7 days for recurrent parents. Agronomic performance of introgressed lines was comparable to their recurrent parents under non-stress conditions, with no significant yield penalty. These Sub1-introgressed lines are ready for multi-location testing in flood-prone areas of Telangana and Himachal Pradesh.