Marker assisted breeding of Sub1 introgressed rice (Oryza sativa L.) lines and identification of stable variety MTU 1232 suitable for flood prone ecosystem

The Development of flood-tolerant rice varieties is a prerequisite for climate resilience in flood-prone areas. The present study aimed to develop a stable, high, yielding, and tolerant rice variety against flash floods and stagnant flooding across multiple environments. Sub1A was incorporated into a popular rice variety MTU 1075 using Swarna-sub1 as a donor to generate BC3F5 families. Sub1BC2 was used as a foreground marker for selection, a proxy for the Sub1A gene. RM23865 and RM464 on Chromosome 9 were used as recombinant markers. Backcross families from the BC3F2 generation were evaluated under two weeks of flash floods 15 days after transplanting. This was followed by stagnant flooding and survived BC3F4 families were used for background selection using a 50K high-density SNP chip. The nine best families identified were included in the field trial evaluation under eight environments. Consequently, MTU Rice 1232 was identified as a high-yielding, flood-tolerant rice variety using Additive Main effects and Multiplicative Interaction stability analysis. The MTU Rice 1232 ranked first by the Best linear unbiased prediction (BLUP) based ranking parameters and 4th based on stability parameters ranking. This flood-tolerant rice variety can tolerate both flash floods and stagnant flooding and possesses an 80% survival rate. It has a yield potential of 3792 Kg ha-1 under severe floods and 6000 Kg ha-1 under normal conditions.