Marker-assisted improvement for submergence tolerance and durable bacterial blight resistance in popular rice variety Hasanta

Flash flooding (FF) and Bacterial blight (BB) are two major constraints of rice production in the rainfed shallow-lowland (RSL) ecosystem. Frequent occurrence of FF and Xoo races dynamics with varying levels of genetic diversity and virulence renders their management extremely challenging. In this context, marker-assisted improvement of plant resistance/tolerance has been proven as one of the most promising strategies for sustainability enhancement crop plants. The present study demonstrates the marker-assisted introgression of the submergence tolerant (Sub1) and bacterial blight resistant genes (xa5+xa13+Xa21) into the background of Hasanta, a popular long duration rice in eastern coastal region of India. The genotypes, Swarna Sub1 (Sub1) and IRBB66 (Xa21, xa13, xa5) had maximum genetic similarity (0.84 and 0.73, respectively) with recurrent parent (RP) were used as donor for trait introgression. Hybridity screening of F1s and IC1F1s, forward analysis of target genes (Sub1+Xa21+xa13+xa5) and genome recovery of RP in each BC/segregating generations was performed utilizing linked and 108 background SSR markers, respectively. The BC and segregating populations were grown under field rapid generation advancement (RGA) facility and phenotyped intensively for accelerative development of improved lines with perfect product profile of RP. The performance of the resulting improved lines, HS 110-224-197-10, HS 110-224-197-13, HS 110-224-197-424, HS232-411-391-702, HS232-411-391-756, HS232-411-391-809, HS232-411-391-831 establishes the utility of marker-assisted selection (MAS) approach for accelerated trait introgression in rice. The MAS-bred lines carrying four introgressed genes (Sub1+Xa21+xa13+xa5) showed 76 to 91% % survival after 14 days of submergence and broad spectrum of BB resistance (plant disease index of 2.55± 0.82 -19.08 ± 0.31 and lesion length of 1.29±0.12 cm to 4.2±0.64 cm). Besides, improved lines carrying Sub1 QTL showed comparatively reduced consumption of soluble sugar, reduced degradation of total chlorophyll contents; enhanced level of Alcohol Dehydrogenase activity (ADH) and proline accumulation under submergence. Further, improved lines also showed the complete product profile of RP along with enhanced submergence tolerant and BB resistance. The improved lines would contribute to sustainable rice production under RSL, particularly in the coastal region that has substantial acreage under Hasanta.