Assessment of submergence stress responses and mining allelic variations of submergence tolerance gene Sub1A in Sri Lankan rice germplasm

Development of submergence tolerant (ST) rice cultivars is a priority in rice breeding programs globally, as floods significantly curtail rice production. Sub1A is the major known gene conveying submergence tolerance in rice, carrying two variants; Sub1A-1 (tolerance allele) and Sub1A-2 (susceptible allele). Sri Lanka hosts a genetically diverse rice germplasm; however, the allelic diversity of Sub1A gene among the Sri Lankan rice germplasm remains unknown. Hence, the current study focuses on assessment of submergence stress responses and identification of the allelic diversity of Sub1A gene in a panel of 64 Sri Lankan rice varieties/accessions. Submergence stress responses of the rice panel were evaluated and Sub1A allelic variations were assessed using a modified gel-based marker, ABUOP0003. A Bayesian approach was used to assess the genetic structure of the rice panel and its association to the Sub1A alleles was explored. Thirteen rice accessions/varieties showed significantly similar (p>0.05) survival percentages (SP - 77 to 93%) as ST reference FR13A. ABUOP0003 marker assay revealed that 13 rice accessions/varieties carry Sub1A-1. The rice accessions Godaheenati, Heenkarayal, Goda wee and Dik wee carried the Sub1A-1 allele as well as expressed a tolerance response to submergence stress. No significant association (p<0.05) was observed between the Sub1A alleles and submergence stress responses indicating additional genes at play. The deduced genetic structure of the rice panel revealed two genetically isolated gene pools and the Sub1A alleles did not associate to any specific gene pool, indicating that the allele divergence pre-dates germplasm introductions and varietal development attempts in Sri Lanka.