Abstract
Floods have destroyed over 2000 acres of rice in Uganda which affected yield and caused losses to farmers. This problem is more pronounced when fields are not well leveled, and the mode of irrigation is by surface flooding. Majority of lowland rice fields in East African region are of this nature and are thus prone to yield losses. There are no submergence tolerance varieties identified in Uganda, so far. To address this problem, breeding for submergence tolerance is the most ideal and promising strategy in rice. As a first step, genotypes tolerant to submergence need to be identified which is the objective of this study. 29 rice genotypes were morphological characterized in screen house and field conditions while 34 rice genotypes were molecularly characterized. Results suggested significant differences in the performance of genotypes both in the screen house and under field conditions in which varieties Swarna, IRRI SUPA 3 and KOMBOKA showed approximately 80% and above survival rate with Swarna variety ranking first. Molecular characterization of rice genotypes revealed that, out of 34 genotypes, 30 genotypes scored presence for Sub 1A-2 allele while, four genotypes were neither Sub1A-1 nor Sub 1A-2 alleles. None of the tested genotypes were carrying Sub 1A-1 allele. Key words: Flash floods, submergence, tolerance, sub1, swarna  
Highlights
Total area under rice cultivation is estimated to be 150 million hectares with annual production averaging 500 million metric tons (Tsuboi, 2004)
Analysis of Sub1-A regions suggested 30 genotypes to have Sub1A-2 allele where four genotypes score absence in Sub1A region. These findings showed that Sub1A is completely absent (Sub1A0) in varieties WITA-4-Sub1, IRRISUPA 3, TXD 306 and Strong-S; the rest of genotypes scored presence for Sub 1A-2 at ~ 0.700 kb where none of the genotypes screened were scored for Sub 1A -1 allele
The study revealed four rice genotypes which are Swarna, IRRI SUPA 3, KOMBOKA and SUPA 5 to be tolerant to submergence at 45 cm water depth for 10 days (≥85% survival) that could be utilized in the Ugandan rice breeding programme for introgression submergence tolerance into susceptible preferred rice varieties
Summary
Total area under rice cultivation is estimated to be 150 million hectares with annual production averaging 500 million metric tons (Tsuboi, 2004). This represents 29% of the total grain crop output worldwide (Xu and Shen, 2003). Due to increase in consumption rate of 7.2% per year, rice demand is expected to rise (Africa Rice, 2012).
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