Submergence tolerance
A gene that enables rice to survive complete submergence has been identified by a team of researchers at the International Rice Research Institute in the Philippines and at the University of California's Davis and Riverside campuses. The discovery allows for development of new rice varieties that can withstand flooding, thus overcoming one of agriculture's oldest challenges and offering relief to millions of poor rice farmers around the world.
More than 22 million hectares of rice paddies are prone to transient flooding due to seasonal rains. This area is home to 140 million farmers of which half live on less than 1$/day. Cultivars that can survive temporal flooding of fields are highly desired to enhance yield.
An international effort, focused on the characterization of the genetic determinants of submergence tolerance, identified an indica landrace, FR13A, as the world's most tolerant of flooding. In collaboration with D. Mackill (International Rice Research Institute) we have now cloned the submergence tolerance (Sub1) locus from FR13A using a map-based cloning approach. The Sub1 locus encodes three putative transcription regulators of the AP2 class and RNA blot analysis indicates that the Sub1A mRNA levels increase dramatically in response to O2 deprivation in sub1 seedlings; whereas Sub1C levels decrease. The sub1A-2 allele possesses a single nucleotide change as compared to the Sub1A-1 allele. All five sequenced sub1A-2 (intolerant) alleles encode a proline at this position whereas the Sub1A-1 alleles from three tolerant lines examined encode a serine. Transgenic lines overexpressing the Sub1A-1 gene into a submergence intolerant line display enhanced submergence tolerance.
Our team has now developed a submergence tolerant version of India and Bangladesh and is grown on more than 5 million hectares. It has good grain quality and high yield. With the submergence tolerant version, which we are temporarily calling Swarna-Sub1, we have found no significant differences compared to the intolerant Swarna in terms of yield or quality under normal (non-submerged) conditions. The yield of both varieties here in the Philippines is about 6 tons grain per hectare. Under submerged conditions, yield is reduced in both varieties, but Swarna-Sub1 has about double the yield of the normal Swarna. This would result in a 1-2 ton/ha yield advantage when submergence is present, a considerable improvement for poor farmers in Asia. Because Swarna is a widely grown variety in areas where submergence is common, we feel that the new submergence-tolerant version of Swarna represents a signficant advance over the previous breeding efforts, and will be acceptable to farmers.
Current experiments involve examining the expression profiles of the Sub1 vs sub1 lines using 45k microarrays, determining the significance of the serine to proline mutation and investigating whether the submergence tolerance phenotype of rice involves differential regulation of other stress response pathways (in collaboration with Julia Bailey-Serres, UCR). We are also testing if sowing of submergent tolerant seed into fields flooded to 15 to 20 cm would effectively limit weed growth and eliminate the need for herbicides.
Xu K, Xu X, Ronald PC, Mackill DJ. 2000. A high-resolution linkage map in the vicinity of the rice submergence tolerance locus Sub1. MGG. 263. 681-689((pdf)
Kenong Xu, Xia Xu, Takeshi Fukao, Patrick Canlas, Sigrid Heuer, Julia Bailey-Serres, Abdel Ismail, Ronald, P.C, David J. Mackill. 2006. Sub1A encodes an ethylene responsive-like factor that confers submergence tolerance to rice. Nature. 442:705-708. (pdf)
Watch time lapse video of submergence tolerance here.
127 days in 40 seconds
IRRI's work on drought and flood tolerance in rice
Ceremonial harvest of Sub1 rice in Bangladesh
Pictures of submergence-damaged fields.
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| Submergence of rice fields in northeast Thailand | After submergence of rice fields in Java, Indonesia | After submergence of rice fields in Java, Indonesia |
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| After submergence of rice fields in Java, Indonesia | Submerged rice fields in Bihar, India | After submergence of rice fields in southern Thailand |
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| Damage of the cultivar Swarna from Submergence (background) compared to tolerant cultivar (foreground) | Submergence damage | flooded rice fields along a river, I think this is in the Philippines (Biggs) |
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| flooded field in Bangladesh(Abdel) | Gina Vergara flooded field, India 2005 | Gina Vergara the flooded field is behind the bridge, India 2005 |
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| Gina Vergara flooded field with post, India 2005 | SWARNA-Sub1 |
