Gene Hettel (2)<strong>Scuba</strong> riceby Adam BarclayNew versions of popular varieties of rice, which can withstand 2 weeks of complete submergence,are set to make a big impact in South AsiaScientists had long knownof an Indian rice variety,unromantically dubbed FR13A,that could handle a week ormore of complete submergenceand recover sufficiently to offer areasonable harvest. Rice, althoughoften grown in standing water, willdrown like any other plant if hit withsevere flooding.Despite its remarkableproperties, FR13A (FR stands for“flood resistant”), as a low-yieldingtraditional variety grown acrosslimited areas in the Indian stateof Orissa, was never expected tomake a big impact on a wide scale.Nevertheless, rice breeders—includingDavid Mackill, a young Californianplant breeder working at theInternational Rice Research Institute(IRRI) in the 1980s—saw the potentialto breed FR13A’s sought-after traitinto some of the modern high-yieldingrice varieties planted over vast floodproneareas across Asia.His reasoning, which emergedfrom discussions with IRRIdeepwater rice breeder DerkHilleRisLambers, was that a floodtolerantversion of a popular modernvariety could have an enormousimpact. In Bangladesh and India,for example, farmers suffer annualcrop losses because of flooding of upto 4 million tons of rice—enough tofeed 30 million people. To the farmfamilies and workers, and to the poorconsumers who rely on rice for thebulk of their food, flooding can betruly disastrous.So, the IRRI breeders—peoplewho spend their careers mixingthe genes of plants to develop newvarieties that can handle harshclimates, or resist diseases and pests,Even after 17 days of submergence in IRRI researchplots, Sub1 rice lines show their “waterproof” trait asthey are still standing to the left, right, and furtherbehind IRRI plant physiologist Abdel Ismail.Stemming the tide in flood-prone South AsiaIRRI plant breeder Dave Mackill (right) swapsnotes at BRRI’s Rangpur station with UC DavisProfessor Pam Ronald.or cope with problem soils—tried.And they succeeded. Sort of. Theycreated higher-yielding rice plantsthat could handle major floods,but they never even got close toreleasing them to farmers. During thebreeding process, which transferredto the modern varieties whichevergenes were giving FR13A its floodtolerance, too many unwanted genesmoved across as well. The resultwas poor-tasting, flood-tolerant ricethat yielded no more than existingvarieties. And so the idea moved tothe back burner.In 1991, Dr. Mackill left IRRIfor the University of California (UC)at Davis. With FR13A still on hismind, he and his graduate studentKenong Xu took up the challenge ofidentifying the genes responsiblefor FR13A’s scuba abilities. Theyeventually pinpointed the precisestretch of DNA that made the varietyso interesting, and named theassumed gene SUB1.The group subsequently teamedup with another UC Davis researcher,Pamela Ronald, an expert in isolatinggenes that give plants particulartraits. Working in Dr. Ronald’s lab,Dr. Xu and his wife, Xia, discovereda single gene, which they namedSUB1A, and demonstrated that thisalone was responsible for most of theflood tolerance.Dr. Mackill, who by now hadreturned to IRRI, realized that theFR13A game was back on. By thattime, 25 years after the first breedingattempts, agricultural science hadcome a long way. A new “precisionbreeding”method, known as markerassistedselection (MAS; see On yourmark, get set, select on pages 28-29of Rice Today Vol. 3, No. 3; also seeFrom genes to farmers’ fields onpages 28-31 of Rice Today Vol. 5, No.4), allowed breeders to do much oftheir work in the lab. The new methodshortened the breeding process andvastly improved the precision withwhich specific traits could be movedfrom one variety into another. Heand his team were able to transfer1A Biblical name used to connote apparent restoration to life.adam barclayDr. Ismail and UC Riverside scientist Julia Bailey-Serres share a laugh at BRRI’s Rangpur station.SUB1A into widely grown modernrice varieties without affecting othercharacteristics—such as high yield,good grain quality, and pest anddisease resistance—that made thevarieties popular in the first place.By 2006, the first Sub1 varietieswere ready for testing at IRRI. Theresearchers set up plots of whatthey hoped would be flood-tolerantversions of several varieties—IR64,Swarna, and Samba Mahsuri—next toplots of their non-Sub1 counterparts.Once the plants had establishedthemselves, the plots were flooded,completely submerging the rice for 15days. Next, the water was drained toreveal muddy plots of limp, flattened,deathly looking plants.Then, a remarkable thinghappened. Within 2 weeks of theflood, almost all of the Sub1 plant<strong>sr</strong>ecovered. They came back to lifeas if coached by Lazarus 1 himself. Afew scattered clumps of the originalversions made a comeback, but therewas no comparison. At harvest, theSub1 rice yielded more than twiceas much as its neighbor (to view adramatic time-lapse video of theexperiment, visit http://snipurl.com/ebql8).Around the same time, followingDr. Ronald’s group’s success inproving that SUB1A was indeed theright gene, Julia Bailey-Serres, ageneticist from UC Riverside who alsoworked on the gene’s identification,began investigating exactly howSUB1A confers flood tolerance. Itturns out that the secret is all aboutsaving energy.With colleague Takeshi Fukao,Dr. Bailey-Serres has determinedthat, when submerged, rice withoutSUB1A responds by increasing thepace of its elongation in an attempt toescape the submergence. Deepwaterrice varieties are able to do thi<strong>sr</strong>apidly enough to succeed. In modernhigh-yielding varieties, however, theelongation is insufficient. If the floodlasts for more than a few days, thenormal varieties expend so muchenergy trying—unsuccessfully—toescape that they’re unable to recover.Submergence of FR13A or any ofthe new Sub1 varieties, on the otherhand, activates the SUB1A gene,which suppresses this elongationstrategy, effectively shunting the riceplant into a dormant state until thefloodwaters recede. Thus, the plantsconserve their energy for a postfloodrecovery.“Understanding things from thisvery basic perspective should allow usto achieve an even better plant morerapidly,” says Dr. Bailey-Serres.According to Dr. Mackill, theSub1 project has shown the advantageof combining practical, applied worksuch as breeding and upstream,fundamental research.““Knowing the exact generesponsible for a trait is not absolutelynecessary for the MAS breedingapproach, because a larger pieceof the chromosome is transferred,normally containing many genes,”he says. “However, by understandingthe processes triggered by SUB1A indetail, “we hope to improve on theexisting Sub1 varieties by identifyingnovel flood-tolerance genes thatallow us to develop hardier plantsthat survive even longer periods of26 Rice Today April-June 2009Rice Today April-June 200927