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34 Rice TodayApril-June 2006

C

rop breeders have enjoyed remarkable successin breeding plant varieties that resist pestsand diseases. As resistance is typically a

qualitative traitmeaning that it arises fromthe effect of just one or a few genesit is

a much more straightforward breeding target thantolerance of such abiotic stresses as drought, salinity,acidity, aluminum toxicity, nutrient deficiency,extreme temperature, or submergence. Abiotic stresstolerance is almost always a quantitative trait, arisingthrough the combined effects of several genes.

Yet, a few genes exist that, like resistance genes,individually confer a degree of abiotic stress tolerance,cracking open the door for researchers to breed thesetraits into popular cultivars. A collaboration led by the

by Peter Fredenburg

TRADITIONAL rice varieties,like the one grown by thisfarmer in the Hindu Kush, mayharbor useful genes for mak-ing hardier modern rice variet-ies that achieve higher yieldsunder stressed conditions.

Researchers zero in on two genes

at opposite ends of the rice genome

that provide tolerance for a dreaded

duo of widespread stresses, high

salinity and phosphorus deficiency

Opposites attract...attention

MATTHIASWISSUWA

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35Rice TodayApril-June 2006

International Rice Research Institute(IRRI) as part of the GenerationChallenge Programan initiativeto use molecular biology to helpboost agricultural production and,consequently, the quality of lifein developing countriesis wellalong the way toward success with

Saltol, a gene on rice chromosome1 that confers salinity tolerance,andPup1, a gene on chromosome 12that improves the plants uptake ofthe essential nutrient phosphorus.Although the two genes governaltogether different processes andoccupy opposite ends of the ricegenome (the sum total of the riceplants genetic information, encodedin its DNA), they are closely linkedin the fields where rice farmersstruggle to make a living.

Both salinity and phosphorusdeficiency are widespread and oftencoexist, especially in the rainfed fieldsof the poorest farmers, explainsAbdelbagi Ismail, the principalinvestigator of the project, whoseavowed aim is to revitalize marginalrice lands. Globally, more than 15million hectares of rice lands aresaline, and more than half of allrice lands are phosphorus-deficient.From the research perspective, we

facilitate their use in crop-breedingprograms, and train nationalscientists in relevant molecular gene-discovery and breeding techniques.

The IRRI team mapped thelocation ofSaltolby crossing Pokkali,a traditional cultivar from India thatexhibits moderate salt tolerance, with

the saline-sensitive variety IR29.Growing a population of eighth-generation inbred descendants withand without salt, the team was able tomap the location ofSaltolon the ricegenome. Fine-mapping of theSaltollocus continues, using descendantsof the hybridization that are almostgenetically identical but differ bythe presence or absence ofSaltol.

The projects many participants,along with IRRI, include theUniversity of California (Davis

and Riverside), AustraliasCommonwealth Scientific andIndustrial Research Organization,Dhaka University in Bangladesh, theIndonesian Center for AgriculturalBiotechnology and Genetic Resourcesand Research Development, JapansNational Institute of AgrobiologicalSciences (NIAS), Irans AgriculturalBiotechnology Research Institute,and the Japan International ResearchCenter for Agricultural Sciences

have a good understanding of thebiology of tolerance of both stresses.And we are in the last stages offine-mapping the location of thegenes, both of which have clear-cuteffects. We expect to have clones ofboth genes within a year or two.

Ismail explains that rice is

particularly sensitive to salt stressduring its seedling and reproductivestages.Saltolconfers tolerance at theseedling stage, which is importantfor good crop establishment incoastal areas, where river water isbrackish early in the growing seasonbefore seasonal rains weigh in.

Its always safer to have salt-tolerant varieties in coastal areas,Ismail adds. The Indian Oceantsunami shocked us with its terribledestruction and loss of life. But the

kind of damage that the tsunamicaused to croplands is more routinethan people realize. Saline floodingfrom relatively small stormsdestroys crops in the Indian stateof Orissa every 2 or 3 years, mostrecently in September 2005. Butsuch events rarely make the news.

The projects main aims are toisolate and cloneSaltolandPup1,validate their respective roles in salttolerance and phosphorus uptake,

ABDELBAGI ISMAIL (holding rice)describes to IRRI visitors how he screensrice plants for salinity tolerance.

LAUROATIENZA

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36 Rice TodayApril-June 2006

where co-principal investigatorMatthias Wissuwa, who left IRRI in2005, continues his work onPup1.

In fact,Pup1 has been followingWissuwa around for years. Havingstarted the project as a EuropeanUnion science and technology fellowat NIAS in 1999, Wissuwa continuedworking on it when he arrived

at IRRI in the Philippines as aninternational research fellow in 2002.

Its good to be able to changejobs and keep working on the samething, Wissuwa says. Whatsexciting aboutPup1 is that it reallydoes something positive in thefield. We observed that plants withPup1 extract up to three timesas much naturally occurring soilphosphorus. These plants cantherefore fill a large portion of theirphosphorus requirement withoutphosphorus fertilizers. This benefitsthe poorest rice farmers, who cantafford to buy enough fertilizer.

AndPup1 is one of thefew cases where were close toisolating the gene andhave a clearpicture of its phenotypic effects,Wissuwa adds. Usually you haveone or the other, not both.

As some traditional rice cultivarstake up 20 times more phosphorusthan other varieties, the projects

mapping population descended froma cross of the tolerant traditionalvariety Kasalath with Nipponbare.Pup1 is clearly associated withvigorous root growth, but the cause-and-effect question remains: Doesstrong phosphorus uptake spur rootgrowth, or the other way around?

Either way, phosphorusuptake is closely linked to droughttolerance. As Wissuwa points out,a plant lacking phosphorus cannot

grow long roots, but one withPup1can. He is nevertheless careful notto oversell the gene he has beenworking for years to isolate.

In an experimental background,Pup1 triples the grain yield anddry weight, he says, referring to astandard measure of plant bulk. Butof course we test with susceptible

varieties. We dont know how muchPup1 will improve normal ricecultivars because we dont know ifthey already have it. If they dont, itshould double their grain yield onseverely phosphorus-deficient soils.

In any case, phosphorus uptakeis an important trait for rainfedfields and uplands, he continues.The risk of phosphorus deficiency ishigher there than in irrigated fields,and those farmers can rarely affordfertilizer. Another thing makes thisresearch worthwhile when youactually have the gene, you can use itin a very targeted way. You can evenput it, for example, into maize.

After cloning, breeding a newgene into popular rice cultivars takes2 years, with another year requiredto multiply enough seed to deliver

the improved variety to farmers.Molecular breeding develops theproduct 46 years more quicklythan conventional breeding, as wellas providing greater understandingof the gene and, as Wissuwa pointsout, more options for its use. Finally,the clean and precise insertion ofa single trait like those conferred

bySaltolandPup1 saves additionaltime following delivery of the newvariety to national programs.

Adding only one trait toa familiar and popular varietyaccelerates its spread and adoption,Ismail explains. In some cases, youmay not need to go through the fullrelease process, which normallytakes an additional 3 years afterdelivery to national programs andmultiplication of seed. When farmfamilies are going hungry, or childrencant go to school because theirparents cant pay the fees, any timesaved can make all the differencein the world to those individuals.

Adapted from Research Highlights 2005,

published by the Generation Challenge

Program (www.generationcp.org).

Nipponbare NIL-C443 Kasalath

IN PHOSPHORUS-DEFICIENT soil, the modernvariety Nipponbare (center) fares poorlyalongside the tall traditional variety Kasalath,the Pup1 donor, and (right) an experimentalline that received Pup1 and is otherwise al-most identical to Nipponbare. By transferringPup1 using the modern technique of marker-assisted selection, the researchers avoidedcarrying over unwanted genes that could havecompromised Nipponbare attributes such asgood grain quality. The corresponding grainsfrom these varieties can be seen below.

MATTHIAS

WISSUWA(2)