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Understanding traits

View of rice plant parents and high-yielding offspring

When a wild O. rufipogon parent, left, is crossed with a popular, high-yielding O. sativa cultivar, such as IR64, right, the offspring are all highly vigorous, center. See larger image

Many answers to breeding new rice varieties that could be grown in a non-flooded system (without paddies) or that could withstand drought or acidic soils with high aluminum toxicity may be found in the plants' roots and the genes that control root architecture. "If you wanted to enhance the ability to explore soil or increase mineral or nutrient uptake, you need to understand the root structure, because the roots are where it happens," says McCouch. "But people simply don't know much about roots."

Janelle Jung, a chief plant breeding graduate student in McCouch's lab, and Randy Clark, a bioengineering graduate student in Kochian's lab, are working to characterize root architecture. Jung has spent the last three years in Cornell's greenhouses growing a diverse set of a wild species that is ancestral to cultivated Asian rice and which is considered a noxious weed in the United States, and phenotyping their above-ground characteristics by measuring 20 to 30 vegetative and seed traits.

Using an advanced 3-D root imaging system and software package developed by Clark in Kochian's lab (see sidebar), Jung and Clark are investigating root architectures – deep and narrow taproots vs. shallow, spreading root systems. By comparing the root and shoot trait data from each plant with each plant's genetic fingerprint using the SNP chip, McCouch and Mezey's labs are able to make associations between traits and the genes underlying those traits. "We now have a chance to get at the genes that determine these different root architectures," McCouch says.

Joshua Cobb, a graduate student in both Kochian's and McCouch's labs, is also using the genotyping power of the new SNP chips to understand the genetics of mineral and heavy-metal uptake in rice. Once he has all his data, he will try and identify what regions of the genome are associated with accumulation or exclusion of these nutrients, minerals and toxic metals such as arsenic and cadmium. "This has implications for human nutrition but also plant nutrition," says Kochian.

Rice grains compared

The O. rufipogon seeds, left, show wild traits such as black hulls and awns (bristles that deter bird predation), as compared with the U.S. Jefferson variety, a cultivated long grain rice with pale yellow hull, right. See larger image

Acidic soils affect half the world's potentially arable land, mostly in the tropics and subtropics. Aluminum in acidic soils becomes toxic to life and binds up phosphorus, creating phosphorus deficiency. "It inhibits root expansion and cell division, and you end up with a stunted and damaged root system that can't take up water and nutrients," adds Kochian.

McCouch, Kochian and their graduate students have also used SNPs to identify genes from divergent strains of rice that confer greater aluminum tolerance and have bred them into rice cultivars that are grown throughout the tropics. Soon, another McCouch and Kochian graduate student, Juan David Arbalaez, will take these new rice lines to Colombia and Indonesia where he will test them in the field for aluminum tolerance under naturally acid soil conditions.

McCouch also has begun collaborating with Cornell agronomist John Duxbury and Bangladeshi soil scientists and rice breeders to identify SNPs related to arsenic tolerance, aiming to reduce arsenic uptake in rice in Bangladesh, where the toxin exists naturally in soils and taints groundwater.

Above all, McCouch stresses that her role is not to produce new, finished varieties of rice, but to give breeders the genomic tools, strategies and enhanced varieties they will need to ensure an abundance of this essential crop by midcentury. "We are working against time to enhance both the productivity and the sustainability – or the resource-use efficiency – of rice production," she says.

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