Genome Wide Association Studies and Rice

To produce the most resilient strain of rice, breeders would conventionally cultivate two different hardy species, but Susan McCouch, a professor of plant breeding and genetics at Cornell University, has found evidence otherwise. In her Friday Oct. 4, 2013 seminar at Dartmouth College, McCouch discussed discoveries about rice and what she believes must be done in order to double rice production within the next 30 years.

Rice cultivation covers 10% of the Earth’s arable land, but not all of it is irrigated. Due to water problems, the rice community hopes to move away from irrigated rice farming to soil-based farming despite the challenges presented by aluminum-toxic soils in the region.

Aluminum, the third most abundant element in the soil, becomes Al³⁺, which inhibits root growth. At concentrations above 160 µM Al³⁺_,grains such as maize, wheat, and sorghum were significantly inhibited, with rice being least affected. McCouch and her colleagues studied the phenomenon and found three mechanisms responsible for rice’s resilience.

In one mechanism, the rice roots secrete negatively-charged, organic ions to bond and neutralize the aluminum ions. In another mechanism, the roots uptake the Al³⁺ into cells and then isolates them into vacuoles or membrane enclosed compartments. In the third mechanism, the roots secrete ADP-glucose, a chemical that prevents Al³⁺ from binding to the rice plant’s cell wall. However, not all rice subspecies grow equally well in aluminum-toxic soils since rice is very diverse compared to other grains.

McCouch and her colleagues studied various species of rice within each two major subdivisions of rice: japonica and indica. Within japonica, there are three genetic subdivisions: temperate japonica, tropical japonica, and aromatic. Within indica, there are two: indica and aus.  For these species of rice, McCouch analyzed the various single-nucleotide polymorphisms (SNPs). These SNPs are single nucleotide differences between the genes of organisms. From their analysis, they found that all the subdivisions of rice have evolved aluminum tolerance independently, so it is possible for breeders to improve rice’s aluminum tolerance by mixing and matching the different rice species to produce an extremely tolerant strain.

From her research, McCouch found some species of indica to be very tolerant, but further analysis of their genome revealed that they also carry genes from temperate japonica rice. The realization that indica rice’s high Al⁺³-tolerance can, in some part, be attributed to genes originating from the less tolerant temperate japonica rice contradicted expectations.

McCouch believes that good genes can came from phenotypically inferior parent plants; in effect, phenotypically superior parents are not necessarily needed to get better traits in offspring. Genome wide association studies such as hers can help find other instances of unexpected gene contributions.