Italian culture boils it into risotto. Cajun culture sautés it into Jambalaya. Japanese culture wraps it around fish and serves it as sushi. As Prof. Susan McCouch, plant breeding and genetics, recognizes, it seems like every culture has its own recipes and preferences for rice. By tracing the past movement of human trade and analyzing the genetic variability of rice subgroups, McCouch hopes to identify genes that may improve the future of agriculture.

“We’re looking at thousands of genetic samples from thousands of varieties of rice from around the world,” McCouch explained. “We help to map diversity across the genome.”

According to McCouch, as one of the world’s main “staple crops”, rice provides invaluable sustenance to cultures around the world. For this reason, McCouch says, the genomes of domestic rice varieties reflect the movement of human civilization, specifically the movement of tradesmen along the Silk Road of Asia — a series of 3000-year-old trade routes that ran from China to the Mediterranean.

Asian rice crops include several sub-groups, namely Japonica rice and Indica rice, as well as many other wild varieties.

“The [Japonica] rice that is distinct to the northeastern cultures,” McCouch described, “is so readily different from that [Indica rice] grown in India.”

McCouch uses enzymes to cut and compare long genetic sequences in what is called a haplotype approach. The goal is to identify both common and unique genes throughout the rice genome, including the genes that control grain size, yield, stress adaptation and fragrance.

Just as humans vary in their blood types, McCouch explained, rice varieties may express alternative genes for many traits. For instance, the Japonica rice of China and Japan possesses short, sticky grains while the Indica rice of Pakistan and India produces long, fragrant grains.

“[The] Indica [variety] and Japonica [variety] are genetically very different,” McCouch said. “All evidence pointed to independent domestication.”

Basmati rice, a fragrant variety from the Indica subgroup, grows primarily in the Punjab region between India and Pakistan. Because of Basmati rice’s geography and distinctive scent, researchers typically classified it within the Indica subgroup. But a growing body of evidence indicates that Basmati rice may have evolved from a Japonica ancestor, suggesting interactive domestication.

On Aug. 17, McCouch, Michael Kovach , grad, and colleagues from the International Rice Research Institute (IRRI) in the Philippines published a research article in the Proceedings of the National Academy of Science of the US. The study documented the discovery of the BADH2 gene — which is responsible for the scent of the Basmati rice — affirming the evidence that Basmati descended from a Japonica-like ancestor.

In addition, the paper proposes a contradictory finding. With support from genetic comparisons, McCouch and her colleagues propose that the fragrance gene could have developed from Indica through gene flow, a process in which genes are transferred from one population to another.

According to McCouch, this kind of gene flow is called “introgression.” Introgression occurs when two plant varieties produce a hybrid offspring with a combination of genes. As these hybrid organisms breed offspring with parent varieties over many generations, genes may move from one parent population to the other.

Historically, breeders believed the two subgroups developed their distinctive genes without interaction. Consequently, they associated fragrance exclusively with Indica rice. However, this research suggests that humans played an instrumental role in the domestication and evolution of rice.

“Fundamentally, I’m interested in the relationship between the world’s major food crops and the people that grow them,” McCouch affirmed. “We know that early on all rice was short-grained, but some cultures favored long-grains.”

McCouch believes that Japonica-like ancestors may have moved from northeastern Asia into India as humans carried the variety along the Silk Road. Humans carried this ancestor into India, allowing it to mate with indigenous, wild varieties. According to McCouch, through introgression, the fragrance gene passed from the Japonica-like ancestor into the Indica population.

McCouch believes that by studying the evolutionary past of rice, biologists may be able to better utilize naturally occurring genes during plant breeding.

According to McCouch, growing populations and rising global temperatures create the need to adjust current agriculture practices. Through her research, McCouch contributes to a growing global effort to improve rice breeding techniques and increase rice crop yields.

“The main issue is trying to grow rice with less nutrients and less water, but then increasing its productivity,” McCouch related.

By mapping the genomes of the different rice varieties, McCouch identifies advantageous genes that scientists may select to breed into hybrid plants. These advantageous traits include size, aroma, yield, disease resistance and stress resistance. Through genetic engineering or artificial selection, biologists may breed superior rice plants that are capable of surviving in harsher, resource-strained conditions.

McCouch added that the future of food production rests on the shoulders of the coming generations. “We also try to train the next generation of plant-breeders and rice-producers,” she explained. “The main mechanism through which we do this is through the students.”