More than three billion people across the globe eat rice every day. The grain makes up 20 percent of the world’s dietary energy supply—more than wheat (19 percent) and maize (5 percent)—and is the number one staple food for the world’s poorest and undernourished people. To say that rice production is critical to global food security is an understatement.
Susan R. McCouch, Plant Breeding and Genetics, is dedicated to improving rice through the power of genomics and breeding. Her lab identifies regions in the genomes of rice species, domesticated and wild, that carry beneficial traits, from grain quality to root growth and nutrient acquisition. McCouch is concerned with developing more efficient breeding strategies that can bring benefits to rice farmers. Her work is grounded on the firm belief that deploying crop diversity is key to feeding the future.
The First Rice Genetic Map
“I don’t believe in silver bullets,” says McCouch, “nor in one-size-fits-all approaches to breeding.” Since rice is grown across a variety of environments, from the tropics to the temperate zone, and from irrigated paddies to dry land hillsides, rice farmers face a range of challenges.
“We have to be able to tailor varieties to the requirements of different farmers, and each farmer needs to make the final choice about what’s best for them. As breeders, we need to keep those choices coming,” says McCouch.
In 1986, McCouch came to Cornell as a graduate student in Plant Breeding and Biometry (the department name at the time) with an interest in breeding plants for disease resistance. That’s when she found rice. Her first research project: create a molecular genetic map of the rice genome, with all 36,000 genes.
“Little was known about rice at that time in the West; it was considered an ‘orphan crop.’ There was no literature, and you couldn’t grow it in Ithaca,” says McCouch. “For all those reasons, I thought, ‘that’s the one for me.’” In 1988, she and her colleagues published the first genetic map of rice, and it opened a whole new chapter. McCouch never looked back.
Making Rice a Durable Crop and a Quality Food
Since then, McCouch has been mining rice’s genetic makeup to understand how its genes determine plant performance in farmers’ fields. After centuries of plant domestication and breeding, many valuable traits that were present in rice’s wild relatives have been eliminated from modern varieties. McCouch seeks to dig up those genes and bring them back into circulation in new varieties.
To do this requires a lot of basic genetics research. McCouch has received funding from the U.S. Department of Agriculture (USDA) and the National Science Foundation (NSF), among others, to identify targets in the rice genome that imbue valuable traits, including resistance to diseases, insects, and environmental stress; eating quality of the grain; and plant architecture.
In a project for the Global Crop Diversity Trust, McCouch looks to tap the genetics of ancestral populations of wild rice. During fall 2015, McCouch will be on sabbatical to work on strategies for enhancing the utility of gene banks that contain millions of wild and cultivated strains of plants.
“We don’t really know much about what’s in these gene banks,” says McCouch. “It’s like not having a card catalog in a library full of books. We’re developing a plan for how to go about sequencing and phenotyping these collections to make them more useful for breeding.”
In another project, McCouch and collaborator Leon Kochian, USDA-ARS and Plant Biology, demonstrated how a rice gene functioned to make rice resilient against soil aluminum toxicity. In a study published in the Proceedings of the National Academies of Science in April 2014, Kochian and McCouch explained how the NRAT1 gene transports aluminum from outside the root, through the root cell wall into the cell, and how variations of the gene affect the plant’s ability to prevent toxicity.
The work is important not only for rice; it can also be translated to other crops where aluminum toxicity is a major problem, including wheat and maize.
For the last eight years, the NSF has funded the Rice Diversity Project, a collaborative research effort between researchers at Cornell, the USDA, and the International Rice Research Institute in the Philippines. The project explores natural genetic variation in rice and its wild ancestors. McCouch is principal investigator (PI) on the project.
Researchers on the project developed a rice diversity research platform that allows people to conduct genome-wide association studies, matching genotype with phenotype, using a suite of publicly available tools and resources. The overall objective is to understand the genetic basis of quantitative variation in rice, and to make it easier for breeders to find and utilize novel genetic variation in plant improvement.
Genetic Discovery and Field Breeding
For McCouch, basic science is intriguing and essential, but translating scientific discoveries into knowledge that people can use to improve their lives is a source of particular satisfaction.
More efforts to closely connect genetic discovery and field breeding are underway. The Bill and Melinda Gates Foundation has recently provided $18.5 million to a team of Cornell plant breeders, computer scientists, and software engineers to develop new tools that will facilitate more efficient breeding strategies for five of the world’s major staple foods: rice, wheat, maize, chickpeas, and sorghum.
McCouch serves as the PI on the project and is working with an interdisciplinary group of researchers, including Edward Buckler, USDA-ARS and Plant Breeding and Genetics; Qi Sun, Computational Biology Service Unit; Jean Luc Jannink, USDA-ARS and Plant Breeding and Genetics; Lukas Mueller, Boyce Thomson Institute; and Mark Sorrells, Plant Breeding and Genetics. The program will work closely with three international breeding centers in India, the Philippines, and Mexico and will operate from a centralized hub at Cornell.
It’s a new concept for the public-sector crop-breeding world, which is typically separated by geographically disparate breeding centers and crop species. But given the developments in genomics and information technology, it’s possible to link breeding centers everywhere.
The research group aims to develop tools that will allow plant breeders to look at the genetic profiles of their breeding lines and to model the agronomic performance of each line based on genomic prediction.
“We aim to employ genomic strategies to facilitate the delivery of productive, stress-tolerant crop varieties to farmers in the developing world.”
“We aim to predict which lines are likely to give rise to the best offspring and to eliminate the worst lines based on genomic information,” says McCouch. “It will allow the breeder to shorten the breeding cycle and focus efforts on the most promising lines, given that field-based evaluation is more expensive and time-consuming than genotyping the same lines. The objective is to increase the rate of genetic gain.”
Another goal is to encourage public breeding programs to work together to incorporate genomic prediction models into their field-breeding programs. These efforts will, in turn, feed information back that will contribute to the development of better models.
It’s a long-term, multi-institutional collaboration that promises to solve problems using an iterative approach, learning together every step of the way, McCouch explains.
“What I hope to do before my career winds down is to take the dream that we had 30 years ago and make it a reality,” says McCouch. “We aim to employ genomic strategies to facilitate the delivery of productive, stress-tolerant crop varieties to farmers in the developing world who are struggling to make a living in very challenging environments.”
Mimicking Nature to Derive Something New from Something Old
When asked why she pursued plant breeding given her literature and history undergraduate degree, McCouch says that it “fit like a glove.”
“My intellectual underpinning is steeped in the concept of things evolving from what comes before—be it language, culture, or plant genetics,” says McCouch. When she ventured into plant breeding, she says that she loved the fact that it was basically a process of accelerated evolution. “We observe and evaluate diverse populations that exist today, make crosses between individuals to recombine their traits, and through this process, we mimic nature to derive something new from something old,” she explains.
In the same way, McCouch’s research has evolved over the decades with changing technologies. In a new NSF-funded project, McCouch will work with Adam Bogdanove, Plant Pathology and Plant Microbe Biology, to apply the new genetic editing tool, CRISPR, to rice.
“The hope is that using CRISPR technology, allele substitution will be faster and more targeted than using backcross breeding, and won’t require disrupting the whole genetic background,” says McCouch. “You’ll be able to make a very specific genetic change in a known location in the genome, and it will be much less disruptive than transgenic technology.”
McCouch’s previous work has laid a strong foundation for knowing which genes in rice are most important to target, and what kind of allelic substitutions will be beneficial.
McCouch is also aware of the need for interdisciplinarity, and she works closely with statisticians, computational biologists, and computer scientists. “We’re more and more dependent on large data processing and analytical capability to understand the quantitative nature of genetic variation,” says McCouch, who today also advises in the graduate field of Computational Biology.
With new genetic and computational technologies, McCouch maintains the importance of being connected to the people who need it most. “If we forget the human dimension as we try to translate scientific discoveries into more productive plant varieties, we’re going to get it wrong,” she says. “We need a feedback loop that connects us very closely to the communities we’re serving.”