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Using Genomics to Unlock the Full Potential of Industrial Hemp

Much of plant breeding and global food production relies on the pollination of flowers to produce fruits that are eaten and used to produce further progeny.

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Plant biologist Alex Harkess, PhD, and his lab at HudsonAlpha Institute for Biotechnology are on a mission to change the future of food and fiber crops, one flowering plant species at a time. Much of plant breeding and global food production relies on the pollination of flowers to produce fruits that are eaten and used to produce further progeny. This process might sound straightforward, but it is actually complicated by the fact that some flowers contain only male or female reproductive organs, others contain both (hermaphrodites), and some can even switch sexes. 

How flowers become male, female, or hermaphroditic is a complex phenomenon. Although not completely understood, it is imperative for crop breeding programs looking to create food and fiber crops better adapted to changing environmental pressures. This is especially true in crop species where one plant sex is more valuable than the other, like female hops that produce cones used in the beer industry, male asparagus plants that live longer in fields, and hermaphroditic papaya fruits that taste better than female fruits. 

While the exact mechanism of sex determination is a mystery in many species, it is widely accepted that genetics plays a major role. Dr. Harkess and the members of his lab are experts at using genomics to understand plant reproduction and the genes that control sex in flowers. Sex-determination genes have only been concretely defined in five plant species, with Harkess playing a critical role in their identification in asparagus.  

Last year, Harkess was awarded a prestigious National Science Foundation (NSF) CAREER grant to characterize sex chromosomes and sex-determining genes across every order of flowering plants. Continuing that momentum, HudsonAlpha, and their collaborators New West Genetics, were recently awarded a United States Department of Agriculture National Institute of Food and Agriculture (USDA-NIFA) grant that aims to unlock the full potential of industrial hemp, a versatile plant used for centuries for a wide variety of purposes. 

New West Genetics is a global leader in creating premium, stable hemp seed genetics that are trait enhanced for sustainability, food, feed, and fiber applications.  For ten years running, the company has built a commercial-scale breeding program across the US and Canada. Applying prior experience from crops like hybrid canola, maize, sorghum, and wheat, the team combines traditional breeding, modern genomics, and agronomic expertise to create non-GMO, proprietary hemp seed bred for multiple markets.

The growing industrial hemp market

Hemp (Cannabis sativa) is an annual flowering plant indigenous to Eastern Asia. It has been cultivated for centuries as a source of industrial fiber, seed oil, food, and medicine. Thanks to popular culture and social media, many people often confuse hemp with its botanical cousin, marijuana, because both are members of the Cannabis family. Unlike marijuana, hemp contains very low levels of tetrahydrocannabinol (THC), the psychoactive compound that produces a “high” when consumed. 

Since hemp was commercially legalized in all 50 states with the passage of the 2018 Farm Bill, the supply chain and demand for grain and fiber products have been steadily building. In addition, ever-increasing data is being published on the higher sustainability marks hemp achieves, with its deep, massive root structure sequestering more carbon than typical row crops and its need for lower inputs and greater drought and pest resistance.  

Hemp is widely recognized for its versatile industrial applications. Its long and durable fibers possess excellent moisture-wicking properties, making them ideal for textiles, building materials, bioplastics, animal bedding, and more. Additionally, hemp seeds are a valuable grain/oilseed crop, offering high levels of protein, healthy fats, and essential nutrients. It is most comparable to the nutrition profile of soy, though its oils are much more nutritious. Hemp seed oil, rich in omega-3 and omega-6 fatty acids, can be used in various edible oil and protein products. This outstanding oil profile, coupled with NWG’s AMPLIFY™ trait, makes it an economically viable candidate for sustainable fuels. 

NWG AMPLIFY, the first commercial, scalable hemp hybrid, genetically skews the sex ratio from its average ancestral ratio of 50:50 female to male to a 90:10 female-to-male ratio. This shift, together with hybrid vigor, results in double the amount of grain and flower yield and more vigor and uniformity overall. 

“NWG AMPLIFY changes the economic dynamics of hemp production, particularly for the grain side,” said Wendy Mosher, New West Genetics CEO. “With double yields of healthy lipids and proteins, we can compete with the economics of soy but with greater carbon sequestration. AMPLIFY enables farmers, ingredient manufacturers, and sustainable fuels processors to adopt a new rotational option that is a much more preferred product by today’s consumers, who express strong preferences for the nutritional value and sustainability of the food they consume.” 

Breeding better industrial hemp for a sustainable source of fiber, proteins, and oil

Hemp is dioecious, having separate male and female sexes. Female hemp plants are typically larger in stature than males and produce more biomass, increasing the yield of hemp fiber per acre. In addition, only female flowers produce seeds that contain high levels of healthy lipids and proteins. For these reasons, hemp breeders want a high percentage of female plants growing in their fields. 

Hemp has an XY sex-determination system, where females have two X chromosomes, and males have an X chromosome and a Y chromosome. Like most XY systems, hemp generally reproduces at a 50:50 male: female ratio. Because the mechanics by which sex is determined in hemp are unknown, breeders currently feminize hemp plants using chemicals to create progeny that is predominantly female. Feminized plants do not make fertile seeds, so the process must be repeated each season. Understanding the genetic mechanism by which plants become male or female would enable genomics-assisted breeding of more female plants without adding chemicals. 

Through their recently awarded USDA NIFA grant, Harkess and his lab aim to build five high-quality hemp genomes that will be used to identify and analyze the hemp sex chromosome pairs. Plant sex chromosomes are hard to identify and difficult to assemble because they differ entirely from species to species. The Harkess lab developed a pipeline called Cytogenetics-by-Sequencing (CBS) to more easily and inexpensively identify and characterize sex chromosomes in plants. They have successfully used the CBS pipeline on nearly 30 dioecious plant and even animal species so far.

“Separate male and female sexes have evolved hundreds if not thousands of times in plants, and finding the genes that control sex determination is so challenging because most plants do it very differently from each other,” said Harkess. “These genes are found on sex chromosomes, which are also the most challenging chromosomes to sequence and assemble in plants. However, with HudsonAlpha’s historical expertise in plant genome sequencing, we are now able to reveal the full complexity of sex chromosomes in species like hemp and finally narrow in on the genes that control this agriculturally and economically valuable trait.”

Using CBS to interrogate the hemp sex chromosomes will allow Harkess and his lab to identify the master sex determination genes in hemp, which can be modified to control sex and increase the proportion of female plants, leading to a higher yield of fiber, oil, and protein. Breeding more female hemp plants will increase the yield and quality of hemp fiber, grain, and oil crops, making it a sustainable and valuable crop for farmers and consumers alike.

“Gaining greater understanding of the genomic basis for gender will be a powerful tool for improving the germplasm,” said John McKay, NWG CTO, and professor of plant genetics at Colorado State University. “We also are curious to see if these discoveries could be instructive for male/female breeding targets in other species, both plant and animal. Working with HudsonAlpha on this grant will be exciting and result in quality research with solid commercial applications.” 

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