By: Audrey Dickinson, Agricultural Genomics Research Specialist
Did you know cranberries are America’s second most consumed berry? Indispensable to Thanksgiving tables, bourgeois salads, and Cosmopolitans alike, they have won the hearts of Americans as a preferred vehicle for sugary enhancement. But cranberry production faces escalating challenges, requiring new research and innovation.
Cranberries are a special case in crop science. Unlike staple cereal crops like wheat and rice, which have been subject to selection for thousands of years of cultivation, cranberries have only been cultivated on farms for around 200 years. Before then, they were gathered from the wild and used for food, dye, and medicine by native people. A formal breeding program focused mainly on disease resistance was established less than 100 years ago, and most commercial cranberry varieties are genetically very close to their wild ancestors. This short period of domestication means that cranberries lack improvements for traits like yield, nutrition, and stress tolerance that have been achieved in other major crops.
As a result of this short domestication history and low selection for environmental stress tolerance, cranberry production is particularly vulnerable to increasing temperature extremes and unpredictable weather patterns brought on by climate change. Both heat waves and unseasonable frosts can damage cranberry plants and fruit, reducing yield and increasing susceptibility to devastating fungal diseases. Increasing resilience to these stressors is a top priority among cranberry producers and breeders. At the San Diego Botanic Garden, in collaboration with the United States Department of Agriculture (USDA) and the Salk Institute for Biological Studies, we are investigating new strategies to increase the resilience of the cranberry crop.
One promising strategy to build resilience in cranberries is to harness the genetic diversity of their crop wild relatives (CWRs): wild plants closely related to cultivated crops that often possess valuable traits lost or underdeveloped in domesticated varieties. In cranberry breeding, our CWR of interest is the wild small cranberry (Vaccinium oxycoccos), which grows at high latitudes in North America and Europe. Though it is better adapted to cold environments, it produces smaller, less commercially desirable fruit. By breeding V. oxycoccos with conventional cranberries (Vaccinium macrocarpon), we aim to combine stress tolerance with high yield, potentially creating new varieties that can persist in a changing climate.
V. oxycoccos, the crop wild relative of cultivated cranberries, growing in the wild.
Fortunately, the two species can interbreed, and USDA scientists have produced a set of hybrids with one parent from each species that we can study with advanced genomic tools. To understand how these hybrids respond at a molecular level to environmental stress, we used RNA sequencing (RNA-seq), a method that distinguishes which genes are active in a plant under various conditions. In a plant, some genes are always “turned on” and present as RNA, whereas others are only turned on in certain conditions. We can sequence and “read” the total RNA in a cell or tissue, then perform analyses that tell us which genes are being turned on and off in response to different treatments.
Using hybridization to bring together desirable traits in cranberry breeding
For our experiment, we exposed conventional cranberry plants as well as cranberry-CWR hybrids to a short heat treatment, and extracted RNA at three different time points. We repeated the experiment with a cold treatment and took more RNA samples. Then, we sequenced the RNA, mapped our sequences to the cranberry genome, and calculated how much each gene was being expressed in each sample. By comparing the RNA profiles of cranberry and cranberry-CWR hybrids exposed to increasing heat and cold stress, we found differences in the behavior of several functional categories.
Cranberries and hybrids in the treatment chamber.
Our findings uncovered encouraging signs of stress resilience in the hybrids. Ribosomal genes, involved in protein production, showed increased expression under heat stress in hybrids, but decreased expression in standard cranberries. Under cold stress, ribosomal gene expression declined in both, but the drop was more pronounced in the cultivated cranberries. Similarly, genes involved in photosynthesis, which allow plants to utilize solar energy, increased expression in hybrids during cold stress but declined in standard cranberries. These patterns suggest that hybrids tend to maintain essential cellular functions during stress whereas standard cranberries shut them down. This characteristic might enable improved survival and yield in unfavorable temperature conditions.
These results highlight the importance of conserving crop wild relatives in their natural habitats and in collections. Crop improvement via CWR hybridization is only possible if there are diverse, healthy populations of plants with valuable genetic variation between individuals that can be adapted for use in agriculture. At SDBG, in addition to working on wild cranberry genomics, we’ve collected and conserved local wild relatives of plums and walnuts. We aim to contribute to the preservation and application of CWR diversity in a world increasingly challenged by climate change and shifting land use.
Our research in CWRs is strengthened by our productive partnership with the Salk Institute, which supports advanced sequencing and bioinformatics efforts at the Garden. Genomics research enhances and accelerates crop breeding by allowing us to identify promising genes or patterns linked to stress tolerance and yield. This research also opens doors to precise gene editing, which could insert beneficial traits directly without lengthy breeding cycles. As environmental change intensifies, these innovations are crucial to sustaining crop productivity amid new and familiar stressors.
Our research on cranberries and their wild relatives reminds us that agriculture must evolve with our changing environment, and that wild genetic diversity is an important natural resource in creating sustainable and resilient food systems. This research complements SDBG’s other efforts in science and conservation, which seek to evaluate and conserve wild plant diversity to support human well-being. While much of our genomics research happens behind the scenes (in my office which is affectionately known as “The Cave” for its windowless insularity), communicating these discoveries is just as important as making them. We value sharing our science with the public because this work is about developing better crops for consumers, and one day, you may find yourself buying elite cranberries bred from USDA–Salk–SDBG hybrids. We look forward to expanding our genomic research in cranberries and other interesting plants while engaging with our community in the years ahead.
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