When Urban Pollinator Gardens Meet Native Plant Communities

Public concern about the state of bees and other pollinating insects has led to increased interest in pollinator gardens. Planting a pollinator garden is often promoted as an excellent way for the average person to help protect pollinators. And it is! However, as with anything in life, there can be downsides.

In many urban areas, populations of native plants remain on undeveloped or abandoned land, in parks or reserves, or simply as part of the developed landscape. Urban areas may also share borders with natural areas, the edges of which are particularly prone to invasions by non-native plants. Due to human activity and habitat fragmentation, many native plant populations are now threatened. Urban areas are home to the last remaining populations of some of these plants.

Concern for native plant populations in and around urban areas prompted researchers at University of Pittsburgh to review some of the impacts that urban pollinator gardens may have and to develop a “roadmap for research” going forward. Their report was published earlier this year in New Phytologist.

Planting a wildflower seed mix is a simple way to establish a pollinator garden, and such mixes are sold commercially for this purpose. Governmental and non-governmental organizations also issue recommendations for wildflower, pollinator, or meadow seed mixes. With this in mind, the researchers selected 30 seed mixes “targeted for urban settings in the northeastern or mid-Atlantic USA” to determine what species are being recommended for or commonly planted in pollinator gardens in this region. They also developed a “species impact index” to assess “the likelihood a species would impact remnant wild urban plant populations.”

A total of 230 species were represented in the 30 seed mixes. The researchers selected the 45 most common species for evaluation. Most of these species (75%) have generalized pollination systems, suggesting that there is potential for sharing pollinators with remnant native plants. Two-thirds of the species had native ranges that overlapped with the targeted region; however, the remaining one-third originated from Europe or western North America. The native species all had “generalized pollination systems, strong dispersal and colonization ability, and broad environmental tolerances,” all traits that could have “high impacts” either directly or indirectly on remnant native plants. Other species were found to have either high dispersal ability but low chance of survival or low dispersal ability but high chance of survival.

This led the researchers to conclude that “the majority of planted wildflower species have a high potential to interact with native species via pollinators but also have the ability to disperse and survive outside of the garden.” Sharing pollinators is especially likely due to super-generalists like the honeybee, which “utilizes flowers from many habitat types.” Considering this, the researchers outlined “four pollinator-mediated interactions that can affect remnant native plants and their communities,” including how these interactions can be exacerbated when wildflower species escape gardens and invade remnant plant communities.

photo credit: wikimedia commons

The first interaction involves the quantity of pollinator visits. The concern is that native plants may be “outcompeted for pollinators” due to the “dense, high-resource displays” of pollinator gardens. Whether pollinator visits will increase or decrease depends on many things, including the location of the gardens and their proximity to native plant communities. Pollinator sharing between the two has been observed; however, “the consequences of this for effective pollination of natives are not yet understood.”

The second interaction involves the quality of pollinator visits. Because pollinators are shared between native plant communities and pollinator gardens, there is a risk that the pollen from one species will be transferred to another species. High quantities of this “heterospecific pollen” can result in reduced seed production. “Low-quality pollination in terms of heterospecific pollen from wildflower plantings may be especially detrimental for wild remnant species.”

The third interaction involves gene flow between pollinator gardens and native plant communities. Pollen that is transferred from closely related species (or even individuals of the same species but from a different location) can have undesired consequences. In some cases, it can increase genetic variation and help address problems associated with inbreeding depression. In other cases, it can introduce traits that are detrimental to native plant populations, particularly traits that disrupt adaptations that are beneficial to surviving in urban environments, like seed dispersal and flowering time. Whether gene flow between the two groups will be positive or negative is difficult to predict, and “the likelihood of genetic extinction versus genetic rescue will depend on remnant population size, genetic diversity, and degree of urban adaptation relative to the planted wildflowers.”

The fourth interaction involves pathogen transmission via shared pollinators. “Both bacterial and viral pathogens can be transmitted via pollen, and bacterial pathogens can be passed from one pollinator to another.” In this way, pollinators can act as “hubs for pathogen exchange,” which is especially concerning when the diseases being transmitted are ones for which the native plants have not adapted defenses.

photo credit: wikimedia commons

All of these interactions become more direct once wildflowers escape gardens and establish themselves among the native plants. And because the species in wildflower seed mixes are selected for their tolerance of urban conditions, “they may be particularly strong competitors with wild remnant populations,” outcompeting them for space and resources. On the other hand, the authors note that, depending on the species, they may also “provide biotic resistance to more noxious invaders.”

All of these interactions require further investigation. In their conclusion, the authors affirm, “While there is a clear potential for positive effects of urban wildflower plantings on remnant plant biodiversity, there is also a strong likelihood for unintended consequences.” They then suggest future research topics that will help us answer many of these questions. In the meantime, pollinator gardens should not be discouraged, but the plants (and their origins) should be carefully considered. One place to start is with wildflower seed mixes, which can be ‘fine-tuned’ so that they benefit our urban pollinators as well as our remnant native plants. Read more about plant selection for pollinators here.

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Growing Plants in Outer Space

Last December I wrote about a mission to the moon that will involve growing plants to determine how they will perform in a lunar environment. That mission is still at least a year away. In the meantime, research involving plant growth in space continues onboard the International Space Station (ISS). Numerous experiments have been carried out so far with the general aim of observing the effects of microgravity and other extraterrestrial environmental factors on plant growth. The larger aim, of course, is to develop methods for growing food in space in order to feed future space travelers as they colonize other celestial bodies, such as the Moon and Mars. Providing oxygen and contributing to psychological well-being are additional benefits of growing plants in space.

International Space Station (photo credit: wikimedia commons)

International Space Station (photo credit: wikimedia commons)

Several weeks ago a spacecraft returned to Earth from ISS carrying samples and data from a variety of studies, including a plant study being carried out by the University of Wisconsin-Madison’s Department of Botany. The study consisted of three groups of Arabidopsis thaliana – a wild type group, a group with a gene involved in gravity sensing always turned on, and a group with that same gene always turned off. The plants were grown from seed on petri dishes, and the seedlings (totaling 1000 plants) were returned to Earth after a few weeks of growth. The petri dishes were placed in deep freeze upon returning to Madison. Eventually, RNA will be extracted from each of the plants and analyzed.

Arabidopsis thaliana is a plant in the mustard family (Brassicaceae) that is commonly used in biological studies because it is fast growing with a short life cycle – it germinates, flowers, and produces seed in about 6 weeks  – and it has a relatively small genome that has been completely mapped. This makes it ideal for studies like this one that aim to observe genes involved in responding to particular environmental factors – in this case microgravity.

Arabidopsis thaliana (photo credit: www.eol.org)

Arabidopsis thaliana (photo credit: www.eol.org)

Plants grown in the weightlessness of space get long, spindly, and weak. Plants grown on Earth in a protected environment without mechanical stresses like wind or rain are more susceptible to pests and diseases compared to those that are subject to such disturbances. It turns out that there is a gene that codes for a protein that senses gravity, and this same protein senses other mechanical stresses as well. This means that studies that help advance the science of growing plants in space could also help improve crop plants here on Earth.

The RNA extracted from the Arabidobsis plants recently returned from space will not only aid in the research being done at UW-Madison, but will also become part of a much larger body of research through NASA’s GeneLab. Access to space is limited, so GeneLab makes available the data recovered from studies like this one to anyone interested in doing studies of their own. The GeneLab will also make it possible to compare the Arabidopsis groups in this study to several other Arabidopsis ecotypes, which will aid in determining plants best suited for microgravity environments.

Read more about this study at NASA, Science Daily, and Plants in Microgravity (a blog produced by Simon Gilroy’s Lab, Department of Botany, UW-Madison). Also, “plants in space” has a Wikipedia page

Speaking of Food: A Recap

The theme for the past 15 posts has been the October 2014 Special Issue of American Journal of Botany, Speaking of Food: Connecting Basic and Applied Plant Science. After a brief introduction to the issue, I spent the next 14 posts (spanning a period of 5 weeks) reading and writing summaries of each of the 17 articles. If you actually read every post, you are a champion in my eyes, and I probably owe you a prize of some sort. And even if you just read one or two, thank you, and I hope you found value in what you read.

I have to admit that it was kind of a grueling process. Many of the articles, along with being lengthy, included high level discussions that were beyond my current understanding, especially concerning topics like genetics, genomics, and phylogenetics. I learned a lot while reading them, but I am still far from truly grasping many of the concepts. For that reason, I did not feel completely comfortable writing summaries of some of these discussions. I made an effort not to misrepresent or oversimplify the research, but I can’t say for sure that my attempts were always successful. I welcome any criticisms, corrections, complaints, or comments in this regard, and I am open to making edits or updates to any of the posts as necessary. I consider this blog my learning platform, as well as a place to share my phyto-curiosity. Perhaps you find it a place for learning, too?

The main purpose of this post is to provide a Table of Contents for the last 14 posts, something that will make it easier to navigate through this series without having to scroll through each post. If you are interested in reading the entire series (again, you’re a champion), you can access them all in order here by clicking on the titles. Otherwise, you can pick and choose whatever topics interest you the most.

  • On the Origins of Agriculture – A deep dive into plant domestication and the beginnings of agriculture, including the revision of theoretical approaches to thinking about the history of plant domestication and a discussion of emerging methods and tools for exploring early domestication and emerging agriculture.
  • The Legacy of a Leaky Dioecy – Does pre-Colombian management of North American persimmon trees explain why non-dioecious individuals are found in an otherwise dioecious species?
  • Dethroning Industrial Agriculture: The Rise of Agroecology – The environmentally devastating effects of industrial agriculture can and must be replaced by a more sustainable, ecologically-focused from of agriculture. This will require reforming our economic system and rethinking our “one size fits all” approach to scientific research.
  • An Underutilized Crop and the Cousins of a Popular One – Safflower, an underutilized oilseed crop, could be improved by introducing genes from wild relatives. Soybean, a very popular and valuable crop, could also be improved by introducing genes from its perennial cousins.
  • Carrots and Strawberries, Genetics and Phylogenetics – An exploration of the genetics and phylogenetics of carrots and strawberries. Better understanding of their genetics will aid in crop improvements; better understanding of their phylogenetics gives us further insight into the evolution of plants.
  • Exploring Pollination Biology in Southwestern China – A fascinating look at the pollination biology of edible and medicinal plants in southwestern China, revealing significant gaps in scientific understanding and the need for conservation and continued research.
  • Your Food Is a Polyploid – Polyploidy is more prevalent in plants than we once thought. This article examines the role of polyploidy in crop domestication and future crop improvements.
  • Tales of Weedy Waterhemp and Weedy Rice – How agriculture influenced the transition to invasiveness in two important weed species.
  • Cultivated Sunflowers and Their Wild Relatives – An investigation into the flowering times of wild sunflowers reveals potential for improvements in cultivated sunflowers.
  • The Nonshattering Trait in Cereal Crops – Is there a common genetic pathway that controls the shattering/nonshattering trait in cereal crops?
  • Apples and Genetic Bottlenecks – Domestication generally leads to a loss of genetic variation compared to wild relatives, but apples have experienced only a mild loss. That loss may increase as commercial apple production relies on fewer and fewer cultivars.
  • Improving Perennial Crops with Genomics – The nature of perennial crops can be an impediment to breeding efforts, which makes the introduction of new perennial crop varieties both time consuming and costly. Advances in genomics may help change that.
  • Using Wild Relatives to Improve Crop Plants – Crop plants can be improved through the introduction of genes from wild relatives. They could potentially experience even greater improvement through systematic hybridization with wild relatives.
  • Developing Perennial Grain Crops from the Ground Up – Some of the environmental issues resulting from agriculture could be addressed by switching from annual to perennial grain crops, but first they must be developed from wild species.
A small harvest of sweet potatoes (Ipomoea batatas ' Hong Hong') from this year's backyard mini-farm. Ipomoea batatas ' Hong Hong.'

A small harvest of sweet potatoes (Ipomoea batatas ‘ Hong Hong’) from this year’s backyard mini-farm.

If I had to pick a favorite article in this issue it would be Think Globally, Research Locally: Paradigms and Place in Agroecological Research (Reynolds et al.). I know I said it in the post, but this article really sums up the reasons why this special issue of AJB is so important. Humans are incredibly resourceful, creative, and resilient, and as we have spread ourselves across the globe and grown our population into the billions, we have found ways to produce enormous amounts of food relatively cheaply. Frankly, the fact that anyone is going hungry or dying of starvation is shameful and appalling as there is plenty of food to go around…for now. But we are doing a lot of things wrong, and the earth is suffering because of it. If the biosphere is in trouble, we are all in trouble. Thus, we are overdue for some major shifts in the way we do things, particularly agriculture as that’s what this series of posts is all about. I advocate for science-based sustainable agriculture, and I am hopeful, thanks to this issue of AJB and other signs I’ve seen recently, that we are moving more in that direction. I’ll step off my soapbox now and leave you with an excerpt from the article by Reynolds, et al.

“There is increasing recognition that the current industrial model of agricultural intensification is unsustainable on numerous grounds. Powered by finite and nonrenewable stores of fossil fuels over the last 200 years, humans have come to see themselves, their technology, and their built environments as controllers of nature rather than interdependent with it, even as our activities threaten to exceed planetary boundaries of resilience in multiple environmental dimensions, such as climate, biodiversity, ozone, and chemical pollution. … In the ‘full world’ we now live in, continuing to use high input, highly polluting methods of food production to support continued economic growth is counterproductive to achieving food security. Continued growth of population and per capita consumption on a finite planet fails to meet the basic requirement of sustainability, that of meeting needs within the regenerative and assimilative capacity of the biosphere. And prolonging the shift to a sustainable economic paradigm risks a harder landing.”

Developing Perennial Grain Crops from the Ground Up

This is the fourteenth in a series of posts reviewing the 17 articles found in the October 2014 Special Issue of American Journal of Botany, Speaking of Food: Connecting Basic and Applied Science.

Useful Insights from Evolutionary Biology for Developing Perennial Grain Crops by Lee R. DeHaan and David L. Van Tassel

The environmental impacts of modern agriculture are diverse and extensive. Our growing population needs to be fed; however, practices that have long-term negative effects on soil, water, and air quality are unsustainable. It is imperative that we find better alternatives. Developing perennial grain crops is one way that plant breeders are working to address this issue.

Moving from annual to perennial grain crops could potentially “increase water quality, reduce soil erosion, increase soil carbon, and improve habitat for wildlife.” It may also help “address the looming challenges of land degradation, food security, energy supply, and climate change.” Sounds like a major win if we can do it, right? And maybe we will, but first we must domesticate perennial grain varieties that perform on a similar level with annual ones. Most plant breeding today involves “improvement of previously domesticated species;” however, new perennial grain crops must be developed “de novo” (i.e. from wild species) in a matter of “decades rather than centuries to millennia.”

The roots of perennial grasses are considerably more extensive than annual grasses. (photo taken from an article about perennial grain crops at nationalgeographic.com)

The roots of perennial grasses are considerably more extensive than annual grasses, which helps reduce erosion and limits the need for fertilizer applications. (photo taken from an article about perennial grain crops at nationalgeographic.com)

Little has been published concerning “strategies for the wholesale remodeling of plants,” and so the authors reviewed findings in other fields, such as evolutionary biology and population genetics, in order to devise strategies for developing perennial grain crops. In this article, the authors summarize the published research they reviewed and describe how it relates to breeding perennial grains. It is a dense and lengthy article, so rather than offering a thorough review, I will briefly describe some of the main areas explored by the authors and then summarize their conclusions.

  • Trade-offs – This occurs when “resources allocated to one trait are unavailable for other traits.” Can perennial grain crops achieve yields comparable to annual varieties when faced with “trade-offs between seed and perennial organs?” Are such yields only attainable by “sacrificing longevity?” Strategies must be devised to “create herbaceous perennial crops with abundant seed production.”
  • Genetic Loads – This is simply defined as “the presence of deleterious alleles in a population.” In perennials, compared to annuals, “highly recessive deleterious alleles can arise at a rate faster than they can be efficiently eliminated.” Low seed set, among other things, may be a result of genetic load, so breeders of perennial grains must “account for and actively reduce genetic load.”
  • Bottlenecks – This refers to the loss of genetic diversity that occurs when population size is reduced. During a bottleneck, “previously rare deleterious recessive genes” can accumulate; however, some models indicate that “inbreeding and the associated bottlenecks may be useful in accelerating domestication.” If the population is isolated and introduced to a new environment simultaneously, “the newly exposed variation could now be adaptive.” Also, “if additional genetic diversity is required,” crosses can be made with wild populations.
  • Pleiotropy – This means that “a single gene [is] affecting multiple traits.” When domesticating wild species, “it would be useful to predict the prevalence of pleiotropy and whether to expect positive or negative pleiotropy to dominate.”
  • Epistatsis – This occurs when the effect of one gene is dependent on the presence of another gene or genes. This is particularly important if “large-effect genes” (pleiotropy) are dependent on a “particular genetic background to function optimally,” because “removing one critical element will severely impact the whole structure.” Perennial grain crops will have to undergo “many generations of plant breeding” in order to ensure that desired genes are found “within a genetic background where their benefits can be used without negative side effects.”
  • Cryptic Variation – Genetic variation is cryptic when “the inheritance of a particular mutated allele has no effect on phenotype and thus is hidden from natural and artificial selection.” New environments or mutations can release cryptic variation. “Ranking candidate species for their likely domesticability” may be an effective approach to cryptic variation. “The best candidates for domestication” originate from areas where conditions are highly favorable for growth and reproduction as opposed to areas that are “resource-limited,” because they have experienced periods of “selective enrichment” that make them suitable for agriculture settings.
  • Past Domestication – Domestication involves a series of “evolutionary changes that may decrease the fitness of a species in the wild but increase it under human management.” Historically this was “likely driven by unconscious selection pressures,” but currently it is “driven by conscious selection.” Studies of past domestication events reveal “somewhat predictable stages” in the process. Even though “current domestication efforts might not follow historical precedent,…the order in which traits are subjected to strong selection may be important.” Investigation into domestication also suggests that “dramatic changes” in plant morphology can be accomplished by selection for a “small number of major-effect genes,” so breeding programs are advised to “first search for useful major genes and evaluate their effects before moving on to strategies designed to accumulate genes of small effect.”
  • Selection – The authors describe “four major limits to selection.” 1.) Desired traits “may only exist in our imagination.” 2.) “The necessary genetic variation may not exist in the population,” and so waiting for or inducing mutations may be required. 3.) There may be “negative genetic correlations between characters being selected,” which will slow response to selection. This can be addressed by subdividing the population, evaluating the population in a new environment, or crossing with other populations. 4.) Conversely, “insufficient genetic correlation between traits may reduce the response to selection.” This makes “finding superior genotypes challenging,” so the authors suggest breeding plants in a “uniform environment,” and then later the plants can “accumulate genes for tolerance to specific stresses in separate populations.”
Intermediate wheatgrass (Thinopyrum intermedium) "produces much larger seeds in the greenhouse during the winter than ever seen in the field during the summer," an example of phenotypic plasticity. (photo credit: www.eol.org)

Intermediate wheatgrass (Thinopyrum intermedium) “produces much larger seeds in the greenhouse during the winter than ever seen in the field during the summer,” an example of phenotypic plasticity. (photo credit: www.eol.org)

The authors determined that the best candidates for perennial grain breeding programs are plant populations that have high diversity between and within individual plants, plastic phenotypes (i.e. adaptable to changes in the environment), and “an evolutionary history that includes adaptation to high resource environments.” They also suggest that breeders “focus more on the required functions [like nonshattering fruits] than on morphological traits” because it will increase the feasibility of evaluating “very large experimental populations.” The ideal experimental set-up would consist of very large populations of widely spaced plants that are subdivided in order to perform evaluations from various angles. Lastly, the authors encourage breeders to embrace new plant forms and breeding strategies and be open to the possibility that perennial grain crops may not “look like modern annual grains.”

Using Wild Relatives to Improve Crop Plants

This is the thirteenth in a series of posts reviewing the 17 articles found in the October 2014 Special Issue of American Journal of Botany, Speaking of Food: Connecting Basic and Applied Science.

Back to the Wilds: Tapping Evolutionary Adaptations for Resilient Crops through Systematic Hybridization with Crop Wild Relatives by Emily Warschefsky, Varma Penmetsa, Douglas R. Cook, and Eric J. B. von Wettberg

The nature of domestication involves the narrowing of genetic diversity through a series of crosses and selections that results in organisms well suited for particular environments and/or purposes. In the short term, this arrangement seems to suit our needs, that is until the climate shifts, novel pests and diseases invade, agricultural soils become degraded, or some other calamity ensues. Then we must select a new form to take the place of the old one that is no longer suitable. Additionally, the varieties currently in use may be doing well within their current parameters, but their performance may be found lacking if placed in different environments or grown in alternate systems, such as one that relies on fewer petrochemical inputs.

The wild relatives of crop plants have a long history of being used in breeding programs to provide specific traits for improving domesticated varieties. Interest in this has increased thanks to technological advancements (such as marker-assisted selection and genomic selection) and the greater availability of germplasm. Introgression (the transfer of genes from one species to another through hybridization and repeated backcrossing) using crop wild relatives has mainly been aimed at introducing traits like resistance to specific pests and diseases, tolerance of certain abiotic stresses, and greater yields. In other words, crop wild relatives are typically screened for a few main traits that might be useful in breeding programs, neglecting the possibility that the introgression of a larger suite of traits may be beneficial long-term.

This article discusses the possibility of using “crop wild relative collections that [have been] systematically built to represent the range of adaptations found in natural populations” to improve crop plants. By using these “purpose-built populations that are hybrids between crops and their wild relatives,” crop plants introgressed with “full sets of wild diversity” will be better adapted to a wide variety of environments, soils, climates, and agricultural systems. In order to “illustrate the gains that are possible,” the authors review published studies of hybridization (both naturally occurring and human mediated). They then “propose a multi-step framework for utilizing naturally occurring variation in wild relatives of crops.”

Grapefruit (Citrus x paradisi) - A hybrid between sweet orange (Citrus sinensis) and shaddock (Citrus maxima) that "occurred far beyond the region of domestication and rather recently [the 18th centruy]." (photo credit: wikimedia commons)

Grapefruit (Citrus x paradisi) – A hybrid between sweet orange (C. sinensis) and shaddock (C. maxima) that “occurred far beyond the region of domestication and rather recently [the 18th century].” (photo credit: wikimedia commons)

Hybridization can occur between two individuals of different cultivars, varieties, subspecies, species, genera, etc. The genetics of the resulting offspring is a combination of the two parents, and depending on the circumstances, a hybridization event “can have drastically different consequences.” For this reason, “hybridization is thought of as both a creative and a restrictive force in evolution.” It is, however, “the potential for the production of novelty that makes hybridization such an intriguing – and potentially useful – phenomenon.”

In their discussion of hybridization between crops and their wild relatives, the authors reveal some “obstacles that limit the use of wild relatives in breeding programs.”

  • Poor Agronomic Performance – “Crop wild relatives often lack important domestication traits.” They may have shattering pods, irregular germination timing, or phenologies that inhibit their use in certain regions.
  • Poor Representation in Germplasm Collections – “Only 2-6% of international germplasm collections are of crop wild relatives.” There are some crop wild relatives that are well-represented, but others have been “poorly collected” or “almost ignored,” and some crops still “lack well-identified wild relatives.” One reason for this disparity is that a large number of these plants “occur in geopolitically unstable areas where collection has long been complicated.”
  • Unpredictability of Phenotypes – “Phenotypes of wild individuals are often assessed in agricultural settings, a largely uninformative practice when the overall wild phenotype is specifically adapted for fitness in the wild but not cultivated settings.” This makes for an inaccurate comparison with domesticated varieties, so when “crop-wild hybrids” are formed, phenotypes are hard to predict. Backcrossing is necessary in order to recover the “essential crop phenotype” while capturing the desired traits of the wild relative.

The authors also highlight the need for conservation of crop wild relatives, as “these species are nearly universally threatened.” The catalog of threats to their survival is similar to so many other threatened species: the loss, fragmentation, and degradation of habitats, climate change, invasive species, and over-harvesting (“in the case of medicinally and pharmaceutically useful species”). One threat, perhaps ironically, is agricultural crops crossing with nearby wild relatives, especially where transgenic genes in crops are being transferred to wild populations. In order to better realize the potential that crop wild relatives have in improving domesticated varieties, they must first be protected in their natural habitats.

Desert sunflower (Helianthus deserticola) - One of three hybrid species born of H. annuus and H. petiolaris, "highlighting the expanded potential of hybrid species...through colonization of extreme habitats where neither parental species can survive." (photo credit: www.eol.org)

Desert sunflower (Helianthus deserticola) – One of three hybrid species born of H. annuus and H. petiolaris, “highlighting the expanded potential of hybrid species…through colonization of extreme habitats where neither parental species can survive.” (photo credit: www.eol.org)

The authors propose a 5 step plan for systematic utilization of crop wild relatives in agricultural breeding programs. The steps include building a comprehensive collection of crop wild relatives, sequencing their genomes, creating purpose-driven hybrid populations between wild relatives and crop plants, developing a predictive network of genotype-phenotype associations, and deploying identified phenotypes into crop breeding efforts. This article is one of the open access articles in this issue. If you are interested in this topic, including this 5 step plan, I encourage you to read the article to learn more. 

Improving Perennial Crops with Genomics

This is the twelfth in a series of posts reviewing the 17 articles found in the October 2014 Special Issue of American Journal of Botany, Speaking of Food: Connecting Basic and Applied Science.

Genomics: A Potential Panacea for the Perennial Problem by Kendra A. McClure, Jason Sawler, Kyle M. Gardner, Daniel Money, and Sean Myles

Compared to annuals, a small but significant portion of our food comes from perennial crop plants. “Approximately one eighth of the world’s total food-producing surface area is dedicated to perennials,” and while that may seem relatively small, there is a good chance that some of your favorite things to eat or drink are perennial crops (apples, bananas, coffee, citrus, sugar cane, coconut, avocados, olives, grapes, cherries, almonds…just to name a few). However, making improvements to and introducing new cultivars of perennial crops is considerably more challenging compared to annual crops simply due to the nature of perennials. This puts perennial crops at greater risk to threats like pests and diseases, climate change, soil degradation, and water and land shortages. Advances in genomics, “the collection and use of DNA sequence information,” could change this.

Because breeding efforts to improve perennial crops is so challenging, “only a small number of elite varieties become popular, and the amount of genetic diversity represented by commercially successful cultivars is therefore often low.” This suggests that there is incredible potential for improvement in these crops, as long as major hurdles can be overcome. Following is a list of some of those hurdles:

  • Time – Most perennial crops have “extended juvenile phases,” meaning they won’t produce fruit for as much as ten years, considerably delaying evaluation of the final product.
  • Space – Perennial crops, especially trees, are large compared to annual crops, so the area required for evaluation is extensive.
  • Infrastructure – “Many perennials require trellis systems, extensive land preparation, and substantial costs for specialized equipment and skilled horticultural labor.”
  • Complex Evaluations – Automated assessments are “either unavailable or poorly developed,” so evaluations that include “size, shape, color, firmness, texture, aroma, sugars, tannins, and acidity” require “tasting panels” to ensure that the final product “satisfies consumer demands.” This process is expensive, and it differs depending on whether the crop will be consumed fresh or processed.
  • Vegetative Propagation – “Many perennials suffer from severe inbreeding depression when selfed,” so cultivars are maintained through vegetative propagation. This is a plus, because it means that the fruits of perennial crops are reliably uniform, so growers and consumers know what to expect year after year. However, this also means that while pests and pathogens evolve, the crops do not, making them more susceptible to such threats. Additionally, the “long histories” of certain cultivars “discourages [growers] from undergoing the risk of trying recently developed cultivars.”
  • Consumer Preferences – “Consumers often exhibit an irrational reverence for ancient or heirloom varieties,” despite the fact that the development of new varieties can result in crops that are higher yielding, resistant to pests and diseases, tastier, more nutritious, more suitable for storage, and require fewer chemical inputs. This obsession with traditional varieties leaves a “tremendous amount of untapped genetic potential for the improvement of perennial crops.”
"Modern avocado breeding still depends heavily on open-pollination because of the difficulty associated with making controlled crosses." (photo credit: wikimedia commons)

“Modern avocado breeding still depends heavily on open-pollination because of the difficulty associated with making controlled crosses.” (photo credit: wikimedia commons)

Apart from issues of social and cultural preference, the challenge of breeding perennial crops comes down to time and money. Advances in genomics can help offset both of these things. Using DNA-based predictions, a plant’s phenotype can be determined at the seed or seedling stage. Genomics techniques can also be “used to reduce the generation time thereby enabling combinations of desirable traits to be combined on a timescale that is more similar to annual crops.” Below are summaries of specific areas discussed in the paper for using genomics in perennial crop breeding programs:

  • Reduction of Generation Time – This can be done using transgenic technology in ways that do not result in transgenic (GMO) cultivars. One method uses virus-induced gene silencing, in which a host plant is infected with “a virus that is genetically modified to carry a host gene;” the host plant then “attacks itself and uses its own endogenous system to silence the expression of one of its own genes.” Early flowering in apples has been induced after seedlings were inoculated with apple latent spherical virus that expresses a flowering gene derived from Arabidopsis thaliana.
  • Genetic Modification – Advances in genomics have brought us transgenic technology, and several commercial crops have been genetically modified using this technology. Most of them are annuals, but one perennial in particular, SunUp papaya, has been a major success. Its resistance to ringspot virus rescued the papaya industry from a devastating pathogen that “almost completely destroyed the industry in Hawaii.” Consumer disapproval, however, poses a major obstacle to commercial production of genetically modified organisms, and unless this changes, “their widespread use is unlikely.”
  • Marker-Assisted Selection – This is the “primary use of genomics in breeding.” The time between initial plant crosses and the introduction of a new cultivar can be dramatically shortened when genetic markers are used to determine the phenotypes of adult plants at the seedling stage. This technology is also useful when crossing domesticated plants with wild relatives, since genetic markers can be used to determine when desired traits are present in the offspring.
  • Ancestry Selection – After crosses with wild relatives, offspring may “perform poorly because wild germplasm often harbors numerous traits that negatively affect performance.” To overcome this, the offspring is crossed with cultivated plants until undesirable traits are eliminated. This is called backcrossing. Using marker-assisted selection, breeders can “select a small number of offspring in each generation that carry both the desired trait from the wild and the most cultivated ancestry.”
  • Genomic Selection – The success of marker-assisted selection is greatest when used for traits that are controlled by one or a few genes. However, many traits involve a complex set of genes. Genomic selection is a new technique that “uses dense, genome-wide marker data to predict phenotypes and screen offspring.” It is “especially useful for predicting complex traits controlled by many small-effect genes.” Genomic selection is in its infancy, so there are kinks to work out, but it is a promising technology for perennial crop breeding efforts.

The use of genomics will not replace every aspect of traditional perennial crop breeding and “should be viewed as a potential supplement…rather than a substitute.” Geneticists and plant breeders are encouraged to work together to develop and implement these technologies in a concerted effort to improve the crop plants that help feed the world.

"Despite the remarkable phenotypic and genotypic diversity in bananas," the Cavendish banana is responsible for the "vast majority" of banana production. (photo credit: wikimedia commons)

“Despite the remarkable phenotypic and genotypic diversity in bananas,” the Cavendish banana is responsible for the “vast majority” of banana production. (photo credit: wikimedia commons)

Tales of Weedy Waterhemp and Weedy Rice

This is the eighth in a series of posts reviewing the 17 articles found in the October 2014 Special Issue of American Journal of Botany, Speaking of Food: Connecting Basic and Applied Science.

Population Genetics and Origin of the Native North American Agricultural Weed Waterhemp (Amaranthus tuberculatus; Amarantheaceae) by Katherine E. Waselkov and Kenneth M. Olsen

Weeds are “the single greatest threat to agricultural productivity worldwide, costing an estimated $33 billion per year in the United States alone.” Understanding the origins, population structures, and genetic compositions of agricultural weeds will not only help us better mitigate current weed problems but may also help prevent the development of future weed species.

In the introduction, the authors present three modes of weed origination: 1. De-domestication (“domesticated species becoming feral”) 2. Hybridization of domesticated species with related wild species 3. Expansion of wild plants into agricultural ecosystems “through plasticity, adaptation, or exaptation [a shift in function of a particular trait].” In this study, the authors focused on the third mode – the wild-to-weed pathway – claiming that it receives “less attention by evolutionary biologists, even though all weeds without close crop relatives must have followed this pathway to agricultural invasion, and even though this type of weed species is the most common.”  Due to the dearth of research, there are several questions yet to be fully addressed: Does invasion require evolutionary changes in the plant and/or changes in agricultural practices? What is more common, single or multiple wild sources? What are the morphological, physiological, and ecological traits that might “predispose a wild species to expand into agricultural habitats?”

To help answer these questions, the authors turned to waterhemp (Amaranthus tuberculatus), a weed that, since first invading agricultural land in the 1950’s, has “become a major problem for corn and soybean farmers in Missouri, Iowa, and Illinois.” Waterhemp is native to the midwestern United States, where it can be found growing along riverbanks and in floodplains. It is a small seeded, dioecious (“obligately outcrossing”), wind-pollinated, annual plant with fruits that can be either dehiscent or indehiscent. Herbicide resistance has been detected in A. tuberculatus for at least six classes of herbicides, making it a difficult weed to control.

There is evidence that A. tuberculatus was previously in the process of diverging into two species, an eastern one and a western one, geographically separated by the Mississippi River. However, “human disturbance brought the taxa back into contact, and possibly gave rise to the agriculturally invasive strain through admixture.” Using population genetic data, the authors set out to determine if the present-day species would show evidence of a past divergence in progress prior to the 20th century. They also hypothesized that “the agricultural weed originated through hybridization between the two diverged lineages.”

Waterhemp, Amaranthus tuberculatus (photo credit: www.eol.org)

Waterhemp, Amaranthus tuberculatus (photo credit: www.eol.org)

After genotyping 38 populations from across the species range, the authors confirmed that A. tuberculatus was indeed diverging into two species. Today, the western variety (var. rudis) has expanded eastward into the territory of the eastern variety (var. tuberculatus), extending as far as Indiana. Its expansion appears to be facilitated by becoming an agricultural weed. Data did not confirm the hypothesis that the weedy strain was a hybridized version of the two varieties, but instead mainly consists of the western variety, suggesting that “admixture is not a pre-requisite for weediness in A. tuberculatus.”

Further investigation revealed that the western variety may have already been “genetically and phenotypically suited to agricultural environments,” and thus did not require “genetic changes to be successful” as an agricultural weed. “Finer-scale geographic sampling” and deeper genetic analyses may help determine whatever genetic basis there might be for this unfortunate situation.

The Evolution of Flowering Strategies in US Weedy Rice by Carrie S. Thurber, Michael Reagon, Kenneth M. Olsen, Yulin Jia, and Ana L. Caicedo

This paper looks at an agricultural weed that originated from the de-domestication of a crop plant (one of the three modes of weed origination stated above). A weed that belongs to the same species as the crop it invades is referred to as a conspecific weed, and weedy rice is “one of the most devastating conspecific weeds in the United States.”  Oryza sativa is the main species of rice cultivated in the US, and most varieties are from the group tropical japonica. The two main varieties of weedy rice are straw hull (SH) and black-hull awned (BHA), which originated from cultivated varieties in the groups indica and aus respectively. Because weedy rice is so closely related to cultivated rice, it is incredibly difficult to manage, and there is concern that cross-pollination will result in the movement of traits between groups. For this reason, the authors of this study investigated flowering times of each group in order to assess the “extent to which flowering time differed between these groups” and to determine “whether genes affecting flowering time variation in rice could play a role in the evolution of weedy rice in the US.”

Rice, Oryza sativa (illustration credit: wikimedia commons)

Rice, Oryza sativa (illustration credit: wikimedia commons)

Crop plants have typically been selected for “uniformity in flowering time to facilitate harvesting.” The flowering time of weed species helps determine their effectiveness in competing with crop plants. Flowering earlier than crop plants results in weed seeds dispersing before harvest, “thereby escaping into the seed bank.” Flowering simultaneously with crop plants can “decrease conspicuousness, and seed may be unwittingly collected and replanted” along with crop seeds. Simultaneous flowering of weeds and crops is of special concern when the two are closely related since there is potential for gene transfer, especially when the crop varieties are herbicide resistant as can be the case with rice (“60-65% of cultivated rice in [the southern US] is reported to be herbicide resistant”).

For this study, researchers observed phenotypes and gene regions of a broad collection of Oryza, including cultivated varieties, weed species, and ancestors of weed and cultivated species. They found that “SH weeds tend to flower significantly earlier than the local tropical japonica crop, while BHA weeds tend to flower concurrently or later than the crop.” When the weeds were compared with their cultivated progenitors, it was apparent that both weed varieties had “undergone rapid evolution,” with SH weeds flowering earlier and BHA weeds flowering later than their respective relatives. These findings were consistent with analyses of gene regions which found functional Hd1 alleles in SH weeds (resulting in day length sensitivity and early flowering under short-day conditions) and non-functional Hd1 alleles in BHA weeds (“consistent with loss of day-length sensitivity and later flowering under short-day conditions”). However, the authors determined that there is more to investigate concerning the genetic basis of the evolution of flowering time in weedy rice.

In light of these results, hybridization is of little concern between cultivated rice and SH weeds. BHA weeds, on the other hand, “have a greater probability of hybridization with the crop based on flowering time and Hd1 haplotype.” The authors “predict that hybrids between weedy and cultivated rice are likely to be increasingly seen in US rice fields,” which, considering the current level of herbicide resistant rice in cultivation, is quite disconcerting.