plants

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Plants Use Mycorrhizal Fungi to Warn Each Other of Incoming Threats

The March 2015 issue of New Phytologist is a Special Issue focusing on the “ecology and evolution of mycorrhizas.” This is the second of two articles from that issue that I am reviewing. Read the first review here.

Interplant signalling through hyphal networks by David Johnson and Lucy Gilbert

When an individual plant is attacked by an insect or fungal pest, it can warn neighboring plants – prompting them to produce compounds that either repel the pests or attract beneficial organisms that can fight off the pests. There are two main pathways for a plant to send these communications: through the air by way of volatile organic compounds (VOC’s) or through the soil by way of a vast collection of fungal hyphae called mycelium. Plant communication by aerial release of VOC’s has been well documented; communication via mycelium, however, is a fairly recent discovery, and there is much left to learn.

“The length of hyphae in the soil and the ability of mycorrhizal fungi to form multiple points of entry into roots can lead to the formation of a common mycelial network (CMN) that interconnects two or more plants.” These CMN’s are known to play “key roles in facilitating nutrient transport and redistribution.” We now understand that they can also “facilitate defense against insect herbivores and foliar necrotophic fungi by acting as conduits for interplant signaling.” The purpose of this research is to explore the “mechanisms, evolutionary consequences, and circumstances” surrounding the evolution of this process and to “highlight key gaps in our understanding.”

interplant signaling

An illustration of plant communication (aka interplant signaling) by air and by soil form the article in New Phytologist.

If plants are communicating via CMN’s, how are they doing it? The authors propose three potential mechanisms. The first is by signal molecules being transported “in liquid films on the external surface of hyphae via capillary action or microbes.” They determine that this form of communication would be easily disrupted by soil particles and isn’t likely to occur over long distances. The second mechanism is by molecules being transported within hyphae, passing from cell to cell until they reach their destination. The third mechanism involves an electrical signal induced by wounding.

If signal molecules are involved in the process, what molecules are they? There are some molecules already known to be transported by fungal hyphae (lipids, phosphate transporters, and amino acids) and there are also compounds known to be involved in signaling between plants and mycorrhizal fungi. Exploring these further would be a good place to start. We also need to determine if specific insect and fungal pests or certain types of plant damage result in unique signaling compounds.

It has been established that electrical signals can be produced in response to plant damage. These signals are a result of a process known as membrane depolarization. “A key advantage of electrical-induced defense over mobile chemical is the speed of delivery.” Movement of a molecule through cells occurs significantly slower than an electrical charge, which is important if the distance to transport the message is relatively far and the plant needs to respond quickly to an invasion. Various aspects of fungal physiology and activity have been shown to be driven in part by membrane depolarization, so involving it in interplant signaling isn’t too far-fetched.

photo credit: wikimedia commons

photo credit: wikimedia commons

How and why does a system of interplant communication involving mycorrhizal fungi evolve? And what are the costs and benefits to the plants and fungi involved? Determining costs and benefits will depend largely on further establishing the signaling mechanisms. Exploring real world systems will also help us answer these questions. For example, in a stable environment such as a managed grassland where CMNs are well developed, a significant loss of plants to a pest or disease could be devastating for the mycorrhizal community, so “transferring warning signals” would be highly beneficial. Conversely, in an unstable environment where a CMN is less established, assisting in interplant signaling may be less of an imperative. Regarding questions concerning the degree of specialization involved in herbivore-plant-fungal interactions: if a “generic herbivore signal” is sent to a neighboring plant that is not typically affected by the attacking herbivore, the cost to the plant in putting up its defenses and to the fungus in transporting the message is high and unnecessary. So, in an environment where there are many different plant species, species-specific signals may be selected for over time; in areas where there are few plant species, a generic signal would suffice.

As research continues, the mysteries of “defense-related” interplant communication via CMN’s will be revealed. Field studies are particularly important because they can paint a more accurate picture compared to “highly simplified laboratory conditions.” One exciting thing about this type of communication is that it may mean that some plants are communicating with each other across great distances, since “some species of fungi can be vast.” CMNs can also target specific plants, and compared to communication via aerial VOC’s, the signal will not be diluted by the wind.

Since I am in the process of reading Robin Wall Kimmerer’s book, Braiding Sweetgrass, I have decided to include her description of a tree-mycorrhizal fungi relationship:

The trees in a forest are often interconnected by subterranean networks of mycorrhizae, fungal strands that inhabit tree roots. The mycorrhizal symbiosis enables the fungi to forage for mineral nutrients in the soil and deliver them to the tree in exchange for carbohydrates. The mycorrhizae may form fungal bridges between individual trees, so that all the trees in a forest are connected. These fungal networks appear to redistribute the wealth of carbohydrates from tree to tree. A kind of Robin Hood, they take from the rich and give to the poor so that all the trees arrive at the same carbon surplus at the same time. They weave a web of reciprocity, of giving and taking. In this way, the trees all act as one because the fungi have connected them. Through unity, survival. All flourishing is mutual.

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Year of Pollination: Hellstrip Pollinator Garden

This month I have been reading and reviewing Evelyn Hadden’s book, Hellstrip Gardening, and I have arrived at the fourth and final section, “Curbside-Worthy Plants.” As the title suggests, this section is a list of plants that Hadden has deemed worthy of appearing in a curbside garden. It’s not exhaustive, of course, but with over 100 plants, it’s a great start. Photos and short descriptions accompany each plant name, and the plants are organized into four groups: showy flowers, showy foliage, culinary and medicinal use, and four-season structure.

This list is useful and fun to read through, but there isn’t much more to say about it beyond that. So I have decided to write this month’s Year of Pollination post about creating a hellstrip pollinator garden using some of the plants on Hadden’s list. Last year around this time I wrote about planting for pollinators where I listed some basic tips for creating a pollinator garden in your yard. It’s a fairly simple endeavor – choose a sunny location, plant a variety of flowering plants that bloom throughout the season, and provide nesting sites and a water source. If this sounds like something you would like to do with your hellstrip, consider planting some of the following plants.

Spring Flowers

Spring flowering plants are an important food source for pollinators as they emerge from hibernation and prepare to reproduce. There are several spring flowering trees and shrubs on Hadden’s list. Here are three of them:

  • Amelanchier laevis (Allegheny serviceberry) – A multi-trunked tree or large shrub that flowers early in the spring. Other small trees or shrubs in the genus Amelanchier may also be suitable.
  • Cercis canadensis (eastern redbud) – A small tree that is covered in tiny, vibrant, purple-pink flowers in early spring.
  • Ribes odoratum (clove currant) – A medium sized shrub that flowers in late spring. Try other species of Ribes as well, including one of my favorites, Ribes cereum (wax currant).

There aren’t many spring flowering herbaceous plants on Hadden’s list, but two that stood out to me are Amsonia hubrichtii (bluestar) and Polemonium reptans (creeping Jacob’s ladder).

Creeping Jacob's ladder (Polemonium reptens) is native to eastern North America and attracts native bees with its mid-spring flowers. (photo credit: www.eol.org)

Creeping Jacob’s ladder (Polemonium reptens) is native to eastern North America and attracts native bees with its mid-spring flowers. (photo credit: www.eol.org)

Summer Flowers

There is no shortage of summer flowering plants, and Hadden’s list reflects that. When planting a pollinator garden, be sure to include flowers of different shapes, sizes, and colors in order to attract the greatest diversity of pollinators. Here are a few of my favorite summer flowering plants from Hadden’s list:

  • Amorpha canescens (leadplant) – A “good bee plant” and also a nitrogen fixer.
  • Asclepias tuberosa (butterfly weed) – “Valuable pollinator plant and larval host for monarch, gray hairstreak, and queen butterflies.” I love the tight clusters of deep orange flowers on this plant.
  • Coreopsis verticillata (threadleaf coreopsis) – I really like coreopsis (also known as tickseed). Try other species in the genus as well.
  • Penstemon pinifolius (pineleaf penstemon) – North America is bursting with penstemon species, especially the western states. All are great pollinator plants. Pineleaf penstemon is widely available and great for attracting hummingbirds.
  • Salvia pachyphylla (Mojave sage) – A very drought-tolerant plant with beautiful pink to purple to blue inflorescences. Salvia is another genus with lots of species to choose from.
  • Scutellaria suffratescens  (cherry skullcap) – A good ground cover plant with red-pink flowers that occur from late spring into the fall.
The flowers of butterfly weed (Asclepias tuberosa). Milkweed species (Asclepias spp.) are essential to monarch butterflies as they are the sole host plant of their larvae.

The flowers of butterfly weed (Asclepias tuberosa). Milkweed species (Asclepias spp.) are essential to the survival of monarch butterflies as they are the sole host plant of their larvae.

Fall Flowers

Fall flowering plants are essential to pollinators as they prepare to migrate and/or hibernate. Many of the plants on Hadden’s list start flowering in the summer and continue into the fall. A few are late summer/fall bloomers. Here are some of my favorites:

  • Epilobium canum (California fuchsia) – “Profuse orange-red tubular flowers late summer into fall furnish late-season nectar, fueling hummingbird migration.”
  • Liatris punctata (dotted blazing star) – Drought-tolerant plant with tall spikes of purple-pink flowers. “Nectar fuels migrating monarchs.”
  • Symphyotrichum oblongifolium (aromatic aster) – Loaded with lavender-blue flowers in the fall. It’s a spreading plant, so prune it back to keep it in check. Hadden recommends it for sloped beds.
  • Agastache rupestris (sunset hyssop) – Spikes of “small tubular flowers in sunset hues attract hummingbirds, butterflies, and bees midsummer to fall.” Try other species in the Agastache genus as well.
  • Monarda fistulosa (wild bergamot) – The unique flower heads are like magnets to a wide variety of pollinators. Also consider other Monarda species.
Lemon beebalm (Monarda citriodora), an annual plant that attracts an array of pollinators.

Lemon beebalm (Monarda citriodora), an annual plant that attracts an array of pollinators.

As with any other garden, your hardiness zone, soil conditions, water availability, and other environmental factors must be considered when selecting plants for your hellstrip pollinator garden. Groups like Pollinator Partnership and The Xerces Society have guides that will help you select pollinator friendly plants that are suitable for your region. Additionally, two plans for “boulevard pollinator gardens” complete with plant lists are included in the book Pollinators of Native Plants by Heather Holm – one plan is for sunny and dry spots and the other is for shady and wet spots (pgs. 268-269). Once your pollinator garden is complete, consider getting it certified as a pollinator friendly habitat. There are various organizations that do this, such as the Environmental Education Alliance of Georgia. If you are interested in such a thing, the public nature of your hellstrip garden makes it an ideal place to install a sign (like the one sold in The Xerces Society store) announcing your pollinator garden and educating passersby about the importance of pollinator conservation.

habsign

Other “Year of Pollination” Posts

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Book Review: Hellstrip Gardening, part one

Keeping a garden alive and thriving is replete with its inherent challenges. Plants have needs, and those needs vary by plant. Lots of sun might be great for one plant but harmful to another. Some plants are very drought tolerant and don’t require much water beyond what falls naturally from the sky, while others insist on regular supplemental irrigation. Plants also have preferred soil types, and that soil must provide a proper balance of nutrients. Then there is the litany of potential pests, diseases, and predators that can present themselves at any given moment. Frankly, it’s surprising that any garden stays alive, all things considered.

Some gardens have added challenges. They may be regularly visited (and trampled) by the public, who may or may not have pets in tow. They may be surrounded by paved surfaces which increase ambient air temperatures significantly and can introduce contaminants to the garden in the form of road salts, petrochemicals, fertilizers, sediments, and animal waste. They may encompass utility boxes, water meters, and road signs that require regular visits and occasional maintenance. All of these things describe the plight of a curbside garden, also known as a hellstrip – that section of green space between the road and the sidewalk. Comparatively, backyard gardens are veritable havens for plants.

Hellstrips have been on my mind for several years now. It all started back in graduate school while studying green roof technology. One of the macro benefits of green roofs is storm water mitigation. During a storm event, green roofs capture a greater proportion of precipitation compared to conventional roofs and slowly release it back into the environment. Storm water is a major issue in urban areas where the percentage of impervious surfaces is high. These surfaces prohibit precipitation from infiltrating the soil and recharging groundwater and nearby waterways. Instead, this water is rushed away and directed into either waste water treatment facilities or local waterways, carrying with it the contaminants that have collected on paved surfaces and rooftops. Gardens along roadways can be engineered to manage storm water in a similar way that green roofs do – capturing it, filtering it, and releasing it back into the environment at a slow pace – thereby minimizing the negative effects of storm water runoff.

A rain garden or bioswale planted in a hellstrip to help mitigate storm water runoff. (photo credit: epa.gov)

A rain garden or bioswale planted in a hellstrip to help mitigate storm water runoff (photo credit: epa.gov)

The hellstrip in front of my parent’s house has been the source of many headaches. It is another reason why hellstrips have been on my mind. It is a weed patch, but not intentionally so. I remember many years ago when my mom told me she was going to replace the weed patch with buffalograss. She was elated by the idea – little or no mowing, very little supplemental water, a cool alternative to conventional lawn. Now, years later after planting dozens of buffalograss plugs and making a concentrated effort to keep them alive and prospering, the hellstrip remains a weed patch. But my mom hasn’t given up hope. The hellstrip will be conquered in due time.

Riding my bike to work last summer, I regularly rode past a house that proudly displayed the potential that curbside gardens could reach. The house sits on the corner lot of an intersection that, due to the angle of the connecting roads, gives the lot a long triangular shape. This makes the hellstrip longer than most of the others in this neighborhood. On this lengthy strip, the owners have planted an expansive and diverse vegetable garden. While once upon a time vegetable gardens were largely confined to backyards, they have lately been making more regular appearances in front yards. Few, however, are as bold and as public as this one – a true hellstrip success.

Last year, garden writer and lawn alternative enthusiast, Evelyn Hadden, put out a book called, Hellstrip Gardening. When I discovered this, I was intrigued, especially considering all of the mulling over hellstrips I had been doing for so long. I was curious to learn what she had to say. It has taken me until now to read it, but it seems like an opportune time to do so. After all, we are in pre-spring, a time when garden planning is being done in earnest. Perhaps this book will give me some ideas and encouragement to tackle some hard to garden spots this year. And maybe this review (and Hadden’s book) will inspire you to do the same. After all, this approach (as Hadden suggests) doesn’t have to be limited to curbside garden beds and can, in fact, be applied to any garden with challenges beyond the norm (like gardens along driveways and in alleyways, for example). The ultimate goal, for me at least, will be to pass along whatever knowledge I gain from this to my parents so that we can address their hellstrip issues once and for all.

hellstrip gardening book

Hellstrip Gardening is organized into four sections: Inspirations, Situations, Creation, and Curbside-Worthy Plants. This review will also have multiple parts that will be posted as I read through the book. The first section of the book is intended to inspire and encourage – to show through words and pictures what others have done and to give you that “if they can do it, so can I” sort of feeling. It also introduces some of the challenges of gardening in hellstrips as Hadden visits 12 gardens across the United States and talks with the people who designed, installed, and maintain them. She tells the story of how the gardens came to be and showcases some of the plants and plant combinations that were used in each situation. The challenges will be fleshed out in the following section; these narratives are meant more to demonstrate what can be done. There are dozens of great photos throughout, and the short plant lists at the end of each profile are sure to be useful.

Now that we’re inspired, next week’s post will take a look at what Hadden has to say about addressing challenges and overcoming obstacles that are unique to hellstrip gardens.

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Botany and Everyday Chemistry

What’s not to love about plants? They provide us with oxygen, food, medicine, fuel, fibers, and countless other things. They help filter groundwater and sequester carbon. They beautify our landscapes and communities. They provide habitat for wildlife and help reduce soil erosion. And the list goes on.

But there is more to plants than meets the eye. There is something deeper within – at their cellular and molecular levels – that is just as worthy of our fascination and appreciation as the blooms that beautify our yards and the fruits that fill our tables, and that is the abundant and diverse world of chemical compounds present in the botanical kingdom.

But how does one gain an understanding and appreciation for such a subject. Luckily, there is a blog for that. It’s called Compound Interest. Authored by UK chemistry teacher, Andy Brunning, Compound Interest explores the “chemistry and chemical reactions we come across on a day-to-day basis.” Much of what Andy writes about doesn’t have anything to do with plants – fireworks, bacon, gunpowder, snowflakes, etc. – but a sizeable portion of his posts do (evidenced particularly by the Food Chemistry category). For example: Did you know nutmeg is hallucinogenic? Have you ever wondered why avocados turn brown so quickly? Why is it that some people have such a strong aversion to cilantro (aka coriander)? What makes coffee bitter, chili peppers spicy, and catnip so attractive to cats?

These and so many other questions are answered by Andy in a fun and approachable way. One thing that makes Compound Interest so approachable is the use of infographics to tell the stories and explain the science. Each post is accompanied by an infographic featuring photos of the subject, structural formulas of the chemicals, and short descriptions.  For example, this infographic explains why beets are red and why our urine turns red after eating them:

Chemistry-of-Beetroot

The infographics can also be downloaded as pdf files, like this one that explains the chemistry behind the smell of fresh-cut grass.

In this manner, the images and files can be easily shared with others. In fact, Andy encourages this practice, provided that the originals are not altered and that Compound Interest is given proper credit. He is particularly interested in seeing his infographics used in a classroom setting. Read more about the content usage guidelines here. Produced by someone who is obviously passionate about chemistry, these posts and graphics are meant to educate and excite people about everyday chemistry both in the botanical world and beyond.

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Why Awkward? Why Botany? Why Now?

Have you ever wondered why this blog is called Awkward Botany? I have. Naming things can be difficult, and there are days that I question whether Awkward Botany was the right choice and if instead another name would have been more appropriate. Most days I am happy with the name, but I also perceive that there might be questions about where it came from and what it means. Or maybe no one cares? Either way, I figured I would start the year off by putting this out there. It may or may not be of interest to anyone, but so be it. Rest assured that regular programming will resume shortly.

Why Awkward?

Awkward is a word that best describes my general state of being. I am uncomfortable in virtually all social situations. The degree to which discomfort manifests itself varies depending on the circumstances, but it is always there. Anxious is another fitting word to describe me. On the surface I may appear calm and collected, but my mind is constantly racing. It’s hard to relax.

I am a high level introvert, and there was a time when this really bothered me. I didn’t like feeling so shy, nervous, and bumbling. I didn’t like that my voice got shaky every time I talked in front of a group of two or more people (no matter how well I knew them). I wanted to be able to make a phone call or start up a conversation without first having to rehearse what I was going to say a dozen times in my head. I envied people who could socialize so freely and who could dance like no one was watching even when plenty of people were. I saw my shell as a curse and thought I was defective because of it.

These feelings haven’t gone away, but they have waned. In my adult years I have grown to accept, even embrace, my awkwardness and introversion. I’m not particularly thrilled about being this way, but I find ways to celebrate it. Claiming the awkward title is one way that I do that. It is nothing to be ashamed of, despite at times feeling shamed for it. Just acknowledging that fact makes tiptoeing out of my comfort zone that much easier.

Awkward can also mean amateurish or inexpert. I am a degree holding and professional horticulturist and I have taken a number of graduate level plant science courses, but I certainly don’t claim to be an expert botanist. I am passionate about botany, and I love to study and explore it, but I am not on the same level as professional botanists. I could be someday, but that isn’t really the point. I would rather illuminate the amateur aspect, the part an enthusiast can play, the role of the citizen scientist…or citizen botanist in this case. The point being that anyone can join in the conversation regardless of their credentials; all that is required is passion, enthusiasm, and a willingness to learn (and to admit when you’re wrong). That is why I have settled on the tagline, “citizen botany for the phytocurious.” Perhaps this approach will inspire other awkward entities to emerge, like awkward history, awkward herpetology, awkward astronomy, awkward linguistics… Just a thought.

Why Botany?

I am unapologetically obsessed with plants. It is not something I fully realized about myself until I was in my twenties; still it feels like it must be in my DNA. I spend significant portions of each day thinking about plants, reading about plants, writing about plants, and working with plants. And I wouldn’t have it any other way. If I am this taken by plants, then why not botany?

But why should people care about plants? Those who already find themselves fascinated by them don’t really need an answer to this question, and the space it would take to enumerate the myriad reasons why plants matter is more than I want to take up in a single post. Suffice it to say that if plants were not around, we would not be around. And if the vital functions of plants don’t convince you to care, just imagine a world without green things and ask yourself if that’s a world you’d want to live in. Dr. Chris Martine, a professor of botany at Bucknell University, defends botany famously in an article he wrote for the Huffington Post last summer.

Why Now?

This is a nebulous question, and I could take it in several directions. To simplify things I will address this line of inquiry: why am I blogging now, rather than expressing myself using some other medium (or none at all)?

When I was in the 7th grade, I discovered that I like to write. It feels wired into my DNA the same way my interest in plants does. I have been writing regularly ever since. At first it was just poetry, short stories, and song lyrics. Then when I was in my teenage years, I discovered punk rock and along with that fanzines, or zines for short. I had been envisioning something similar to zines before I knew about them, so once I came across them, I knew that I had to make one. Over the course of about 17 years, I produced at least 66 zines under 9 different titles. My two main titles were Elephant Mess and The Juniper. While I haven’t completely given up on zine writing, I have been on hiatus for about two years now.

juniper 16_edit 2

My hiatus is largely due to the expense of doing zines (photocopies, postage, office supplies, etc.) and the markedly reduced interest in them (a PO Box full of mail used to be a fairly common sight for me; now it never happens). So I blog instead. I hesitate to compare blogs to zines, though. For a seasoned zinester like me, that feels blasphemous. But there are clearly some similarities, and now that the internet has become nearly ubiquitous, for someone who likes to write and publish content regularly, blogs seem like the way to go.

But I don’t see this blog as the end goal either. I love to write, and I have long wanted to be a writer. Maintaining a blog doesn’t necessarily mean I’m on the road to a successful writing career, but it certainly doesn’t hurt. For now, Awkward Botany is where I hang my hat, and I am more than happy to call it home.

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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.”

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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.”

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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)

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Apples and Genetic Bottlenecks

This is the eleventh 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.

Genetic Diversity in Malus x domestica (Rosaceae) through Time in Response to Domestication by Briana L. Gross, Adam D. Henk, Christopher M. Richards, Gannara Fazio, and Gayle M. Volk

Domestication is a selection process. Plants with desirable traits are selected (consciously or unconsciously) and removed from the larger population to be grown out and selected from again. Over time, this series of selections results in a cultivated variety that differs substantially from the larger, origin population. This process, while yielding crop varieties that feed a growing population of humans, also results in a series of genetic bottlenecks, meaning they experience a reduction in genetic variation compared to their wild relatives.

There are two points were bottlenecks occur in the domestication process. The first takes place “during the initial domestication event as a subset of the wild population is brought into a cultivated setting.” This is called a “domestication bottleneck.” The second, known as an “improvement bottleneck,” happens when “modern, elite cultivars are selected from the broad variety of landraces [locally adapted varieties]” that were developed during the original domestication event. This stepwise reduction in genetic diversity “limits the options of plant breeders, even as they face the need to increase crop productivity and sustainability” in today’s changing climate.

Most of what we know about genetic bottlenecks during domestication is derived from studies of annual fruit and grain crops. However, “non-grain crops, and perennials in particular, respond to domestication or are domesticated in ways that are fundamentally different.” For this reason, the authors investigated genetic bottlenecks in apple (Malus x domestica), “one of the most widely distributed perennial fruit crops.” They then compared what they learned to other published studies of annual and perennial fruit crops in order to gain more insight into how genetic diversity is affected in these types of crops during domestication.

The common apple was domesticated in central Asia around 4,000 years ago and is a hybrid of at least three species: Malus sieversii, Malus orientalis, and Malus sylvestris. Today, apples are grown throughout the world, and there are more than 7,500 known cultivars with new cultivars being released regularly. Despite this impressive diversity, just fifteen cultivars make up 90% of apple production in the U.S. The authors of this study analyzed DNA from 11 of the 15 major cultivars as well as DNA from the three main wild progenitor species.

Malus x domestica 'Gala' - One of the top 15 apple varieties produced in the U.S. (photo credit: wikimedia commons)

Malus x domestica ‘Gala’ – One of the top 15 apple varieties produced in the U.S. (photo credit: wikimedia commons)

Perennial fruit crops typically experience “mild genetic bottlenecks” compared to annual fruit crops, and the authors confirmed this to be the case with domesticated apples, finding “no significant reduction in genetic diversity through time across the last eight centuries.” Because apple cultivars are maintained by clonal propagation, they can often be traced back to when they were originally developed, making bottlenecks easier to observe. The authors found that “the most recently developed or described cultivars of apples show little to no reduction in genetic diversity compared with the most ancient cultivars.” Cultivars developed since the 1950’s show increased diversity, which may partly be the result of plant breeders introducing genes from another wild species, Malus floribunda.

After a review of the literature, the authors found that apples have retained the highest amount of genetic diversity through the domestication process compared to other fruits, both annual and perennial. More studies are needed in order to confirm the accuracy and extent of these findings; however, the unique story of apple domestication may help explain why it has been “particularly prone to retaining diversity through time.” First, it was widely distributed across Eurasia during its early days of domestication. Second, it experienced “admixture with cultivars” as it expanded its range. For example, after being introduced to North America, it became naturalized, resulting in gene flow occurring between naturalized individuals and cultivated varieties. Offspring of these populations (“chance seedlings”), were then selected, cloned, and became named cultivars.

Despite the mild genetic bottleneck observed in apples, the authors warned that a “dependence on a small number of cultivars” for the majority of U.S. apple production may be resulting in some loss of genetic variation. Relying on so few cultivars may leave apple production vulnerable to pests, diseases, and climate change. “Careful management” is advised as “the continued genetic resilience of the crop is dependent on the genetic diversity of cultivars that are present in living and cryopreserved collections around the world.”

Malus sylvestris (common crabapple) - One of the three main players involved in the apple domestication story (photo credit: www.eol.org)

Blossoms of Malus sylvestris (common crabapple) – One of three main species involved in the history of apple domestication (photo credit: www.eol.org)

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The Nonshattering Trait in Cereal Crops

This is the tenth 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.

Morphological Diversity and Genetic Regulation of Inflorescence Abscission Zones in Grasses by Andrew N. Doust, Margarita Mauro-Herrera, Amie D. Francis, and Laura C. Shand

Seed dispersal is a key aspect of reproduction in plants. Producing seeds requires large amounts of energy and resources, and if the seeds don’t find their way to a suitable environment where they can germinate and grow, then it may be all for naught. There are several modes of seed dispersal (wind, gravity, water, animals, ballistics), and each plant species has its own story to tell in this regard. However, one commonality that most all seed dispersal stories share is “disarticulation [separation] of the seed or fruit from the body of the plant via means of the formation of an abscission zone.”

Seeds are typically dispersed inside fruits, and attached to the fruits may be other plant structures (such as parts of the inflorescence or, in the case of tumbleweeds, the whole plant). The entire dispersal unit (seed, fruit, etc.) is known as a diaspore. In the grass family, a fruit is called a caryopsis. It is a unique fruit because the fruit wall is fused to the seed, making it difficult to distinguish between the two. Methods of disarticulation in grasses are diverse, with diaspores varying greatly in their sizes and the plant parts they contain. Below is a figure from this article showing this diversity. Abscission zones are depicted using red dotted lines.

Domesticated crop plants do not exhibit the same levels of disarticulation that their wild relatives do. This is because “nonshattering forms” were selected during early stages of domestication due to their ease of harvest. Today, all domesticated cereal crops are nonshattering, and all began by selecting “a nonshattering phenotype where the grain [did] not fall easily from the inflorescence.”  However, the wild relatives of cereal crops, “as well as grasses as a whole, differ widely in their manner of disarticulation [as indicated in the figure above].” A mutation in the genes that control abscission is what leads to nonshattering phenotypes. Because all domesticated cereal crops began as nonshattering mutants, the authors of this study were interested in investigating whether or not there is a common genetic pathway across all cereal crops and their wild grass relatives that controls the abscission trait.

The “genetic control of loss of shattering” is important to those interested in domestication, thus it “has been studied in all major crops.” Some of these studies suggest that there is a common genetic pathway that controls abscission in cereal crops, while others suggest there may not be. The authors of this study suspect that “there is potential for considerable genetic complexity” in this pathway, and so before we can determine “the extent to which there are elements of a common genetic pathway,” we must first develop “a better understanding of both diversity of disarticulation patterns and genetic evidence for shared pathways across the grasses.”

In an effort to begin to answer this question, the authors used herbaria vouchers to analyze “morphological data on abscission zones for over 10,000 species of grasses.” They also reviewed published scientific studies concerning the genetics of disarticulation in grasses and cereal crops. They determined that “the evidence for a common genetic pathway is tantalizing but incomplete,” and that their results could be used to inform a “research plan that could test the common genetic pathway model more thoroughly.” Further studies can also “provide new targets for control and fine-tuning of the shattering response” in crop plants, which could result in “reducing harvest losses and providing opportunities for selection in emerging domesticated crops.”

Foxtail millet, Setaria italic (photo credit: www.eol.org)

Foxtail millet (Setaria italica), a widely cultivated species of millet, has “shattering genes” similar to those found in sorghum and rice (photo credit: www.eol.org)