genetics

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Apriums and Plumcots and Pluots, Oh My!

I was once a teenage paper carrier in small town Idaho. One of my stops was an apartment complex, and for much of the year, this was an uneventful stop. But for a few weeks in the summer, the purple-leaved plum trees out front had ripe fruit on them, and each time I was there, I would stop and take a few. In general, I don’t get that excited about fruit, but I enjoyed eating these plums. This variety of plum is typically planted for its looks rather than its fruit, and it may even be the tree that recently received a pitifully low score on an episode of Completely Arbortrary. Ornamental plum or not – and low cone score or not – I thought the fruit was good.

Many of the things we eat are a result of crosses between two related species, and plums are a great example of this. Species are species because they are reproductively isolated. A species does not typically mate with a member of another species and create viable offspring, except this happens all the time both naturally and artificially. In many cases, the offspring isn’t actually viable, but there is offspring nonetheless, and in the case of plants, that offspring can then reproduce asexually – by leaf, stem, or root cuttings or by some other means – and the resulting hybrid can exist indefinitely. One species mating with another species (specifically two species that are members of the same genus) is called interspecific hybridization, and there is a good chance that you’ve eaten something recently that is a result of this.

One of the most widely grown species of plum, Prunus domestica (commonly known as European plum), is a result of interspecific hybridization that occurred many centuries ago. A paper published in Horticulture Research (2019) confirmed that P. domestica originated as a cross between Prunus cerasifera and Prunus spinosa, the latter of which may have also been a result of interspecific hybridization. There are over 400 species in the genus Prunus that are distributed across temperate regions in the northern hemisphere. Within this genus is the subgenus Prunus (or Prunophora), a group that includes dozens of familiar species such as the plums, apricots, peaches, and almonds. Due to their close relationship, both natural and artificial hybridization among members of this subgenus is common, which explains the origin of Prunus domestica, as well as the majority of the plums we grow today.

Current commercial production of plums in North America is largely thanks to work done by Luther Burbank in the late 19th to early 20th centuries. Burbank was obsessed with plant breeding and released hundreds of new varieties of all kinds of different plants during his decades long career. He seemed particularly interested in plums, developing 113 different cultivars, which account for more than half of all his fruit releases. Probably his most well known plum variety is ‘Santa Rosa,’ which thanks to modern day genetics has been determined to be a cross between at least four different species of plum.

apriums

Early colonizers to the American continent were mainly growing varieties of the European plum they had brought over from Europe. North America is also home to several species of plums, which are used by indigenous populations. Shortly before Burbank began working with plums on his farm in California in 1881, Asian plum species were imported to the U.S., and breeders began using them in crosses with both European and North American plum species. Burbank became particularly engulfed in these efforts. In an article published in HortScience (2015), David Karp writes, “In the history of horticulture it is rare to find an individual who almost single-handedly created a new commercial industry based on a novel fruit type as Luther Burbank did for Asian-type plums in the United States.” Most Asian-type plums sold in stores today are hybrids of several different plum species due to the numerous complex crosses that Burbank made.

Burbank is also said to be the first to cross plums and apricots, creating the first of many cultivars of the plumcot. Plum and apricot crosses didn’t really catch on for a few more decades, and when they did, it was thanks to the work of Floyd Zaiger of Zaiger Genetics who developed and released numerous varieties. Apriums and Pluots are Zaiger Genetics trademarks, along with a few other unlikely crosses with plums and their related counterparts.

plumcots

A plumcot is the simplest cross. It is said to be 50% Asian plum (Prunus salicina) and 50% apricot (Prunus armeniaca). However, due to all the breeding of Asian plums carried out by Burbank and others, the Asian plum involved in the cross is typically a hybrid with other plum species, as discussed in a recent paper published in Plants (2022). An aprium is the result of a cross between a plumcot and an apricot, making it 75% apricot and 25% plum, while a pluot is a cross between a plumcot and a plum, making it 75% plum and 25% apricot. There is typically much more that goes into making these crosses, but that’s the general idea. If you’re lucky, you can find all three of these intraspecific crosses in a produce section near you, but it may not be clear what cultivar you’re purchasing. Myriad cultivars have been released of each of these hybrids – each one varying in color, size, flavor, disease resistance, etc. – and unfortunately most grocery stores don’t include cultivar names on their products, so it’s difficult to know what you’re getting.

At Awkward Botany Headquarters, there is a plum tree growing in our front yard. We didn’t plant it, so at this point I have no idea what species or cultivar it is. The plums are delicious though, and the leaves aren’t purple like the plums I used to eat on my paper route. Considering all of the intraspecific crossing that has gone on with plums, it’s quite likely that it is a combination of different species, which isn’t going to make it easy to figure out. But I’ll do my best.

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Seed Shattering Lost – The Story of Foxtail Millet

For a plant to disperse its seeds, it must first let go of them. Sounds obvious, but it is a key step in the dispersal process and an act that is actually coded in a plant’s DNA. As fruits ripen and seeds mature, an abscission layer is formed that separates the seed-bearing fruits from the plant. No longer attached to their parents, seeds are left to their own devices. If all goes well, they will find themselves in a suitable location where they can germinate and grow into a whole new plant, fully equipped to make seed babies of their own.

The releasing of mature seeds is known as shattering, a term most commonly used in reference to grasses and plants with dehiscent seed pods (i.e. fruits that split open when ripe, such as those in the bean and mustard families). In grasses, seeds form along a central stem called a rachis. As the seeds ripen, they separate from the rachis and drop from the plant. In some cases, the rachis is brittle and a section of it breaks off with each seed that falls.

Seed shattering is not a desirable trait when it comes to food crops. It’s easy to see how yields can be poor if seeds disperse before they are harvested. Thus, an essential step in domesticating certain agricultural crops was selecting plants that lacked this particular trait. Instead of dropping mature seeds, such plants hold on to them, making them easy to collect. A simple and naturally occurring mutation in the genes of these plants allowed early farmers to select varieties that were more ideal for agriculture than their wild progenitors.

Genetic studies of agricultural crops have located genes in a number of species that code for seed shattering, confirming that domestication in many cases involved selecting plants with this gene turned off. A recent study, published in Nature Biotechnology (October 2020), took a different route in locating this gene, looking instead at a weedy, wild relative of a crop that was domesticated at least 8000 years ago. Green foxtail (Setaria viridis) is the wild antecedent of foxtail millet (Setaria italica), a crop that, while still commonly grown for food in parts of Asia, is mostly grown for hay, silage, and bird seed in North America. Recently, interest in foxtail millet and other millets (a term used to refer to the grains of several different species of grasses) is on the rise due to the ability of these crops to tolerate drought and heat.

Illustration of three Setaria species from Selected Weeds of the United States (Agriculture Handbook No. 366) published in 1970

Setaria viridis is an abundant, widespread weed adapted to human disturbance. It’s of Eurasian origin but has been present in North America since the early 1800’s and was likely introduced both intentionally and accidentally. It’s an annual grass with prominent, bristly flowerheads that are easily recognizable and the reason for its common name, green foxtail. A handful of other closely related, similar-looking species are also common weeds in North America. Due to useful traits including its short life cycle, small genome, and self-fertility, S. viridis has been used frequently as a model species to carry out a variety of scientific studies. The study referred to above aimed to further enhance the use of green foxtail, particularly when it comes to crop science.

Researchers traveled across the United States collecting nearly 600 samples of green foxtail in order to better understand its genome. They found that the North American population of green foxtail is composed of multiple introductions and that, as the species has followed humans around, it has quickly adapted to diverse climates found across the continent. In examining the genome, they were able to identify the genetic underpinnings for three traits that have importance to agriculture: response to climate, leaf angle (which is used as a predictor of yield in grain crops), and seed shattering.

foxtail millet (Setaria italica) via wikimedia commons

The seed shattering gene – which the researchers named Less Shattering 1 (SvLes1) – was an especially interesting discovery. When compared to the orthologous gene found in foxtail millet, they found that a frameshift mutation had caused a disruption in the gene, turning it off. Using CRISPR (a gene editing tool) they were able to recreate a similar interruption in green foxtail, which resulted in a loss of seed shattering similar to that of foxtail millet. It became clear that selecting plants with this mutation was an essential step in the domestication of this ancient grain.

An excerpt about seed shattering from Fruit from the Sands by Robert N. Spengler III: 

In many of the world’s domesticated grains, especially those from the founder crops of southwest Asia (i.e. wheat and barley), the earliest phenotypical trait of domestication that archaeobotanists look for is a tough rachis, the small stem by which an individual grain or small cluster of grains is attached to the ear. In their wild form, most grains are programmed to detach easily after the grain ripens; however, in domesticated cereals, the grains remain attached to the ear throughout the harvesting process. This change is an inadvertent result of human harvesting with sickles: as people reap their harvest, the grains with a brittle rachis are dropped and those with a tough rachis are collected, stored, and replanted for successive harvests.

Further Reading:

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Lettuce Gone Wild, part two

The lettuce we eat is a close relative to the lettuce we weed out of our gardens. Last week we discussed the potential that wild relatives may have for improving cultivated lettuce. But if wild lettuce can be crossed with cultivated lettuce to create new cultivars, can cultivated lettuce cross with wild lettuce to make it more weedy?

Because so many of our crops are closely related to some of the weeds found along with them or the plants growing in nearby natural areas, the creation of crop-wild hybrids has long been a concern. This concern is heightened in the age of transgenic crops (also known as GMOs), for fear that hybrids between weeds and such crops could create super weeds – fast spreading or highly adapted weeds resistant to traditional control methods such as certain herbicides. To reduce this risk, extensive research is necessary before such crops are released for commercial use.

flowers of prickly lettuce (Lactuca serriola)

There are no commercially available, genetically modified varieties of cultivated lettuce, so this is not a concern when it comes to crop-wild hybrids; however, due to how prevalent weedy species like prickly lettuce (Lactuca serriola) are, hybridization with cultivated lettuce is still a concern. So, it is important to understand what the consequences might be when hybridization occurs.

In a paper published in Journal of Applied Ecology in 2005, Hooftman et al. examined a group of second-generation hybrids (L. sativa x L. serriola), and found that the hybrids behaved and appeared very similarly to non-hybrid prickly lettuce. They also found that the seeds produced by the hybrids had a significantly higher germination rate than non-hybrid plants. This is an example of hybrid vigor. Thus, “if hybridization does occur, this could lead to better performing and thus potentially more invasive (hybrid) genotypes.” However, the authors cautioned that “better performing genotypes do not automatically result in higher invasiveness,” and that much depends on the conditions they are found in, the level of human disturbance, etc.

Another thing to consider is that hybrids are not stable. In an article published in Nature Reviews Genetics in 2003, Stewart et al. adress the “misunderstanding that can arise through the confusion of hybridization and … introgression.” It is wrong to assume that hybrids between crops and wild relatives will automatically lead to super weeds. For this to occur, repeated crosses with parental lines (also known as backcrossing) must occur, and “backcross generations to the wild relative must progress to the point at which the transgene [or other gene(s) in question] is incorporated into the genome of the wild relative.” That is what is meant by “introgression.” This may happen quickly or over many generations or it may never happen at all. Each case is different.

prickly leaf of prickly lettuce (Lactuca serriola)

In a paper published in Journal of Applied Ecology in 2007, Hooftman et al. observe the breakdown of crop-wild lettuce hybrids. They note that “fitness surplus through [hybrid vigor] will often be reduced over few generations,” which is what was seen in the hybrids they observed. One possible reason why this occurs is that lettuce is predominantly a self-crossing species; outcrossing is rare, occurring 1 – 5% of the time thanks to pollinating insects. But that doesn’t mean that a stable, aggressive genotype could never develop. Again, much depends on environmental conditions, as well as rates of outcrossing and other factors relating to population dynamics.

A significant expansion of prickly lettuce across parts of Europe led some to hypothesize that crop-wild hybrids were partly to blame. In a paper published in Molecular Ecology in 2012 Uwimana et al. ran population genetic analyses on extensive data sets to determine the role that hybridization had in the expansion. They concluded that, at a level of only 7% in wild habitats, crop-wild hybrids were not having a significant impact. They observed greater fitness in the hybrids, as has been observed in other studies (including the one above), but they acknowledged the instability of hybrids, especially in self-pollinating annuals like lettuce.

seed head of prickly lettuce (Lactuca serriola)

It is more likely that the expansion of prickly lettuce in Europe is due to “the expansion of favorable habitat as a result of climate warming and anthropogenic habitat disturbance and to seed dispersal because of transportation of goods.” Uwimana et al. did warn, however, that “the occurrence of 7% crop-wild hybrids among natural L. serriola populations is relatively high [for a predominantly self-pollinating species] and reveals a potential [for] transgene movement from crop to wild relatives [in] self-pollinating crops.”

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Charles Darwin and the Phylogeny of State Flowers and State Trees

This is a guest post by Rachel Rodman. Photos by Daniel Murphy.

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Every U.S. state has its own set of symbols: an official flower, an official tree, and an official bird. Collectively, these organisms form the stuff of trivia and are traditionally presented in the form of a list.

But, lists…well. As charming as lists can sometimes be, lists are rarely very satisfying.

So I decided to try something different.

I am not, of course, the first person to be unhappy with the eclectic, disordered nature of many biological assemblages. In the 18th century, Linnaeus developed a classification system in order to make sense of that untidiness. Kingdom, Phylum, Class, and so on.

In the 19th century, Darwin set biodiversity into an even more satisfying intellectual framework, outlining a model that linked organisms via descent from a series of common ancestors. And, as early as 1837, he experimented with a tree-like structure, in order to diagram these relationships.

Following Darwin’s lead, I’ve worked to reframe the state flowers and state trees in terms of their evolutionary history (*see the methods section below). And today, in honor of Darwin’s 209th birthday, I am delighted to present the results to you.

Let’s start with the state flowers.

In this tree, Maine’s “white pine cone and tassel” forms the outgroup. Among all the state “flowers,” it is the only gymnosperm—and therefore, in fact, not actually a flower.

Notice, also, that the number of branches in this tree is 39—not 50. Most of this stems from the untidy fact that there is no requirement for each state to select a unique flower. Nebraska and Kentucky, for example, share the goldenrod; North Carolina and Virginia share the dogwood.

With the branch labeled “Rose,” I’ve compressed the tree further. The state flowers of Georgia, Iowa, North Dakota, New York, and Oklahoma are all roses of various sorts; with my data set (*see methods below), however, I was unable to disentangle them. So I kept all five grouped.

This is a rich tree with many intriguing juxtapositions. Several clades, in particular, link geographical regions that are not normally regarded as having a connection. Texas’ bluebonnet, for example, forms a clade with Vermont’s red clover. So, similarly, do New Hampshire’s purple lilac and Wyoming’s Indian paintbrush.

Texas bluebonnet (Lupinus texensis) – the state flower of Texas

The second tree—the tree of state trees—is similarly rewarding. This tree is evenly divided between angiosperms (19 species) and gymnosperms (17 species).

Iowa’s state tree is simply the “oak”—no particular species was singled out. To indicate Iowa’s selection, I set “IA” next to the node representing the common ancestor of the three particular oak species: white oak, red oak, and live oak, which were selected as symbols by other states.

Arkansas’ and North Carolina’s state tree, similarly, is the “pine,”—no particular species specified. I’ve indicated their choice in just the same way, setting “AR” and “NC” next to the node representing the common ancestor of the eight particular pine species chosen to represent other states.

In this tree of trees, as with the tree of flowers, several clades link geographical regions that are not usually linked—at least not politically. Consider, for example, the pairing of New Hampshire’s white birch with Texas’ tree, the pecan.

Another phylogenetic pairing also intrigued me: Pennsylvania’s eastern hemlock and Washington’s western hemlock. It evokes, I think, a pleasing coast-to-coast symmetry: two states, linked via an east-west cross-country bridge, over a distance of 2,500 miles

The corky bark of bur oak (Quercus macrocarpa). Oak is the state tree of Iowa.

In this post, I’ve presented the U.S. state flowers and U.S. state trees in evolutionary framework. The point in doing that was not to denigrate any of the small, human stories that lie behind these symbols—all of the various economic, historical, and legislative vagaries, which led each state to select these particular plants to represent them. (Even more importantly, I have no wish to downplay the interesting nature of any of the environmental factors that led particular plants to flourish and predominate in some states and not others.)

The point, instead, was to suggest that these stories can coexist and be simultaneously appreciated alongside a much larger one: the many million year story of plant evolution.

With Darwin’s big idea—descent with modification—the eclectic gains depth and meaning. And trivia become a story—a grand story, which can be traced back, divergence point by divergence point: rosids from asterids (~120 mya); eudicots from monocots (~160 mya); angiosperms from gymnosperms (~300 mya), and so on and so on.

So today, on Darwin’s 209th, here, I hope, is one of the takeaways:

An evolutionary framework really does make everything—absolutely everything: U.S. state symbols included—more fun, more colorful, more momentous, and more intellectually satisfying.

Thanks, Darwin.

*Methods:

To build these two trees, I relied on a data set from TimeTree.org, a website maintained by a team at Temple University. At the “Load a List of Species” option at the bottom of the page, I uploaded two lists of species in .txt format; each time, TimeTree generated a phylogenetic tree, which served as a preliminary outline.

Later, once I’d refined my outlines, I used the “Get Divergence Time For a Pair of Taxa” feature at the top of the page in order to search for divergence time estimates. As I reconstructed my trees in LibreOffice, I used these estimates to make my branch lengths proportional.

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Rachel Rodman has a Ph.D. in Arabidopsis genetics and presently aspires to recontextualize all of history, literature, and popular culture in the form of a phylogenetic tree. Won’t you help her?

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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. 

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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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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. 

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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)