March 30, 2022 by awkwardbotany

Dispersal by Open Sesame!

In certain instances, “open sesame” might be something you exclaim to magically open the door to a cave full of treasure, but for the sesame plant, open sesame is a way of life. In sesame’s case, seeds are the treasure, which are kept inside a four-chambered capsule. In order for the next generation of plants to have a chance at life, the seeds must be set free. Sesame’s story is similar to the stories of numerous other plant species whose seeds are born in dehiscent fruits. But in this instance, the process of opening those fruits is fairly unique.

Sesamum indicum is a domesticated plant with a 5000 plus year history of cultivation. It shares a genus with about 20 other species – most of which occur in sub-Saharan Africa – and belongs to the family Pedaliaceae – the sesame family. Sesame was first domesticated in India and is now grown in many other parts of the world. It is an annual plant that is drought and heat-tolerant and can be grown in poor soils and locations where many other crops might struggle. However, the best yields are achieved on farms with fertile soils and adequate moisture.

Depending on the variety and growing conditions, sesame can reach up to 5 feet tall and can be unbranched or highly branched. Its broad lance-shaped leaves are generally arranged directly across from each other on the stem. The flowers are tubular, similar in appearance to foxglove, and are typically self-pollinated and short-lived. They come in shades of white, pink, blue, and purple and continue to open throughout the growing season as the plant grows taller, even as fruits formed earlier mature. The fruits are deeply-grooved capsules with at least four separate chambers called locules. Rows of tiny, flat, teardrop shaped seeds are produced in each chamber. The seeds are prized for their high oil content and are also used in numerous other ways, both processed and fresh. One of my favorite uses for sesame seeds is tahini, which is one of the main ingredients in hummus.

The fruits of sesame are dehiscent, which means they naturally split open upon reaching maturity. Compare this to indehiscent fruits like acorns, which must either rot or be chewed open by an animal in order to free the seeds. Dehiscence is also called shattering, and in many domesticated crop plants, shattering is something that humans have selected against. If fruits dehisce before they can be harvested, seeds fall to the ground and are lost. Selecting varieties that hold on to their seed long enough to be harvested was imperative for crops like beans, peas, and grains. In domesticated sesame, the shattering trait persists and yield losses are often high.

Most of the world’s sesame crop is harvested by hand. The plants are cut, tied into bundles, and left to dry. Once dry, they are held upside down and beaten in order to collect the seeds from their dehisced capsules. When harvested this way, naturally shattering capsules may be preferred. But in places like the United States and Australia, where mechanical harvesting is desired, it has been necessary to develop new, indehiscent varieties that can be harvested using a combine without losing all the seed in the process. Developing varieties with shatter-resistant seed pods, has been challenging. In early trials, seed pods were too tough and passed through threshers without opening. Additional threshing damaged the seeds and caused the harvest to go rancid. Mechanically harvested varieties of sesame exist today, and improvements in these non-shattering varieties continue to be made.

In order to develop these new varieties, breeders have had to gain an understanding of the mechanisms behind dehiscence and the genes involved in this process. This research has helped us appreciate the unique way that the capsules of the sesame plant dehisce. As in the seed bearing parts of many other plant species, the capsules of sesame exhibit hygroscopic movements. That is, their movements are driven by changes in humidity. The simplest form of hygroscopic movement is bending, which can be seen in the opening and closing of pine cone scales. A more complex movement can be seen in the seed pods of many species in the pea family, which both bend and twist as they split open. In both of these examples, water is evaporating from the plant part in question. As it dries it bends and/or twists, thereby releasing its contents.

dehisced capsules of sesame (Sesamum indicum); photo credit: **wikimedia commons (Dinesh** **Valke)**

The cylindrical nature and cellular composition of sesame fruits leads to an even more complex form of hygroscopic movement. Initially, the capsule splits at the top, creating an opening to each of the four locules. The walls of each locule bend outward, then split and twist as the seed falls from the capsule. In a study published in Frontiers in Plant Science (2016), researchers found that differences in the capsule’s inner endocarp layer and outer mesocarp layer are what help lead to this interesting movement. The endocarp layer is composed of both transvere (i.e. circumferential) and longitudinal fiber cells, while the mesocarp is made up of soft parenchyma cells. The thicknesses of these two layers gradually changes along the length of the capsule. As the mesocarp dries, the capsule initially splits open and starts bending outwards, but as it does, resistance from the fiber cells in the endocarp layer causes further bending and twisting (see Figure 1 in the report for an illustration). As the researchers write, “the non-uniform relative thickness of the layers promotes a graded bi-axial bending, leading to the complex capsule opening movement.”

All this considered, a rock rolling away from the entrance of a cave after giving the command, “Open sesame!” almost seems simpler than the “open sesame” experienced by the fruit of the sesame plant.

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.

The Dispersal of Ancient and Modern Apples by Humans and Other Megafauna

Crop domestication often involves selection for larger fruits. In some crops, humans took plant species with relatively small fruits and, over many generations of artificial selection, developed a plant with much larger fruits. Consider giant pumpkins as an extreme example. Yet in the case of apples, relatively large fruits already existed in the wild. Producing larger apples happened quickly and, perhaps even, unconsciously. Apples were practically primed for domestication, and as Robert Spengler explains in a paper published last year in Frontiers in Plant Science, looking back in time at the origins of the apple genus, Malus, can help us understand how the apple we know and love today came to be.

via wikimedia commons

Apples are members of the rose family (Rosaceae), a plant family that today consists of nearly 5000 species. According to the fossil record, plants in the rose family were found in large numbers across North America as early as the Eocene (56 – 33.9 million years ago). They were present in Eurasia at this time as well, but Spengler notes, “there is a much clearer fossil record for Rosaceae fruits and seeds in Europe and Asia during the Miocene and Pliocene (20 – 2.6 million years ago).” Around 14 million years ago, larger fruits and tree-form growth habits evolved in Rosaceae subfamilies, giving rise to the genera Malus and Pyrus (apples and pears). Small, Rosaceae fruits were typically dispersed by birds, but as Sprengler writes, “it seems likely that the large fruits [in Malus and Pyrus] were a response to faunal dispersers of the late Miocene through the Pliocene of Eurasia.” Larger animals were being recruited for seed dispersal in a changing landscape.

Glacial advances and retreats during the Pleistocene (2.6 million – 11,700 years ago) brought even more changes. Plants with effective, long distance seed dispersal were favored because they were able to move into glacial refugium during glacial advances. Even today, these glacial refugium are considered genetic hot spots for Malus, and could be useful for future apple breeding. As the Pleistocene came to a close, many megafauna were going extinct. This continued into the Holocene. Large-fruited apple species lost their primary seed dispersers, and their ranges became even more contracted.

Humans have had an extensive relationship with apples, which began long before domestication. Foraging for apples was common, and seeds were certainly spread that way (perhaps even intentionally). Favorable growing conditions were also created when forests were cleared and old fields were left fallow. Apple trees are early successional species that easily colonize open landscapes, gaps in forests, and forest edges, so human activity that would have created such conditions “could have greatly promoted the spread and success of wild Malus spp. trees during the Holocene.”

via wikimedia commons

The earliest evidence we have of apple domestication (in which “people were intentionally breeding and directing reproduction”) occurred around 3000 years ago in the Tian Shan Mountains of Kazakhstan, where Malus sieversii – a species that is now facing extinction – was being cultivated. This species was later brought into contact with other apple species, a few of which were also being cultivated, including M. orientalis, M. sylvestris, and M. baccata. These species easily hybridized, giving us the modern, domesticated apple, M. domestica. As Spengler writes, “the driving force of apple domestication appears to have been the trans-Eurasian crop exchange, or the movement of plants along the Silk Road.” Continued cultivation and further hybridization among M. domestica cultivars over the past 2000 years has resulted in thousands of different apple varieties.

The unique thing about domesticated apples is that their traits are not fixed in the same way that traits of other domesticated crops are. Growing an apple from seed will result in a very different apple than the apple from which the seed came. Apple traits instead have to be maintained through cloning, which is accomplished mainly through cuttings and grafting. Apples hybridize with other apple species so readily that most apple trees found in the wild are hybrids between wild and cultivated populations.

via wikimedia commons

Spengler considers the study of apple domestication to be “an important critique of plant domestication studies broadly, illustrating that there is not a one-size fits-all model for plant domestication.” The “key” for understanding apple domestication “rests in figuring out the evolutionary driver for large fruits in the wild – seed dispersal through megafaunal mammals – and the process of evolution for these large fruits – hybridization.” He notes that “domestication studies often ignore evolutionary processes leading up to human cultivation,” which, in the case of apples, involves “hybridization events in the wild” that led to the evolution of large fruits “selected for through the success in recruiting large megafaunal mammals as seed disperses.” Many of those mammals went extinct, but humans eventually assumed the role, selecting and propagating “large-fruiting hybrids through cloning and grafting – creating our modern apple.”

Excerpt from Fruit from the Sands by Robert N. Spengler:

Indeed, the relationship between apples and people is close and complex, spanning at least five millennia. The story of the apple begins along the Silk Road… In recent years genetic studies have resolved much of the debate over these origins. Nevertheless, the ancestry of the apple is highly complex. Cloning, inbreeding, and reproduction between species have created a genealogy that looks more like a spider’s web than a family tree. To growers, the beauty of the apple lies not in its rosy skin but in its genetic variability and plasticity, its ability to cross with other species of Malus and other distant lines of M. domestica, and the ease with which it can be grafted onto different rootstocks and cloned.

Eating Weeds: Lambsquarters

Last year during the Summer of Weeds I inadvertently wrote about several edible weeds, one of which I even ate. It’s not surprising that so many weeds are edible; there are plenty of plants out there – both native and introduced – that are, despite the fact that most of us stick with whatever is made available at the grocery store. Some edible weeds, dandelion included, were once commonly grown for food, while other weeds are close relatives of present day agricultural crops. The more I read about these things and the more my weeds obsession grows, the more I feel compelled to eat them (the edible ones, at least). Hence, a new series of posts: Eating Weeds.

I might as well start with an easy one. Chenopodium album, or lambsquarters, which I wrote about last summer, is a close relative of a number of common crops and a spitting image of quinoa. It happily grows alongside other plants in our vegetable gardens without even being asked to. It is highly nutritious and palatable – particularly the young leaves – and can be eaten raw or cooked. It is often compared to spinach and can be prepared and used in similar ways.

lambsquarters seedling (Chenopodium album)

For the purposes of this post, I decided to try lambsquarters pesto. While pesto is traditionally made using basil leaves, all kinds of other leaves – or combinations thereof – can be substituted. I have made pesto with parsley, which was interesting, as well as watercress, which was delicious. The possibilities are endless. So, why not lambsquarters?

Making pesto is incredibly simple. Blend together a combination of leaves, garlic, nuts or seeds, Parmesan cheese (or something similar), olive oil, salt, and pepper. Pine nuts are traditionally used to make pesto, but like the leaf component, a number of different nuts or seeds can be substituted. I rarely make pesto with pine nuts because, despite being delicious, they are pricey.

lambsquarters pesto

I made two batches of lambsquarters pesto. For the first I used walnuts, and for the second I used sunflower seeds. Both batches were delicious. How could they not be with all of that garlic and cheese in there? Lambsquarters is not a very bitter or strong-tasting green, so lambsquarters pesto might be perfect for anyone who is otherwise not fond of pesto (although that is a stance that I personally cannot fathom).

This is definitely something I will make again. I understand the frustration people have with lambsquarters. It can be prolific and hard to eliminate from a garden. Luckily, it makes an excellent pesto.

Resources:

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This series of posts was inspired in part by the book Dandelion Hunter, in which the author, Rebecca Lerner, attempts to go a full week eating only things she is able to forage in her hometown of Portland, Oregon. As you might imagine, many of the plants she forages are weeds.

February 28, 2018 by awkwardbotany

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.”

February 21, 2018 by awkwardbotany

Lettuce Gone Wild, part one

Lettuce, domesticated about six thousand years ago in a region referred to as the Fertile Crescent, bears little resemblance to its wild ancestors. Hundreds of years of cultivation and artificial selection eliminated spines from the leaves, reduced the latex content and bitter flavor, shortened stem internodes for a more compact, leafy plant, and increased seed size, among several other things. The resulting plant even has a different name, Lactuca sativa (in Latin, sativa means cultivated). However, cultivated lettuce remains closely related to its progenitors, with whom it can cross to produce wild-domestic hybrids. For this reason, there is great interest in the wild relatives of lettuce and the beneficial traits they offer.

image credit: wikimedia commons

Crop wild relatives are a hot topic these days. That’s because feeding a growing population in an increasingly globalized world with the threat of climate change looming requires creative strategies. Utilizing wild relatives of crops in breeding programs is a potential way to improve yields and address issues like pests and diseases, drought, and climate change. While this isn’t necessarily a new strategy, it is increasingly important as the loss of biodiversity around the globe threatens many crop wild relatives. Securing them now is imperative.

There are about 100 species in the genus Lactuca. Most of them are found in Asia and Africa, with the greatest diversity distributed across Southwest Asia and the Mediterranean Basin. The genus consists of annual, biennial, and perennial species, a few of which are shrubs or vines. Prickly lettuce (L. serriola), willowleaf lettuce (L. saligna), and bitter lettuce (L. virosa) are weedy species with a wide distribution outside of their native range. Prickly lettuce is particularly common in North America, occurring in the diverse habitats of urban areas, natural areas, and agricultural fields. It is also the species considered to be the main ancestor of today’s cultivated lettuce.

In a paper published in European Journal of Plant Pathology in 2014. Lebeda et al. discuss using wild relatives in lettuce breeding and list some of the known cultivars derived from crosses with wild species. They write that in the last thirty years, “significant progress has been made in germplasm enhancement and the introduction of novel traits in cultivated lettuce.” Traditionally, Lactuca serriola has been the primary source for novel traits, but breeders are increasingly looking to other species of wild lettuce.

bitter lettuce (Lactuca virosa) – image credit: wikimedia commons

Resistance to disease is one of the main aims of lettuce breeders. Resistance genes can be found among populations of cultivated lettuce, but as “extensive screening” for such genes leads to “diminishing returns in terms of new resistance,” breeders look to wild lettuce species as “sources of new beneficial alleles.” The problem is that there are large gaps in our knowledge when it comes to wild lettuce species and their interactions with pests and pathogens. Finding the genes we are looking for will require “screening large collections of well defined wild Lactuca germplasm.” But first we must develop such collections.

In a separate paper (published in Euphytica in 2009), Lebeda et al. discuss just how large the gaps in our understanding of the genus Lactuca are. Beginning with our present collections they found “serious taxonomic discrepancies” as well as significant redundancy and unnecessary duplicates in and among gene banks. They also pointed out that “over 90% of wild collections are represented by only three species” [the three weedy species named above], and they urged gene banks to “rapidly [acquire] lettuce progenitors and wild relatives from the probable center of origin of lettuce and from those areas with the highest genetic diversity of Lactuca species” as their potential for improving cultivated lettuce is too important to neglect.

Lactuca is a highly variable genus; species can differ substantially in their growth and phenology from individual to individual. Lebeda et al. write, “developmental stages of plants, as influenced through selective processes under the eco-geographic conditions where they evolved, can persist when plants are cultivated under common environmental conditions and may be fixed genetically.” For this reason it is important to collect numerous individuals of each species from across their entire range in order to obtain the broadest possible suite of traits to select from.

One such trait is root development and the related ability to access water and nutrients and tolerate drought. Through selection, cultivated lettuce has become a very shallow-rooted plant, reliant on regular irrigation and fertilizer applications. In an issue of Theoretical and Applied Genetics published in 2000, Johnson et al. demonstrate the potential that Lactuca serriola, with its deep taproot and ability to tolerate drought, has for developing lettuce cultivars that are more drought tolerant and more efficient at using soil nutrients.

willowleaf lettuce (Lactuca saligna) – image credit: wikimedia commons

Clearly we have long way to go in developing improved lettuce cultivars using wild relatives, but the potential is there. As Lebeda et al. write in the European Journal of Plant Pathology, “Lettuce is one of the main horticultural crops where a strategy of wild related germplasm exploitation and utilization in breeding programs is most commonly used with very high practical impact.”

Coming Up in Part Two: Can cultivated lettuce cross with wild lettuce to create super weeds?

December 13, 2016 by awkwardbotany

What Is a Plant, and Why Should I Care? part four

What Is a Plant?

Part one and two of this series have hopefully answered that.

Why should you care?

Part three offered a pretty convincing answer: “if it wasn’t for [plants], there wouldn’t be much life on this planet to speak of.”

Plants are at the bottom of the food chain and are a principle component of most habitats. They play major roles in nutrient cycling, soil formation, the water cycle, air and water quality, and climate and weather patterns. The examples used in part three of this series to explain the diverse ways that plants provide habitat and food for other organisms apply to humans as well. However, humans have found numerous other uses for plants that are mostly unique to our species – some of which will be discussed here.

But first, some additional thoughts on photosynthesis. Plants photosynthesize thanks to the work accomplished by very early photoautotrophic bacteria that were confined to aquatic environments. These bacteria developed the metabolic processes and cellular components that were later co-opted (via symbiogensis) by early plants. Plants later colonized land, bringing with them the phenomena of photosynthesis and transforming life on earth as we know it. Single-celled organisms started this whole thing, and they continue to rule. That’s just something to keep in mind, since our focus tends to be on large, multi-cellular beings, overlooking all the tiny, less visible beings at work all around us making life possible.

Current representation of the tree of life. Microorganisms clearly dominate. (image credit: nature microbiology)

Food is likely the first thing that comes to mind when considering what use plants are to humans. The domestication of plants and the development of agriculture are easily among the most important events in human history. Agricultural innovations continue today and are necessary in order to both feed a growing population and reduce our environmental impact. This is why efforts to discover and conserve crop wild relatives are so essential.

Plants don’t just feed us though. They house us, clothe us, medicate us, transport us, supply us, teach us, inspire us, and entertain us. Enumerating the untold ways that plants factor in to our daily lives is a monumental task. Rather than tackling that task here, I’ll suggest a few starting points: this Wikipedia page, this BGCI article, this Encylopedia of Life article, and this book by Anna Lewington. Learning about the countless uses humans have found for plants over millennia should inspire admiration for these green organisms. If that admiration leads to conservation, all the better. After all, if the plants go, so do we.

Humans have a long tradition of using plants as medicine. Despite all that we have discovered regarding the medicinal properties of plants, there remains much to be discovered. This is one of the many reasons why plant conservation is imperative. (photo credit: wikimedia commons)

Gaining an appreciation for the things that plants do for us is increasingly important as our species becomes more urban. Our dense populations tend to push plants and other organisms out, yet we still rely on their “services” for survival. Many of the functions that plants serve out in the wild can be beneficial when incorporated into urban environments. Plants improve air quality, reduce noise pollution, mitigate urban heat islands, help manage storm water runoff, create habitat for urban wildlife, act as a windbreak, reduce soil erosion, and help save energy spent on cooling and heating. Taking advantage of these “ecosystem services” can help our cities become more liveable and sustainable. As the environmental, social, and economic benefits of “urban greening” are better understood, groups like San Francisco’s Friends of the Urban Forest are convening to help cities across the world go green.

The importance of plants as food, medicine, fuel, fiber, housing, habitat, and other resources is clear. Less obvious is the importance of plants in our psychological well being. Numerous studies have demonstrated that simply having plants nearby can offer benefits to one’s mental and physical health. Yet, urbanization and advancements in technology have resulted in humans spending more and more time indoors and living largely sedentary lives. Because of this shift, author Richard Louv and others warn about nature deficit disorder, a term not recognized as an actual condition by the medical community but meant to describe our disconnect with the natural world. A recent article in BBC News adds “nature knowledge deficit” to these warnings – collectively our knowledge about nature is slipping away because we don’t spend enough time in it.

The mounting evidence for the benefits of having nature nearby should be enough for us to want to protect it. However, recognizing that we are a part of that nature rather than apart from it should also be emphasized. The process that plants went through over hundreds of millions of years to move from water to land and then to become what they are today is parallel with the process that we went through. At no point in time did we become separate from this process. We are as natural as the plants. We may need them a bit more than they need us, but we are all part of a bigger picture. Perhaps coming to grips with this reality can help us develop greater compassion for ourselves as well as for the living world around us.

October 26, 2016 by awkwardbotany

Maize Anatomy and the Anatomy of a Maze

Commonly known as corn throughout much of North America, maize is a distinctive emblem of the harvest season. It is one of the most economically important crops in the world (the third most important cereal after rice and wheat) and has scads of uses from food to feed to fuel. The story of its domestication serves as a symbol of human ingenuity, and its plasticity in both form and utility is a remarkable example of why plants are so incredible.

The genus Zea is in the grass family (Poaceae) and consists of five species: Z. diploperennis, Z. perennis, Z. luxurians, Z. nicaraguensis, and Z. mays. Maize is the common name of Zea mays subsp. mays, which is one of four Z. mays subspecies and the only domesticated taxon in the genus. All other taxa are commonly and collectively referred to as teosintes.

The domestication of maize, apart from being an impressive feat, has long been a topic of research and a challenging story to tease apart. The current understanding is that maize was first domesticated around 9000 years ago in the Balsas River valley in southern Mexico, the main progenitor being Zea mays subsp. parviglumis. It is astonishing how drastically different in appearance teosintes are from modern day maize, but it also explains why determining the crop wild relative of maize was so difficult.

Teosinte, teosinte-maize hybrid, and maize – photo credit: wikimedia commons

Teosintes and maize both have tall central stalks; however, teosintes generally have multiple lateral branches which give them a more shrubby appearance. In teosinte, each of the lateral branches and the central stalk terminate in a cluster of male flowers; female flowers are produced at the nodes along the lateral branches. In maize, male flowers are borne at the top of the central stalk, and lateral branches are replaced by short stems that terminate in female flowers. This is where the ears develop.

Ears – or clusters of fruits – are blatantly different between teosintes and maize. To start with, teosinte produces a mere 5 to 12 fruits along a short, narrow cob (flower stalk). The fruits are angular and surrounded in a hard casing. Maize cobs are considerably larger both in length and girth and are covered in as many as 500 or more fruits (or kernels), which are generally more rounded and have a softer casing. They also remain on the cob when they are ripe, compared to teosinte ears, which shatter.

Evolutionary biologist, Sean B. Carroll, writes in a New York Times article about the amazing task of “transform[ing] a grass with many inconvenient, unwanted features into a high-yielding, easily harvested food crop.” These “early cultivators had to notice among their stands of plants variants in which the nutritious kernels were at least partially exposed, or whose ears held together better, or that had more rows of kernels, and they had to selectively breed them.” Carroll explains that this “initial domestication process which produced the basic maize form” would have taken several hundred to a few thousand years. The maize that we know and love today is a much different plant than its ancestors, and it is still undergoing regular selection for traits that we find desirable.

Female inflorescence (or “ear”) of Zea mays subsp. mays – photo credit: wikimedia commons

To better understand and appreciate this process, it helps to have a basic grasp of maize anatomy. Maize is an impressive grass in that it regularly reaches from 6 to 10 feet tall and sometimes much taller. It is shallow rooted, but is held up by prop or brace roots – adventitious roots that emerge near the base of the main stalk. The stalk is divided into sections called internodes, and at each node a leaf forms. Leaf sheaths wrap around the entirety of the stalk, and leaf blades are long, broad, and alternately arranged. Each leaf has a prominent midrib. The stalk terminates in a many-branched inflorescence called a tassel.

Maize Anatomy 101 - image credit: Canadian Goverment

Maize Anatomy 101 – image credit: Canadian Government

Maize is monoecious, which means that it has separate male and female flowers that occur on the same plant. The tassel is where the male flowers are located. A series of spikelets occur along both the central branch and the lateral branches of the tassel. A spikelet consists of a pair of bracts called glumes, upper and lower lemmas and paleas (which are also bracts), and two simple florets composed of prominent stamens. The tassel produces and sheds tens of thousands of pollen grains which are dispersed by wind and gravity to the female inflorescences below and to neighboring plants.

Female inflorescences (ears) occur at the top of short stems that originate from leaf axils in the midsection of the stalk. Leaves that develop along this reduced stem wrap around the ears forming the husk. Spikelets form in rows along the flower stalk (cob) within the husk. The florets of these spikelets produce long styles that extend beyond the top of the husk. This cluster of styles is known as the silk. When pollen grains land on silk stigmas, pollen tubes grow down the entire length of the silks to reach the embryo sac. Successful fertilization produces a kernel.

The kernel – or fruit – is known botanically as a caryopsis, which is the standard fruit type of the grass family. Because the fruit wall and seed are fused together so tightly, maize kernels are commonly referred to as seeds. The entire plant can be used to produce feed for animals, but it is the kernel that is generally consumed (in innumerable ways) by humans.

There is so much more to be said about maize. It’s a lot to take in. Rather than delve too much further at this point, let’s explore one of the other ways that maize is used by humans to create something that has become another feature of the fall season – the corn maze.

Entering the corn maze at The Farmstead in Meridian, Idaho

Exploring the corn maze at The Farmstead in Meridian, Idaho

December 12, 2014 by awkwardbotany

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.

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.”

December 4, 2014 by awkwardbotany

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)

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.

awkward botany

amateur botany for the phytocurious

crop wild relatives

Dispersal by Open Sesame!

See Also: Seed Shattering Lost – The Story of Foxtail Millet

Seed Shattering Lost – The Story of Foxtail Millet

Further Reading:

The Dispersal of Ancient and Modern Apples by Humans and Other Megafauna

See Also: Science Daily – Exploring the Origins of the Apple