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:

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.

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.”

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.

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.

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


Interested in learning more about how plants get around? Check out the first issue of our new zine Dispersal Stories.

Book Review: Fruit from the Sands

“By dispensing plants and animals all around the world, humans have shaped global cuisines and agricultural practices. One of the most fascinating and least-discussed episodes in this process took place along the Silk Road.” — Fruit from the Sands by Robert N. Spengler III


My understanding of the origins of agriculture and the early years of crop domestication are cursory at best. The education I received was mostly concerned with the Fertile Crescent, as well as crops domesticated by early Americans. The Silk Road, as I understood it, was the route or routes used to move goods across Asia and into eastern Europe well after the domestication of many of the crops we know today. Other than the fact that several important crops originate there, little was ever taught to me about Central Asia and its deep connection to agriculture and crop domestication. I suppose that’s why when I picked up Fruit from the Sands by Robert N. Spengler III, published last year by University of California Press, I wasn’t entirely prepared for what I was about to read.

It wasn’t until I read a few academic reviews of Fruit from the Sands that I really started to understand. Spengler’s book is groundbreaking, and much of the research he presents is relatively new. The people of Central Asia played a monumental role in discovering and developing much of the food we grow today and some of the techniques we use to grow them, and a more complete story is finally coming to light thanks to the work of archaeologists like Spengler, as well as advances in technology that help us make sense of their findings.

This long history with agricultural development can still be seen today in the markets of Central Asia, which are loaded with countless varieties of fruits, grains, and nuts, many of which are unique to the area. Yet this abundance is also at risk. Crop varieties are being lost at an alarming rate with the expansion of industrial agriculture and the reliance on a small selection of cultivars. With that comes the loss of local agricultural knowledge. Yet, with climate change looming, diversity in agriculture is increasingly important and one of the tools necessary for maintaining an abundant and reliable food supply. Unveiling a thorough history of our species’ agricultural roots will not only give us an understanding as to how we got here, but will also help us learn from past successes and failures. Hence, the work that Spengler and others in the field of archaeobotany are doing is crucial.

To set the stage for a discussion of “the Silk Road origins of the foods we eat,” Spengler offers his definition of the Silk Road. The term is misleading because there isn’t (and never was) a single road, and the goods, which were transported in all directions across Asia, included much more than silk. In fact, some of what was transported wasn’t a good at all, but knowledge, culture, and religion. In Spengler’s words, “The Silk Road … is better thought of as a dynamic cultural phenomenon, marked by increased mobility and interconnectivity in Eurasia, which linked far-flung cultures….This network of exchange, which placed Central Asia at the center of the ancient world, looked more like the spokes of a wheel than a straight road.” Spengler also sees the origins of the Silk Road going back at least five thousand years, much earlier than many might expect.

Most of Spengler’s book is organized into chapters discussing a single crop or group of crops, beginning with grains (millet, rice, barley, wheat) then moving on to fruits, nuts, and vegetables before ending with spices, oils, and teas. Each chapter compiles massive amounts of research that can be a bit overwhelming to take in all at once. Luckily each section includes a short summary, which nicely distills the information down into something more digestible.

Spengler’s chapter on broomcorn millet (Panicum miliaceum) is particularly powerful. While in today’s world millet has largely “been reduced to a children’s breakfast food in Russia and bird food in Western Europe and America,” it was “arguably the most influential crop of the ancient world.” Originally domesticated in East Asia, “it passed along the mountain foothills of Central Asia and into Europe by the second millennium BC.” It is a high-yielding crop adapted to hot, dry conditions that, with the development of summer irrigation, could be grown year-round. These and other appealing qualities have led to an increase in the popularity of millet, so much so that 2023 will be the International Year of Millets.

The “poster child” for Spengler’s book may very well be the apple. Popular the world over, the modern apple began its journey in Central Asia. As Spengler writes, “the true ancestor of the modern apple is Malus sieversii,” and “remnant populations of wild apple trees survive in southeastern Kazakhstan today.” As the trees were brought westward, they hybridized with other wild apple species, bringing rise to the incredible diversity of apple cultivars we know today. Sadly though, most of us are only familiar with the small handful of common varieties found at our local supermarkets.

Of course, as Spengler says, “No discussion of plants on the Silk Road would be complete without the inclusion of tea (Camellia sinensis),” a topic that could produce volumes on its own. Despite the brevity of the section on tea, Spengler has some interesting things to say. One in particular involves the transport of tea to Tibet in the seventh century, where “an unquenchable thirst for tea” had developed. But the journey there was long and difficult. Fermented and oxidized tea leaves traveled best. Along the way, “the leaves were exposed to extreme cold as well as hot and humid temperatures in the lowlands, and all the time they were jostled on the backs of sweaty horses and mules.” This, however, only improved the tea, as teas exposed to such conditions “became a highly sought-after commodity among the elites.”

“In Central Asia, Mongolia, and Tibet, tea leaves were oxidized, dried, and compressed into hard bricks from which chunks could be broken off and immersed in water.” – Robert N. Spengler III in Fruit from the Sands (photo via wikimedia commons)

As dense as this book is, it’s also quite approachable. The information presented in each of the chapters is thorough enough to be textbook material, but Spengler does such a nice job summing up the main points, that there are plenty of great takeaways for the casual reader. For those wanting a deeper dive into the history of our food (which in many ways is the history of us), Spengler’s book is an excellent starting point.

More Reviews of Fruit from the Sands:


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