White Rot and the Quarantine Zone, revisited

This is a revised version of a post I wrote in July 2013 during the inaugural year of Awkward Botany.

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It’s garlic planting season in the northern hemisphere. A few years ago, while helping out with the garlic harvest at a local farm, I had the chance to learn about some of the challenges involved in growing garlic in southern Idaho. Apart from the fact that it is a very labor intensive crop to grow, one of the major challenges stems from a disease called white rot – easily one of the worst diseases that garlic and onion growers face.

White rot is caused by a fungus (Sclerotium cepivorum), and it affects all plants in the Allium genus, including garlic, onions, chives, and ornamentals. The disease causes the leaves of alliums to die back, their bulbs to decay, and their roots to rot, ultimately turning the plants to mush. Sclerotia, the dormant stage of the fungus, are small (about the size of a poppy seed), black, spherical structures that can survive in soil for more than 20 years. They remain dormant until the exudates of allium plants awaken them, at which point they begin to grow, unleashing their destruction. Sclerotia can be moved around by farm equipment, floods, irrigation water, wind, and by attaching themselves to plant material. Once this fungus has established itself in a field, it is extremely difficult to eradicate, making the field virtually unfit for allium crops.

The threat of white rot and the monetary damage that it can cause led to the establishment of a quarantine zone in southern Idaho in order to protect its $55 million dollar a year onion industry. Due to the quarantine zone (which encompasses 21 counties), all garlic that is grown for seed within the zone must be inspected and certified. [“Seed” in this case refers to the garlic cloves themselves; onions, on the other hand, are grown from actual seeds and are not subject to the same protocol.] Any seed garlic that is brought into the zone must go through a rigorous testing process in order to ensure that it is free of the white rot pathogen before it can be planted. Garlic is a specific threat because the cloves can readily carry sclerotia, compared to onion seeds, which are not likely to harbor them.

This process significantly limits the amount and variety of garlic that can be grown in the quarantine zone. While the quarantine is essential for warding off the threat of this particular pathogen, it stifles the garlic growing industry and makes it difficult for new garlic growers to establish themselves.

Garlic farming is already incredibly demanding due to the amount of time and physical labor that goes into planting, harvesting, drying, grading, etc. The quarantine, while understandable, is an added challenge. Learn more about this issue by listening to this story on PRX.

See Also:

Garlic emerging in the spring.

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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.”

Developing Perennial Grain Crops from the Ground Up

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

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

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

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

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

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

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

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

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

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

Using Wild Relatives to Improve Crop Plants

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Improving Perennial Crops with Genomics

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

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

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

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

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

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

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

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

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

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

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

The Nonshattering Trait in Cereal Crops

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

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

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

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

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

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

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

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

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

 

Cultivated Sunflowers and Their Wild Relatives

This is the ninth 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.

Transistions in Photoperiodic Flowering Are Common And Involve Few Loci in Wild Sunflowers (Helianthus; Asteraceae) by Lucas P. Henry, Ray H. B. Watson, and Benjamin K. Blackman

The seasonal timing of flowering is an important trait to consider in crop plants, because it dictates where geographically a particular crop can be grown and also plays a role in fitness and yield. Flowering time is determined by a combination of genetics and environmental factors. One of the major environmental factors is day length, a phenomenon known as photoperiod response (or photoperiodism).  There are three main types of photoperiod response: short-day (plants flower when “grown in day lengths below a critical maximum threshold”), long-day (plants flower when “grown in day lengths above a critical minimum threshold”) and day-neutral (“plants flower at the same time under all day length conditions”). A plant’s response to day length can be obligate – restricted to a particular response – or facultative – capable but not restricted. Understanding the genetics of photoperiod response is important for breeding efforts, and can help in the development of crop varieties that have improved yields and that can be either grown in broader geographic areas or that are specifically selected for local regions.

Agricultural breeding programs often investigate wild relatives of crop plants for potential traits that could lead to improvements. There is “renewed interest” in these investigations “because genome-enabled methods [of identifying desirable genes] and international investment in germplasm resources have dramatically reduced the associated labor, time, and risk.” The authors of this study, recognizing extensive variation in flowering time in both common sunflower (Helianthus annuus) and its wild relatives, examined the genetic basis for this variation in an effort to support sunflower breeding programs.

Common Sunflower, Helianthus annuus (photo credit: Wikimedia commons)

Common Sunflower, Helianthus annuus (photo credit: wikimedia commons)

Helianthus is a genus consisting of around 70 species, most of which are native to North America (a few occur in South America). Several species in this genus are cultivated as food crops and/or as ornamental plants. H. annuus is the most commonly cultivated species, valued for its edible seeds and the oil they produce as well as for various other things. Wild relatives of H. annuus have “been a frequent source of genetic raw material for agricultural innovation,” aided by the fact that “barriers to interspecies crosses are incomplete or can be overcome through embryo culture or chromosomal doubling.” Helianthus is a diverse genus, including generalist species occurring in “diverse environments over broad geographic regions” and specialist species occurring in “habitats characterized by high temperature, water, or salt stress.” For this reason, “wild sunflowers are prime sources to mine for alleles that confer higher yield in new or marginal” agricultural settings.

A relatively small subset of Helianthus species were involved in this study; however, the subset represented a “phylogenetically dispersed sample.” One interesting finding was that the evolution of an obligate short-day requirement for flowering has occurred in several species, “particularly those with ranges restricted to the southern United States.” The authors suggest that a reason for this finding could be that “long, hot, and humid summers” in this region “may be unfavorable for growth or reproduction.” Thus, while populations of H. annuus “likely escape these conditions by flowering in the long days of late spring,” other Helianthus species put off “flowering until the arrival of cooler, less humid falls.” Flowering during cooler times is beneficial because pollen fertility decreases and seed maturation slows at high temperatures. The risk of fungal pathogens attacking flowers and dispersed seeds is also reduced during periods of lower humidity.

Another important finding was that the diversity in photoperiod response in Helianthus appears to have a “relatively simple genetic architecture.” If this is the case, it could “greatly facilitate rapid crop improvement by marker-assisted selection.” Further studies are necessary, specifically those involving “intra- and interspecific crosses segregating for variation in photoperiod response,” in order to confirm the authors’ findings and justify “broader investment of resources into these applied efforts.”

Nuttall's Sunflower (Helianthus nuttallii), one of Common Sunflower's wild relatives (photo credit: www.eol.org)

Nuttall’s Sunflower (Helianthus nuttallii), one of Common Sunflower’s wild relatives (photo credit: www.eol.org)

While much was learned from this study, the authors acknowledge the need for “future investigations with greater taxonomic and environmental sampling.” Researchers recently produced a “draft genome” for sunflower. This additional resource will greatly aid breeding programs and further inform studies, like this one, that are interested in the “mechanistic factors and ecological agents that have promoted the emergence of the great diversity and lability in photoperiod response observed in wild sunflowers.”