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.”

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)