User:Cat&Donkey/Perennial grain

Updating the "methods for developing perennial grains" section. Hi Emelyn,

I like how you’ve set up the problems of agriculture and a potential solution, while explaining that it has not yet been utilized. This sets up your second paragraph on why this is true for the reasons you have listed. In the third section, you expand on this by explaining typical domestication methods and how this can be hard but maybe skirted around and then following up with current projects underway. I think this flow works well. I would just be careful with the final paragraph to make sure these aren’t discussed at any length elsewhere. Some of the topics you touch on may be on other wiki pages, so just check ahead so you are not repeating info.

5/5 Evol&#38;Glass (talk) 16:26, 9 March 2021 (UTC)

Outline:

_______________________
 * 1) Introduction
 * 2) Current agricultural practices present many sustainability issues (erosion of top soil, heavily dependent on chemical inputs like fertilizers and herbicides, large fossil fuel use)
 * 3) The extensive root systems present in the soil year typical of perennial plants could alleviate these problems if applied to agriculture
 * 4) Annuals have been domesticated for 10,000 years
 * 5) No perennials have been domesticated in this time
 * 6) Domestication needs to be drastically accelerated if we want to benefit from perennial grains in our lifetime
 * 7) Plausibility of domesticating
 * 8) Why perennial grains haven't been domesticated (Van Tassel et al. 2010)
 * 9) Longer generation time, selection happens slower
 * 10) Management practices like tilling are not compatible with perennials
 * 11) Annuals tend to have higher yield than perennials
 * 12) Are high yielding perennial grains physiologically possible
 * 13) actual yield is more important that percent allocation to grain
 * 14) Evidence from Van Tassel et el. 2010
 * 15) Counter arguments from Smaje 2015
 * 16) Methods of domestication (Cox et al. 2010; Wagoner & Shaeffer, 1990)
 * 17) De novo domestication of wild plants
 * 18) Domestication pipeline (Schlautman et al. 2018)
 * 19) Candidate species selection
 * 20) Limitations of De novo domestication
 * 21) Low yield starting point
 * 22) High heterozygosity, obligate outcrosser
 * 23) Perennialization of annual crops through hybridization (Cox et al. 2002; Wagoner & Shaeffer, 1990)
 * 24) Ex: Perennial wheat
 * 25) Limitations of hybridization
 * 26) Most hybrids are infertile
 * 27) Result in intermediate yield and perennialism
 * 28) Genetic methods (DeHaan et al. 2020)
 * 29) Genomic Selection (Crain et al. 2020)
 * 30) Transgenics of annual crops into perennial species
 * 31) Target "domestication gene" orthologs in perennials
 * 32) Limitations of genetic methods
 * 33) Limited genetic information available
 * 34) Methods need to be optimized for candidate species
 * 35) Some candidate species (Intermediate wheat grass, wild rye) have complex polyploid genomes
 * 36) Progress of domestication (Cox et al. 2002)
 * 37) Current species
 * 38) Kernza
 * 39) Silphium
 * 40) Sourghum
 * 41) Legumes

Second draft

Perennial Crop Development
The current agricultural system is predominantly composed of herbaceous annuals. The development of perennial grains could improve the sustainability of agriculture. Annual systems depend heavily on tilling and chemical applications, like pesticides and fertilizers, and thus contribute to sustainability issues like erosion, eutrophication and fossil fuel use. In contrast, perennial systems involve plants with deep, long lived roots, and are not dependent on tilling, could to reduce the demand for chemical applications, build soil health, and sequester carbon.

Annual crops have been domesticated for nearly 10,000 years, whereas no commercial perennial grains have been developed. Thus, to capitalize on the potential benefits of perennial crop domestication, the domestication process needs to be accelerated. It is unclear exactly why perennial grains were not domesticated alongside annual grains during the agricultural revolution. Annuals may have been predisposed to domestication for several reasons. For one, wild annuals were likely easier targets for early domestication efforts because they generally have greater yields than wild perennials. The fitness of annual plants depends on the reproductive output of a single year so plants naturally invest heavily in seed production (the product of interest for agriculture). In contrast, perennials have to balance seed production with overwinter survival and thus produce lower yields. Second, annual plants have a shorter generation time, facilitating faster gains through the artificial selection process. Third, early agriculture utilized plowing to clear fields for the following year’s crop and the practice of annual tilling is not compatible with perennial grains. Finally, once annual grains were domesticated there was no longer a reduced incentive to pursue the domestication of new perennial grains.

If the limitations of early domestication efforts explain the lack of perennial grains, there may not be an insurmountable physiological barrier to high yielding perennials. For instance, the trade off between survival and yield in perennials should primarily be observed in the plant's first year when they are establishing root structures. In subsequent years, perennials may actually benefit from having a longer growing season and greater access to soil resources due to pre-established root systems ( which can also reduce reliance on fertilizer). However, even if physiological limitations limit resource allocation to seed production in perennials, their yields may still be comparable to or exceed annual grain yields due to improved resource acquisition and higher overall biomass.

While perennial crop domestication could alleviate some of the sustainability issues caused by reliance on annual crops, the gains may still be fundamentally limited by general agricultural practices. Producing grain on scales large enough to meet the world demand depends on the conversion of massive tracts of native grassland to agriculture, regardless of the perennial or annual nature of the crop.

Crop Development Methods
Serious efforts to develop new perennial grains began in the 1980s, largely driven by Wes Jackson and The Land Institute in Salina, Kansas. Approaches to perennial crop development generally fall under three main methods: perennialization, de novo domestication, and genetic manipulation. These methods are not mutually exclusive and can be used in tandem.

Perennialization
Hybridizing existing annual crops with perennial wild relative is a common approach to perennial crop development. This approach aims to conserve the important agronomic traits that have been developed in annual grain crops while converting the plant to a perennial life cycle with well-developed long-lived root systems. However, it is not without challenges.

For one, plants produced through hybridization are often infertile so successful breeding of plants beyond the F1, or initial hybrid generation is rare. Second, perennial traits are often polygenic (controlled by multiple genes) so conferral of a perennial lifecycle to domesticated annual crops depends on a full suite of genes being transferred to the hybrid offspring from the perennial parent. Yield traits are generally less polygenic so single genes can have positive effects on yield. Perennial crop development through hybridization may be more effective if the goal of hybridization is to introduce increased yield to perennials rather than introducing perenniality to annual crops.

De Novo Domestication
De novo domestication of perennial wild plants provides another avenue for perennial crop development. This approach involves selection of wild perennial grasses based on their domestication potential, followed by artificial selection for agronomically important traits like yield, seed shattering (the tendency of seeds to fall off the plant or stay attached until harvest), free-threshing seeds (the tendency of seeds to easily detach from the chaff) and plant height. Existing pipelines  have established criteria for evaluating the potential of candidate species to be successful for domestication programs—e.g. high variability and heritability of agronomically important traits—and also guide what traits should be focused on during breeding efforts. Extensive lists of potential candidate species can be found in Wagoner & Schaeffer and Cox et al..

Domesticating new perennial species has a couple of major drawbacks. For one, wild perennial grains have very low yields compared to domesticated annuals so breeding efforts have a lot of ground to make up before perennial grains are commercially viable. This problem is exacerbated by the fact that many candidate species are polyploid (i.e. they have extra sets of genetic material). Polyploidy makes it harder to breed undesirable alleles out of the population and create uniform plants that grow and mature simultaneously for easy harvest.

Genetic Methods
Several genetic methods can help the perennial crop development process. Genomic selection, a method of predicting plant traits based on analysis of their genome, shows promise as a method to accelerate selection of plants in domestication programs. If adult plant phenotypes can be predicted from the genomes of young plants, plants can be artificially selected at an earlier age, reducing time and resources needed to identify individuals with desirable traits. Transgenics and gene altering can add or target “domestication genes” and their orthologs (genes with similar sequences and functions) in perennial plants. Domestication genes have known effects on traits that are relevant to domestication, and have been discovered in annual crop species. Genome sequencing indicates that many orthologs also exist in perennial species that may be useful targets for genetic alteration.

Current applications of genetic manipulation are limited because the genomes of many candidate species have not been sequenced. Furthermore, methods of genetic manipulation have not yet been optimized in most candidate species. Despite these limitations, there have been rapid gains the development of genetic techniques and these methods are likely to be a useful aid for the development of perennial crops in years to come.