Finding Genes to Create Perennial Crops
Finding Genes to Create Perennial Crops
I want to create perennial crops that are better for people and the environment. This project is to identify "perennialism" genes.
I want to create perennial crops that are better for people and the environment. This project is to identify "perennialism" genes. Read more
The shipping is included with the reward.
Modern agriculture is reliant on annual crops that have to be planted each year. This project is a first step to developing perennial crops, crops that are planted once and then harvested for multiple years. I believe perennial crops will address many of modern agriculture's problems. Perennial crops will allow farmers, in both the developing and developed worlds, to grow more food, on less land, with less water, and with fewer chemicals. Perennial crops will reduce pollution and protect soil, wild lands, and water ways. Perennial croplands will be better habitat for wildlife. Indirectly, perennial crops will impact everything from eliminating childhood malnutrition and increasing the resources farm families have to send their children to school in developing nations, to ending the need for crop subsidies and reducing the carbon foot print of developed nations. (For more detailed discussions of the potential benefits of and concerns with perennial wheat see Appendix A and B.)
Despite the potential, there are only a few groups in the entire world trying to breed perennial grains using classical methodologies and there is no research team of which I am aware dedicated to understanding the basic genetic mechanisms that give rise to perennialism.
I am requesting Kickstarter help to fund a small $15,000.00 project to do the first subtraction of the genes expressed by the perennial/annual model plant pair: Arabidopsis lyrata and Arabidopsis thaliana. The goal of the subtraction is to pare down over the next year the list of 30000 genes in the perennial plant to just a few “differentially expressed” genes that have a high probability of being able to transform a plant that normally only lives for one year into a plant that survives multiple years. (The plan is more fully explained in Appendix C. The genetics of perennialism are presented in Appendix D.)
RNA Extraction $ 2,700
Illumina Deep Sequencing and Subtraction $ 7,400
Expression Verification (for first 20 genes) $ 2,400
Postage (for rewards) and Miscellaneous $ 2,500
TOTAL REQUEST $15,000
I am requesting only funds to pay for the supplies necessary to do the project. Wilmington College is providing the needed equipment and lab space. Anything else required for the project I will provide. No salary is included in the budget. This is part of my commitment to the project.
This is a lean budget permitting a single sequencing run each for the perennial and annual. Statistical analysis improves with additional runs. If the project’s funding request is exceeded the additional resources will be used to do more sequencing and to begin the characterization of the differentially expressed genes that are identified through this project.
Perennial research has suffered from the inconsistent support of traditional funding agencies. Part of the reason for seeking Kickstarter funds is to try to circumvent the chicken-and-egg problem that my project is currently experiencing. Funding agencies want more results before they will commit to the project, and it’s difficult to provide them with more results until I receive some funding.
Once the gene candidates have been identified and verified the next step will be to functionally characterize them. In the case of perennialism, the goal is to introduce genes from the perennial Arabidopsis lyrata into the annual Arabidopsis thaliana. If the annual becomes a perennial then the gene will be proved to be responsible. The assay is simple, does the plant live when it otherwise wouldn’t.
Once it has been worked out which genes give rise to perennialism in the model plant Arabidopsis, the research will move into wheat. It will need to be shown that the wheat versions of the Arabidopsis genes allow perennialism in wheat. Then the genetic information can be used for the marker-assisted breeding of the perennial wheats that have been created through traditional breeding, or for genetic engineering of perennialism into annual wheat. (See Appendix B, Section 4 for a discussion of the two approaches to create a perennial wheat.)
Appendix A- The Benefits of Perennial Wheat
Eventually I would like to see perennial varieties of all of the cereal crops (corn, wheat, rice, oats, rye, barley). Initially I am focusing on wheat because it is already capable of overwintering. It only needs to be breed to re-grow after it is harvested, or perhaps more accurately not to die completely after its seeds have ripened. A perennial wheat could have numerous advantages over annual wheat. Least among these is the obvious advantage that perennial wheat would not have to be planted every year saving fuel, the farmer’s time, wear and tear on equipment etc. Other important advantages are:
Perennial wheat could re-use its roots from year to year.
Re-use of its roots opens up two possibilities for a perennial. It can direct the resources into the shoot and grain that it would otherwise have needed to build its roots thus increasing its yield. Alternatively it can still use the same proportion of resources to build roots each year but instead of starting from scratch it can expand the root system it already has. In the later case, the larger, deeper root system should increase the perennial wheat’s drought tolerance and improve its nutrient acquisition lessoning fertilizer and irrigation needs.
Perennial wheat could have its roots in place at the beginning of the growing season.
Since the roots of perennial wheat should already be in place at the beginning of the growing season, the plant can direct its resources into building the shoot. Quick canopy closure could lessons competition from weeds. It also means that the plant can reach its maximum rate of photosynthesis quicker which will contribute to improved yields.
With roots already in place, nutrients can immediately be mobilized from the soil in support of photosynthesis and any fertilizer applied can be quickly bio-incorporated perhaps in a single application. In the case of dry years, growth can commence immediately without the need to wait for rain because the existing roots can access deep soil moisture.
Perennial wheat has a longer growing season.
Typically winter annual wheat is harvested around the Summer Solstice, the day when there is the most sunlight and when there is the greatest opportunity for the plant to photosynthesize. This means that in July, August, and September if nothing is planted in the field about 1/3 of the yearly potential sunlight that could be captured by crops in the field is lost. Even if the field is double cropped, often the soybeans planted after the annual wheat are so small in July that they are only able to capture a tiny fraction of the sunlight available to them. There is also a risk that double-cropped soybeans won’t have enough rain to germinate.
Perennial wheat will end most tillage.
Tillage of fields is one of the top causes of erosion of top soils. It also is responsible for the loss of up to half of the organic matter in soils. Erosion and the loss of organic matter have led to the degradation of soil properties (tilth, water infiltration, fertility, etc.) which has cost farmers productivity and led to increased fertilizer use and irrigation. It has also meant that rather than buffering climate change by storing carbon in soil, agriculture has made the problem worse by contributing CO2 to the atmosphere.
No-till farming which requires the extensive use of herbicides has helped to eliminate most erosion where it is practiced. However there are questions as to the sustainability of the practice as weeds evolve resistance to the herbicides.
Perennial wheat straw could be an excellent biofuel.
Natural prairies have vast soil stores of carbon generated from the deep expansive root systems of the perennial grasses of which they are composed. If similar expansive root systems are replicated in perennial wheat it may be possible to build soil carbon in crop fields while harvesting the straw as an environmentally-sound and economical feedstock for biofuel production. As it stands now, removal of annual crop residues is met with skepticism based on the belief that without the non-grain portions of the plant being returned to the soil each year the agricultural soil carbon pool would disappear entirely.
Perennial wheat can be grown vegetatively.
Hybridization has contributed greatly to the productivity of modern corn/ maize, but similar benefits have not accrued in other crops, like wheat, because of the difficulty and cost of emasculating their flowers. Perennial wheat changes the equation in two ways. First the male sterile plants needed for easily and cheaply creating hybrids with higher yields and vigor can be maintained and multiplied vegetatively. Secondly the hybrid wheat itself can be propagated vegetatively. Vegetative propagation imparts longevity to a hybrid allowing the cost of its creation and multiplication to be amortized over multiple years.
Perennial wheat will be better cover for wildlife.
The expectation is that perennial wheat fields will function more like natural grasslands with all of the associated benefits to wildlife because of their lush and extended season of growth. Bare fallow fields are for all practical purposes deserts for wildlife, without cover and food. Since perennial wheat fields won’t need as many herbicides to prevent yield-affecting levels of weeds from growing, they should have more non-crop plants. At least in some circumstances, non-crop plants have been shown to provide refuge for pollinators, and refuge for beneficial insects, etc that control crop pests. Perennial wheat should reduce pollution of waterways both because fewer fertilizers and herbicides should be required and because the plant should be more effective at stopping erosion and leaching of the chemicals that are applied.
Perennial wheat will be more profitable to grow.
In every way, perennial wheat should be more profitable to grow because the farmer won’t have to spend as much to obtain similar or higher yields compared to its annual counterpart. This has several ramifications: Farmers will make better livings. Because their farms are more profitable, farmers won’t need regular federal crop subsidies as often. This should over the long run result in less of a burden on taxpayers to support these vital, but expensive farmer assistance programs. (The wildlife benefits may also allow agriculturally targeted conservation programs to be adjusted.)
The cost savings to grow high yielding perennial wheat will be especially significant in the developing world where capital for investment in agriculture is scarce and inputs are expensive and difficult to obtain. Even small reductions in the need for inputs could have major ramifications for the logistics of providing assistance to isolated developing world farmers. Crops that yield well with fewer inputs often mean the difference between food security and malnutrition. Farm profit also very directly translates into whether or not children, especially girls, are sent to school, medical care is obtained, houses have mosquito nets and running water, etc.
Appendix B- Potential Concerns with Perennial Wheat
Pest control and Hessian Flies
Hessian flies infestations in annual wheat are controlled by restricting its planting to no sooner than a week before the first frost. Obviously this wouldn’t apply to perennial wheat. To control Hessian flies in perennial wheat breeders will have to incorporate the natural genetic resistance to the pest already found in many annual wheat cultivars. Other wheat pests will have to be dealt with similarly if they were previously controlled through cultural methods.
Winter Damage From “Excessive Fall Growth”
It is expected that perennial wheat will have a heavy stand well beyond what is referred to as “excessive fall growth” in annual winter wheat which is susceptible to winter damage. Rather than a liability though, I see several opportunities. Firstly, it is possible that the perennial wheat may be able to be bred so that it can be harvested a second time in the fall. Secondly, the perennial wheat stand may be able to be grazed. Thirdly, perennial wheat stands may be able to be mowed. Finally it may be the case that perennial wheat behaves less like annual wheat and more like a natural prairie grasses. In this respect, the new wheat shoots in the spring are protected by and then grow through the dried shoots from the previous season.
Perennial wheat is not expected to be invasive though extensive testing of perennial wheat will have to done to prove this definitely. To survive in high density plantings, perennial wheat, just like annual wheat, will be limited in its ability to produce allelopathic compounds (chemicals secreted by the roots that restrict the growth of neighboring plants.). Also, as with annual wheat, almost all of perennial wheat’s seed will be consumed by people leaving little to escape into wild lands. Any of the large nutritious seeds that do escape are likely to fall victim to a myriad of seed eaters-birds, insects, small mammals, etc.
Genetically Modified (GMO) Perennial Wheat
Attempts have periodically been made to develop perennial wheat using traditional breeding methodologies. The earliest attempts were made by Russian scientists in the 1920’s. The latest attempts are underway at the University of Washington and the Land Institute. All of the traditional breeding attempts have involved crossing domesticated annual wheat with a wild perennial relative of wheat. All of the traditional breeding attempts have been successful at creating perennial wheats, but all except for the most recent attempts were abandoned when funding dried up because the perennial wheat’s yields couldn’t be quickly raised to the levels of annual wheat. Whether this proves to be the case for the current efforts remains to be seen. They have been at work breeding perennial wheat for 20 years and predict that it will take another 20 years to achieve yield parity with annual wheat.
One thing that could help the current efforts to beat the odds to quickly produce a commercially- viable perennial wheat is if breeders know which genes were required for a plant to be perennial. They could screen for the gene(s) when the plant is just a few weeks old, eliminating the need to grow them for over a year, and at great expense, to assess whether or not they are perennial.
Traditional breeding in some ways substitutes one problem, perennialism, for another, yield. Even if this is overcome, several other issues could arise. It is not known how easily the newly created perennial wheat will able to be crossed with existing wheat varieties. If it is not easy to cross, introducing disease resistance, local adaptations, and other novel traits from other wheat varieties in the future becomes very difficult. Immediately, this problem will apply to the perennial wheat’s grain qualities. Wheat markets currently recognize five categories of wheat based on the baking qualities of their flour (hard red, soft red, hard white, soft white, and durum). It is not clear into which category perennial wheat will fall, whether a new category/ new market will have to be created for it, or if varieties of perennial wheat can be developed that will fit in the five existing categories. Finally, assuming all of these problems are overcome and perennial wheat is a great success, the question remains as to how the work to perennialize wheat can be translated to all of the other annual cereal crops- rye, oats, secale, barley, rice, maize, and sorghum without going through similar 40 to 50 year development programs for each crop.
Genetic engineering of perennialism cuts through all of this. It is applicable to any species or variety of those species. It involves transferring only those genes needed for perennialism without affecting any of the other traits (yield) of the plant. The resulting GMO perennial plants can then be easily crossed by anyone anywhere in the world trying to improve a crop through traditional methods. It should also be rapid and relatively inexpensive. Importantly in the case of perennializing wheat, it is not being used to do something that isn’t possible through traditional breeding, it is only being used to overcome some of the problems inherent in traditional breeding.
High-Yielding Perennial Wheat Is Unnatural
I believe there are at least four main reasons why we have annual domesticated cereals today, keeping in mind that the annual cereals are nothing like their wild ancestors. The first is historical. In almost all of the places where agriculture took root, annual wild grasses were dominant. Once work was begun to domesticate these annual grasses, their head start was an overwhelming advantage even when agriculture spread into areas where it probably would have been better to switch to a perennial grain. Secondly, early domestication was a race to identify rare agronomically favorable traits in plants. Annual grasses provided many more opportunities to do so because of their shorter generation times. Thirdly, the annual grasses that become our domesticated crops were all self pollinating. This means that it was much easier to develop in-breeding populations with individual plants that were homozygous for rare beneficial recessive mutations. Lastly, annual plants have few if any requirements to germinate or flower. Contrast this with perennials which have lots of requirements to germinate and flower which often translates to them not having a harvest the first year from seed
None of the reasons for why I believe we have annual crops precludes perennials having high yields. Further most of the reasons annuals were domesticated instead of perennials are no longer insurmountable in light of our modern understanding of genetics and biology.
Appendix C- Details of the Project Plan
The objective of this project is to winnow down the list of Arabidopsis lyrata genes to only those required for the plant to be perennial. Arabidopsis lyrata has about ~30000 predicted genes. About ¼ or 7500 are not paired with Arabidopsis thaliana genes according to the fully aligned senteny map that shows which gene in the perennial Arabidopsis lyrata genome corresponds to which gene in the annual Aarabidopsis thaliana genome, and vice versa. (Meaning there are immediately 7500 candidates for perennialism genes in Arabidopsis lyrata if you assume the perennialism genes are completely missing in Arabidopsis thaliana.) Not all of the 7500 genes are going to being actively transcribed at the relevant time and in the relevant tissues that I predict are important for perennialism. Therefore, expression analysis and subtraction should allow the list of 7500 Arabidopsis lyrata genes to be pared down to less than 1000 genes, perhaps as few as 500. The orthologues of the 1000 to 500 genes will be identified in wheat and the other sequenced grass genomes. The genes whose orthologues lie in regions predicted to be important for perennialism by earlier studies will then be the priority for additional research. It is hoped that this final level of analysis will eliminate all but one hundred candidate genes or so, a reasonably small number for additional characterization.
Arabidopsis lyrata and Arabidopsis thaliana
To identify the genes that regulate perennialism, we propose to use the perennial Arabidopsis lyrata (CS22696) and the annual Arabidopsis thaliana (CS6688, Edi-0, an accession that flowers under the same condition as Arabidopsis lyrata). These two species are superior for studies with a heavy bioinformatic/ deep sequencing component, like the project we are proposing, because they are the only co-generic perennial/ annual pair of plants with fully sequenced genomes and a senteny map. Further, abscission zones and senescence restriction are predicted to be important for perennialism. Arabidopsis thaliana does not have an abscission zone at the base of its peduncles and its rosette begins to show signs of senescence even before its seed pods (siliques) dehisce (Patterson, 2001). This is contrary to Arabidopsis lyrata which does seem to have abscission zones at the base of its peduncles and shows no signs of rosette senesce even after all of its seeds have been shed (pers. observation). Finally these two species are superior for doing knock-out (RNAi) and gain-of-function mutagenesis through simple and easy floral-dip methods (Literally the flowers are soaked in a solution containing the bacteria with the mutagenizing construct.) This is critical for determining the function of any genes that have roles in perennialism as implicated by the subtraction analysis. (Most of the genes responsible for “perennialism” phenotypes and QTLs seem to be uncloned precisely because of the relative difficulty, time, and expense of doing genetics and molecular biology in crop species.)
Plant material comprising the organ boundary zone between the peduncle and the rosette just before and after flowering has been harvested and is now in a freezer at Wilmington College. Precautions were taken to make certain that the two sets of plants were grown and treated as identically as possible to ensure that the only variables are those directly associated with perennialism. The time period just before and after flower and the location at the base of the peduncle are hypothesized to encompass the critical time and tissues for perennialism.
The RNA will be extracted from the plant material using an Invitrogen Trizol and Column RNA Extraction Kit according to the kit’s protocol. The kit based extraction is the suggested method for RNA isolation by the Molecular and Cellular Imaging Center (MCIC) of The Ohio State University for Illumina deep sequencing.
Illumina Deep Sequencing and Subtraction
MCIC will process and sequence one RNA sample from the perennial Arabidopsis lyrata and one RNA sample from the annual Arabidopsis thaliana. Each Illumina column run is expected to return 25 million short sequence reads that can then be aligned against the respective genomes. The level/ frequency of expression will be determined based on how many times a given sequence shows up in a run. With the assistance of the staff of MCIC, the web-based Galaxy genomic analysis platform will be used to automate the removal of the linker sequences, the aligning of the high quality sequences against their respective genomes, and the assigning of the expression frequencies to the individual genes.
Once candidate genes are identified for further study their differential expression will be verified by RTPCR. New RNA will be extracted from the perennial and annual plants as stated above. The RNA will be reverse-transcribed into DNA. An equal quantity of DNA for the perennial and the annual will be used as template for standard short, 20-25 cycle PCR amplification of the genes of interest. The PCR products will be checked on a gel to see if there is more amplification product for genes that are more highly expressed.
Genes with Orthologues on the 4E Chromosome of Thinopyrum elongatum
To prioritize gene candidates for further study the list of differentially expressed genes will be sorted using several additional criteria. The first criterion is whether an Arabidopsis species differentially expressed gene has an orthologue (best sequence match) on or near the proximal quarter of the short arm of the 4E chromosome of Thinopyrum elongatum, the region that has been shown to contain a required gene(s) for perennialism in perennial wheat.
Unfortunately Thinopyrum elongatum whole genome sequence is not available, but comparable chromosomal regions of wheat, switchgrass, or another of the sequenced grass species can be used as a substitute to the degree that these regions are sentenous (their gene order conserved). The whole switchgrass genome has just become available. It is especially valuable because it is the first perennial grass to be sequenced, and is likely the only perennial that shares senteny with Thinopyrum elongatum and the other grain crops (rice, maize, sorghum). Some genes may only be present in the genomes of perennial plants, so switchgrass opens up the possibility of establishing their location when otherwise it wouldn’t be possible.
Differentially Expressed Genes near “Perennialism” QTLs
As for the 4E chromosome of Thinopyrum elongatum, orthologues of the Arabidopsis species differentially expressed genes near QTLs for a perennialism-associated trait will also be a criterion for giving priority to genes for further study. There are approximately 50 QTLs (about 25 unique genes) that have been identified for perennialism-associated traits in maize, sorghum and rice. While not all of the phenotypes represented by the QTLs are present in Arabidopsis species, it is expected that at least some of the genes they represent are involved in senescence restriction, abscission zone processes, and/ or organ boundary zone processes.
Genes Unique to Perennial Plants
In addition to prioritizing gene candidates that are near QTL’s or on the 4E chromosome of Thinopyrum elongatum for further evaluation, differentially expressed genes will be given a high priority if they have orthologues in perennial species, but not in annual species, particularly not in Arabidopsis thaliana. Arabidopsis lyrata, and Arabidopsis thaliana, diverged over ten million years ago. If annualism is a result of a non-functional gene(s) then that amount of time should be sufficient for the gene(s) to accumulate enough random mutations for the gene’s signature to be lost.
Besides genes that are perennial specific, near QTL’s, or on the 4E chromosome of Thinopyrum elongatum, generally, genes will be given priority for further study if they have very strong differential expression, have interesting predicted functions, belong to interesting classes of genes, or otherwise stand out. MADS-box transcription factors, like the tomato JOINTLESS gene, and receptor-like kinases, like the Arabidopsis thaliana HAESA gene, for example will be pursued because they have previously have been shown to be involved in regulating abscission zone formation. CUC gene family members will be investigated because they have previously been implicated in organ boundary zone formation. Zinc finger (Knuckles/ C2H2-type) transcription factors will be tested because of their suspected role in rhizome formation in perennial rice.
Appendix D- Genetics of Perennialism
Inflorescence (flower and associated peduncle (floral stems)) ripening in perennials follows a very precise pattern. It proceeds to the base of the peduncle, the place where the inflorescence originates from the main stem, or rosette, and then stops. At the base of the peduncle is an organ boundary zone that is morphologically and physiologically distinct from surrounding tissues. Early on, the organ boundary zone is important as a region that separates two tissues with different developmental fates. Later it is important when it becomes an abscission zone, the place where the peduncle physically detaches from the rest of the plant once ripening (senescence) is complete. Recently I have begun to wonder if it has a third function as a barrier that contains the senescence signals emitted by the developing seeds so that they ripen normally without the rest of the plant dying.
The Arabidopsis thaliana SOC1/ FUL Double Mutant
Recently researchers produced an Arabidopsis thaliana suppressor of overexpression of constans 1 (soc1)/ fruitful (ful) double mutant which produces a rosette in place of flowers, which in turn produces a rosette in place of flowers, without apparent end. The mutant does not senesce and the plant becomes a pseudo-perennial. Soc1 and ful interact in a pathway that permits flowering of Arabidopsis thaliana plants when they are exposed to long-days. My hypothesis for the pseudo-perennial phenotype of the double mutant is that flowering is initiated, but because of the mutations, the plant defaults to the production of leaves. The leaves then produce auxin and decreased amounts of ethylene which inhibits normal senescence. If this is true, then it is reminiscent of how abscission zone processes are controlled in the organ boundary zone.
The double mutant is evidence that the life history of a plant can be radically changed with relatively few genetic manipulations, but it does not provide insight into how normal perennial plants limit senescence to just the meristems that have flowered because the mutant appears to produce few normal inflorescences. It does, however, beg the question as to whether the previously observed absence of an abscission zone at the base of the peduncle in Arabidopsis thaliana is the reason for its annualism, because the species is clearly physiologically capable of surviving longer. Arabidopsis thaliana does have abscission zones, and similar dehiscence zones, that permit flower petal shedding, pollen maturation, silique opening, and seed shattering, so most of the mechanism for abscission must be functional. This suggests that there may be a regulatory reason as to why Arabidopsis thaliana’s does not form an abscission zone at the base of the peduncle.
Candidates for “Perennialism” Genes
There are as of yet no published papers specifically addressing the genetic differences between perennial and annual abscission and organ boundary processes, particularly with a focus on senescence regulation. However, there have been a number of studies to identify “perennialism” and “perennialism- associated” genes more generally. Unfortunately none of the individual genes for the phenotypes or QTLs discussed in these studies have yet been cloned and published. Despite this, the studies do suggest that the likely number of regulatory genes that lead to the gaining of senescence restriction in perennial plants is relatively few in number, assuming that senesce restriction genes are a small subset of all “perennialism” genes.
Annual wheat x perennial Thinopyrum elongatum hybrids are said to exhibit post-sexual cycle regrowth (PSCR). Plants that show PSCR survive multiple seasons, each season producing new tillers after their ripe seed is harvested. PSCR is very likely the result of senescence restriction and abscission zone processes though it has not been discussed in that context. Deletion analysis has revealed that the proximal quarter (closest to the centromere) of the short arm of chromosome 4E of Thinopyrum elongatum, estimated to contain fewer than 500 genes, is required for any degree of PSCR in wheat x Thinopyrum elongatum hybrids, although the region is insufficient for 100% penetrance of the PSCR phenotype.
In crosses between the perennial Zea diploperennis and a primitive annual popcorn, perennialism appeared to be inherited as a single recessive gene. However, when Zea diploperennis was crossed with WMT corn the results suggested that perennialism was governed by two dominant genes. In the latter case the “perennial” maize was scored for evergreen stalks, a trait that again suggests that in the perennial there has been a change in the transmission or receptivity of the plant to senescence signals.Qualitative trait loci (QTL) analysis of perennial and annual teosinte crosses complimented the segregation analysis, showing just a few QTLs for each of the eight traits associated with perennialism that the researchers measured, including: three for withered stems (the opposite of evergreen stalks), two of which were on the same chromosome.
Risks and challenges
After the initial project to compile the list of candidate senescence restriction/ perennial genes, the next phase of the research will be to determine what the genes do in the Arabidopsis species. This functional characterization will begin with mutagenizing the candidate genes and studying the changes to the plants. It is hoped that the mutations will result in the perennial Arabidopsis lyrata becoming an annual and the annual Arabidopsis thaliana becoming a perennial. If this turns out to be the case then it should be relatively straight forward to find the wheat/ grass versions of the genes and then test to see if they have the same activity in wheat as the Arabidopsis genes have in Arabidopsis. If this best case scenario holds true then the gene information could be ready for marker-assisted traditional breeding or genetic engineering perhaps in as little as five years.
The gene mutations in Arabidopsis may not produce clear perennials and annuals. This could be because the relevant genes weren’t unmasked by the subtraction. It is recognized that this approach may exclude the identification of expressed genes with very low copy number, important genes that differ only in their coding sequences, and miRNAs. However it is felt that subtraction, followed by mutating the differentially expressed genes, is more cost and time effective per gene of interest characterized than the alternative, random mutagenesis of the entire Arabidopsis lyrata genome.
Another reason gene mutations in Arabidopsis may not produce clear perennials and annuals is that several distinct genetic pathways interact to determine if a plant is a perennial or an annual. If this is the case, it may require several years of creating double and triple mutants plants to investigate how the genes interact. It may also require additional expression studies to determine which genes are turned off or on by different mutations. It is conceivable too that we may end up with genes acting relatively late in the senescence restriction. Then it may be necessary to “walk’ upstream to find the key regulatory genes in the senescence restriction/ perennialism pathways.
The critical “perennialism” genes in Arabidopsis may be different than the critical genes in wheat and the other grasses. I could start by working with grasses. A fair amount of work on perennial genes has been done in crop species, but it is far easier to start from scratch with the Arabidopsis species because of their superior genetic and molecular biology resources, than to try to pick up on the existing crop research. Until there is information to the contrary, I have proposed what I believe will be the easiest, quickest and least expensive path to finding the genes required for senescence restriction and perennialism.
Several facts buffer my belief that the perennialization of wheat will proceed according to the best case scenario. Perennials have evolved from annuals multiple times and in multiple lineages. This suggests that it is relatively easy to alter plant life histories genetically and it involves relatively few genes. Similarly annuals have evolved multiple times and in multiple lineages from perennials. It is believed that all of the annual ancestors of today’s annual cereal crops evolved from perennial lineages. In almost every case when the perennials are crossed with the annual crop relatives the progeny are perennial. This suggests that perennialism is dominant, that the cross likely restores a gene function that is missing in the annual, and that perennialism again involves relatively few key genes.Learn about accountability on Kickstarter
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