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.)
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.)
Deep Sequencing and Subtraction $
Verification (for first 20 genes) $
(for rewards) and Miscellaneous $
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.
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
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
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.
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
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.
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.
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.
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
Pest control and 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
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
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.
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.
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
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
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.
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.
D- Genetics of Perennialism
(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
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
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.
Perennial crops should increase the income of farmers in absolute terms and provide more consistent income year over year. When farmers particularly in developing nations have sufficient income they send their kids to school. When they do not have enough income they don't send their kids to school. If a choice has to be made of which child gets sent to school if there isn't enough money to send them all generally it is the girls who are not educated. I'm not talking huge sums. A few tens of dollars in increased profits for the farmer could make the difference.
An envelop of 50 cockscomb seeds with planting instructions. Cockscomb begins to bloom in late summer. The red flower expands until the plant is killed by frost, sometimes getting 12 inches or more in width. Very showy.
A signed glossy photograph of an Arabidopsis lyrata plant for framing or a digital picture of an Arabidopsis lyrata plant that can be used as a screen saver, etc. Primarily for Overseas pledgers and those who can't grow my seeds and plants. They might be worth someting when this project succeeds:)
A Frozen Rose- A video of a rose frozen in liquid nitrogen and then shattered into a million pieces only in reverse with dramatic music. A floral version of the evil robot fromTerminator III. Primarily for Overseas pledgers and those who can't grow my seeds and plants.
Planting and care instructions plus A 3-inch pot with a lisianthus (echo series), campanula (champion pink or blue), or larkspur (imperial mix) plant. These plants will all bloom during the summer of 2013 and are excellent for cutting. Only 350 for the summer of 2013.
A virtual larkspur- a time lapse video of of the growth of larkspur flower from seed to bloom over the course of five months with dramatic music. Primarily for overseas pledgers and those who can't experience the real thing.
An Arabidopsis gene identified through the project will be named in your honor (assuming a gene is found without a previous name). Genes will be named in the order of sponsership until all genes are named.
Be immortalized by having a future perennial wheat cultivar named in your honor. This will be a whole new class of crops that will be grown for centuries into the future. When farmers and researchers study the history of perennial wheat your name will be indelibly linked to it as the one whose funding made it possible. Also be one of the first to receive a 50 pound sack of perennial wheat seed, enough to plant an acre of wheat.