Importance of Natural Resources

Oil palm & the rainforest – Genome sequencing for sustainability – October 7, 2013


Thanks for that lovely introduction back
here it’s a great pleasure to talk here always and for those of you who saw my
last public lecture of Cold Spring Harbor is about a year ago at the plant biology
symposium this is going to be a update on where we were then and I entitled it
send in the clones part two for that reason so clones are very important in
plant biology I’m gonna explain why and then I’m going to tell you about the oil
palm genome sequencing project which I’ve been involved in actually for the last
ten years now and has some recent discoveries that we made and then
finally I’m going to tell you about the potential for other sorts of plants as
biofuels and perhaps to do something about climate change in the long term
okay so clones well when we when we think of human clones especially human
reproductive cloning it’s obviously a very controversial matter has been the
subject of many movies in the last few years but clones of course much much
more common and widely propagated in plants in fact the word klónos in greek
means a little twig or branch that you can propagate as a vegetative cutting
which will completely recapitulate the genetic material found in the parent
tree and so effectively as a clone clones are actually very very common in
nature the oldest and probably the largest organism on earth is a clone
it’s a stand of quaking aspen in utah it’s called pando which is the latin for
i spread and it’s estimated to be about 50,000 years old the entire clone is
male so it’s it’s an interesting life habit and it weighs at the moment with
the 40,000 or so stems more ramets it weighs something like 6,000 tons over
the years it’s expanded over many many acres and actually it’s thought to be
older than the last two ice ages it propagates through the roots so the
roots are the other the way in which these stands are related but of course
over time as well as being entirely male pando has lost most of its fertility and
so it probably hasn’t sexually reproduced in something like 10,000
years which is as I said an interesting life strategy and there are other clones
plant clones that you’re probably more familiar with than panda grapes are
propagated as clones they’re propagated as cuttings actually by grafts and they
can occupy huge areas this is a vineyard in Chile I was up fairly recently and of
course each each variety of grape is highly prized for its uniformity so if
you have a Pinot Noir you want it to be Pinot Noir Pinot Gris you wanted to be
Pinot Gris but in fact many of these many of these prized clonal varieties
would derive from each other and that’s because they can be unstable and so for
example Pinot Blanc is actually a derivative of Pinot Noir and it’s a
derivative that arose through vegetative propagation probably sometime
in the middle ages and we now know a lot more about this variation we sometimes
call this epigenetic variation between otherwise genetically identical clones
between individuals that are clonely related much of this variation in clones
is caused by epigenetic effects on something called a transposable element
these were of course discovered here the Cold Spring Harbor in the 1940s
and 50s by by mcclintock and they can cause actually genetic as well as
epigenetic changes in clones as as using mechanisms and principles that she
discovered a long time ago and in fact those varieties of grapes that I just
showed you turn out to be caused by the insertion of these transposable elements so transposable elements are responsible for for much of this
variation so Pinot Noir has this beautiful dark color anthocyanins in the
skin whereas Pinot Blanc has this insertion of a transposable element
or sometimes called jumping gene these are pieces of DNA that can move around
the genome and when they integrate next to a gene or within a gene they can
actually change the way that gene behaves a subsequent rearrangement in which
most of the transposon was lost has led to Pinot Gris and so the the full range
of color that is in these Pinot grapes can be explained by by the just the sort
of variation that I was just talking about okay so why are clones successful in
nature considering the fact that they often sacrifice fertility as pando has
done over the last 80 thousand years but they still survive very well and each of
their individual members survives and part of the reason for this is that they
maintain something called heterozygosity what that is is the genetic contribution
that comes from both the original parents this is something you’re
probably very familiar with it’s often called hybrid vigor and hybrid vigor is
really the key to much of modern plant breeding hybrid vigor is still not fully
understood there’s a lot of theories about hybrid vigor and I’d be delighted
to tell you that we think we are getting a little bit close to at least one of
them even in the oil palm but it’s still one of the great mysteries of plant
genetics but this is why clones which of course maintain that hybridity
because they don’t sexually reproduce they don’t shuffle the genes the
combinations from the parents they just maintain them from one from one
propagated propagule as they call to the next and in contrast of course sexual
inbreeding which is practiced in many plant reading schemes leads to poor
performance at least as something called inbreeding depression and actually
that’s true of inbred animals and inbred humans as well just think of the British
royal family for example I didn’t really say that so you know you did the the the
success of clones really results on this on this maintenance while the principles
of hybrid vigor were actually first here at Cold Spring
Harbor more than 100 years ago now in 1908 by George Shull who perfected the
art of embedding parents of corn and then crossing them together so they
generated a uniform hybrid population now there’s inbreds
weren’t particularly high yielding they were just stable and that was difficult
to do but he did it but the hybrids were very high yielding because again they
got both contributions from both parents and as I said at least in maize the
molecular the sort of DNA basis for this hybrid vigor is still not fully
understood but working here as well as in Israel with his former adviser Danny
Zamir this is Zach Lippmann who’s assistant professor in the plant group
and he was able to show that one of the most important genes involved in tomato
breeding it’s called the S gene is in fact one of these genes that exhibits
it’s what’s called single gene heterosis hybrid vigor in which just a single
allele at each gene is enough to give you a heterozygote a hybrid that’s
better than both parents and way better so these hybrids are used in commercial
breeding and they produce a lot more yield than than that than other other
tomatoes this is a very important discovery made a few years ago okay so
what I’m really going to be focusing on today is how are the principles of plant
genetics I told you about clones and hybrids and so on can potentially be
used to solve some of the major problems in agriculture and also importantly in
bioenergy in the impact of bioenergy on for one thing providing energy which is
itself valuable but also solving one of the you know great crises of today which
is of course the carbon problem you probably don’t need me to remind you of
this but essentially fossil reserves which are essentially ancient plants and
ancient animals which have contributed carbon to these fossil deposits are
consumed in the most crude way by burning to produce energy and that
energy unfortunately also gives rise to the release of atmospheric carbon
atmospheric carbon would normally through various mechanisms of climate
change have some pretty nasty effects but plants can fix that carbon they can use photosynthesis and reduction power that
comes from photosynthesis to to make sugars initially out of that carbon and
that fixes it it takes it out of the atmosphere so if you can use plants
existing plants instead of fossilized plants as fuel you could potentially
close this circle and prevent the release of excess atmospheric carbon so
that’s the real promise of biofuels in addition to issues like you know oil
dependence and and economic issues this is really the much more long-term value
of biofuels okay well if we look at what sort of crops have been used for
biofuels there’s a number that have been used I’m just giving a little a little
taste of them here one of the most popular in the United States has been
corn itself but actually corn has of course been bred and domesticated
actually have a thousands of years and bred over hundreds of years to produce
food not fuel and it’s in fact not that efficient that producing fuel and the
reason for that is you need a lot of high input so fertilizer you need to
carry it around you need decent land irrigation and so on to make high
yielding corn and we have very high yielding corn but after you’ve put all
that energy in the amount of energy you get out is at best a ratio of about 1.5
which isn’t very good and that’s actually a generous estimate some people
think it’s actually less than one kind of oil crops are often better than that
so rapeseed oil for example is decent at around two or three or so but really to
get up to the the really high value energy crops we need to look at a much
more recent or recently domesticated plants such as sugar cane which is one
of the biggest biofuel crops in the world palm oil which I’ll be telling a
lot more about and some new technologies that I’m not going to tell you about in
which we’re trying to directly convert cellulose material think of you know
paper if you like but the stems the stove
plants into ethanol this is this is not yet been done at any sort of efficiency
that makes sense but industrial plants will already exist so this is a
potential hope for the future but right now the most the most high yielding
energy crops are in fact clones or what are propagated as clones that includes
oil palm trees as I’ve explained in a moment but also probably more familiar
sugar cane plants so in Brazil a sugar cane has been a very very effective
source of biofuels of course the way that works is you get the sugar out of
the plants you can you then convert it into ethanol using fermentation and use
the ethanol as liquid transportation fuel you just add it as an additive to
gasoline and in fact their sugar cane is propagated as clones the
way that’s done is as vegetative propagation from year to year you can
plant a little piece of the stem you can’t actually do that for every year it
only lasts about six or seven years and then you have to go back and replant but
nonetheless you get these very uniform and very high yielding populations of
clonal sugar cane and sugar cane of course can only be grown in
certain parts of the world but nonetheless in those parts of the world
like Brazil it said it’s a very important part of biofuel production but
oil palm is actually right now the most efficient producer of bioenergy on the
planet for every unit of energy you put in you get something like nine units out
and furthermore it comes out as biodiesel which is an extremely
efficient fuel you can easily convert into jet fuel and so on and in fact a
Richard Branson flew one of his one of these planes on palm oil to demonstrate
this about five years ago and there’s been a lot of interest in palm oil as a
potential biofuel then because of this there are numerous problems with palm
oil and I’ll be getting into that in a big way in a moment but anyway it was a
it was a number of years ago now that we started our collaboration on the oil
palms I I’ve got a lot of pictures from my
various collaborators or in the world I hope you don’t mind I’m not terrific
cameramen but you get the idea the biggest and nicest collection of palm
trees I know of is in the Botanic Garden in Rio and this is the royal palm avenue
from the from that garden and just gives you an idea of the sort of tremendous
growth capacity of these wonderful plants there are many species of palm
but it’s the oil palm trees that really give rise to to all that oil this palm
trees are actually monocots this is a branch and order of flowering plants so
flowering plants you’d be very familiar with and monocots actually include the
grasses so corn wheat sorghum and sugarcane are all monocots and so are
palm trees and they’ve just been placed on this evolutionary tree which was
actually constructed from DNA sequence in a collaboration with some very good
friends of mine at the Museum of Natural History here in New York who
collaborated with us on the oil palm project as well and they were able to
place oil palm molecularly as botanists had before which is good so we
all agreed in little clade here of tropical crop plants which include
ginger and turmeric funnily enough which you would have thought didn’t look
anything like palms right but from a DNA standpoint from an evolutionary
standpoint they’re actually very closely related plants so oil palm trees then
are in this genus called Elias and they come in a couple of different species as
I tell you in a moment which turned out to be very important for the for the
genome sequencing project which we began as I said about ten years ago now oh
sorry first tell you about those two species so the two species are elaeis
guineensis which is the African oil palm so it’s native to West Central and East
tropical Africa sub-saharan Africa whereas elaeis oleifera is found in Central
and South America and so for example in Brazil both of them exist coexist in in
tropical rainforests that is their natural habitat or at least related
tropical niches and they are surprisingly interfertile the reason that surprising is that from an evolutionary standpoint new
and old world plants are separated usually at the time when the two
continents separated which was about 60 or 70 million years ago that two
continents refused at one time called Gondwana and so one of the interests of
sequencing the genomes of these plants to find out how on earth that could have
happened that these these two species could have retained this this this
ability to still cross to each other and one idea of course was that in fact
they’re much more closely related to each other than you might imagine that
in fact one migrated to the other most likely from South America to Africa or
perhaps the other way around and one reason that that’s a popular idea is
that if you look at the palm tree lineage here are date palms northern
Africa of course there are many many species of date-palms and I thought I
think they’re all almost all from the old world but oil palms are actually
quite closely related to coconuts as you’ll see in a moment that turns out to
be important for the gene that we found called the shell James think of a coconut
shell and so one idea then of course coconuts can can essentially propagate
anywhere in the world because they float on water and they could just float
anywhere and that’s why coconut trees are all over the beaches in the South
Pacific and so on but these are so one idea then was an oil plants might have
been derived from some ancient coconut that had been able to propagate in that
way turned out not to be true just to spoil the suspense but that it was a
good idea it was actually my favorite theory of the time ok so as I said we
established a collaboration about 10 years ago now headed by the malaysian
palm world board which is based in Kuala Lumpur in Malaysia a place that I spend
quite a bit of time as well as Orion genomics which is a cold spring harbor
spin-off company cold spring harbor itself of course and our friends at the American
Museum of Natural History between us we were able to
sequence the oil palm genome it’s big big genome it’s almost 2 billion bases
in size 16 chromosomes and it’s highly repeated and doesn’t really have any any
what we call reference that you can you can look at you have to assemble the
whole thing like one huge jigsaw puzzle in which most of the pieces are
identical and and so it’s a it’s an extremely difficult genome to to
sequence but we did it and and we’re able to publish it very satisfying in nature
earlier this year in July and at the same time as publishing the genome
sequence we are also able to identify the gene that the single gene that has
the biggest effect on yield of oil that’s the amount of oil you get per
tree you can also think of it perhaps more provocatively the amount of oil you
get per acre of rainforest that has been sacrificed to allow growth of these
trees and so it’s a very important thing to get at this all yield and finding
that gene is quite a fun story this is going to be the scientific part of the
talk through you see those of you who don’t don’t have taken too many details
I thought I’d throw in some real science just to give you an idea of what that’s
like so oh before I do that this is the Malaysian part of the team actually
these are the guys from Orion genomics and this is the more that the leaders of
the Malaysian team including Datuk Choo who’s actually the director general of
the malaysian palm oil board and we really had a great deal of fun with
these guys they’re amazing amazing group and this is rajinder singh who’s the
first author actually on both papers ok so the genome as I said it’s 1.8 giga
bases in size that’s an awful lot of zeros and is equivalent in size to the
human genome in size and actually worse in terms of complexity there are 16
chromosomes and we estimate from informatics something like 38 maybe
forty thousand genes so in that sense it’s quite similar to the the grasses
that we know so well like rice or maize and actually the maize genome is
similarly difficult and complex and difficult sequence as I
said there are only two species known which is unusual for palm trees and
quite unusual for angiosperms in general and perhaps it’s the fact that there are
only two species which allows the interfertility which I’ll forget in a
moment we also discovered that palms in general have these ancient duplications
where one chromosome looks a lot like another and these ancient duplications
and only duplications not triplication suggest that the genome as a whole was
doubled something like 30 million years ago leading to both date palms and oil palms it’s like 60 million years ago lead to both date palms and oil palms so we discovered all these genes there are lots of nice chromosomal
features it was a it’s a very satisfying genome importantly of course we wanted
to find out what was going on with a will in this genome and I’ll they’ll get
to that in a moment but first I’ll tell you the evolutionary results which was
which was a lot of fun and turned out to be the title of the paper and in fact so
our friends at the Museum in New York were able to use the genome sequences or
what’s called transcript sequences of more than 150 species of plants
worldwide these have been collected in computer databases over the years and
were able to get a really accurate picture of the evolution of all of these
species and when they did that they found that the African and American
palms were separated by about the same distance as other old world and new york
world crops for example here sorghum which is an old world grass and zea
mays which of course is a new world grass and they are actually closer
together than the two oil palm species are and for those of you plant
biologists of course you can’t successfully get fertile hybrids from
maize and sorghum you can’t cross these together and expect to get anything that
looks like a fertile and successful plant whereas oil palm breeders are
actually using the interfertility of the american and african palms in breeding
schemes so it’s quite extraordinary that palm trees the oil palm trees have
remained fertile for all that time you know 60 million years
that’s a really long time and and there’s actually a theory that says that
the fewer species you have the more likely that is to have happened so if
you think about it there’s only one species in each continent they never see
in other species so there’s no need to build up reproductive isolation so that
was a very interesting result we also as I said we looked at the genes
responsible for oil biosynthesis and we compared those genes in oil palm to date
palm and also to banana which is recently sequenced it by African
American South American consortium and when we did that comparison we found
perhaps not surprisingly that genes responsible for oil biosynthesis are
over-represented there’s more of them there’s more types of them which
probably means they’re they’re actually used in more different tissues of the
plant and if you think about it the fact that oil palm produces all this oil and
its fruit is its unique defining feature most plants only produce all in their
seeds not in their fruit and so that this made was made a lot of sense and
I’ll I’ll get back to that point again in a moment okay but we were also able
to take advantage of the extraordinary genetic resources that the Malaysians
had built up over the last few decades and actually much of this work was
started by Belgian breeders in the Congo before oil palm was introduced into
Southeast Asia which was something like the late 19th century actually mostly as
an ornamental palm I and only rarely used commercially from the 1920s onwards
and it was in the 1920s that a Belgian breeder working the Congo realized that
there was an example of single gene heteros exactly the same sort of
phenomenon that I told you about those in the Zach Lippman finding in tomato was
happening in oil palm and the gene responsible actually had a name the gene
is called the shell gene or SH and it’s responsible for the thickness of the
shell so I told you that oil palm and coconut are quite closely related if you
slice open an oil palm fruit either one way or the other you’ll notice the
inside is a white endosperm looks a lot like coconut a flesh and it’s surrounded
by this thick fibrous shell which is the equivalent to that
awful thing that you need a machete for to get off to eat a coconut and of
course it’s much smaller but it does decrease the amount of oil because it
occupies so much of the surrounding fruit now what this breeder realized was
that commercially grown and actually a large number of wild x sessions of oil
palm were something called the tenera or thin-shelled form and they could be
produced by crosses between the thick shelled and a rare type of oil palm
called the pisifera which didn’t have a shell at all and he was able to trace
this to the single gene by classical genetics in other words it behaved its
segregated as a single gene which he called shell and he realized then that
the the tenera palms which a thin shelled were heterozygous so they got
the alleles from both parents and so they were hybrids and those hybrids
yielded something like thirty percent or even more oil than either parent and
part of the reason for that was the pisifera ones which you would have
thought might yield a lot of oil are actually mostly sterile a female sterile
so you can only use pollen from these plants and that’s why they’re so rare in
nature okay so given that these these genes were discovered in the 1920s
they’ve been used genetically for for breeding oil palms since breeding began
mostly after World War Two and so this is just a summary of what I just told
you oil palms exhibit this thing called single gene heterosis in which the
amount of oil that you gather the mesocarp that’s the fruit is much higher and
actually it has much high quality because the shell is thin enough to allow
accumulation of that oil and thick enough to allow fertility you have to
have both it’s sort of like the Goldilocks hypothesis if you like it’s
just right and the most potent most productive a bunch composition then
these fruit bunches and you really do get a huge amount of oil I mean weight
for weight you get something like forty percent of the weight of one of these
bunches after steaming is just oil it’s remarkable
and this meant of course that these pisifera pounds which I said we’re quite
rare in nature have this recessive shell shell-less allele what that meant is
that we could take advantage of the extraordinary breeding that have been
going on in Malaysia since the 1950s to find the shell gene and I just sort of it’s
an atmospheric photograph here of a shell oil palm plantation in Malaysia
you can see sort of how dark it is and how mysterious the shell gene was had
always been the sort of holy grail of biotechnology for the for the Malaysians
so what they had a forest were pedigrees they’ve been maintaining pedigrees from
their breeding schemes for decades going back to the 1950s where some of the
earliest palms and amazingly enough of course these are quite long live trees
so many of these trees are still around you could still get DNA from them for
example and and and they develop these pedigrees where they cross together
palms of differing allele at the shell gene so they’re either too narrow or
pisifera and then we could we could select some of the more recent versions
of this from this pedigree in which the genes had all been shuffled up
enormously as much as you as much as you could and try to find the shell gene in
those in those palms and and we did that using something that we could only have
done in the last five years or so which is something called next-generation
sequencing in which you can once you’ve got a good quality sequence of the plant
you’re interested in you can then sequence many hundreds of other plants
using this this very highly throughput instrumentation that allows you to to
get all of the variation that’s found in those plants from the original reference
and when we did that we used a technique called homozygosity mapping again this
is this is for the cognoscenti but it was fun because it had been first
proposed by Eric Lander and David Botstein in the 1980s before this
technology was available and they did propose it as a way to find actually
human diseases that arise in inbred human populations and so
this was a this was a perfect opportunity to use this using
next-generation sequencing and so within the rough genetic interval where we knew
the shell gene had to be there was just one region that was homozygous that
means there’s no no variation this is just plotting variation here along the
genome and sequencing just about 50 trees was enough when we compared this
to the genetic interval there was literally one gene that was in that in
that overlap and that’s that’s amazing for for those you do positional cloning
and any organism to get that sort of resolution and this is what we can do
with these next-generation sequencing technologies so this was really applying
the cutting edge of DNA technology to the to the Malaysian Malaysian problem
so the shell gene it was very satisfying in terms of what it encoded it encodes a
gene which I’ll tell you in a moment it’s already known to have a similar
function in other plants but what was really neat is it turned out that the
Malaysians who collected something like 10,000 x sessions of oil palm from
africa so they’d gone out on collecting expeditions over the last few decades
actually led by an incredible guy called dr. Rajan Naidu who must be in his 70s
but still goes out there and climbs into compounds and takes this stuff it’s a
he’s amazing now anyway they’d it turns out that they had collected two
different alleles of the shell gene which they’d used in the in their
breeding and actually had shown unwittingly controlled the same
phenotype because they cross them together and these two mutations were
only six base pairs apart in the in the genome sequence and remember the genome
sequence is two billion bases so the fact that we found these two mutations
so close to each other is like finding two flags at the North Pole you know
you’re in the right place this is definitely the shell gene so that was
that was extremely satisfying and you can see that they they differ also in
their geographical location so more or less one of them is an East African
allele most different Tanzania and as far away as Madagascar actually whereas
the other arose in Nigeria we think but ended up in Ango and Congo as well so they made a nice geographical distribution okay so what
is the shell gene well it encodes something that we’re very familiar with
at cold spring harbor these things are transcription factors what that means is
there they encode proteins that bind DNA and regulate other genes so their master
genes if you like and that makes sense because it’s a really important gene
that clearly has major major effects it’s a class of genes that’s that’s well
known in in other plants especially the model plant arabidopsis where the gene
is actually called seed stick which you can almost tell it’s got to be the right
gene just from the name and what was really nice about it was that the two
mutations that we found were found in the DNA binding domain which is where we
would like them to be and they influence the interaction with another related
protein called sepallata which we were able to demonstrate using something
called yeast two-hybrid you don’t have to remember any of that but but it was
it was extremely satisfying and the reason it was satisfying because it
provides at least for this example an explanation for single gene heterosis
and that’s because these two proteins interact with each other and they need
to interact with each other in order to bind the DNA the DNA is this double
helix around here here are the proteins which actually form a multimeric sort
of complex of these proteins and and that need to form a complex with other
proteins form the basis of a theory from an old friend of mine called Jim Birchler
who’d come up with this many years ago where if you do the mathematics if you
need three blobs to be functional okay blue red blue then if you vary the dose
of either of those of those components you will end up with something worthy
though the heterozygote can actually look better than either homozygous like
this is because of dose dependence so this really was wonderful scientifically
because first of all we found the gene and secondly it had this wonderful
explanation for single gene heterosis but of course most importantly what what
this gene does is it increases yield it means that we can now use this as a
genetic test just as you would any other genetic test to find the trees that are
going to have the biggest yield in any breeding scheme and that will make a
huge difference to the oil palm breeding industry and so they were very excited
about that and you know one reason they’re excited about that is because
they can take these elite hybrids so they use the marker gene to find the
best tree just one tree maybe not one but it’s a few hundred trees that are
that are elite and they can take them and clone them they can generate
thousands of copies of the same tree by using something called micropropagation
in which they take what amounts to the heart of palm if you like which is the
whole leaf at the top of the palm tree and they take that and put it into into
tissue culture and can regenerate literally thousands of little seedlings
from that one that one pair of palm and because they’re clones they all have
exactly the same genetic constitution they both got you know that the two
copies the shell gene from one parent and not from the other and so they
should thoroughly in theory have fantastic in the yield and often they do
these days but sometimes they don’t and in fact the first time this this was
tried before it was perfected some some some aberrations arose and those of you
follow the cloning literature and animals shouldn’t be too surprised at
that of course famously Dolly the sheep was not quite the you know paragon of
sheep health that she could have been and her clones suffered from a number of
these epigenetic maladies that even though they were genetically identical
and the same is true in palm trees we often find problems like this where the
fruit failed to form properly these are actually they’re very
interesting phenotype in many ways but they don’t produce much oil compared to
the normal ones and this is bad news because you don’t even see these fruit
until the trees are about 10 years old which means of course you’ve already
planted your plantation and again you know if you occupied a lot of land that
you didn’t want to occupy and so the next thing that a Orion Genomics is
trying to do is use epigenetic technology actually much of it developed
here at Cold Spring Harbor to to find the responsible culprit for this for
this effect okay so palm trees then our oil palm trees are a very effective way
of harvesting oil from the land but of course there’s a problem and that
problem is they coexist with the rainforest and this picture was actually
taken by by Meilina one of the year or a palm team from a helicopter of
a Borneo and you really get the idea here are the palm trees being grown in
uniform plantations and here’s the rainforest so you know increasing the
yield of oil palm is all very well but we first and I think it has has great
potential to you know restrict the the expanded use of land but of course
because of course you can now produce more oil from the same amount of land
but in order for that to work you really need you know governments to work
hand-in-hand with biology and make this work and the Malaysians to their great
credit actually put a moratorium on expanding into the rainforest any
further in the 1990s and the Indonesians have just recently done the same thing
two or three years ago however you know this is a really important area and we
all know why I’ve actually spent quite a bit of time in Borneo myself
and I just have to introduce you to this right this guy who are sadly has passed
on this picture was taken four years ago and read recently that he died of old
age but this is Ritchie he’s the alpha male in the arid orangutang or was in
the orangutan sanctuary in Santubong in Borneo and actually I have to say it’s
not a bad life for an orangutan this particularly sanctuary it’s they get they
get fed and so on but the reason they have to they have to have these
sanctuaries I’m just going to show you a few more pictures but he’s got amazing
hair because all the way over is of course because the even even with you
know these these rainforest conserved rain forest areas it’s difficult for the
orangutans to move around and actually what’s worse is that there are poachers
who will attempt to steal the babies in order to sell them as pets which is
actually probably the biggest threat right now but they are marvelous
creatures so you know a wren forest conservation you know has to go
hand-in-hand with increased oil yield but oil yield increase through biology
does have the potential to reduce a rainforest impact needless to say this
has been an issue for a long time and it was very interesting to see the reaction
to the popular press to the genome of oil palm have to say in general it was
very positive the BBC World Service gave us lots of lots of coverage which is
terrific and even more surprising as a Brit was the guardian who you know who
really had a lot to say about oil palm plantations over the years and and we
really we really got great coverage is very balanced I’m very reasonable and
even now I mean I think the Guardian produces a article and oil column every
every few weeks it seems and and they’ve really been investigating you know this
issue this this idea that maybe by regulation and biological improvement
you know we can really do something realistic with that with the system I
mean you have to realize that most of the rain forest that’s being destroyed
in Southeast Asia is being destroyed by smallholders and the reason for that
these guys are poor and they need product predictable yields in order to
maintain their plantation and without that you know the temptation
to burn down accidentally of course then the nearby rain forest is overwhelming
and if we can provide them with seeds that will always give high yields than
perhaps that will make a difference to that that practice as well as the law I
mean it is illegal anyway yeah the debate that is one that’s still very
much going on given that and also given another another issue that that you’ll
find raised here too is another big problem with biofuels and this is
something that has been realized especially with the production of corn
ethanol over the years and that is that corn and oil palm are foods and actually
providing food is as important as providing fuel perhaps more so given the
increase in the world population which is predicted to go up to 9 billion by
2050 and so if you have to sacrifice food in order to get fuel a lot of bad
things happen the first thing that happens is economic of course which is
that the price of that food goes up and that’s exactly what happened with corn
ethanol when corn ethanol became much more widespread in its use the price of
corn went up quite dramatically and there were riots in Mexico and so on for
very good reason I mean you know this this competition is a bad one so
although we’ve done a lot I think we have a lot of potential to improve the
situation of oil palm respect to the rain forest we’re not really going to be
able to deal with this biofuel problem unless we deal with it in some other way
and I’m not saying that oil palms not not going to be used for biofuel it is
and part of the reason for that is actually Dagnia is introducing before
is that the oil that comes from the kernel the inside the shell that is
actually mostly of a type that’s better for bio is saturated so it’s better for
biofuels and plastics and detergents and all that sort of thing than it is for
food so to some extent oil palm is a versatile crop that can do both but what
we’re really looking for is a plant that we can use for biofuels that is not
going to compete for food and so I just want to finish and you
heard Bruce saying something about this on that video with one of my favorite
plants environment which I think has a lot of potential in this direction it’s
called you’ll know it as duckweed it’ll cover your pond especially if your pond
is in a golf course where it gets lots of runoff fertilizer from the
surrounding greens because it loves actually to consume waste water and a
cleans waste water extremely efficiently as a result you can grow it on municipal
waste you can grow it on agricultural waste there are even mining companies in
in Australia that are growing it on a mine water which is which is quite
remarkable cuz they can take up heavy metals as well but the other thing about
duckweed is that it grows incredibly fast oh yeah just quickly friends at the
Botanic at the American Museum of Natural History are placing it on the
tree at the moment they’re not quite finished yet but we know it’s going to
end up somewhere around here so again it’s a monocot it’s quite distant from
palm trees but nonetheless we can we can we can sequence the genome just as we
did the palm tree and and and and hope to get a lot of good information from
that not tell you about that in a second so here are the vital statistics
duckweed or most of the species of lemna species are in this family lemnaceae
they’re the smallest flowering plants in the world fully enough they come from
the same order the arcadia oh sorry aroid plants which are actually have the
biggest plants in the world as well so they seem to span the gamut there are
aquatic plants which means they float of course on the surface of the water that
means they don’t need all the lignin and all the heavy stuff that trees and corn
have in order to be terrestrial plants to stand up they don’t need any of that
so they’re much softer much easier to process and they don’t have a lot of the
chemicals that make processing bad news they bud so they’re clones they bud
fronds just from one another if you put one of these things in a flask in the
laboratory they’re quite scary after a week or two the flask will be full and
they and they really double incredibly fast roughly every two days and as a
result they actually have one of the largest biomass productions per hectare
known even in industrial production you know commercially viable production
there are at least two or three times more than things like switchgrass and
and corn and i’m not i don’t mean corn kernels i mean the whole plant so that
these are producing more biomass than than anything else so they really have a
fantastic potential from that point of view there are several different species
i’m not showing it all here the tiny little ones here are wolffia globosa
which are you can get five thousand plants into a thimble which is quite fun
but although they grow clonally they do produce flowers and although they don’t
produce and they can produce seeds much of that you know some species without
question they also produce another sort of resting form which they overwinter in
and these things are called turions you can see the dark here these actually
contain almost pure starch and so that they have as much starch as a corn
kernel does so so duckweed actually is a very promising biofuel just from the
starch point of view think about sugar cane or something like that but our our
our goal at Cold Spring Harbor is to actually make them make oil to convert
that starch inside the plant in vivo if you like into oil and we think that’s
possible we think that’s possible for a variety of reasons first of all we’ve
sequence the genome so just like the genome of oil pump we’ve sequence the
genome of lemna gibba which is what sometimes called common duckweed and
this is the the form that you’ll it’s everywhere it’s not invasive it’s it’s
it’s normally found in a very wide latitude and it’s been used extensively
in various types of research especially in things like remediation and so here
are the vital statistics we’ve got a nice genome it’s much smaller than the
oil palm genome and pleased to say it has a lot fewer genes may be half as
many genes as oil palm but it does have a lot of the genes that we think are
going to be important this is just an example this is a gene required for oil biosynthesis it’s found in oil palms found in other crops as well it’s
actually one of my favorite classes of genes it’s a chromatin gene a chromatin
remodeling but but anyway it controls again it’s a regulatory master gene that
controls many others so we’re going to take a leaf if you excuse the pun or the
from the oil plant book and and and see what sort of genes we can put in to duck
weed to try to persuade it to make oil instead of starch now in order to do
that you have to first of all develop the technology that allows you to put
genes in this is the genetic modification technology we were talking
about earlier and that’s been extremely challenging with duckweed a lot of
people have tried in the past and have not got anything anything good but I’m
very delighted to say that a couple of people in the lab have been able to do
this extremely efficiently now what you’re looking at here is that cell
culture remember the callous that I showed you an oil palm this is a very
similar idea that’s being transformed with a gene from jellyfish that gives
you a fluorescent a green fluorescence it’s sometimes called gfp and that made
it very easy to find the transformed frogs which were then selected and these
are very stable the whole process is done within six weeks which is
comparable to some of our favorite plants that we use every day in the lab
and so this is really very good news so we’re very happy about this and this is
really provide going to provide us with the tools to to make it happen and these
clones are very stable this is a typical duck weed plant you’ve got a
little stipe here you’ve got a thing called a pocket where the two new fronds
are emerging and you can just pick these things off and they’ll and they’ll grow
like the clappers so when as I said we’re going to take a leaf from the oil
palm genome and actually other other oilseed genomes which have been looked
at by others in the past we understand a lot about shell gene of course but
that’s likely to be quite specific for oil palm because it has a shell and
we’re not dealing with seeds anymore but what we are dealing with is genes that
are expressed and that’s what these little these little graphs are in the
fruit which is unusual for plants because it’s a it’s a non seed tissue
and it’s accumulating massive amounts of oil so if we can take those same genes
and put them into the fronds of duck weed or maybe in the turians of duck
weed then we should be able to make oil at least that’s the idea
and so this has been done at a sort of model level in in other plants again
this is our favorite model plant and it works reasonably well we think we can
get it to work even better than that but that’s using these very same these are
very same genes and so these are some of our target genes and I’m delighted to
say I think we’ve got the first one the first one in already and so we should
know fairly soon if we can at least it a sort of model level get duckweed to make
oil and then we’ll have to really play with the the conditions to get it to do
it and grow fast at the same time that’s the hard part but I’m confident we can
we can give it a shot okay I just want to finish on one climate change last two
slides a climate change note and I gave this talk recently a summer school in
Utrecht without realizing that much of the work that I’m about to talk about
was done there and so they were delighted they came up to me afterwards but it
was it was interesting so in the nineteen 1990s actually the Arctic
survey went out with ice breakers into the Arctic Ocean in those days you
needed ice breakers in the Arctic Ocean not sure you do anymore but they went
out there and they drilled into the into the core into the sediments and pulled
out cause which they could then determine the plant life that had grown
in the Arctic back to many many millions of years ago and what they found was
that in the early eocene about 50 million years ago they could tell from
the carbon dioxide trapped in the ice that atmospheric carbon concentrations
were much much higher than they are now and so the world was much hotter the
average Arctic sea temperature for example was you know about what it is in
Long Island Sound 13 degrees centigrade so you know there were palm trees and
hippos in the Arctic Ocean in those days but what was really interesting was that
the because of the the plate shifts the Arctic Ocean was actually partially
landlocked and so it had a top layer of freshwater after all that rainfall and
as a result duckweed actually a species called azolla was able to grow
really really well and they recovered something like 8 to 20 meters thick
deposits of azolla can you imagine these carpets of duckweed spanning the entire
Arctic Ocean this is an amazing biomass and a theoretical calculation suggests
that this may have actually changed the climate that there may have been
sufficient carbon dioxide of carbon fixation to change the climate from the
from the glass house that we had then to the relatively cool climates that we’ve
been used to ever since and so really these are these blooms of duckweed have
some tremendous potential for climate change as well now whether we could ever
really seriously propose that as another matter but these guys in in Holland are
actually working on the genome sequence now with this duckweed is over and and
we’re in touch with them and we’re going to try and stay in touch with them about
these projects that they have a fantastic video which I don’t think I
have time to show you what do I have time to show you yeah okay present-day society is strongly
dependent on fossil fuels not only for our energy needs but also as a resource
for countless household products but fossil fuel reserves are finite
increasing costs and affect our climate and environment to maintain welfare for
the growing human population industry is permanently seeking alternatives
resources that are sustainable co2 neutral cheap and practical to produce
solutions can be found closer to home than one may expect in nature itself
plant material is particularly viable as a natural resource because plants use
naturally existing nutrients water and carbon dioxide that’s why in the
pre-industrial era wood and cotton were typically used as natural resources more
recently soy palm oil rapeseed and many other candidates have substituted for
fossil fuel each with special qualifications in terms of quality and
quantity but all these alternatives came with downsides they compete with food
production for the use of arable land and require expensive and large amounts
of fertilizers all that is except for one one plant species can change the
entire ballgame it is the aquatic freshwater firm azolla I won’t you make you watch the whole
thing but you get the idea see how we’re running out of time
but i recommend you have a look at this youtube video it’s really it’s really
fun and they actually point out a lot of the industrial uses of the products you
can get from these aquatic plants as well so as I said we’re going to stay in
touch with these guys and hopefully we’ll be able to make some progress on
using aquatic plants as biofuels okay well we’re at the end of our time so I
just want to give you some conclusions so what I told you oil palm is the most
productive oil crop in the world and we’ve been able to you know get to the
basis of some of the hybrid vigor that’s responsible for that production by
cloning the shell gene however oil palm is also a food and although you can make
clones from oil palm there are problems with cloning oil palm which I think we
can address but ultimately you know in order to maintain the sustainability the
balance between the rain forests and the plantations we’ve got to consider other
other possibilities for biofuels and I told you about our excitement about
clonal duckweed and it’s it’s it’s successful if very ancient history in
being able to solve some of our climate change issues and so I’ll leave you that
that food for thought I’ve put up some some names here this is my duck we group
here at Cold Spring Harbor many of them i think maybe all of them are here
hopefully they’ll be around to talk to you if you want to afterwards the oil
pan genome project was run by the malaysian palm oil board and really the
sequencing and a lot of the the genetic sort of thought came from Orion genomics
as well as our friends at the American Museum of Natural History and also
contributions from the Botanic Garden in NYU which I didn’t tell you about
and then thanks to its Sjef Smeekens at the Azolla project in Utrecht who gave me
that video actually this morning so that was good timing okay and my friend Paulo
Ferreira in brazil who i talked to a lot about sugar cane and so also the
worldwatch institute provided much the statistics that i showed you and thanks
to Cold Spring Harbor as well I’d be happy to take some questions


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