Perennial rice: Improving rice productivity for a sustainable upland ecosystem

Abstract

The world population will reach a staggering 9 billion by 2050. Recent statistics show
that an additional 40 million hectares of rice paddy is needed to increase rice
production to 118 million tons by 2035, a figure that is more than double the current
rice production. Every year, rice is planted in approximately 14 million hectares of
upland areas. Current benchmark yields of annual upland rice are lower than 1 t/ha. If
upland rice yield can be increased to 3-4 t/ha, a reasonable yield under barren and
infertile soil conditions, 40 Mt of rice can easily be secured. Traditionally, the uplands
suffer from drought, infertile soils, weed infestation and plant diseases. Compounding
these problems is the continuous erosion and degradation of upland soils due to
agricultural use. A practical solution to these problems would be to breed and cultivate
perennial upland rice that would not have to be planted annually. Not only would
perennial upland rice reduce soil erosion by providing permanent groundcover. It
would also improve the sustainability of the uplands for agricultural use and lower the
annual inputs related to field operations, thus increasing the income of farmers.

Full text

191
SABRAO Journal
of Breeding and Genetics
44 (2) 191-201, 2012
PERENNIAL RICE: IMPROVING RICE PRODUCTIVITY FOR
A SUSTAINABLE UPLAND ECOSYSTEM
JUNGHYUN SHIM
International Rice Research Institute (IRRI), Philippines
Corresponding author email: j.h.shim@irri.org
SUMMARY
The world population will reach a staggering 9 billion by 2050. Recent statistics show
that an additional 40 million hectares of rice paddy is needed to increase rice
production to 118 million tons by 2035, a figure that is more than double the current
rice production. Every year, rice is planted in approximately 14 million hectares of
upland areas. Current benchmark yields of annual upland rice are lower than 1 t/ha. If
upland rice yield can be increased to 3-4 t/ha, a reasonable yield under barren and
infertile soil conditions, 40 Mt of rice can easily be secured. Traditionally, the uplands
suffer from drought, infertile soils, weed infestation and plant diseases. Compounding
these problems is the continuous erosion and degradation of upland soils due to
agricultural use. A practical solution to these problems would be to breed and cultivate
perennial upland rice that would not have to be planted annually. Not only would
perennial upland rice reduce soil erosion by providing permanent groundcover. It
would also improve the sustainability of the uplands for agricultural use and lower the
annual inputs related to field operations, thus increasing the income of farmers.
Key words: rice, perennial rice, sustainable agriculture, food security.
Manuscript received: June 28, 2012; Decision on manuscript: October 10, 2012; Manuscript
accepted in revised form: October 27, 2012.
Communicating Editor: Bertrand Collard
INTRODUCTION
Rice is the staple food source in
Asia. In Africa and Latin America,
rice is quickly becoming an
important crop. For over 40 years
after the 1960s Green Revolution,
the improved rice varieties and
cultural management practices
have kept rice production in pace
with the rice demand. In fact,
between mid-1960s and mid-
1980s, the annual rice output grew
by almost 3%. After the mid-1980s
however, a slower growth rate for
rice production was observed as
influenced by both supply and
demand factors. By the 1990s, the
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SABRAO J. Breed. Genet. 44 (2) 191-201, 2012
192
technology that spurred the Green
Revolution that saved millions
from the threat of famine was
diminished and the yearly 3%
increase in rice production slipped
to 1.25%. This decline in
productivity was observed in an
increasing number of favorable rice
growing areas and may be
attributed to the long-term
degradation of the paddy resource
base. Despite the declining growth
rate in rice production, the demand
for rice continuously increased
with the ever-growing human
population. Recent statistics show
that by 2035, rice production must
increase to 116 million tons to meet
the demands of the rice-consuming
population (GRiSP, 2010). This
increase will have to be achieved
using less land, less water and less
labour, in a more efficient and
environment-friendly production
systems.
Uplands as the stage for new
yield frontiers in rice
Based on general surface
hydrology, rice ecologies can be
classified as irrigated, rainfed
lowland and rainfed upland. Some
80 million hectares of the world’s
rice land is irrigated, whereas 60
million hectares is rainfed lowland
(IRRI Rice facts, 2012). Modern
rice varieties grown in favorable
environments of in irrigated and
rainfed lowland regions produce
96% of the world’s rice. An
additional 14 million hectares of
land that produces 4% of the
world’s rice comprise rainfed
upland areas (Figure 1).
Nearly two-thirds of all
upland rice areas are in Asia.
Bangladesh, Cambodia, China,
India, Indonesia, Laos, Myanmar,
Thailand, and Vietnam are
important rice producing nations.
Unlike the irrigated rice areas in
these countries, most of the upland
rice fields are unfavorable due to
the slopes, high altitude, and
infertile and acidic soils. Only 15%
of upland rice grows in a favorable
upland sub-ecosystem that has
fertile soil and a long growing
season.
Yields in the uplands are
generally low and the prospect of
major increases are lower
compared to irrigated and rainfed
lowland rice environments
(Swaminathan, 1989). The current
benchmark yields of annual upland
rice are actually lower than 1 t/ha.
Still, nearly 100 million people
depend on upland rice for their
daily staple food. Many upland rice
farmers plant local rice varieties
that do not respond well to
improved management practices.
But these cultivars are well adapted
to the variable constraints in the
ecosystem and have grain quality
characteristics that meet specific
local needs.

193
Figure 1. (a) World rice cultivation area. (b) Yield production percentage in rice
ecosystem (IRRI Rice facts, 2012).
In recent years, the
dramatic rise in population has
resulted in heavy pressure on the
fragile uplands of South and
Southeast Asia, as well as of Africa
where slash and burn is still the
most widely practiced cropping
system. The availability of this
system depends on a fallow period
that is long enough to allow the
vegetation to re-grow and the soil
to regenerate (Fujisaka 1993). Due
to land pressure however, fallow
periods became shorter, resulting in
gradual soil erosion and
degradation and, eventually,
abandonment. This destruction of
watersheds adversely affects the
lowlands too, as sediment loads
resulting from erosion cause
siltation of reservoirs and drainage
canals, as well as increased
flooding (Crosson, 1995).
Permanent and sustainable land use
systems are therefore critical in the
use of upland areas for agriculture,
particularly if rice production will
be intensified.
In the early 1990s at IRRI,
scientists embarked on a “new
frontier” project to develop a
perennial rice plant that would be
suitable for upland rice ecology. A
perennial rice won’t have to be
planted annually, thereby providing
permanent groundcover and
reducing soil erosion. Ultimately,
this cultural practice would
improve the sustainability of the
uplands for agricultural use and
lower the annual inputs related to
field operations, thus increasing the
income of farmers.
PERENNIAL UPLAND RICE
Considering the existing problems
in upland rice production, the
potential impact of perennial
upland rice is valuable. A rice plant
that would not have to be planted
annually could help reduce soil
erosion by providing permanent
groundcover. In this way, rice
cultivation is considerably
intensified while improving the
76%
20%
4%
Yield Percentage
Irrigated Rainfed lowland
Rainfed upland
80Mha
52%
60Mha
39%
14Mha
9%
Area (M/ha)
Irrigated Rainfed lowland
Rainfed upland
(a)
(b)

SABRAO J. Breed. Genet. 44 (2) 191-201, 2012
194
sustainability of the uplands for
agricultural use and lowering the
annual inputs related to field
operations because the soil does
not have to be prepared each year
(Schmit, 1996).
Perennial rice, like many
other perennial plants, can spread
by horizontal stems belowground
(i.e. rhizomes) (Fig. 2d) or just
aboveground (i.e. stolon).
Nevertheless, they can also
reproduce sexually by producing
flowers, pollen and seeds. The
wild ancestor of African rice,
Oryza longistaminata often lives
for many years and spreads
vegetatively. O. officinalis, O.
australiensis, and O. rhizomatis
also spread by underground stems,
called rhizomes (Khush, 1997).
The wild ancestor of Asian rice, O.
rufipogon sometimes spreads
vegetatively by above-ground
stems, called stolons. O.
longistaminata has been reported
to have dominant, vigorous
rhizomes (Sacks et al. 2005). The
species is also characterized to
have high pollen fertility, strong
seed dormancy and a reproductive
barrier relative to other species of
the genus Oryza.
Breeding program for perennial
grains
For several decades, breeding for
perennial wheat, rye, triticale, oat,
rice, sorghum, Johnson grass, pearl
millet, maize, soybean and Illinois
bundle flower had been carried out
in a number of institutes and
countries (Cox et al., 2002). Wheat
for example, had been crossed with
a number of Triticum species and
perennial grasses. None of these
efforts, however, produced a
perennial wheat cultivar because of
the complicated chromosome
number of Triticum, as well as the
limited perennial Triticum source.
Efforts to develop perennial wheat
were hence diverted into producing
improved annual cultivars.
Another promising perennial grain
crop is rye. A perennial rye cultivar
Perenne had already been released
in Hungary for grain and forage
production (Hodosne-Kotvics et
al., 1999). Perenniality is also a
trait that can be observed in
sorghum. In a tropical
environment, a new sorghum plant
can regrow from the basal nodes of
the main plant to produce a rattoon.
Rhizomatousness has also been
reported in the crop (Paterson et
al., 1995). For sorghum grown in
temperate regions, perenniality
would have to be combined with
winter hardiness for the crop to
survive the winter season. The real
challenge would be to exploit the
limited genetic resources of
sorghum that are mostly adapted to
tropical climate to find genes that
would allow the crop to
overwinter.
Unlike sorghum, rice is
genetically diverse and is
distributed worldwide. This
diversity made available perennial
wild Oryza relatives that can be
used for crosses.
Early perennial rice research by
IRRI and partners
IRRI had worked on the Perennial
Upland Rice (PUR) project, which
was one of the several “New
Frontier” projects established at
IRRI. The PUR project was long-
term and considered high-risk but it
has the potential to largely advance

Shim (2012)
195
not only rice research but also rice
production. Because the concept
was still in its infancy, the project
was given a 10-15 years timeline.
The PUR project ran for 6 years,
generating valuable new
information pertinent to developing
perennial rice.
A review of literature on
IRRI’s PUR generated new
information on the genetics of
drought and nematode resistance.
But more important was the
development of early stage
breeding lines that might require
further development to fit a
suitable agronomic type, but are
nevertheless able to perenniate.
In the years that followed,
interest in perennial rice but other
perennial crops did not waver and
studies showing the critical role of
perennial crops in sustainable
agriculture found its way in many
published works. The first QTLs
controlling rhizome formation was
identified in chromosomes 3
(between RM119 (2.2 cM) and
RM273 (7.4 cM)) and 4 (between
OSR16 (1.3 cM) and OSR13 (8.1
cM)) (Hu et al., 2003). In 2006,
Sacks et al. clearly demonstrated
the feasibility of perennial rice by
crossing interspecific genotypes
(IGs) from an intermated O. sativa/
O. longistaminata population with
male-fertile IG selections from the
intermated population, and with O.
sativa cultivars and found out that
the most important traits are
perenniality and survival by
rhizome. They reported that
rhizome presence and expression
were positively associated with
survival and vigor of the survivors.
Sacks et al. (2005) suggest that
backcross progenies of
RD23/O.longistaminata that have
moderate to long rhizomes would
be a useful source of genes for
developing perennial upland rice.
Because of the less expansive
rhizome formation, more
assimilated carbon would be
allocated to the grains and less will
be pumped to storage organs
(rhizome) thereby increasing the
size of the grains. In fact, the yield
of elite rhizomatous perennial
progenies was reported to range
from at least 5 to 10 g/plant
compared to the 11g/plant of O.
sativa, indicating the potential to
break the yield barrier for a
perennial variety. Earlier, Sacks et
al. (2003) also reported that the
most strongly perennial F4 and
BC1F4 families derived from
crosses between O. sativa and O.
rufipogon showed high yields
without any indication of a
negative correlation between yield
and survival (Sacks et al., 2003;
DeHaan et al., 2005). These results
indicate that backcrossing
perennial selections to cultivated
rice would be an efficient strategy
to improve the yield in perennial
rice.
Strategic approach to perennial
upland rice breeding
The major constraint in utilizing
wild rice species as a source of
perenniality is the existing
reproductive barriers that result in
sterile seeds or low seed setting in
the progenies. An approach to
overcome this specific constraint is
to construct chromosome segment
substitution lines (CSSLs) using a
wild rice with perennial traits such
as O. longistaminata as donor.
CSSLs are powerful tools to
identify genes or QTLs controlling

SABRAO J. Breed. Genet. 44 (2) 191-201, 2012
196
a trait because each line has a
specific chromosome segment
substituted from a donor in the
background of any elite rice variety
(Xu et al., 2010; Ebitani et al.,
2005; Doi et al., 1997). Using
CSSLs, conventional breeding
methods can be used to transfer
gene(s) for perenniality (i.e.
rhizome formation) in existing rice
cultivars without transferring the
unfavorable genes of the wild rice
parent. With collaborations
between IRRI and Nagoya Univ.,
Dr. Ashikari developed CSSLs of
O. longistaminata in the
Nipponbare background. From the
interspecific progenies, 3 major
rhizome formations were observed:
(1) vigorous rhizome that grows
and propagate individually, (2)
intermediately vigorous rhizomes
that grow and produce tillers, (3)
short rhizomes that grow and give
rise to more than hundred rhizomes
that grow like tillers (Figure 2).
Identification of the QTLs
controlling the different kinds of
rhizomes would be the major key
to perennial rice breeding.
The second approach to
perennial rice breeding is to
pyramid genes/QTLs for
perenniality into existing varities.
Once specific CSSLs carrying
fragments covering the QTLs for
rhizomes are ready, they will be
used for crossing with O. sativa to
pyramid the rhizome loci and other
genes controlling perenniality in
existing rice cultivars. The
candidate O. sativa cultivars are
selected for their fitness to specific
target regions as well as for other
traits including grain quality and
resistance to pathogens and
diseases.
Another approach for
perennial rice breeding is the use of
mutagenesis. O. rufipogon (Acc.
105491) has good agricultural traits
that are closer to O. sativa (D.
Brar, personal communication). It
often lives for many years, setting
seed each year and spreading
vegetatively although it does not
have rhizome. One strategy would
be to conduct mutagenesis (1 kg
seed) via chemical mutangenesis
system (CMS) treatment and
screen the mutants showing good
agricultural traits, alongside the
perennial trait. Penetrance for the
traits will be evaluated in the M2
population and the selected
mutants will be crossed with O.
sativa to recover other favorable
agricultural traits (D. Brar,
personal communication). O.
longistaminata (Acc. 110404)
showing vigorous rhizomes will
also be mutagenized with CMS and
mutants at the M2 generation will
be observed and selected for
desirable agricultural traits. The
methodology for perennial upland
rice breeding is below (Figure 3).

Shim (2012)
197
Figure 2. Characteristics of O. longistaminata progenies. a) scattered rhizome growth
pattern b) localized rhizome growth pattern c) very short rhizome but high tiller
number d) 2-month-old O. longistaminata from one seedling e) high panicle numbers
f) progenies with rhizome derived from cross between O. longistaminata and O. sativa
(Picture taken in 2011 at IRRI screen house).
(a)
(b)
(c)
(d)
(e)
(f)

Shim (2012)
198
CSSLs
Elite recurrent
varieties
Perennial
BILs &
CSSLs with
rhizome
BC3F2,,, F5
BILs & CSSLs
Crosses
between
intergenic
lines
Select
Perennial &
Intermediate
rhizome with
high yeild
M2: Good
agronomic
traits as well as
perenniality
Transferring
Genes &
Pyramiding
Intermediate
rhizome &
high yield lines
Recovered
agronomic
favored lines
crossed toward
Developed
Yea r
1
2
3
4
5
6
7
8
9
10
11
12 Breeding for higher yield and grain quality have to be followed
O. sativa O. longistaminata
X
BC1F1
BC2F1
BC3F1
Selfing,,,
O. rufipogon or O. nivara
20,000 seeds mutagenesis
F2 : Mapping
Finding rhizome
gene/QTLs
F3, F4, F5,,,
Select
promising
Perennial
lines
Field trial
Multi-locational
yield trial
PerennialRILs
with various
rhizome
Field trial
Multi-locational
yield trial
X
Field trial
Multi-locational
yield trial Field trial
Multi-locational
yield trial
Figure 3. Perennial rice breeding scheme.
CHALLENGES IN
PERENNIAL UPLAND RICE
CULTIVATION
Sustainability of intensified
upland rice production.
Sustainable agriculture is the
practice of farming following the
principles of ecology. This refers to
making the most efficient use of
non-renewable resources and on-
farm resources and integrating,
where appropriate, natural
biological cycles and controls.
With the current agricultural
landscape, perennial crops will
have a critical role to play in
sustainable agriculture. Perennial
upland rice that will reduce costs to
farmers and the environment by
reducing the need for plowing
while obtaining similar yields as
for annual systems is a realistic
objective. However, even with
only a 2 tons/ha/season rice yield,
perennial upland rice would
represent a substantial benefit to
society as long as it’s cultivation
preserves the natural resource base.
Perennial crops have two
major sustainable agricultural
benefits, water management and
carbon storage. Shifting from
annual to perennial food crops
would likely have important
consequences for how water is
managed in agricultural
landscapes, just as shifting from

Shim (2012)
199
perennial-dominated native
vegetation to annual crops has had
dramatic, but generally detrimental,
impacts (Glover et al., 2010a,
2010b). The adoption of perennial
grain crops would likely be
advantageous in terms of climate
change. Greater soil carbon storage
and reduced input requirements
mean that perennials have the
potential to mitigate global
warming. Adding grains to the
inventory of available perennial
crops would give farmers more
choices in what they can grow and
where, while sustainably producing
high-value food crops for an
increasingly hungry planet (Bell et
al., 2010).
Disease and pest resistance
Because there would be no break
period in the cultivation of
perennial rice, there would be a
higher risk of a disease and/or pest
epidemic than if annual rice would
be cultivated. To address this
challenge, breeding for genetic
resistance to a wide range of pests
and diseases would be an important
aspect of perennial rice
development. Newly developed
elite lines at IRRI that can be used
for perennial upland rice breeding
as sources of multi-resistance to
many diseases. Once perenniality
is fixed on the target rice variety,
genes for disease resistance can be
pyramided into the line.
Grain yield and quality
The yield of perennial rice is
expected to be lower than those of
existing cultivars because the
limited photosynthetic products
have to be distributed into the more
vigorous root system of the former.
On the other hand, a trade-off that
could possibly give better quality
grains might be expected from this
kind of system. In rice production,
yield increases are expected with
increased fertilizer application,
although a reduction in grain
quality is also observed. In a
perennial rice cultivation system,
ratooning will allow harvesting at
least six times in a year cultivation
period without a need for fertilizer
application. This means, an
augmented harvest within a year
cultivation of grains that meet
significant yield level.
Perennial rice was not
chosen by farmers during
domestication due to its low yield
as well as characters that are
similar to those of wild species
including small grain size, grain
number shattering, and awn traits.
With the use of CSSLs, a perennial
rice that is more similar to existing
rice cultivars could be bred. CSSLs
having small chromosome
fragments from wild perennial
Oryza species could be used for
crossing followed by a series of
backcrossing to the recurrent parent
to reconstitute the genetic
background of the preferred
cultivar to which perenniality is
being introduced. Grain quality
concerns could also be addressed
by backcrossing to the recurrent
parent which are good grain quality
varieties such as IR64 and NSIC
Rc222. once perennial rice lines are
developed.
Prospects
The yields of mega-varieties in
each country are widely grown and
yield production has almost

SABRAO J. Breed. Genet. 44 (2) 191-201, 2012
200
reached a plateau. The available
land area for rice cultivation is
continuously shrinking due to
industrialization and urbanization.
To break the existing ceiling in rice
yields, the utilization of
unfavorable rice fields such as the
uplands represents a viable option.
However, the feasibility of turning
uplands to irrigated rice terraces is
very limited. The rice breeder
therefore, has to develop a variety
that is adaptable under upland rice
ecosystem. One realistic strategy is
to develop perennial rice. Current
benchmark yields for annual
upland rice are lower than 1 t/ha.
An increase of 3 tons/ha of upland
rice yield is a relatively feasible
target yield that could overcome
the current maximum in rice yields.
This increase in upland rice yield is
reasonable even in barren and
infertile soils, and could secure an
estimated 40 million tons of rice.
With perennial rice, farmers could
reduce the rice production cost
from field preparation, seeding,
and transplanting. Upland
perennial can also prevent from
soil erosion. Increased yield will
give higher income and food
security for the world population.
Breeding for perennial upland rice
is highly innovative and
challenging especially for the poor
farmers of the fragile upland
ecosystem.
International working groups on
perennial rice and collaborators
International Perennial Grain Crops
Workshop was held in Wagga
Wagga, NSW Australia in
September 2010. From Yunnan
Academy of Agricultural Sciences,
Fengyi Hu presented the progress
in recent years in obtaining
perennial lines with reasonable
fertility and that grow well in
paddies. Initial testing of these
lines would be carried out in LAO
PDR as part of the ACIAR project
that Len Wade from Charles Sturt
University leads. The latest
movement on perennial rice is
quite active.
ACKNOWLEDGEMENTS
The authors are grateful to Dr. Rosalyn
A. Shim and Dr. Bertrand Collard for a
critical comment and support. The
content of this paper was submitted to
New Frontier Research proposal call of
GRiSP (2011).
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