identifying and exploiting grain yield genes in rice

Available online at www.sciencedirect.com

Identifying and exploiting grain y
ield genes in riceTomoaki Sakamoto1 and Makoto Matsuoka2
Improved grain yield has been a major focus of crop breeding

programs around the world. With the accomplishments of the

Rice Genome Project, genes regulating several agronomically

important traits related to grain yield, such as tiller number,

grain number, grain size, and plant height, have recently been

identified. Although these findings have not been enough to

fully characterize the mechanisms that regulate each trait,

these genes and knowledge of the molecular mechanisms

involved provide a set of tools that can be combined to achieve

tailor-made breeding suitable for various programs aimed at

higher grain yield.

Addresses1 Institute for Advanced Research, Nagoya University, Chikusa, Nagoya,

Aichi 464-8601, Japan2 Bioscience and Biotechnology Center, Nagoya University, Chikusa,

Nagoya, Aichi 464-8601, Japan

Corresponding author: Matsuoka, Makoto ([email protected]

u.ac.jp)

Current Opinion in Plant Biology 2008, 11:209–214

This review comes from a themed issue on

Plant Biotechnology

Edited by Jan Leach and Andy Greenland

1369-5266/$ – see front matter

# 2008 Elsevier Ltd. All rights reserved.

DOI 10.1016/j.pbi.2008.01.009

IntroductionFood shortage is becoming a serious global problem

because the rate of world population growth currently

exceeds the rate of increase in food production. The

recent tussle for arable land between staple crop cultiva-

tion and energy crop cultivation is contributing to the

food shortage. To adequately feed the 9 billion people

projected by 2050, food crop productivity will have to be

increased.

The grain yield potential of rice can be dissected into

four major components: grain weight, grain number per

panicle, panicle number per plant (closely related to

tiller number per plant), and ratio of filled grains.

Grain weight is nearly completely governed by genetic

factors, whereas the ratio of filled grains is strongly

affected by environmental factors [1]. In addition to

these direct components, other traits, such as plant

height and tillering, are also crucial to grain yield in

modern agriculture.

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The International Rice Genome Sequencing Project,

launched in 1997, has provided useful tools and infor-

mation that have greatly facilitated the analysis of import-

ant agronomic traits of rice, the model grain crop,

including grain yield. Using such information and tools,

rice researchers have identified several genes involved in

the regulation of grain number, grain size, plant height,

and tiller number. Such molecular biological knowledge

can now be used to generate new cultivars with increased

grain yield. In this review, we summarize the current

situation in the isolation and characterization of genes

involved in three direct components of grain yield —

grain number, grain weight, and grain filling — and two

indirect components — plant height and tillering.

Grain numberDuring the past decade, many attempts have been made

to characterize quantitative trait loci (QTLs) for grain

number. Recently, Gn1, a QTL that increases grain

number in rice, has been identified on the short arm of

chromosome 1 [2��]. It was identified also on syntenous

chromosomes of other cereals, viz., chromosome 3 in both

wheat and maize [3�]. Gn1 has two loci, Gn1a and Gn1b;

Gn1a encodes a cytokinin (CK) oxidase/dehydrogenase

(CKX), OsCKX2 [2��]. CKs are best known as phytohor-

mones that promote cell division [4], and CKX prefer-

entially and irreversibly degrades CKs [5]. The

expression of OsCKX2 in inflorescence meristems

regulates the CK level and thus controls the number of

flowers. Transgenic rice with antisense OsCKX2 cDNA

had reduced expression of endogenous OsCKX2 and

developed more grains [2��]. Conversely, overexpression

of AtCKX3, the Arabidopsis ortholog of rice OsCKX2, in

transgenic Arabidopsis reduced the number of flowers

because of a decreased rate of primordium formation in

the floral meristem [6]. These findings demonstrate the

feasibility of genetic improvement of grain number by the

modulation of CK catabolism and levels of bioactive CK.

Grain number per panicle is basically determined by the

panicle architecture (i.e. the number and length of

primary branches of a panicle, the number and length

of secondary branches on each primary branch, and the

number of branches on secondary and higher order

branches; Figure 1a and b). Interestingly, a near-isogenic

line (NIL) containing Gn1a had the same number of

primary branches as the control line but generated more

secondary branches on primary branches at the panicle

base (M Ikeda et al., unpublished results). Therefore,

other genes control the number of primary branches and

the number of secondary branches on primary branches at

the panicle top. The cloning and characterization of such


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http://dx.doi.org/10.1016/j.pbi.2008.01.009

210 Plant Biotechnology

Figure 1

Various rice phenotypes related to grain productivity. (a) Gross morphology of panicle. Left: Japanese leading cultivar, Koshihikari. Right: a New Plant

Type (NPT) cultivar for increased grain yield bred at the International Rice Research Institute. (b) Panicle architecture of Koshihikari (left) and NPT

cultivar (right) in (a). (c) Sizes and shapes of grains (left) and hulled rice (right). From top to bottom, Koshihikari ( japonica cultivar), Kasalath (indica), VC-

65 (wild rice), LG10 (wild rice), and d1 (short-grain mutant). (d) Appearance of translucent (upper) and chalky (lower) grains after polishing. (e) Gross

morphology of sd1 mutants. Left to right, Woo-gen (progenitor of Dee-geo-woo-gen), Dee-geo-woo-gen, Calrose (progenitor of Calrose76), Calrose76,

Fujiminori (progenitor of Reimei), and Reimei. The moderately dwarfed phenotype conferred by sd1 increased grain yield in combination with the

application of large amounts of nitrogen fertilizer. (f) Erect-leaf phenotype of BR-related mutant. The degree of bending between the leaf blade (lb) and

leaf sheath (ls) of the mutant (right) is less than that of the wild type (left). (g) Gross morphology of BR-related erect-leaf plants. Left to right: Nipponbare

(progenitor of osdwarf4-1), osdwarf4-1 (BR-deficient mutant), Taichung 65 (wild-type control for BKD11), and BKD11 (BR-insensitive transgenic line). In

addition to a moderately dwarfed phenotype, these plants showed very erect leaves. Photographs in (a) and (b) were kindly provided by Prof H Kitano

(Nagoya University).

Current Opinion in Plant Biology 2008, 11:209–214 www.sciencedirect.com

Rice yield genes Sakamoto and Matsuoka 211

genes will allow fine-tuning of panicle architecture favor-

able to the breeding of high-yielding rice.

Grain weightGrain weight is determined by grain length, width, and

thickness (Figure 1c). Grain size is a major target of

breeding, not only as a component of grain yield but

also as a quality trait, because increased grain size may

reduce grain quality. Many QTLs for grain weight have

been detected, two of which were identified recently:

GS3, located on the pericentromeric region of chromo-

some 3, is a major QTL for grain length and weight [7�].The candidate gene for GS3 encodes a transmembrane

protein containing an intercellular phosphatidylethano-

lamine-binding protein (PEBP)-like domain, an extra-

cellular von Willebrand factor type C (VWFC) module,

and a tumor necrosis factor receptor (TNFR)/nerve

growth factor receptor (NGFR) family cysteine-rich

domain. Comparative sequencing analysis revealed

that all large-grain cultivars tested share the same

nonsense mutation in the PEBP-like domain resulting

in a truncated form of the protein. These results

suggest that GS3 negatively regulates grain size, in

agreement with the recessive nature of the long-grain

phenotype.

Another grain weight-related gene, GW2, was identified

from a QTL on the short arm of chromosome 2 that

controls grain width and weight [8��]. The candidate

gene for GW2 encodes a RING-type ubiquitin E3

ligase. A NIL containing a loss-of-function allele

(NIL-GW2) showed an increase in grain width and

weight. The width of the spikelet hull was also

increased in NIL-GW2, caused largely by an increased

cell number. These results suggest that GW2 negatively

regulates grain width through the control of cell

division in the spikelet hull by targeting unknown

substrates for the ubiquitin-dependent degradation

by the 26S proteasome.

Although the functions of the genes in these two QTLs

have not yet been clarified, cloning of such genes will

provide the opportunity for characterizing the regulatory

mechanism during grain development and a potential tool

for improving grain size.

Grain fillingGrain filling is a dynamic and complex process that

determines the grain yield of cereal crops. A high-yielding

rice cultivar bearing a large number of grains had insuffi-

cient carbohydrate supply to fill all grains completely [9].

Rice leaf sheaths and culms accumulate carbohydrates

before heading and then supply them after heading,

exporting carbohydrates into panicles. Therefore, it is

important to increase the carbohydrate supply not only

by photosynthesis during the grain-filling period but also


from the nonstructural carbohydrate (NSC) in leaf

sheaths and culms reserved before heading.

Takai et al. [10�] detected two QTLs on chromosome 8

and 12 that were strongly associated with increased filling

percentage per panicle. The QTL on chromosome 8

exactly overlapped that for NSC content in leaf sheaths

and culms during the grain-filling period, and the allele

associated with an increased grain-filling ratio was associ-

ated with a decreased NSC content, suggesting that this

QTL is involved in NSC translocation from leaf sheaths

and culms to panicles. Interestingly, these QTLs were

not linked with QTLs controlling grain number per

panicle, allowing the possibility of improving both

grain-filling ratio and sink size.

Higher night temperatures during the grain-filling stage

associated with global warming reduce rice grain yield

and quality [11]. High temperatures impair dry matter

production and decrease grain size and weight of cereals,

including rice. They also cause a chalky appearance of

rice grains (Figure 1d), which is a serious problem

because chalky grains have inferior polishing ability

and palatability. Comprehensive gene-expression

analysis by microarray and semiquantitative RT-PCR

during the grain-filling stage at high temperature

revealed the down-regulation of several genes for

starch or storage protein synthesis and the up-regulation

of genes for starch-consuming a-amylases and for heat-

shock proteins [12��]. Interestingly, chalky grains

contained amylopectin with longer chains than in nor-

mal grains, consistent with the reduced expression

of genes for starch-branching enzyme under high

temperature.

Although further research is needed to clarify the

mechanism regulating carbohydrate translocation and

chalky grain occurrence, integration of molecular

genetic, transcriptomic, proteomic, and biochemical

analyses will allow breeders to improve grain filling,

which is controlled by dynamic and complex metabolic

processes.

Plant heightThe major factor that made the Green Revolution

possible was the introduction of semi-dwarf cultivars

of wheat and rice in combination with the application of

large amounts of nitrogen fertilizer (Figure 1e). Nitro-

gen fertilization is essential to increase grain yield.

However, it also promotes leaf and stem elongation,

which results in an overall increase in plant height that

makes plants more susceptible to being flattened by

wind and rain, thus leading to dramatic yield losses.

This is a particular problem in the monsoon season in

Asia. By contrast, semi-dwarf cultivars are more resist-

ant to damage by wind and rain (lodging-resistant), and

the reduced plant height improves the harvest index



(the ratio of grain to grain plus straw) and enhances

biomass production [13].

It is noteworthy that two Green Revolution genes —

wheat Reduced height1 (Rht1) and rice semi-dwarf1(sd1) — are involved in gibberellin (GA) signaling and

biosynthesis, respectively [14,15]. The characterization of

Green Revolution genes has taught us that controlling GA

metabolism or sensing is the best target for producing

high-yielding semi-dwarf cultivars by means of traditional

crop breeding. Indeed, the genetic manipulation of GA

metabolism has generated agronomically significant,

semi-dwarf, transgenic rices [16].

Another agronomically important semi-dwarf gene, the

barley uzu, encodes a homolog of Arabidopsis BRASSI-NOSTEROID INSENSITIVE1 (BRI1) [17]. BRI1 func-

tions as a brassinosteroid (BR) receptor, and Arabidopsisbri1 mutants showed BR-insensitive severe dwarf phe-

notypes [18]. The BRI1 ortholog in rice, OsBRI1, is found

in the d61 mutant [19]. Interestingly, d61 plants are not

only semi-dwarf but also show an erect-leaf phenotype

(Figure 1f). BR-deficient rice mutants and BR-insensitive

transgenic rice, both of which have a moderately dwarfed

phenotype with very erect leaves (Figure 1g), had an

increased grain yield under high planting density without

the use of extra fertilizer [21��,22�] because erect leaves

are advantageous for light capture [20].

TilleringRice tillers form as branches on the short basal internodes

of the main culm or on primary or higher order tillers.

Each tiller has the ability to generate a panicle, but tillers

that develop late in the growing season fill grains incom-

pletely, thus increasing the straw biomass only. Con-

sequently, it is necessary to strictly regulate the

number of tillers in order to maximize the yield potential.

TEOSINTE BRANCHED1 (TB1) is one of the most

famous genes contributing to the domestication of maize

(Zea mays ssp. mays) from its probable wild ancestor

teosinte (Z. mays ssp. parviglumis). The expression pattern

of TB1 and the morphology of tb1 mutants suggest that

TB1, a TCP-domain transcription factor, negatively

regulates the outgrowth of axillary buds [23]. The rice

ortholog OsTB1/FINE CULM1 (FC1) shows similar

characteristics and therefore also negatively regulates rice

tillering [24].

Another tillering-related gene MONOCULM1 (MOC1) was

identified by positional cloning with a loss-of-function

mutant moc1 [25]. Plants with moc1 almost completely

lose their tillering ability and produce only one main

culm. MOC1 encodes a GRAS family nuclear transcription

factor that is highly homologous with the tomato Lateralsuppressor (Ls). Ls loss-of-function mutations cause a

branchless phenotype owing to a failure in axillary mer-


istem initiation [26]. These results suggest that both Lsand MOC1 function as positive regulators of lateral

branching.

Recent studies have identified a series of branching

mutants in dicots, including pea ramosus (rms), petunia

decreased apical dominance (dad), and Arabidopsis moreaxillary branching (max), suggesting that the upward

inhibitory signal produced by the RMS, DAD, and MAXgenes transmits the downward auxin signal [27,28�].Molecular cloning of these genes revealed that MAX3and RMS5 are orthologs, and that MAX4, RMS1, and

DAD1 are orthologs and encode carotenoid cleavage

dioxygenases [29–33]. By contrast, MAX2 and RMS4encode F-box/leucine-rich repeat (LRR) proteins appar-

ently involved in the perception or transduction of the

branching inhibitor [33,34]. Rice genes for several dwarf

mutants with increased tiller number have been charac-

terized. Among them, DWARF3 (D3), identified by pos-

itional cloning of the d3 locus, encodes an F-box/LRR

protein orthologous to MAX2/RMS4 [35�]; high tilleringdwarf1 (htd1) is caused by the mutation of a MAX3/RMS5 ortholog [36�]; and DWARF10 (D10), identified

from the d10 mutant, is an ortholog of MAX4/RMS1/DAD1 [37��]. These findings suggest that shoot branching

is controlled by common mechanisms conserved across

monocot and dicot plants.

Tillering involves two developmental processes: for-

mation and outgrowth of axillary buds. MOC1 is involved

in the positive regulation of bud formation because no

tiller primordia are generated in the moc1 mutant. On the

contrary, OsTB1/FC1 plays a role in the negative regula-

tion of the outgrowth process because tiller primordia

develop normally in transgenic rice overexpressing

OsTB1/FC1. D10 also functions as a negative regulator

and works independently of OsTB1/FC1 [37��]. As key

regulators of tillering, these genes could make significant

contributions to future improvement of rice through the

regulation of tiller and panicle numbers per plant.

ConclusionGene isolation from mutants by positional cloning is a

powerful tool for revealing the mechanisms regulating

target traits, though in many cases mutations are too

severe to introduce directly for crop improvement. Many

important agronomic traits, including heading date, plant

height, grain yield and quality, and stress tolerance, show

continuous phenotypic variation that is usually governed

by a number of QTL genes [38]. Thanks to the growing

infrastructure of plant genomics, more genes regulating

important agronomic traits will be identified, providing a

set of tools that can be combined to achieve tailor-made

breeding suitable for various breeding programs. In

addition, as the rice genome is similar to those of other

major cereal crops, such as maize, barley, and wheat, rice


Rice yield genes Sakamoto and Matsuoka 213

genomics will support not only rice breeding but also

other cereal crop breeding programs.

References and recommended readingPapers of particular interest, published within the annual period ofreview, have been highlighted as:

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36.�

Zou J, Zhang S, Zhang W, Li G, Chen Z, Zhai W, Zhao X, Pan X,Xie Q, Zhu L: The rice HIGH-TILLERING DWARF1 encoding anortholog of Arabidopsis MAX3 is required for negativeregulation of the outgrowth of axillary buds. Plant J 2006,48:687-696.

A rice tillering gene, HTD1, encodes a carotenoid cleavage dioxygenaseorthologous to a dicot shoot-branching gene, MAX3/RMS5. Expressionof HTD1 was induced by auxin treatment suggesting that auxinmay regulate rice tillering partly through up-regulation of HTD1 geneexpression.

37.��

Arite T, Iwata H, Ohshima K, Maekawa M, Nakajima M, Kojima M,Sakakibara H, Kyozuka J: DWARF10, an RMS1/MAX4/DAD1ortholog, controls lateral bud outgrowth in rice. Plant J 2007,51:1019-1029.

A rice tillering gene, D10, encodes a carotenoid cleavage dioxygenaseorthologous to a dicot shoot-branching gene, MAX4/RMS1/DAD1. Theauthors discuss the relationship between D10 and other tillering genes inrice.

38. Yano M: Genetic and molecular dissection of naturallyoccurring variation. Curr Opin Plant Biol 2001,4:130-135.


identifying and exploiting grain yield genes in rice

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