This document summarizes a study on the rice gene PAY1 and its effects on plant architecture. PAY1 was identified through mutagenesis of a wild rice introgression line. The PAY1 mutant showed changes to traits like plant height, tiller number, and panicle morphology. PAY1 was mapped and cloned, found to encode a protein that regulates polar auxin transport. Overexpression of PAY1 in the introgression line replicated the mutant phenotype. Introduction of PAY1 into an elite rice variety through backcrossing improved plant architecture and increased yield. The identification of PAY1 provides insights into molecular mechanisms of plant architecture and a tool for breeding higher-yielding rice varieties through modification of architecture.

1. WELCOME

2. Molecular Basis of Aerial Plant Part
Architecture in Rice
2
Presented By
VANISHRI, B.R.
PALB 4249

3. Introduction
Tillering
Panicle morphology
Plant height
Case study
Conclusion
3

4. Plant Architecture
4
 Plant architecture is referred to as the three
dimensional organization of the plant.
 Crop plants with desirable architecture are able to
produce much higher grain yields.
 In case of the “Green Revolution” in which grain
yields have been significantly increased by growing
lodging-resistant semi- dwarf varieties of wheat and
rice.

5. Rice is an annual grass with round, hollow and
jointed stems (culms) that bear panicles.
Generally, rice plant growth is divided into
three stages:
1. Vegetative stage
2. Reproductive
3. Grain filling stage
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6. Rice plant architecture
• Rice is an ideal system for studying plant architecture
of cereal crops.
• Rice plant architecture, a collection of the important
agronomic traits that determine its grain
production, is mainly affected by factors including
1. Tillering
2. Plant Height
3. Panicle Morphology
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7. Tillering
Rice tillering occurs in a two-stage process: the
formation of an axillary bud at each leaf axil and its
subsequent outgrowth.
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8. Genes Controlling Tillering
• MONOCULM 1 (MOC1)
• LAX PANICLE (LAX 1)
Genes involved in strigolactone biosynthesis
and signalling
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9. 9
Wang and Li, 2011
Genes Involved In Tillering

10. • Neither the extremely spreading nor the compact
plant type is beneficial to rice grain production.
Genes involved in regulating the tiller angle in rice:
• LAZY1 (LA1)
• TAC1 (Tiller Angle Control 1)
• PROG1 (PROSTRATE GROWTH1 )
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11. LAZY1 (LA1)
Negative regulator in polar auxin transport
(PAT).
Mutations of LA1 enhance PAT greatly and alter
the endogenous IAA distribution in shoots,
leading to the tiller-spreading phenotype of rice
plants.
It regulates the lateral organ angle and mediates
branching and leaf formation (Li et al., 2007).
11

12. TAC1 (Tiller Angle Control 1)
• TAC1, positive regulator of rice tiller angle.
Mutation in TAC1
• Sharp upward asymmetrical growth of the base of
the culm.
• Compact plant architecture with erect tillers (Yu et
al., 2007).
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13. PROSTRATE GROWTH1 (PROG1)
• Prostrate growth habit to erect tiller growth of rice.
• Transcription factor.
• Expression site: unelongated basal internodes of the
culm.
• Mutation in PROG1 leads to a phenotype of
significantly less vertical tiller angle.
13

14. • Tiller has the potential to produce a panicle by
transitioning from a vegetative SAM(shoot
apical meristem) into a reproductive SAM.
• Tillers that produce panicles are termed
effective tillers, and they contribute to the
grain yield.
Panicle Morphology
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15. • Rice panicle develops into three types of axillary
meristems,
Rachis-branch Meristems,
 Lateral Spikelet Meristems
Terminal Spikelet Meristems.
• The initiation and outgrowth of these meristems
determines rice panicle morphology.
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16. Major Steps In The Rice Panicle Development
(A) Formation of the first bract primordium
indicating the transition from the
vegetative phase to reproductive phase;
(B) Formation of the primordia of the
primary branches(PB) from the base of
bracts;
(C) Formation of the primordia of the
secondary branches(SB) from the base
of each PB primordium;
(D) Formation of the terminal and lateral
spikelet meristem primordia on the
rachis-branches (primary and/or
secondary branches) and differentiation
of the spikelet primordia
16
Wang and Li,2005

17. Key Genes Controlling Rice Panicle
Architecture
17
Wang and Li, 2008

18. Models representing the function of FZP during the
development of rice spikelets
18Komatso et al., 2003

19. Plant Height
Rice stem elongation starts at the beginning of
panicle initiation and is mainly ascribed to the rapid
elongation of cells in the top 4–6 internodes.
Gibberellins(GA) and Brassinosteroids(BR) have
been revealed to play major roles in modulating rice
plant height.
19

20. 20Wang and Li,2008

21. CASE STUDY
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22. INTRODUCTION
 Plant architecture, a complex of the important
agronomic traits that determine grain yield, is a
primary target of artificial selection of rice
domestication and improvement.
 Genetic identification and functional analysis of the
PLANT ARCHITECTURE AND YIELD 1 (PAY1) gene in
rice.
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23. MATERIALS AND METHODS
Plant materials :
• YIL55 (a wild rice introgression line )
• The PAY1 mutant
YIL55 mutagenized with EMS to generate a library for
genetic screening of mutants with altered plant
architecture.
They identified a mutant with greatly changed plant
architecture, referred to as PLANT ARCHITECTURE AND
YIELD 1 (PAY1).
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24. 24
Phenotype of wild-type (YIL55) and PAY1 mutant.
(a) Introgression line YIL55 and the PAY1 mutant at maturity stage.
(b) Main panicle of YIL55 and PAY1 mutant.
(c) Stem structure of YIL55 and PAY1 mutant.
(d) Cross-sections of the fifth internode
(e) The diameter of the fifth internode between YIL55 and PAY1 mutant.
(f) Comparison of plant height, number of panicles per plant, grain number per
panicle and grain yield per plant between YIL55 and PAY1 mutant plants.

25. Cloning and Characterization of PAY1
• The F1 plants from the cross between PAY1 and YIL55
showed a similar phenotype to the PAY1 mutant .
• F2 plants, showed a segregation rate of the PAY1
mutant and YIL55 plants fitting a 3:1 ratio.
• These results indicated that the PAY1 mutant
phenotype was controlled by a single dominant
gene.
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26. CLONING
• F2 populations were generated from the cross
between the PAY1 mutant and Nipponbare
• PAY1 mapped between the single sequence
repeat markers RM339 and RM223 on the
long arm of chromosome 8.
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27. 27
Molecular identification of PAY1
(a) PAY1 was mapped in the interval of RM339 and RM223 on the long arm of
chromosome 8.
(b) PAY1 was delimited to a 51-kb region between the sp5 and sp7 markers.
(c) Annotation of the 51-kb region harboring PAY1 on Nipponbare BAC AP004691.
(d) PAY1 structure and the mutation site in PAY1 mutant

28. Genetic Confirmation
• To verify altered plant architecture caused by the
single nucleotide change in the LOC_ Os08g31470
gene.
• They generated transgenic YIL55 plants with
overexpression of cDNA of the PAY1 mutant
• Real-time quantitative PCR (RT- qPCR) analysis
showed that the expression levels of PAY1 were
much higher in transgenic than in control plants.
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29. Experimental Procedure
• The entire coding sequence of PAY1 cDNA , a 1773-bp
fragment, was inserted into the vector pCAMBIA1301
driven by the maize Ubiquitin promoter to form the
over expression construct pOE.
• The construct was introduced to Agrobacterium
tumefaciens strain EHA105 and subsequently
transferred into YIL55.
• There were 18 independent transgenic lines harvested,
and two lines (pOE6 and pOE8) were used for
phenotypic evaluation.
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30. 30
Comparison of control plant (CL3) and PAY1-overexpression transgenic plants .

31. The PAY1 mutant shows reduced
polar auxin transport(PAT) activity
 PAT plays a key role in the regulation of many aspects
of plant growth and development.
 The basipetal and acropetal indole-3-acetic acid (IAA)
transport in etiolated coleoptiles of wild-type and
PAY1 plants were compared.
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32. 32
3 groups of 5 days old Coleoptile Segments of 2cm length
incubation
Liq. Half strenght MS media, 100 rpm for 2hr
One end of apical/basal end is submerged in Half strenght MS media
To remove endogenous IAA
0.35% phytagel
500nm [3H]IAA
Dark
RT
2hr
NPA (N-1-naphthylphtalamic acid) applied to media for one group
Submerged end is washed with Half strenght MS media, 3times
Radioactivity of each section was counted by Liquid scintillation counter.
20 hr incubation in scintillation liquid
PAT Assay

33. 33
Results and Discussion
Comparision of PAT between YIL55 and PAY1 mutant in dark grown coleoptiles

34. 34
Comparision of auxin content in the tip of dark grown
coleoptiles between YIL55 and PAY1 mutants

35. PAY1 Used For High-yield Breeding
To evaluate the PAY1 potential application for
optimizing rice plant architecture and increasing
grain yields
They introduced the PAY1 into Teqing (TQ)
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36. • The NILs were generated using continuous
backcrossing between PAY1, as the donor, and
elite indica variety Teqing as the recurrent
parent.
• BC3F3 generation plants were used for
phenotype analysis.
36
Continued

37. 37
Phenotype of TQ and TQ-PAY1 NIL Plants
(a) Gross morphologies of TQ and TQ-PAY1-NIL plants at the maturity stage.
(b) Stem structure of TQ (left) and TQ-PAY1-NIL (right) plants.
(c) Comparison of the main panicle between TQ and TQ-PAY1-NIL plants.
(d) Cross-sections of the fifth internode between TQ and TQ-PAY1-NIL plants.

38. 38
CContd…….

39. • The PAY1 mutant showed characteristics of ideal plant
architecture compared with the wild-type YIL55 via affecting
PAT activity and altering endogenous indole-3-acetic acid
distribution.
• The NILs with Teqing genetic background demonstrated that
PAY1 could shape better plant architecture and enhance
grain yield of rice.
• PAY1 is an important dominant regulator of rice plant
architecture and would be useful for rice genetic
improvement and breeding of new varieties with increased
grain yield, thus contributing to global food security.
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CONCLUSION

40. SUMMARY
Rice is one of the most important staples and feeds more
than half of the world’s population.
The ability to produce more food in the same acreage is
crucial to feeding an increasing world population, and
therefore rice attracts tremendous attention in crop
improvement.
Elucidation of the molecular mechanisms underlying rice
plant architecture will provide a solid basis for modifying
the plant and in turn help to increase the yield.
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