Alteraton of plant type through mi-RNA expression

Presented By: Nilesh Joshi
Roll. No: 20827
Course Leader: Dr. V.S. Hegde
Chairman: Dr. Gopala Krishnan S.
Division Of Genetics
ICAR-Indian Agricultural Research Institute
ICAR-INDIANAGRICULTURALRESEARCHINSTITUTE

OUTLINE
• Introduction
• Types of Ideotype
• Features of Ideotype
• Breeding for Ideotype-conventional approaches
• mi-RNA discovery
• mi-RNA biosynthesis
• Genetic diversity related to plant architecture
• Genes involve in controlling plant architecture
• Molecular basis of shoot and root architecture
• miR156 regulating plant architecture
• Case studies

introduction
• Model plant
type
synonymous
• Ideal model
plant type
synonymous
• Plant type
synonymous
Ideotype concept was given by C.M. DONALD in the year 1968
Ideotype is a biological model which is expected to perform or behave
in a predictable manner within defined environment
Source: C.M. Donald(1968)

Types of Ideotype
• Isolation Ideotype: perform well when plants spaced planted
• Competition Ideotype: perform well in genetically heterogeneous
population
• Crop Ideotype: perform best at commercial crop densities (poor
competitor)

Features of Ideotype
• It should be weak competitor
• It will be the most efficient in utilizing environmental resources
• Each unit of dry matter production will include such a number of
flowers or florets
• Ideotype should have high harvest index
• A crop Ideotype must grown , as for as possible in a weed - free
situation
• The design of crop Ideotype is likely to involve concurrent modification
of the environment

Crop Ideotype breeding
Wheat Ideotype features
C.M. Donald(1968)

Contd…
Rice Ideotype
• Given by Jennings 1964
• Semi-dwarf stature
• Greater Culm diameter
• More number of panicles
• High tillering capacity
• Erect ,short and thick leaves
features
Lacharme,2001

mi-RNA Discovery
• 1st mi-RNA to be discovered in
1993 in Lin-4 gene of C.elegans
• By Victor Ambros’s and Gary
Ruvkun’s
• In nematode C.elegans
heterochronic gene control
temporal development pattern of
all larval stages
Victor ambros and gary ruvkun
Source: victor ambros and gary ruvkun(1993)

mi-RNA biosynthesis
 mi-RNA a class of small
endogenous RNAs of 21-25
nucleotides in length
 RNA pol-2 is mainly responsible
for transcription of mi-RNA
genes
Source: victor ambros and gary ruvkun(1993)

Genetic diversity related to plant architecture
Crop Plant
height
Branching
/tillering
Leaf
angle
Branch
angle of
tassel/panic
le
References
Rice Sd1 IPA ,
MOC1&ta
d1/te,OsT
B1
LPA-1&
PROG-1
osLG-1 Li ,X Quin
Q.,
2003&Zeng D
et al.,2009
Wheat Rht-
D1b&Rht-
B1b
MOC1 LC2 mos1 S.Pearce.,201
1
&Spielmeyer
W.et al.,2002
Maize d8 &d11 TB-1 &
ramosa2
LPA-1 LG-1 Choi, M.S., et
al.,2012
Arabidopsi
s
GAI BRC1
&BRC2 TAC1&L
AZY1
AtSPL8 Mooney &
Freeling.,1997
&Takeda et
al.,2003

Contd …
crop Plant
height
branching Leaf angle Root
architecture
References
Soybean dt1 Br1&Br2 LFY Slow anion
channel
associated
like-1
Zhang et
al.,2015&Rendall
nelson
Tomato dwarf1 fasciated FLO ara1 Molinero et
al.,1999
pea dt1 ramosus1-
5
UNIFOLAT
A
cra2 Emeline et
al.,2014&beveridge
2006&hofer et
al.,2001
pigeonpe
a
dt ramosus1-
5
LFY Auxin1 Bennet et al.,1996

PAY1 improves plant architecture in rice
Phenotype of wild type and PAY1 mutantSource:Lei zhao et al.,2015
PAY1 mutant
exhibit increased
plant height ,low
tiller number,
reduced tiller
angle and larger
panicle

osmiRNA156h is associated with semi dwarf and high
tillering phenotype
• WD44-sdt OsmiR156h
transgenic plant exhibit
increased tiller number and
dwarf stature
• OsmiR156h-OSPL14 is a
regulatory module
• Over expression of OsmiR156h
in transgenic plants
OsmiRNA156h expression in transgenic plant
Source: Meng Zhao et al.,2015

Zmbri1-RNAi alters maize plant architecture
Zmbri-RNAi plant architectureSource:Gokhan kir,et al.,2015

Molecular basis of shoot architecture
 MOC1 a key gene controlling rice
shoot development
 tad1/te mutants increased tiller
number
 OsMADS57 negatively regulated
by miR444a
source: Jianru Zuo.,2013
Network of tillering in rice

mi-RNA 156 controlling branching and tillering
• miR156s positive regulator of
branching
• OsTB1 and BRC1&2 suppress
branch/tiller outgrowth
Hai wang et al.,2015 miRNA156/SPL regulatory hub

IPA1 control by miR156
IPA interacting protein a ring
finger E3 ligase that can
interact with IPA1 in the
nucleus
IPI1 promotes degradation of
IPA1 in panicles while it
stabilize IPA1 in shoot apex
IPI1 ubiquitinate IPA1
mediated complex with different
poly ubiquitin chains
Adding K-48 linked
polyubiquitin chains in panicles
and K-63 linked polyubiquitin
chains in the shoot apex
IPA1 regulation mechanism
Source: Wang et al.,2017

mi-RNA156 controlling leaf angle/panicle branch angle
Mutation in the OsmiRNA156
target site in IPA1 leads to
reduced tiller number and
increased plant height
Hai wang et al.,2015

miRNA in root architecture development
 miR165/166 repression of HD-
ZIP TFs in embryonic root
development
 miR160 is a major regulator of
root growth and graviotropism
 miRNA negatively regulates
3ARFs (ARF10,16&17)
 Over expression of miR160
gene reduced levels of ARFs
mRNAs
miRNA in root developmentKhan,G.A.et al.,(2011)

miR172 regulate tassel formation
 Ids1 is a target gene of ts4
 Ids1 encodes an AP2 like gene
 Mutation in the 5` end of the
miR172 target binding site in
AP2 like gene leading to
dominant phenotype
Source: Chuck G et al.,2007

ramosa2 controlling inflorescence branching in maize
ra2 mutant phenotypeSource: Bortiri Estaben,et al.,(2006)

Contd…
 a typical ra2 mutant tassel
shows an abnormal, gradual
transition from long branches to
spikelet pairs
 All ra2 mutant alleles, the
spikelet pair pedicel is longer
Source: Bortiri Estaben,et al.,(2006)
Tassel Branching Patterns in A188, B73, and
W22 Maize Inbred Lines and ra2 Mutants

miR156-Targeted SPL genes in determining plastochron
length in Arabidopsis
 miRNA is limiting for the
delay of initiation of new leaf
primordia
 miR156 cause shortening of
the plastochron
a) Modulation of plastochron lengthSource:Jia-Wei Wang ,et al.,(2008)

BRI1 regulates cell division and cell expansion in maize
leaf growth
Reduced leaf growth in
zmbri-RNAi
Number of dividing cell
reduced in zmbri-RNAi
a) zmbri-RNAi leaves reduced in length
e) zmbri-RNAi show decreased cell elongation
Source:Gokhan kir,et al.,2015

Zmbri1-RNAi plants show leaf auricle phenotypes
In strongly affected leaves auricle
are largely missing
BR signalling might have a
specific function in maize auricle
development
Auricle band of zmbri-RNAi gets
narrower than wild type
a) Wild type auricle
b) Zmbri-RNAi lacking auricle
c) Zmbri-RNAi ligules reduced
Source:Gokhan kir,et al.,2015

Case study-1
Materials: backcrossing SNJ (shaonienjing) with TN1 and generated Bc2F2
population.

Map based cloning of IPA1 QTL
 Using 110 BC2F2 population
 IPA1 mapped b/w marker
RM149 and RM1345
 IPA1 located on the
chromosome 8
a)Plant architecture of SNJ and TN1
c) Coarse linkage map of IPA1
e) annotation of candidate gene on BACSource:Yongqingjiao et al.,2010

Expression pattern of OsSPL14 and confirmation of
OsmiRNA156 directed regulation
 OsSPL14 was predominantly
expressed in shoot apex ,
primordia of primary and
secondary branches
 OsSPL14 transcripts products
cleaved by OsmiR156 in vivo
Expression pattern of OsSPL14 and confirmation of
OsmiR156 direct regulation on OsSPL14
Source:Yongqingjiao et al.,2010

Effects of the point mutation in OsSPL14ipa1 on the
OsmiR156-directed regulation of OsSPL14.
 We generated transgenic
plants carrying the
OsSPL14IPA7m-GFP
transgene, which contained
seven mismatches to
OsmiR156
 Mutation of OsSPL14 in SNJ
perturbed the cleavage of the
OsSPL14 transcripts by
OsmiR156
Effect of point mutation OsSPL14 ipa1Source:Yongqingjiao et al.,2010

Phenotypic characterization of NIL OsSPL14ipa1 plants
 Generate NIL in the HUI7
background that contains
OsSPL14ipa1 allele
 NIL OsSPL14ipa1 show
increase level of OsSPL14
transcripts
Conclusion: mutation in the target binding site of OsmiR156 in OsSPL14
perturbs cleavage of OsSPL14 transcripts by OsmiR156 results into reduced
tillering
Phenotypic characterization of OsSPL14ipa1
Source:Yongqingjiao et al.,2010

Case study-2
Materials: a multi tillering and dwarf rice mutant Osmtd1 was obtained by
a T-DNA insertion mutant collection

Osmtd1 mutant exhibited dwarf and bushy phenotype
Phenotypes of Osmtd1
Qing Liu,et al.,2015

T-DNA insertion caused Osmtd1 phenotype
Phenotype of Osmtd1 and wild type after removing
axillary tiller

Location of T-DNA insertion
 T- DNA insertion localized in
unknown gene Os08g34258
 OsmiR156f located in the 3.3Kb
downstream of it
d) Over expression of Os08g34258 gene complemented
the phenotype of Osmtd1

OsmiR156 up regulated in Osmtd1
Conclusion: over expression of OsmiR156 caused high tillering and dwarf
phenotype which due to suppression of OsSPL14 genes

Application in crop improvement
 OsmiR156/SPL module can be intentionally exploited as a set of tools to genetically modify
crops for better agronomic traits
 Osmtd1 mutant ,PAY1,ra2 and IPA1 genes play important role in development of new plant
type in rice and other crops
 RNAi can be use in the development of ideal plant architecture using transgene approach
 LPA1,PROG1 and LAZY1 regulating tiller angle and leaf angle can be use to develop new
plant type in rice
 CFL1,LIC1,DLT,ILA, and LC2 helpful genes for development of new leaf architecture using
miR156
 TB1,MOC1 and TAD1/TE genes may be helpful in the development of new ideal rice plant
architecture using miR156

Alteraton of plant type through mi-RNA expression

Recommended

Recommended

More Related Content

What's hot

What's hot (20)

Similar to Alteraton of plant type through mi-RNA expression

Similar to Alteraton of plant type through mi-RNA expression (20)

Recently uploaded

Recently uploaded (20)

Alteraton of plant type through mi-RNA expression