The document discusses plant ideotypes and genes that regulate plant architecture. It describes how the ideotype concept was proposed by Donald in 1968 to define an optimal plant model. Ideotypes can be isolation, competition, or crop types. Key features of ideotypes are discussed. Various genes that control traits like plant height, tillering, leaf angle, and root architecture in different crops are summarized. The role of miRNAs like miR156 in regulating genes like IPA1, SPLs, and TB1 to influence branching and tillering is described. Two case studies on mapping the IPA1 QTL in rice and characterization of the Osmtd1 mutant provide examples of genes regulating architecture.
Editing rice-genome with CRISPR/Cas9: To improve agronomic traits for increa...apaari
Editing rice-genome with CRISPR/Cas9: To improve agronomic traits for increased crop productivity by MK Reddy during the Regional Expert Consultation on Gene Editing in Agriculture and its Regulations Technical Session III
CRISPR Agbio San Diego April 2017 AgendaDiane McKenna
CRISPR AgBio Congress is the first and only end-to-end meeting dedicated to helping agricultural biotech ad agrochemical companies leverage the power of CRISPR/Cas9 advanced trait breeding technology and precision genome editing, to overcome productivity challenges, increase yield and pioneer sustainable agriculture in plants breeding, crop protection and livestock. Commercialize the next generation of sustainable and superior agricultural products and help meet the world’s growing food demands.
Targeted Breeding Applications of CRISPR-CasKate Barlow
Doane Chilcoat, Director, Applied Technology Systems, DuPont Pioneer
CRISPR-Cas as an advanced plant breeding tool is a more efficient way to improve plants and help farmers produce more and better food, with fewer resources. The superior properties of CRISPR-Cas allows DuPont Pioneer scientists to develop innovative and sustainable seed products for growers similar to those realized through conventional plant breeding, but with even greater efficiency, accuracy and quality. Pioneer is leading the application of this tool to develop customized agriculture solutions. In this talk, potential product targets of this promising technology will be discussed. Approaches to fostering social license and developing an open innovation model for CRISPR-Cas will also be reviewed.
Editing rice-genome with CRISPR/Cas9: To improve agronomic traits for increa...apaari
Editing rice-genome with CRISPR/Cas9: To improve agronomic traits for increased crop productivity by MK Reddy during the Regional Expert Consultation on Gene Editing in Agriculture and its Regulations Technical Session III
CRISPR Agbio San Diego April 2017 AgendaDiane McKenna
CRISPR AgBio Congress is the first and only end-to-end meeting dedicated to helping agricultural biotech ad agrochemical companies leverage the power of CRISPR/Cas9 advanced trait breeding technology and precision genome editing, to overcome productivity challenges, increase yield and pioneer sustainable agriculture in plants breeding, crop protection and livestock. Commercialize the next generation of sustainable and superior agricultural products and help meet the world’s growing food demands.
Targeted Breeding Applications of CRISPR-CasKate Barlow
Doane Chilcoat, Director, Applied Technology Systems, DuPont Pioneer
CRISPR-Cas as an advanced plant breeding tool is a more efficient way to improve plants and help farmers produce more and better food, with fewer resources. The superior properties of CRISPR-Cas allows DuPont Pioneer scientists to develop innovative and sustainable seed products for growers similar to those realized through conventional plant breeding, but with even greater efficiency, accuracy and quality. Pioneer is leading the application of this tool to develop customized agriculture solutions. In this talk, potential product targets of this promising technology will be discussed. Approaches to fostering social license and developing an open innovation model for CRISPR-Cas will also be reviewed.
Heat Shock Transcription Factors (HSFs) In Pearl Millet: Identification and c...ICRISAT
As a response to heat stress, plants rapidly accumulate HSPs which are regulated by the heat shock transcription factors (HSFs). Pearl millet (Pennisetumglaucum(L.)R.Br.)is an important crop of arid and semi-arid regions. Pearl millet genome opened an opportunity to study the HSFs present in its genome.
Transgene-free CRISPR/Cas9 genome-editing methods in plantsCIAT
"Transgene-free CRISPR/Cas9 genome-editing methods in plants" by Matthew R. Willmann, Ph.D. Director, Plant Transformation Facility College of Agriculture and Life Sciences, School of Integrative Plant Science, Cornell University.
CRISPR Is On The Move: Genome Editing From Rice To WheatFabio Caligaris
Presented at Plant Genomics and Gene Editing Congress: Europe. For more information visit: www.global-engage.com
Success in rice is not equalled in wheat: CRISPR/Cas9 efficiency is around 5% and requires a time-consuming downstream identification of the genome edited plants.
An overview of agricultural applications of genome editing: Crop plantsOECD Environment
The presentation gives an overview of genome editing applications in relation to crop plants. The aim is to have a better understanding of the specific features of genome editing in comparison with classical breeding and genetic engineering techniques. It will give an overview of some examples of agricultural applications that may be on or close to the market or under research and development. It will also consider the possibility of foreseeing future applications (e.g. variations in CRISPR/Cas applications, DNA-free application, agricultural pest control), if possible.
Loss of pollen-specific phospholipase NOT LIKE DAD triggers gynogenesis in maizePGS
This lecture was a part of Plant Genetics Seminars - PGS 2017/2018 at Assiut University. These seminars organized by Dr. Ahmed Sallam, Department of Genetics, Faculty of Agriculture, Assiut University
Abstract
Gynogenesis is an asexual mode of reproduction common to animals and plants, in which stimuli from the sperm cell trigger the development of the unfertilized egg cell into a haploid embryo. Fine mapping restricted a major maize QTL (quantitative trait locus) responsible for the aptitude of inducer lines to trigger gynogenesis to a zone containing a single gene NOT LIKE DAD (NLD) coding for a patatin-like phospholipase A. In all surveyed inducer lines, NLD carries a 4-bp insertion leading to a predicted truncated protein. This frameshift mutation is responsible for haploid induction because complementation with wild-type NLD abolishes the haploid induction capacity. Activity of the NLD promoter is restricted to mature pollen and pollen tube. The translational NLD::citrine fusion protein likely localizes to the sperm cell plasma membrane. In Arabidopsis roots, the truncated protein is no longer localized to the plasma membrane, contrary to the wild-type NLD protein. In conclusion, an intact pollen-specific phospholipase is required for successful sexual reproduction and its targeted disruption may allow establishing powerful haploid breeding tools in numerous crops.
microRNA in Plant Defence and Pathogen Counter-defenceMahtab Rashid
The presentation is about the role of microRNA in plant defence and the pathogen counter-defences which they adopt to escape or evade the plant defence mechanism.
microRNAs in Arabidopsis : discovery, functions & involvment in the control o...Frédéric Bouché
Discovered about 20 years ago, microRNA are small non-coding RNA (21-23 nt) involved in the post-transcriptional regulation of gene expression. They are involved in numerous regulatory pathways. However, the analysis of their function and their expression level is a bit tricky, explaining that they were only integrated in the molecular pathways during the last decade.
Here, we present a brief summary of the events that lead to the discovery of microRNAs, as well as the molecular tools used for their analysis and their role in the molecular control of flowering time.
Of course, feel free to leave any constructive comment about those slides !
Persistent neglect of the crop has resulted in continual loss of essential AYB germplasm with implications on its variability
Research on diversity and yield evaluation of this crop is
germane to its improvement
Using more recent genomic tools to understand the extent of genetic variability present in AYB will be beneficial to breeders
Heat Shock Transcription Factors (HSFs) In Pearl Millet: Identification and c...ICRISAT
As a response to heat stress, plants rapidly accumulate HSPs which are regulated by the heat shock transcription factors (HSFs). Pearl millet (Pennisetumglaucum(L.)R.Br.)is an important crop of arid and semi-arid regions. Pearl millet genome opened an opportunity to study the HSFs present in its genome.
Transgene-free CRISPR/Cas9 genome-editing methods in plantsCIAT
"Transgene-free CRISPR/Cas9 genome-editing methods in plants" by Matthew R. Willmann, Ph.D. Director, Plant Transformation Facility College of Agriculture and Life Sciences, School of Integrative Plant Science, Cornell University.
CRISPR Is On The Move: Genome Editing From Rice To WheatFabio Caligaris
Presented at Plant Genomics and Gene Editing Congress: Europe. For more information visit: www.global-engage.com
Success in rice is not equalled in wheat: CRISPR/Cas9 efficiency is around 5% and requires a time-consuming downstream identification of the genome edited plants.
An overview of agricultural applications of genome editing: Crop plantsOECD Environment
The presentation gives an overview of genome editing applications in relation to crop plants. The aim is to have a better understanding of the specific features of genome editing in comparison with classical breeding and genetic engineering techniques. It will give an overview of some examples of agricultural applications that may be on or close to the market or under research and development. It will also consider the possibility of foreseeing future applications (e.g. variations in CRISPR/Cas applications, DNA-free application, agricultural pest control), if possible.
Loss of pollen-specific phospholipase NOT LIKE DAD triggers gynogenesis in maizePGS
This lecture was a part of Plant Genetics Seminars - PGS 2017/2018 at Assiut University. These seminars organized by Dr. Ahmed Sallam, Department of Genetics, Faculty of Agriculture, Assiut University
Abstract
Gynogenesis is an asexual mode of reproduction common to animals and plants, in which stimuli from the sperm cell trigger the development of the unfertilized egg cell into a haploid embryo. Fine mapping restricted a major maize QTL (quantitative trait locus) responsible for the aptitude of inducer lines to trigger gynogenesis to a zone containing a single gene NOT LIKE DAD (NLD) coding for a patatin-like phospholipase A. In all surveyed inducer lines, NLD carries a 4-bp insertion leading to a predicted truncated protein. This frameshift mutation is responsible for haploid induction because complementation with wild-type NLD abolishes the haploid induction capacity. Activity of the NLD promoter is restricted to mature pollen and pollen tube. The translational NLD::citrine fusion protein likely localizes to the sperm cell plasma membrane. In Arabidopsis roots, the truncated protein is no longer localized to the plasma membrane, contrary to the wild-type NLD protein. In conclusion, an intact pollen-specific phospholipase is required for successful sexual reproduction and its targeted disruption may allow establishing powerful haploid breeding tools in numerous crops.
microRNA in Plant Defence and Pathogen Counter-defenceMahtab Rashid
The presentation is about the role of microRNA in plant defence and the pathogen counter-defences which they adopt to escape or evade the plant defence mechanism.
microRNAs in Arabidopsis : discovery, functions & involvment in the control o...Frédéric Bouché
Discovered about 20 years ago, microRNA are small non-coding RNA (21-23 nt) involved in the post-transcriptional regulation of gene expression. They are involved in numerous regulatory pathways. However, the analysis of their function and their expression level is a bit tricky, explaining that they were only integrated in the molecular pathways during the last decade.
Here, we present a brief summary of the events that lead to the discovery of microRNAs, as well as the molecular tools used for their analysis and their role in the molecular control of flowering time.
Of course, feel free to leave any constructive comment about those slides !
Persistent neglect of the crop has resulted in continual loss of essential AYB germplasm with implications on its variability
Research on diversity and yield evaluation of this crop is
germane to its improvement
Using more recent genomic tools to understand the extent of genetic variability present in AYB will be beneficial to breeders
Fast forward genetic mapping provides candidate genes for resistance to fusar...ICRISAT
Fast forward genetic mapping combined with whole genome sequencing (WGS)and bulked segregantan alysis (BSA)approach was used to identify the candidate genes for Fusarium wilt (FW)and sterility mosaic disease (SMD) resistance in pigeonepa.
3 Jul 2014
Genetic Improvement of Indica Group Rice Through Wide HybridizationDr. Md. Nashir Uddin
Indica Group Rice Cultivar IR64 was recurrently crossed with Japonica Group Rice (New Plant Type originated from Indonesia) and developed the Introgression lines (INLs). These INLs showed 30 to 40% increment of Yield than IR64. This wide hybridization method is very useful for crop improvement including rice.
Role of miRNA for Nutrient Use Efficiency in cropsRahul kumar
NUE of major nutrients like N, P and K are very low within the plant systems. In the enhancement of NUE in the plant system miRNA can play a very important role.
miRNA diversity related to NUE indicates different miRNA sequences and their target sequence in respect of Nutrient uptake ,translocation and their assimilation in plants. miRNAs are vital for maintaining nutrient homeostasis in plants by regulating the expression of transporters that are involved in nutrient uptake and mobilization. The alteration of nutrient levels in soil trigger specific signaling molecules that act as repressors of target nutrient responsive- miRNAs . The decreased accumulation of miRNAs subsequently stabilizes the expression of transporters. The identification of promoter regions of specific up- or down- regulated miRNAs that are responsive to micronutrient stresses and the subsequent development of knock-out mutants by inducing mutation in cis-acting elements using targeted genome- editing technologies ,such as TALEN or CRISPR-Cas9 techniques, may lead to essential crop-improvement strategies in the future.
Genome Sequencing in Finger Millet
Genome size estimation
SOLiD Sequencing Technology
Illumina Sequencing Technology
Gene prediction and functional annotation of genes
Mining of plant transcription factors and other genes
Gene silencing techniques for crop improvementJhilickBanerjee
Gene silencing is a technique that aims to reduce or eliminate the production of a protein from its corresponding gene. Gene silencing is the regulation of gene expression in a cell.
Gene silencing can occur during either transcription or translation.
Gene silencing is often considered as “Gene knockdown’ i.e their expression is reduced. In contrast , when genes are knocked out they are completely erased from the organism’s genome and thus have no expression.
Methods used to silence genes include RNAi, CRISPR or siRNA, these reduce the expression of the gene by 70% but do not completely eliminate it.
Similar to Alteraton of plant type through mi-RNA expression (20)
DERIVATION OF MODIFIED BERNOULLI EQUATION WITH VISCOUS EFFECTS AND TERMINAL V...Wasswaderrick3
In this book, we use conservation of energy techniques on a fluid element to derive the Modified Bernoulli equation of flow with viscous or friction effects. We derive the general equation of flow/ velocity and then from this we derive the Pouiselle flow equation, the transition flow equation and the turbulent flow equation. In the situations where there are no viscous effects , the equation reduces to the Bernoulli equation. From experimental results, we are able to include other terms in the Bernoulli equation. We also look at cases where pressure gradients exist. We use the Modified Bernoulli equation to derive equations of flow rate for pipes of different cross sectional areas connected together. We also extend our techniques of energy conservation to a sphere falling in a viscous medium under the effect of gravity. We demonstrate Stokes equation of terminal velocity and turbulent flow equation. We look at a way of calculating the time taken for a body to fall in a viscous medium. We also look at the general equation of terminal velocity.
The ability to recreate computational results with minimal effort and actionable metrics provides a solid foundation for scientific research and software development. When people can replicate an analysis at the touch of a button using open-source software, open data, and methods to assess and compare proposals, it significantly eases verification of results, engagement with a diverse range of contributors, and progress. However, we have yet to fully achieve this; there are still many sociotechnical frictions.
Inspired by David Donoho's vision, this talk aims to revisit the three crucial pillars of frictionless reproducibility (data sharing, code sharing, and competitive challenges) with the perspective of deep software variability.
Our observation is that multiple layers — hardware, operating systems, third-party libraries, software versions, input data, compile-time options, and parameters — are subject to variability that exacerbates frictions but is also essential for achieving robust, generalizable results and fostering innovation. I will first review the literature, providing evidence of how the complex variability interactions across these layers affect qualitative and quantitative software properties, thereby complicating the reproduction and replication of scientific studies in various fields.
I will then present some software engineering and AI techniques that can support the strategic exploration of variability spaces. These include the use of abstractions and models (e.g., feature models), sampling strategies (e.g., uniform, random), cost-effective measurements (e.g., incremental build of software configurations), and dimensionality reduction methods (e.g., transfer learning, feature selection, software debloating).
I will finally argue that deep variability is both the problem and solution of frictionless reproducibility, calling the software science community to develop new methods and tools to manage variability and foster reproducibility in software systems.
Exposé invité Journées Nationales du GDR GPL 2024
Phenomics assisted breeding in crop improvementIshaGoswami9
As the population is increasing and will reach about 9 billion upto 2050. Also due to climate change, it is difficult to meet the food requirement of such a large population. Facing the challenges presented by resource shortages, climate
change, and increasing global population, crop yield and quality need to be improved in a sustainable way over the coming decades. Genetic improvement by breeding is the best way to increase crop productivity. With the rapid progression of functional
genomics, an increasing number of crop genomes have been sequenced and dozens of genes influencing key agronomic traits have been identified. However, current genome sequence information has not been adequately exploited for understanding
the complex characteristics of multiple gene, owing to a lack of crop phenotypic data. Efficient, automatic, and accurate technologies and platforms that can capture phenotypic data that can
be linked to genomics information for crop improvement at all growth stages have become as important as genotyping. Thus,
high-throughput phenotyping has become the major bottleneck restricting crop breeding. Plant phenomics has been defined as the high-throughput, accurate acquisition and analysis of multi-dimensional phenotypes
during crop growing stages at the organism level, including the cell, tissue, organ, individual plant, plot, and field levels. With the rapid development of novel sensors, imaging technology,
and analysis methods, numerous infrastructure platforms have been developed for phenotyping.
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...Sérgio Sacani
We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest
imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters
spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data
at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and
30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric
redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts
z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of
M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1
. Our search finds no candidates
at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to
infer the properties of the evolving luminosity function without binning in redshift or luminosity that
marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the
impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results,
and that the luminosity function normalization and UV luminosity density decline by a factor of ∼ 2.5
from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical
models for evolution of the dark matter halo mass function.
Salas, V. (2024) "John of St. Thomas (Poinsot) on the Science of Sacred Theol...Studia Poinsotiana
I Introduction
II Subalternation and Theology
III Theology and Dogmatic Declarations
IV The Mixed Principles of Theology
V Virtual Revelation: The Unity of Theology
VI Theology as a Natural Science
VII Theology’s Certitude
VIII Conclusion
Notes
Bibliography
All the contents are fully attributable to the author, Doctor Victor Salas. Should you wish to get this text republished, get in touch with the author or the editorial committee of the Studia Poinsotiana. Insofar as possible, we will be happy to broker your contact.
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...Ana Luísa Pinho
Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required. Yet, to date, both structural atlases and parcellation-based activations do not fully account for cognitive function and still present several limitations. Further, they do not adapt overall to individual characteristics. In this talk, I will give an account of deep-behavioral phenotyping strategies, namely data-driven methods in large task-fMRI datasets, to optimize functional brain-data collection and improve inference of effects-of-interest related to mental processes. Key to this approach is the employment of fast multi-functional paradigms rich on features that can be well parametrized and, consequently, facilitate the creation of psycho-physiological constructs to be modelled with imaging data. Particular emphasis will be given to music stimuli when studying high-order cognitive mechanisms, due to their ecological nature and quality to enable complex behavior compounded by discrete entities. I will also discuss how deep-behavioral phenotyping and individualized models applied to neuroimaging data can better account for the subject-specific organization of domain-general cognitive systems in the human brain. Finally, the accumulation of functional brain signatures brings the possibility to clarify relationships among tasks and create a univocal link between brain systems and mental functions through: (1) the development of ontologies proposing an organization of cognitive processes; and (2) brain-network taxonomies describing functional specialization. To this end, tools to improve commensurability in cognitive science are necessary, such as public repositories, ontology-based platforms and automated meta-analysis tools. I will thus discuss some brain-atlasing resources currently under development, and their applicability in cognitive as well as clinical neuroscience.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
Comparing Evolved Extractive Text Summary Scores of Bidirectional Encoder Rep...University of Maribor
Slides from:
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Track: Artificial Intelligence
https://www.etran.rs/2024/en/home-english/
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
1. 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
2. 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
ICAR-INDIANAGRICULTURALRESEARCHINSTITUTE
3. 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
ICAR-INDIANAGRICULTURALRESEARCHINSTITUTE
Source: C.M. Donald(1968)
4. 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)
ICAR-INDIANAGRICULTURALRESEARCHINSTITUTE
5. 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
ICAR-INDIANAGRICULTURALRESEARCHINSTITUTE
7. 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
ICAR-INDIANAGRICULTURALRESEARCHINSTITUTE
8. 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)
ICAR-INDIANAGRICULTURALRESEARCHINSTITUTE
9. 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)
ICAR-INDIANAGRICULTURALRESEARCHINSTITUTE
10. 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
ICAR-INDIANAGRICULTURALRESEARCHINSTITUTE
11. 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
ICAR-INDIANAGRICULTURALRESEARCHINSTITUTE
12. 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
ICAR-INDIANAGRICULTURALRESEARCHINSTITUTE
13. 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
ICAR-INDIANAGRICULTURALRESEARCHINSTITUTE
15. 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
ICAR-INDIANAGRICULTURALRESEARCHINSTITUTE
16. 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
ICAR-INDIANAGRICULTURALRESEARCHINSTITUTE
17. IPA1 control by miR156
ICAR-INDIANAGRICULTURALRESEARCHINSTITUTE
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
18. 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
ICAR-INDIANAGRICULTURALRESEARCHINSTITUTE
19. 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
ICAR-INDIANAGRICULTURALRESEARCHINSTITUTE
miRNA in root developmentKhan,G.A.et al.,(2011)
20. 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
ICAR-INDIANAGRICULTURALRESEARCHINSTITUTE
Source: Chuck G et al.,2007
22. 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
ICAR-INDIANAGRICULTURALRESEARCHINSTITUTE
Source: Bortiri Estaben,et al.,(2006)
Tassel Branching Patterns in A188, B73, and
W22 Maize Inbred Lines and ra2 Mutants
23. 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
ICAR-INDIANAGRICULTURALRESEARCHINSTITUTE
a) Modulation of plastochron lengthSource:Jia-Wei Wang ,et al.,(2008)
24. 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
ICAR-INDIANAGRICULTURALRESEARCHINSTITUTE
25. 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
ICAR-INDIANAGRICULTURALRESEARCHINSTITUTE
27. 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
ICAR-INDIANAGRICULTURALRESEARCHINSTITUTE
28. 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
ICAR-INDIANAGRICULTURALRESEARCHINSTITUTE
29. 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
ICAR-INDIANAGRICULTURALRESEARCHINSTITUTE
30. 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
ICAR-INDIANAGRICULTURALRESEARCHINSTITUTE
31. Case study-2
Materials: a multi tillering and dwarf rice mutant Osmtd1 was obtained by
a T-DNA insertion mutant collection
ICAR-INDIANAGRICULTURALRESEARCHINSTITUTE
32. Osmtd1 mutant exhibited dwarf and bushy phenotype
Phenotypes of Osmtd1
Qing Liu,et al.,2015
ICAR-INDIANAGRICULTURALRESEARCHINSTITUTE
33. T-DNA insertion caused Osmtd1 phenotype
Phenotype of Osmtd1 and wild type after removing
axillary tiller
Qing Liu,et al.,2015
ICAR-INDIANAGRICULTURALRESEARCHINSTITUTE
34. 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
Qing Liu,et al.,2015
ICAR-INDIANAGRICULTURALRESEARCHINSTITUTE
35. OsmiR156 up regulated in Osmtd1
Conclusion: over expression of OsmiR156 caused high tillering and dwarf
phenotype which due to suppression of OsSPL14 genes
Qing Liu,et al.,2015
ICAR-INDIANAGRICULTURALRESEARCHINSTITUTE
36. 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
ICAR-INDIANAGRICULTURALRESEARCHINSTITUTE