Milestones
and outputs (including HRD activities) - For the Consortium
Moisture stress, salinity, heat, cold
and submergence tolerance – Microbes
Time schedule of activities and activity
milestones
|
S.No. |
Objective/Activity |
Activity Milestones |
Expected
Output |
Responsibilitiy |
|||
|
|
1 |
2 |
3 |
|
|
||
|
1. |
Selection of different extreme enviornments for survey and collection of soil, water and
sediment samples. The sites proposed to be
surveyed are with regards to extreme conditions of a) Salinity/ Sodicity/ Acidity |
Survey and collection of soil
samples from extreme enviornments. |
Yes |
|
|
Samples from different sites
will be available for isolation of microbes. |
NBAIM. Mau, IARI, CIFRI,
Barrackpur, CMFRI,
Cochin, CIFT,
Cochin NRCG, Junagarh |
|
|
b) Moisture |
Survey and collection of soil
samples from extreme enviornments. |
Yes |
|
|
Samples from different sites
will be available for isolation of microbes. |
NBAIM. Mau, IARI, NRCG, Junagarh |
|
|
b) Temperature (Low
and High) |
Survey and collection of soil
samples from extreme enviornments. |
Yes |
|
|
Samples from different sites
will be available for isolation of microbes. |
NBAIM. Mau, IARI, CIFA, NRCG, Junagarh |
|
|
c) Temperature (Low
and High) |
Survey and collection of soil
samples from extreme enviornments. |
Yes |
|
|
Samples from different sites
will be available for isolation of microbes. |
NBAIM. Mau, IARI, CIFA, NRCG, Junagarh |
|
|
d) Submergence (Anoxia) |
Survey and collection of soil
samples from extreme enviornments. |
Yes |
|
|
Samples from different sites
will be available for isolation of microbes. |
CRRI,
Cuttuck, CIFT,
Cochin, CMFRI,
Cochin, |
|
2. |
Analysis of diversity of
predominant genera from various extreme enviornments |
Isolation of microbes from
samples collected from extreme environments of the country |
Yes |
Yes |
|
Development of database for
microbes isolated from extreme environments. Generation of baseline
information in the country. |
NBAIM. Mau, IARI, CIFA, CIFRI, Barrackpur, CMFRI, CRRI, Cuttuck, CIFT, NRCG, Junagarh |
|
3. |
Sequencing of rDNA genes for identification of selected
isolates/strains. |
Generation of sequence database
of native isolates and identification of isolates. |
|
Yes |
|
Submission of DNA sequences in GenBank of native isolates. |
NBAIM. Mau, IARI, CIFA, CIFRI, Barrackpur, CMFRI, CIFT, CRRI, Cuttuck, NRCG, Junagarh |
|
4. |
Specific primers for known
genes will be used in PCR to identify and isolate candidate genes from
microbes. |
PCR amplification of relevant
genes using specific primers |
Yes |
|
|
Allelic variants from
indigenous isolates will be identified. |
NBAIM. Mau, IARI, CIFA, CIFRI, Barrackpur, CMFRI, CRRI, Cuttuck, CIFT, NRCG, Junagarh |
|
5. |
Construction of genomic library
in suitable vector and screening of clones for identification of novel genes. |
Genomic library construction. |
|
Yes |
Yes |
Identification of novel genes
for abiotic stress tolerance. |
NBAIM. Mau, IARI, CIFA, CIFRI, Barrackpur, CMFRI, CRRI, Cuttuck, CIFT, NRCG, Junagarh |
|
6. |
Transposon mutagenesis of the seleted strains
for screening and isolation of the mutants of interest. |
Development of mutants using Transposons. |
|
Yes |
Yes |
Mutants of negative for relevant
trait Will be developed. |
NBAIM. Mau, IARI, CIFA, CIFRI, Barrackpur, CMFRI, CRRI, Cuttuck, CIFT, NRCG, Junagarh |
|
7. |
Identification of the genes
disrupted by transposon insertion in the mutants by
cloning and DNA sequence analysis of transposon
flanking sequences. |
DNA sequences and
identification of new genes. |
|
Yes |
Yes |
Validation of novel genes for
abiotic stress tolerance. |
NBAIM. Mau, IARI, CIFA, CIFRI, Barrackpur, CMFRI, CRRI, Cuttuck, CIFT, NRCG, Junagarh |
|
8. |
Metagenomic library construction and sequence based screening for novel
genes for candidate traits. |
Isolation DNA from soil and
construction of metagenomic library. |
Yes |
Yes |
Yes |
Metagenomic library construction for unculturables. |
NBAIM. Mau, IARI, CRRI, Cuttuck, |
|
9. |
Bioinformatics analysis of the identifies genes and the encoded proteins and putative
biochemical pathways responsible for the stress tolerance. |
Identification of the genes and
genes sequences. |
|
Yes |
Yes |
Novel genes from indigenous
isolates identified. |
NBAIM. Mau, IARI, CIFA, CIFRI, Barrackpur, CMFRI, CRRI, Cuttuck, CIFT, NRCG, Junagarh |
Trait-wise
Distribution of work elements among participating Institutes - microbes
|
Trait |
Species |
Location/Resources |
Activity |
Institute |
|
Salt tolerance, dessiccation,
high temperature |
Fungi |
Both aquatic and soil |
Fungal isolation and
identification, gene identification by Molecular & Metagenomic
approach |
NBAIM. Mau, NRCG, Junagarh |
|
Heat & cold tolerance,
Desiccation & Acid soil |
Soil Bacteria |
|
Isolation & Identification
of microbes, variable tolerance study, Gene
identification by Molecular & Metagenomic
approach. |
Microbiology Lab, IARI, |
|
Salt tolerance |
Aquatic bacteria, Phytoplankton
(Blue-green algae) and Zooplankton |
Esturine mangrove ecosystems (Sunderbans
in west |
Microbe isolation &
identification, salt tolerance study, ,Gene identification by Molecular &
Metagenomic & Bioinformatic
analysis (metagenomic
component to the carried out in collaboration with CRRI, |
CIFRI, Barrackpur, CRRI, |
|
High Temperature Tolerance |
Aquatic Bacteria |
Orissa and west |
Microbe identification, heat
tolerance study, Gene identification by Molecular & Metagenomic
& Bioinformatic analysis |
CIFA, |
|
Salt Tolerance and Anoxia/
Submergence |
Marine Microbes |
Marine environments of Kerala and Lakshwadeep coast
and Kutch region in |
Microbe identification, identification,
salt tolerance study, transposon mutagenesis and
Molecular & Metagenomic & Bioinformatic analysis |
CIFT, |
|
Salt Tolerance and Anoxia/
Submergence |
Marine Microbes |
Marine environments of Tamilnadu,Kerala and Andhra Pradesh |
Algal identification,
identification, salt tolerance study, transposon
mutagenesis and Molecular & Metagenomic & Bioinformatic analysis |
CMFRI, |
|
Anoxia/ Submergence |
Soil and Aquatic Microbes |
Orissa, |
Microbe identification, Gene identification and Bioinformatic
analysis. Metagenomic study of samples collected by
CIFRI, Barrackpur |
CRRI, |
|
Validation of genes for abiotic
stress tolerance |
|
|
Aiotic stress tolerance gene validation |
NRCPB, |
Moisture
stress, salinity/sodicity, acidity, heat/cold and
submergence tolerance - Rice
Time schedule of activities and activity
milestones
|
S.No. |
Objective/Activity |
Activity Milestones |
Milestones
and when to be attained |
Expected Output |
Responsibilitiy |
||
|
|
1 |
2 |
3 |
|
|
||
|
1. |
Identification of core
collection of rice that would represent total diversity |
Analysis of the available
passport data as well as agro-ecological, morphological and molecular data on
the whole germplasm collection of rice to constitute a core collection |
Yes |
|
|
A core collection of about 6000 rice accessions including
landraces and wild relatives |
NBPGR |
|
2. |
Validation of cire and Identification
of mini-core collection of rice |
Phenotypic and Molecular
markers-based analysis of core collection of rice and constitute a mini-core
collection |
Yes |
Yes |
|
A mini-core collection of about
1000 accessions representing and diversity |
NRCPB, NBPGR, DRR, CRRI. IARI,
IGKVV, CAU-B & RCNEHR |
|
3. |
Generation of phenotypic information for the mini-core
collection |
Phenotypic evaluation of the
mini-core collection in multiple environments for target traits (stress tolerance,yield,cooking and nutritional quality |
|
Yes |
Yes |
Phenotypically characterized mini-core set of rice |
NBAIM. Mau, IARI, CIFA, NRCG, Junagarh |
|
4. |
Identification of candidate genes through differential expression
analysis for selected traits. |
To use rice DNA chips in gene
expression analysis for identifying possible candidate genes for trait such
as abiotic stress tolerance. |
Yes |
Yes |
|
Information on candidate genes
related to target traits. |
DUSC, CAU-B, DRR |
|
5. |
Selection of SNPs and SSRs for whole genome and candidate gene based
genotyping. |
Study of the whole genome SSR
and SNP information as well as genic region of the
rice gemone, standalone assays for high throughput
genotyping. |
Yes |
|
|
Selected set of SSR and SNP
markers (Total about 4000) covering the whole genome spaced at an physical
interval of about 100kb and standardized genotyping methods. |
NRCPB, DUSC, CAU-B |
|
6. |
Generation of SSR and SNP database for mini-core collection. |
SSR and SNP genotyping Of the mini-core collection and
understanding the diversity pattern and haplotype
structure. |
|
Yes |
Yes |
|
NRCPB, NBPGR, DRR, CRRI, IGKVV,
IARI, CAU-B, & RCNEHR |
|
7. |
Allele mining for the
selected/known candidate genes. |
Association the phenotypic
information of the mini-core collection with the known candidate gene based genotypic
information |
|
Yes |
Yes |
Novel alleles of genes for the
target traits. |
NRCPB, NBPGR, DRR, IIT-K, IARI,
CAU-B & RCNEHR |
|
8. |
Association mapping and
identification of new genes/QTLs for the target
traits. |
Associating the phenotypic
information on the mini-core collection with the whole genome genotypic
information |
|
Yes |
Yes |
Novel genes/QTLs
for the chosen trait. |
NRCPB, NBPGR & IASRI |
|
9. |
Validation of marker-trait associations in biparental mapping populations. |
Use of the available mapping
population segregating for abiotic stress tolerance for validation of
linkages. |
|
|
Yes |
Validated markers for QTLs for abiotic
stress tolerance |
NRCPB, DRR, IGKVV, CRRI, IARI |
|
10. |
Marker associated Backcross
transfer of useful genes/QTLs |
Generation of backcross derived
lines with new gene combinations. |
|
Yes |
Yes |
New genotypes for use in Rice
improvements/function analysis of traits. |
DRR, IGKVV, CRRI, IARI |
|
11. |
Validation of candidate gene in transgenic
of model systems. |
Genetic transformation of
Arabidopsis/Rice using identified candidates/transcription factors. |
|
Yes |
Yes |
Functionally validated genes. |
DUSC, VPKAS, IIT-K, CAU-B, RCNEHR |
|
12, |
Cloning and characterization of orthologs of new/candidate genes from bajra.
|
Pcr CLONING, Sequencing and sequence analysis of new genes for
stress analysis from pearl millet. |
|
|
Yes |
Novel orthologs
of rice from pearl millet, which is highly stress tolerance. |
NRCPB, IIT-K |
*Responsibility:
NRCPB,
NBPGR,
DRR,
CRRI, Cuttack: G.J.N. Rao, J.N.
Reddy, R.K. Sarkar, P. Swain, P. Krishnan, H.N. Subudhi, S Marndi, and J. Meher
IARI,
IASRI,
DUSC,
IGKVV,
CAU, Barapani: W. Tyagi and M. Rai
Res Comp NEHR: A. Pattanayak,
IIT, Kharagpur: S. K. Sen, A. Basu, M.K. Maiti and B. S. Das
VPKAS, Almora: P.K. Agrawal, K.
Babu, J.P. Aditya and A. Kumar
Work
allocation & sharing: Rice across traits
|
Name & Designation |
Institute/ Organization |
Work Allocation |
|
T. Mohapatra, PS |
NRCPB, |
Coordination
of whole activities in rice, selection
of markers, Genotyping of core and
mini-core collections, expression analysis,
phenotyping for abiotic stress tolerance,
association analysis to discover new
genes and alleles |
|
N. K. Singh, PS |
NRCPB, |
Expression analysis, genotyping and phenotypic of
the mini-core collection |
|
K. Gaikwad, SS |
NRCPB, |
Genotyping and phenotyping
of the mini-core collection, allele mining using the candidate genes |
|
V. Rai, SS |
DRR, |
Genotyping
of the core and mini-core using SSR
markers, expression analysis to
identify candidate gene for drought tolerance and candidate gene based
allele mining |
|
N. Sarla, PS |
DRR, |
Genotyping of the core using SSR markers |
|
T. Ram, PS |
DRR, |
Generation of core and mini-core, phenotyping of the mini-core |
|
L. V. Subbaro, PS |
DRR, |
Generation of core and mini-core, phenotyping of the mini-core |
|
D. Subrahmanyam, SS |
DRR, |
Physiological analysis of core and mini-core |
|
G.J.N. Roa |
CRRI, |
Generation of core and mini-core, SSR genotyping,
QTL mapping, allele mining |
|
J. N. Reddy |
CRRI, |
Generation of core and mini-core, phenotyping for submergence tolerance, SSR genotyping,
QTL mapping, AS |
|
R. K. Sarkar |
CRRI, |
Phenotyping for salinity and submergence tolerance, MAS |
|
P. Swain |
CRRI, |
Phenotyping for drought tolerance, MAS |
|
P. Krishnan |
CRRI, |
Phenotyping for high temperature tolerance, MAS |
|
J. Mehar |
CRRI, |
Phenotyping for high temperature tolerance, MAS |
|
H. N. Subudi |
CRRI, |
Generation of core and mini-core, phenotypic of the
mini-core collection |
|
S. Marandi |
CRRI, |
Phenotyping for Salinity tolerance |
|
A. K. Singh |
IARI, |
Phenotyping and genotyping of the core and mini-core using SSR
markers, candidate gene based allele mining for BLB resistance, MAS for BLB
and BPH resistance. |
|
C. Viswanathan |
IARI, |
Phenotyping of the mini-core for drought tolerance |
|
K.V. Bhatt |
NBPGR, |
Generation of
core and mini-core collection, and genotyping using SSR markers,
allele mining using known/candidate genes |
|
I.S. Bisht |
NBPGR, |
Generation of
of
core and mini-core collection, and genotyping using SSR markers,
allele mining using known/candidate genes |
|
R.K. Singh |
NBPGR, |
Generation of
of
core and mini-core collection, allele mining, and genotyping using SSR
markers |
|
A. Singh |
NBPGR, |
Allele mining, and genotyping using SSR markers |
|
J. P. Khurana |
DU, South Campus |
Expression analysis using microarrays
and functional validation |
|
S. Kapur |
DU, South Campus |
Expression analysis using microarrays
and functional validation |
|
G. Chandel |
IGKVV, |
Phenotyping for drought tolerance, SSr
genotyping of core and mini-core, validation for association in biparental populations |
|
S. Verulkar |
IGKVV, |
Phenotyping for drought tolerance, SSr
genotyping of core and mini-core, validation for association in biparental populations |
|
P.K. Agarwal |
VPKAS, Almora |
Phenotyping for drought and cold tolerance, validation for gene
function in transgenics |
|
K. Babu |
VPKAS, Almora |
Phenotyping for drought and cold tolerance, validation for gene
function in transgenics |
|
J. P. Aditya |
VPKAS, Almora |
Phenotyping for drought and cold tolerance |
|
A. Kumar |
VPKAS, Almora |
Phenotyping for drought and cold tolerance |
|
W. tyagi |
CAU, Barapani |
Phenotyping for cold and acidity tolerance, allele mining for
cold tolerance, functional validation in trangenics |
|
M. Rai |
CAU, Barapani |
Phenotyping for cold and acidity tolerance, allele mining for
cold tolerance, functional validation in trangenics |
|
A. Pattanayak |
ICAR Res Compl
for NEHR, BArapani |
Phenotyping for cold and acidity tolerance, allele mining for
cold tolerance, functional validation in trangenics |
|
S. Gupta |
ICAR Res Compl
for NEHR, BArapani |
Phenotyping for cold and acidity tolerance |
|
P. K. Ghosh |
ICAR Res Compl
for NEHR, BArapani |
Phenotyping for cold and acidity tolerance |
|
S. K. Sen and associates |
IIT, Kharagpur |
Identification of candidate and their functional
validation in transgenics |
|
A. R. Rao and associates |
IASRI, |
Statistical and computational genomics support |
Moisture stress
tolerance: Maize
Time schedule of activities and activity
milestones
|
S.No. |
Objective/Activity |
Activity Milestones |
Milestones
and when to be attained |
Expected Output |
Responsibilitiy |
||
|
|
Y1 |
Y2 |
Y# |
|
|
||
|
14. |
Collection of relevant
germplasm for the target trait, including targeted exploration in the country
|
Assembling a core panel of atleast 300 genotypes for drought stress tolerance |
Yes |
|
|
Avaliability of relevant indigenous and exotic germplasm for bioprospecting
and allele mining for drought stress tolerance |
BMP & FH (in collaboration with other partners) |
|
15. |
Phenotyping of ~300 genotypes under drought stress at multiple locations ( |
Intensive evaluation of atleast 100 genotypes each year under control and stress
condition at three locations |
Yes |
Yes |
Yes |
Identification of sources of tolerance to drought stress
suitable to different agro-ecologies |
BMP; FH; RP; DP; PKA; AK |
|
16. |
Intensive molecular
characterization of 96 selected genotypes using genomic and genic SSRs and SNP markers |
SSR and SNP genotyping of
selected genotypes (complete by Y2) |
Yes |
Yes |
|
Profiles and database of
genomic and genic SSRs
and SNPs on phenotypically
contrasting genotypes |
BMP; FH; PKA; BKB |
|
17. |
Allele mining for 10 selected candidate
genes associated with drought stress tolerance |
Primer design, sequence
analysis and/or SNP analysis of selected genotypes for 10 candidate genes |
|
Yes |
Yes |
Analysis of candidate gene
variation in selected contrasting genotypes for drought stress tolerance |
BMP; FH |
|
18. |
SNP and haplotype
pattern mining based on sequence analysis of candidate genes |
Computataional analysis of sequence data for SNP and haplotyp
pattern mining in candidate genes |
|
|
Yes |
Detection of a series of SNPs and haplotypes in
candidate genes |
BMP; FH |
|
19. |
Association genetic analysis
for identification of marker-trait associations |
Statistical analysis of
genotypic and phenotypic datasets for identification of functionally relevant
SNP/haplotype in candidate genes |
|
|
Yes |
Identification of favourable alleles )SSRs & SNPs_ and haplotypes for
potential use in molecular brreding |
BMP; FH |
IARI, New Delhi: BMP:
BM praanna; FH: Firoz Hossain
VPKAS, Almora
PKA: PK Aggarwal;
BKB: B Kalyan Babu; AK: Arun Kumar
CCSHAU, Uchani
RP: Rishi
Pal; DP: Dharam Pal
Excess water Stress
Tolerance: Maize
Time schedule of activities and activity
milestones
|
S.No. |
Objective/Activity |
Activity Milestones |
Milestones
and when to be attained |
Expected Output |
Responsibilitiy |
||
|
|
Y1 |
Y2 |
Y3 |
|
|
||
|
1. |
Collection of relevant
germplasm for the target trait, including targeted exploration in the country
|
Assembling a core panel of atleast 300 genotypes for drought stress tolerance |
Yes |
|
|
Avaliability of relevant indigenous and exotic germplasm for bioprospecting
and allele mining for drought stress tolerance |
BMP & FH (in collaboration with other partners) |
|
2. |
Phenotyping of ~300 genotypes under excess water stress at four locatons (Pantnagar; Barapani; |
Intensive evaluation of atleast 100 genotypes each year under control and stress
condition at three locations |
Yes |
Yes |
Yes |
Identification of sources of tolerance to excess water stress in
North Eastern India |
FH; MZKW; SSV; NKS; AP; SG; PKG; RP; DP |
|
3. |
Intensive molecular characterization of 96 selected genotypes
using genomic and genic SSRs
and SNP markers |
SSR and SNP genotyping of
selected genotypes (complete by Y2) |
Yes |
Yes |
|
Profiles and database of genomic and genic
SSRs and SNPs on phenotypically contrasting genotypes |
BMP; FH; NKP |
|
4. |
Transcriptome profiling for excess water stress tolerance and identification
of fiffrentially expressed genes |
Microarray analysis for excess water stress using selected highly
contrasting genotypes |
|
Yes |
Yes |
Identification of significant differentially expressed genes
under excess water stress |
BMP; FH |
|
5. |
Allele mining for 6 selected candidate genes associated with
excess water stress tolerance |
Primer design, sequence
analysis and/or SNP analysis of selected genotypes for 6 candidate genes |
|
Yes |
Yes |
Analysis of candidate gene variation
in selected contrasting genotypes for excess water stress tolerance |
BMP; FH |
|
6. |
SNP and haplotype pattern mining based
on sequence analysis of candidate genes |
Computational analysis of
sequence data for SNP and haplotype pattern mining
in candidate genes |
|
|
Yes |
Detection of series of SNPs and haplotypes in candidate genes |
BMP; FH |
|
7. |
Association genetic analysis for identification of marker-trait
associations |
Statistical analysis of genotypic
and phenotypic datasets for identification of functionally relevant SNP/haplotype in candidate genes |
|
|
Yes |
Identification of favourable alleles )SSRs & SNPs_ and haplotypes for potential use in molecular brreding |
BMP |
IARI,
GBPUAT; Pantnagar: MZKW:
MZK Warsi; SSV: SS Verma;
NKS: NK Singh
ICAR-NEH, Barapani: AP:
A Pattnayak; SG:
CCSHAU, Ucani: RP:
Rishi Pal; DP: Dharam Pal
Moistue Stress: Sorghum
|
S.No. |
Objective/Activity |
Activity Milestones |
Milestones
and when to be attained |
Expected Output |
Responsibilitiy |
||
|
1. |
Scrrning of available sorghum genetic stocks for drought/heat tolerance |
Phenotypic trait such as stay green,
Root mass, length and density, yield components, total biomass will be analysed under stress and controlled conditions |
Yes |
|
|
A core set of Sorghum defined for carryuing
out allele mining |
NRCS |
|
2. |
Allele mining in selected set from the core set of sorghum |
A Pcr
based method will be followed for allele mining using candidate genes primers |
|
Yes |
|
Cloned and sequenced alleles available |
NRCS |
|
3. |
Search for polymorphism and molecular marker development |
In silico
analysis of sequences and identification of SNPs
will be done. Molecular makers will be designed |
|
Yes |
|
Useful alleles identified and molecular markers developed |
NRCS |
|
4. |
Genotyping in remaining core set |
Using the SNP markers larger
set will be genotyped |
|
|
Yes |
Core set genotyped and alleles identified |
NRCS |
|
5. |
Validation of genotypes of sorghum for drought tolerance and
susceptibility |
Selected genotypes will be
given stress treatment and will be characterized based on phenotypic markers |
|
Yes |
|
True drought tolerant and susceptibility genotypes identified |
MPKV |
|
6. |
Construction of cDNA library
(subtracted cDNA) |
Isolation of total RNA from
tolerant and susceptibe genotypes after stress and
mRNA isolation and RT-PCR |
|
Yes |
|
cDNA library (subtracted cDNA) ready |
MPKV |
|
7. |
Sequencing of cDNA library |
`cDNAs
will be sequenced by outsourcing |
|
Yes |
|
Sequences available |
MPKV |
|
8 |
Expression analysis of identified clones |
Expression will be checked in Yeast.bacterial expression system |
|
|
Yes |
Validation of identified genes |
MPKV |
Work allocation & sharing:
Sorghum
|
Name & Designation |
Institute/ Organization |
Work Allocation |
|
Monica Dalal, SS |
NRCS, |
Phenotyping of
available genetic stock for drought stress tolerance, allele mining.
Molecular marker development genotyping and cloning and expression analysis of
genes |
|
R. MAdhusudhan, SS |
NRCS, |
Phenotyping of
available genetic stock for drought stress tolerance, allele mining.
Molecular marker development genotyping and cloning and expression analysis
of genes |
|
H. S. Talwar, SS |
NRCS, |
Phenotyping of
available genetic stock for drought stress tolerance, allele mining.
Molecular marker development genotyping and cloning and expression analysis
of genes |
|
Ashok Jadhav, Professor |
MPKV, Rahuri |
Validation
of genotypes for drought tolerance and susceptibility cDNA
(subtractive), screening and analysis of new genes |
|
A.A. Kale |
MPKV, Rahuri |
Validation
of genotypes for drought tolerance and susceptibility cDNA
(subtractive), screening and analysis of new genes |
|
V. P. Chimote |
MPKV, Rahuri |
Validation
of genotypes for drought tolerance and susceptibility cDNA
(subtractive), screening and analysis of new genes |
Moisture
Stress Tolerance: Cucumis
sp.
|
S.No. |
Objective/Activity |
Activity Milestones |
Milestones
and when to be attained |
Expected Output |
Responsibility |
||
|
1. |
Analysis of ecogeographical data and
identification of core collection in cucumber, muskmelon, C. callosus |
Core collection of cucumber
(250) and muskmelons(150) |
X |
|
|
Designation of cores in cucumber and melons |
NBPGR |
|
2. |
Multi-location characterization
of core collection for tolerance to drought. |
Characterization of core
collections |
X |
X |
|
Diversity in core |
NBPGR, IIHR, IIVR, RAU |
|
3. |
Identification characterization
of SSR primers and construction of saturated linkage maps in cucumber.
Muskmelons |
Markers (1000) for genotyping |
|
X |
X |
Polymorphic SSR markers |
NBPGR, IIHR, RAU |
|
4. |
Phenotyping of the core collection under standard controlled condiation in four location |
Characterization of core for
target traits |
|
X |
X |
Accession with specific traits |
NBPGR, IIHR, IIVR, RAU |
|
5. |
Genotypic of the core collection
using AFLP, SSR and SNPs for candidate genes |
AFLP, SSr
and SNP profiles of core accessions (~450 markers) |
X |
X |
X |
Molecular profiles of core
accessions |
NBPGR, IIHR, IIVR, RAU |
|
6. |
Association analysis to identify
genes/markers for target traits |
Identification of accessions
and marker tags |
|
X |
X |
Donor accessions for target
traits |
NBPGR, IIHR, RAU |
|
7. |
Fine mapping of selected genes
for validation & use in markler assisted
transfer of the trait |
Tagging of target genes |
|
X |
X |
Marker tags for MAS |
NBPGR, IIHR, RAU |
|
8. |
Identification of putative
genes through differential expression analysis for selected traits |
To use differential display and
subtractive hybridization for identifying putative genes for moisture stress
tolerance |
|
X |
X |
Information on candidate genes
related to moisture tolerance |
NBPGR, IIHR, IIVR, RAU |
|
9. |
Cross validation of results in Cucumis Arabidopsis among the patterns for
specific traits identified |
Identification nof genes and allele for tarfet
traits |
|
X |
X |
Allelic variation for
deployment |
NBPGR, IIHR, RAU |
NBPGR: KVB- KV Bhat, MKR- MK Rana;
RAU, Bikaner: RAS-
RAmavtar Sharma
IIVR, Varanasi: SP-Sudhakar Pandey, ML-M.
Lokanath
IIHR: MP-M. Pitchaimuthu, ASK-
Ashokan, VR- V. Ravindram, RS- Ravishanker
Moisture Stress
Tolerance: Lathyrus sp.
|
S.No. |
Objective/Activity |
Activity Milestones |
Milestones
and when to be attained |
Expected Output |
Responsibility |
||
|
1. |
Analysis of ecogeographical data and
identification of core collection in Lathyrus |
Core collection of Lathyrus (300 accessions) |
X |
|
|
Designation of cores in Lathyrus |
NBPGR |
|
2. |
Multi-location evaluation of core collection for tolerance to
drought |
Characterization of core
collections |
X |
X |
|
Diversity in core |
NBPGR, IIT (KGP) |
|
3. |
Identification and
characterization of SSR primers and construcation
of saturated linkage in maps in Lathyrus |
Markers for genotyping
(500 SSRs) |
|
X |
X |
Polymorphic SSR markers |
NBPGR |
|
4. |
Phenotyping of the core collection under standard and controlled conditions
in three locations |
Characterization of core for
target traits |
|
X |
X |
Accessions with specific traits |
NBPGR, IIT (KGP) |
|
5. |
Genotyping of core collection using AFLP, SSR and SNPs for candidate genes |
AFLP, SSR and SNP haplotypes of core collection |
X |
X |
X |
Molecular profiles of core accessions |
NBPGR |
|
6. |
Assocaition analysis to identify
genes for target traits |
Identification of accessions
and marker tags |
|
X |
X |
Donor accessions for target traits |
NBPGR |
|
7 |
Fine mapping of selected genes for use in marker assisted transfer of the traits |
Tagging of target genes |
|
X |
X |
Markers tags for mAS |
NBPGR |
|
8. |
Cross validation of results in Arabidopsis system |
Identification of genes and alleles
for target traits |
|
X |
X |
Allelic variations for deployment |
NBPGR, IIT (KGP) |
IIT, KGP: SKS- S. K. Sen,
AB- Asitava Basu, MKM- MK Maity, BSD- BS Das
NBPGR: KVB- K. V. Bhat,
MKR- MK Rana
Moisture Stress
tolerance: Ziziphus sp.
|
S.No. |
Objective/Activity |
Activity Milestones |
Milestones
and when to be attained |
Expected Output |
Responsibility |
||
|
1. |
Collection, screeing and
identification of reference collection in Ziziphus |
Reference collection of Ziziphus |
X |
|
|
Designation of cores in Ziziphus |
CIAH |
|
2. |
Phenotypic of the reference collection using lab. Based
techniques |
Characterization of reference
for target traits |
|
X |
X |
Accession with specific traits |
CIAH |
|
3. |
Isolation and cloning of candidate genes through subtractive
analysis |
Putative genes for tolerance to
drought |
|
X |
X |
Information on candidate genes related to drought tolerance |
CIAH, NRCPB |
|
4. |
Expression profiling and identification of putative genes for
drought tolerance |
Confirmation of genes
identified |
|
X |
X |
Identification of putative genes for drought tolerance |
NRCPB |
|
5. |
Validation of genes in Arabidopsis |
Confirmation of genes for
tolerance |
|
X |
X |
Novel genes for plant transformation |
NRCPB |
CIAH: PNS-PN
Sivalingam, DS-Dhurinder Singh
NRCPB: JCP-JC Padaria,
KNK-Kanika, PKA-PK Ananda Kumar
Heat Tolerance: Vigna sp.
|
S.No. |
Objective/Activity |
Activity Milestones |
Milestones
and when to be attained |
Expected Output |
Responsibility |
||
|
1. |
Analysis of ecogeographical data and
identification of core collection in moth bean including wild species |
Core collection of moth bean (225
accessions) |
Yes |
|
|
Designation of cores in moth bean |
NBPGR |
|
2. |
Screening and classification of core collection for the
tolerance |
Characterization of core
collection |
Yes |
Yes |
|
Diversity in core |
NBPGR, RAU |
|
3. |
Isolation and cloning of candidate genes for heat tolerance
based on homology |
Identification & cloning of
genes for heat tolerance |
|
Yes |
|
A set of cloned genes involved in heat tolerance mechanism from
moth bean |
NBPGR, RAU |
|
4. |
Validation of isolated genes through transformation in moth
bean/ Arabidopsis |
Functional validation |
|
Yes |
Yes |
A system to study genes further through expression analysis |
RAU |
|
5. |
Identification of candidate genes through differential expression
profiling |
Information on heat stress
induced genes |
|
Yes |
Yes |
Information on heat stress induced genes |
NBPGR, RAU |
|
6. |
Allele mining for the selected genes |
Identification of elite
germplasm lines |
|
Yes |
Yes |
Novel alleles of genes for the target traits |
NBPGR, RAU |
RAU, Bikaner : RAS-Ramavtar
Sharma
NBPGR : KVB_KV
Bhat, MKR-MK Rana
Heat and Cold Stress
tolerance: Camel and Goat
Milestones and outputs (including HRD activities)
|
S.No. |
Activity |
1 |
2 |
3 |
Expected Output |
Responsibility |
|
1. |
To identify population structure and breed specific haplotypes-under extremes of temperature conditions.Identification of various in camels and goats for various candidate genes associated
with thermoregulatory mechanisms in mammals in different geographical
locations having extremes of temperature variations. |
Yes |
|
|
Allele associated with heat and cold stress in camels and goats |
NBAGR |
|
2. |
Transcriptome analysis of goats and camels inhabiting the extreme climatic
regions of the country |
|
Yes |
|
|
|
|
3. |
Extimating of relative frequency of the SNPs
between extreme temperature conditions |
|
Yes |
|
|
|
|
4. |
Association of the SNP/haplotypes with
the adaptive traits |
|
Yes |
Yes |
|
|
|
5. |
Analysis of expression of genes associated with thermoregulatory
mechanism in camel and goat. Approach
to Research: Comparative analysis of apparently normal goat and camel blood lymphocytes
at normal conditions and under heat stress at various temperatures and
duration of exposure |
Yes |
Yes |
|
Quantification of mRNA profile for heat and cold stress In camels and goats under hot arid and temperate regions. |
CIRF, NDRI Comparison of hot arid
region goats with thermoneutral conditions. IVRI, NDRI Comparison of temperate
region goats with thermoneutral
conditions. SKUAST Comparison of temperate
region goats and camel at thermoneutral conditions
and stress NRCC Comparison of hot arid region camels under thermoneutral and stress conditions |
|
6. |
In vitro
differential gene expression related to heat/cold temperatures |
|
Yes |
|
|
|
|
7. |
Establishment of relationship between the identified differential
heat/cold (Thermoregulatory) gene in different
genetic groups. |
|
Yes |
Yes |
|
Anoxia: Catfish
|
S.No. |
Objective/Activity |
Activity Milestones |
Milestones
and when to be attained |
Expected Output |
Responsibility |
||
|
9. |
Identification and characterization of genes for Anoxia
resistance in Clarius batrachus
and Channa striatus |
· Collection of Clarius batrachus from different locations · Construction of cDNA libraries by Suppression
Subtractive Hybridization (SSH) technique · Full length normalized cDNA library
construction of different tissues |
Yes Yes |
Yes Yes |
Yes |
·
Availability of
base material with abiotic stress (anoxia) |
NBFGR, CIFA |
|
10. |
Full length normalized cDNA library
construction of different tissues. |
The Normalized cDNAs Illumina GA-sequencing Gene annotation Cloning |
Yes Yes |
Yes Yes Yes |
Yes Yes |
Genome resource for abiotic stress Anoxia transcriptome characterization |
NBFGR, CIFA |
|
11. |
Quantitaive Real-Time PCR for differentially expressed genes. RACE |
Designing of RT primers Differential expression Full length cDNA
construction |
|
|
Yes Yes Yes |
Genome Resorce Expression profile Sequence information |
NBFGR, CIFA |
CIFA: Dr. H.K.
Burman, Dr. K. Kumar, Dr. C. Debaraj
NBFGR: Dr. Vindhya Mohindra, Dr. Ravindra Kumar
Salt tolerance: Shrimp
and Scrampy
|
S.No. |
Objective/Activity |
Activity Milestones |
Milestones
and when to be attained |
Expected Output |
Responsibility |
||||
|
9. |
Identification and characterization of genes for salinity stress
in giant freshwater prawn. M. Rosenbergii/ M. malcolmsoni-CIFA, Bhubneswar and P. Mondon (CIBA) |
· Collection of larval populations of M. Rosenbergii/
M. malcolmsoni and P. Mondon
under varied salinity conditions · Collection & preservation of different tissue samples from
brackish water during season and from freshwater · Construction of cDNA libraries by SSH
techniques from wild and acclimatized samples. · Construction of cDNA libraries by
normalized cDNA from wild & acclimatized
samples · Conversion of normalized cDNAs to Illumina GA-sequencing ready libraries followed by · Assembling sequences for cutom
bioinformatics. · Cloning normalized cDNA into pGEMT-easy vector. · Sequencing of full length cDNA by RACE · Estimation of transcript levels by Real-Time PCR · Report writng |
Yes Yes Yes Yes |
Yes Yes Yes Yes |
Yes Yes Yes Yes Yes Yes |
·
Availability of
base material with abiotic stress (anoxia) |
NBFGR, CIFA |
||
|
2. |
Fuvtional characterization of novel genes identified in P. mondon-CIFE, Mumbai |
Sequencing
og 5’ and 3’ ends of the 3 genes over-expressed in P.mondon acclimatized to 35 ppt and 1
gene over-expressed in specimens acclimatized to 0 ppt.
using RACE Estimating
transcripts levels at different salinities in P.mondon
gill and muscle tissue using Real time PCR and valiadating
relation with adaption to salinity stress Cloning
of cDNA sequences in a constitute His-tag
expression vector and over-express in a eukaryotic cell lines Purification
of the His-tagged protein using Ni coloumn and
raise antibodies in rabbit. Sub-cellular
localization of the novel proteins involved in salt homeostasis in the gill
and muscle tissues of marine tiger shrimp using antibodies Tracing
the change in expression levels of these proteins in different salinities
using immuno-histochemical techniques and
hypothesizing their roles in salt homeostasis Report
writing |
Yes Yes Yes |
Yes Yes |
Yes Yes Yes |
Complete cDNA sequences pf 3 P. mondon genes over-expressed during saline stress and
1 over-expressed in freshwater Validation of the importance of these sequences for saline
adaptation Purified proteins that are important for saline adaptation Sub-cellular location of the above proteins Validation of the role of these proteins in saline adaptation Final report |
CIFE, Mumbai |
||
CIFA: Dr. H. K. Barman, Dr. P. Jayashanker
CIBA: Dr.
M.S. Shekhar, Dr. G. Gopalkrishna, Dr. C. Gopal, Dr. K. Vinaya Kumar, Dr. S. Kannappan
CIFE: Dr.
Aparna Chaudhari, Dr. Gayatri Tripathi, Mr. Gireesh Babu P.
Cold Tolerance: Trout
|
S.No. |
Objective/Activity |
Activity Milestones |
Milestones
and when to be attained |
Expected Output |
Responsibility |
||
|
1. |
Collection of fish samples from different high altitude colder environments
for the study of cold tolerant. The sites proposed to be surveyed with
regards to extreme cold conditions in J&K, Himachal
Pradesh and Uttarakhand upland regions, |
Survey
and collection of fish samples from extreme environments, |
Yes |
|
|
Samples collected from different sites. |
DCFR |
|
2. |
Isolation of DNA/RNA samples collected following standard
techniques and optimized protocols. |
Isolation
of DNA/RNA |
Yes |
|
|
Development of standardized protocols. |
DCFR |
|
3. |
Molecular identification and sequence variation between the
exotic and indigenous trout sp. Of collected samples for cold tolerant genes |
Identification
of known genes through public domain. |
Yes |
|
|
Allele mining |
DCFR |
|
4. |
Specific primers for known genes will be used in PCR to identify
and isolate candidate genes from fishes |
PCR
amplification of relevant genes using specific primers |
|
Yes |
|
Allele variants from indigenous fish species will be identified |
DCFR |
|
5. |
Construction of genomic library in suitable vector and screening
of clones for identification of novel genes. |
Genomic
library construction |
|
Yes |
|
Identification of novel genes for cold tolerance |
DCFR |
|
6. |
Cloning and sequencing of genes in vectors |
Genomic
library construction |
|
|
Yes |
Development of cDNA library |
DCFR |
|
7. |
Bioinformatic analysis of the identified genes |
Submission
in GenBAnk |
|
|
Yes |
Bioinformation available of cold tolerant genes in indigenous fish species |
DCFR |
DCFR: Dr. A. Barat,
Senior Scientist and Dr. G.K. Sivaraman, Scientist
Statistical and
Computational Genomics
Time Schedule of activity and activity milestones
|
S.No. |
Objective/Activity |
Activity Milestones |
Milestones
and when to be attained |
Expected Output |
Responsibility |
||
|
|
1 |
2 |
3 |
|
|||
|
1. |
Statistical and Computational analysis of genomic data generated
from plants, animals and fish genetic resources |
Identification,
procurement and installation of statistical and computational software; Statistical
analysis of generated molecular and phenotypic data; Undergoing
national and international trainings |
Yes |
Yes |
Yes |
Establishment of centralized facility for statistical and
computational analysis or genomic data Establishing association between genomic and marker data |
ARR, VKB, |
|
2. |
Development of algorithms for supporting need based genomic
analysis |
New
user friendly analytical tools for gene discovery |
|
Yes |
Yes |
Efficient gene prospecting in genetic resources |
ARR, VKB, |
|
3. |
Training scientific personnel in the field of statistical
genomics and Bioinformatics |
Providing
training to 2 batches of 20 participants each year. |
Yes |
Yes |
Yes |
Upgrading skills and building expertise among the scientists
working in genomics and Bioinformatics |
ARR, VKB, |