Vill. Kharibil, P.O. Eranch, Distt. Cuttack, Orissa -754105, India
B.Sc. (Agriculture) from OrissaUniversity
of Agriculture and Technology, Bhubaneswar in 1985
M.Sc. (Genetics) from Indian Agricultural Research Institute, New Delhi
Ph.D (Genetics) from Indian Agricultural Research Institute, New Delhi
·Scientist Probationer (3.12.1991 to 2.5.1992), NationalAcademy of Agricultural Research Management, Hyderabad,
·Scientist (3.5.1992 to 25.3.1999), National Research Centre on Plant
Biotechnology, Indian Agricultural Research Institute, New Delhi
·Senior Scientist (26.3.1999 to 11.9.2005), National Research Centre
on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi
·Principal Scientist (12.9.2005 to date), National Research Centre
on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi
·National Rural Talent Search Merit Scholarship from
class VIII to class XI (for four years)
·National Scholarship during Intermediate in Science
(for two years)
·National Scholarship during B.Sc (Ag) (for four years)
·Junior Research Fellowship of the IARI during M.Sc
·Senior Research Fellowship of the IARI during Ph.D
TEACHING AND TRAINING EXPERIENCE
·Teaching Molecular Genetics of Eukaryotes to Post Graduate
students at IARI since 1993
·Guided 36 M. Sc. and 50 Ph.D students of the Indian
Agricultural Research Institute as a member in the Advisory Committee
·Guided six Post-Doctoral Fellows, six DBT National
Associates and three SERC Visiting Fellows of DST.
·Imparted laboratory training on Molecular Breeding
to more than 25 individual scientists from various Universities/Institutions in the country and abroad
Visited Clemson University Genomics Institute, Clemson,
South Carolina, USA from 9th October 2000 to 30th December 2000
through the Exchange Visitor Program on Rice Genomics under the Indian Rice Genome Project funded by the DBT, Govt. of India.
The purpose of this visit was to undergo training in various aspects of Rice Genomics. During this period a physical map of
the chromosome 11 of rice was constructed using Bacterial Artificial Chromosomes, which provides the framework for an ordered
clone-by-clone sequencing of the genomic region being sequenced by India.
Visited the Arizona Genomics Institute, The University of Arizona, Arizona, USA from 20-08-2003
to 30-01-04 through the Exchange Visitor Program on Rice Genomics under
the Indian Rice Genome Project funded by the DBT, Govt. of India. The overall objective of the visit was to learn the recent
tools and techniques that are being employed to generate Finished quality DNA sequence of the Rice Genome and apply those
to a selected set of BAC clones belonging to the Indian Region of the rice Chromosome 11.
Visited the National Institute of Agricultural Biotechnology, Rural Development Administration, Suwon,
the Republic of Korea from 19-08-04 to 22-08-04 as an expert
on Germplasm Characterization on invitation by the Director General, NIAB, Suwon, Korea
Membership of Academies/Societies/Professional
·Life Member, Indian Society of Genetics and
Plant Breeding, IARI, New Delhi
·Life Member, Society of Plant Biochemistry and
Biotechnology, IARI, New Delhi
Physical mapping and genome sequencing in rice (Oryza sativa)
India is a collaborator in the International Rice Genome
Program and had committed to sequence about 57cM region of long arm of chromosome 11 of rice. The basic input for sequencing
is the large genomic DNA fragments cloned in Bacterial Artificial Chromosomes (BACs), which belong to this genomic region.
To meet this requirement a BAC based physical map was constructed for the rice
chromosome 11 in collaboration with Clemson University Genomics Institute, USA.
In an elaborate effort, 70 overgo probes were designed from the markers available on the linkage of the rice genome and used
to screen the BAC library filters. The BACs hybridizing with the probes were identified, fingerprinted and arranged into contigs.
The BACs constituting the minimum tiling path were then identified. These BACs were subsequently sub-cloned and sequenced
by both the Indian centers involved in the Rice Genome Project. This contribution formed a component of an international publication
in the reputed journal THE PLANT CELL (Impact Factor >10). Rice genomic DNA sequences of sixty BAC clones totaling
about 8.1 million base pairs have been submitted in the public database. This work thus enabled the country to meet an
important international commitment within a stipulated time frame leading to a publication in the international journal Nature.
Genome mapping and gene tagging
a. Generation and characterization of a permanent
mapping population in Indian mustard (Brassica juncea)
genome mapping and gene tagging requires availability of a permanent mapping population such as recombinant inbred lines (RILs).
The RILs are developed by repeated selfing of the F2 plants for at least six generations.In mustard, 225 RILs have been generated which are now in the F10
generation. These have been characterized
in replicated field trials for three seasons. Wide range of variation for oil content, fatty acid profile, days to
flowering, plant height and yield contributing traits has been observed, which makes RILs ideal for mapping of the underlying
genetic factors and eventually their isolation using the functional genomic tools.
b. Construction of molecular maps of mustard genome
Molecular linkage maps are useful in understanding genome structure and its
evolution pattern, gene mapping and tagging, map based gene isolation and genome sequencing. In a completely indigenous effort,
a large number
of DNA based markers developed and used to construct a molecular map of mustard. First a RFLP linkage map was developed based on segregation of 66 markers in F2 population. This map consisted of 14 linkage
groups and covered 407.9cM length of mustard genome. Subsequently, 190 RAPD
markers were used in the RILs to develop a map, which consisted of 21 linkage
groups and covered 790.4 cM of the mustard genome. The molecular map of mustard is
the first of its kind in any crop in the country and the first RIL based map of the mustard in the world. While new markers such as AFLP are being added to this map, it has been already used for mapping useful genes in mustard.
Tagging of a gene for the white rust resistance in mustard
White rust is a serious disease of oilseed Brassica
crops. Breeding varieties for this trait requires screening of a large segregating population over generations for disease
reaction to select the desirable ones. Since the field screening depending upon natural infestation is not reliable, artificial
epiphytotic conditions need to be created. This requires special efforts, facilities and therefore is difficult. Availability
of a suitable marker linked to the gene for resistance can aid identification of the desirable segregants at seedling stage
in early generations. This enables selection in absence of any selection environment and saves time, effort and money. The
genome map of mustard was used to tag a gene designated as Ac2(t) conferring
resistance against the white rust pathogen, Albugo candida. Two markers flanking
the target gene were identified. The tightly linked flanking marker was converted to a CAPS marker and validated in different
segregating populations. Selection of desirable rust resistant segregants in early generations after hybridization can now
be practiced at seedling stage without creation of artificial epiphytotic condition.
d. Interval mapping of loci for fatty acid levels
Quantitative traits such as oil content and fatty acid levels in mustard show quantitative inheritance
and are influenced by environment that makes selection based on phenotype unreliable. Molecular markers linked to the loci
(QTLs) affecting such traits if identified can be used in indirect selection irrespective of growth stage and environment.
Using the linkage map of mustard, common, linked and independent loci influencing the levels of oleic, linoleic, linolenic
and erucic acids were mapped to marker intervals. The RILs were also used to identify markers for the content of oil in
mustard seed. This is the first such effort in mustard.
e. Molecular mapping and isolation of the candidate
gene for fertility restoration in Basmati rice hybrid
Cytoplasmic male sterility based on wild abortive cytoplasm has been used
to develop hybrids in rice. In case of Basmati hybrid developed at IARI, PRR78 is used as the fertility restorer. In collaboration
with the Division of Genetics, IARI, sequence tagged
microsatellite markers were employed in bulk segregant analysis of F2 population and one STMS marker was found
linked to the fertility restorer gene on the long arm of Chromosome 10 of rice.Subsequently an AFLP marker showing tighter linkage with the restorer gene was identified. These markers have facilitated
physical positioning of the gene on a BAC contig that has led to positional cloning of the gene.
Marker assisted selection
assisted selection for bacterial blight resistance genes in rice
Bacterial Blight (BB) caused by Xanthomonas
oryzae pv. oryzae is a major disease of rice in tropical Asia.
Since all the Basmati varieties are highly susceptible and the disease is prevalent in the entire Basmati growing region of
India, BB is a severe constraint in Basmati rice production.
A collaborative study with the Division of Genetics, IARI, was undertaken to combine the important Basmati quality traits
with resistance to BB by a combination of phenotypic and molecular marker-assisted selection (MAS).The two BB resistance genes xa13 and Xa21 present in IRBB55 were combined with the Basmati
quality traits of Pusa Basmati-1 (PB-1), the most popular high yielding Basmati rice variety used as recurrent parent.
Molecular marker-assisted selection for the two resistance genes was carried out in BC1F1, BC1F2and
the previous years. The presence of the two genes was confirmed in all the desirable BC1F5recombinants. Enhanced level of resistance in the recombinants
was confirmed by disease reaction after inoculation. Background analysis carried out using AFLP markers in the previous year
was extended with mapped STMS markers that confirmed more of recurrent parent (Pusa Basmati1) genome in the segregants. Recombinants
having enhanced resistance to BB, Basmati quality and desirable agronomic traits were evaluated in a replicated trial. One
of the promising lines that out-yielded the National Check variety is now in the advanced stage of testing in the All India
b. Marker assisted selection (MAS) for powdery mildew
resistance in pea
In collaboration with the Division of Genetics, IARI, a sequence characterized amplified region (SCAR) marker
was designed for the powdery mildew resistance gene er. The efficiency of this marker in MAS was demonstrated in germplasm lines as well as in backcross populations. Although all the
plants in the BC1 generation were phenotypically susceptible, use of the SCAR marker enabled identification of
the carriers of the recessive alleles for resistance.
DNA fingerprinting for germplasm characterization and variety identification
a. Development DNA fingerprinting technology in rice, wheat and
is rich in biodiversity. Protection of this rich heritage requires precise identification of the important varieties, elite
genotypes and valuable germplasm resources. Morphology based variety identification is subjective and it is difficult to resolve
morphologically similar genotypes. Analysis based on DNA is free from environmental influences and thus is objective. In this
regard, DNA profiling systems such as RFLP, RAPD, STMS, ISSR, ASSR and AFLP were standardized for variety identification in
rice including the Basmati varieties, wheat and mustard. Various parameters including the type and number of markers required
for a meaningful and usable fingerprint, relevance of mapped molecular markers, levels of intra-varietal DNA polymorphism
etc. were worked out. DNA fingerprints were created for 120 varieties including the commercially important traditional
Basmati cultivars in rice, 137 cultivars in wheat and 42 cultivars in Brassica,
which provides molecular descriptors for variety identification.
b.Molecular marker analysis of species clones and commercial varieties in sugarcane
Sugarcane is a crop of commercial importance in the country.
The commercial varieties of sugarcane have been evolved through inter-specific hybridization involving Saccharumofficinarum
and S. spontaneum. They possess complex polyploid genomes with varying chromosome numbers.With a view to developing molecular marker systems that would aid the conventional breeding, microsatellite
and AFLP analysis of the species clones and important commercial varieties was carried out. Contribution of the progenitor species namely S.officinarum and S. spontaneum to the genomic constitution of the commercial cultivars was determined. Cross
transferability of maize microsatellite markers to sugarcane species and varieties was demonstrated for the first time. Only a limited number of microsatellite
markers could precisely differentiate 32 varieties and establish the species relationships. A large number of species-specific
AFLP markers were identified, which can be used in identification of varieties and inter-specific hybrids, gene mapping and
introgression of useful genes from different species.
c. Identification of pearl millet hybrids and parental lines
In collaboration with the Division of Seed Science and Technology, IARI, RAPD markers
were identified which could precisely identify 24 genotypes of pearl millet including seven hybrids and their parental lines.
Identification key based on four RAPD primers was developed for the pearl millet genotypes, which can be used as when
d. Differentiation of races of root knot nematode using RAPD
In a collaborative study with the division of Nematology, IARI,
four races of the root knot nematode identified on the basis of host differentials were characterized using RAPD profiling.
Nineteen primers detected polymorphism among the races. One RAPD primer was identified that could differentiate all the
races of the nematode.
e. Differentiation of sex in kiwi fruit using RAPD
Kiwi fruit is a dioecious fruit plant, which has become commercially important in the low and mid-Himalayan regions
of India. Prior to planting, it is essential to identify the
male and female lines so that a desirable ratio is maintained. In a collaborative work with the Department of Biotechnology,
Dr. Y.S Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, RAPD profiling was used to characterize male
and female plants of this fruit crop. Diagnostic markers were identified that could efficiently differentiate the male
and female genotypes from each other thus can be used as markers in idenyification of the sex of the planting material.
f.Molecular marker analysis of somatic cell hybrids of mustard and its wild relative
Molecular markers were employed to characterize a number of somatic cell hybrids to understand
the structure of mitochondrial and chloroplast genomes. During the period under consideration RFLP analysis was used to identify
somatic hybrid plants produced from Diplotaxis catholica and Brassica juncea. The hybrids carrying desirable recombinant mitochondrial genome and a chloroplast genome similar
to the cultivated species were identified, which facilitated development of a stable cytoplasmic male sterile (CMS) line of
mustard from this somatic hybrid. Random segregation of chloroplast genomes in the somatic hybrids was clearly evident. Besides,
based on restriction mapping, recombination between chloroplast genomes of Trachystoma
ballii and Brassica juncea was demonstrated in a CMS line developed from the
somatic hybrid of these two species. These were the first reports on random chloroplast segregation and recombination in Crucifereae.
g. AFLP based genetic diversity analysis and variety identification in ber
Ber (Ziziphus spp.) belonging to the buckthorn family Rhamnaceae
is an important fruit crop that naturally grows in harsh environmental conditions. Commercial cultivars have been developed
in India mostly through selection of productive natural variants
that are being propagated through budding on wild rootstocks and used for orchard plantations. Genetic diversity among 41 accessions of cultivated Ziziphus. mauritiana (lam.) and its wild relative Z. nummularia (burm.f.) was determined using AFLP. The wild relative that is being used as rootstock showed greater diversity than the cultivated
species. The range (0.37 to 0.86) and the average similarity (0.62)among the accessions of
the cultivated species indicated a broad genetic base of the commercial cultivars. Nine of the primer combinations used detected many accession specific amplified fragments and individually
gave a discrimination rate of 1.
Any one of these informative primers thus can be used for maintenance of the quality of both the scions and the rootstocks
for establishing productive orchards. This is the first such effort on molecular characterization of ber.
h. Evaluation of genetic diversity and variety identification
Jute (Corchorus spp.) is an important fibre crop that has ruled the packaging sector for over one
and a half century in India. For sustenance of the trade in
the face of tough competition from synthetics, there is an urgent need to redesign the breeding strategy for improving both
yield and quality of jute fibre. To understand the pattern of diversity in this important commercial crop species 20 exotic
germplasm lines and 20 commercial varieties of the two cultivated species (C. olitorius and C. capsularis) and
two wild relatives of jute (C. aestuans and C. trilocularis) were characterised using STMS, ISSR and RAPD markers. The first set of six STMS markers developed
from the genomic sequence of C. olitorius was not fully transferable
to the related species C. capsularis. Level of intraspecific polymorphism revealed
by these markers was very low. The level of polymorphism was found significantly low within a species. The commercial varieties
particularly those of the C. capsularis had an extremely narrow genetic base that demands immediate effort for diversification.
The germplasm accessions in both species showed considerably higher levels of diversity and thus should be used in broadening
the base of the varieties. This is the first report of the use of STMS markers and comparative analysis of three different
molecular markers in intra and interspecific diversity analysis of jute.
PRODUCTS (VARIETIES, CONCEPTS, PROCESSES, TECHNOLOGIES AND PATENTS)
A cytoplasmic male sterile line of mustard (Brassica juncea) designated
as CMS Trachy carrying a recombinant mitochondrial genome (INGR No. 97007) for
use in hybrid breeding program (Plant Breeding 114:434-438).
A rice line Pusa1121 (INGR No. 02001) possessing exceptionally high cooked
kernel elongation and basmati traits (Intl. Rice Res. Notes, 48:81-86). This line has been released for commercial cultivation.
DNA fingerprinting technologies developed for rice (including the Basmati varieties), wheat, brassica, sugarcane, jute,
tobacco, pearlmillet, kiwi fruit and ber. DNA fingerprints
of more than 430 varieties belonging to the above crop species were developed. Molecular marker parameters were also defined
for variety identification in these crops.
DNA sequence of eighteen resistance gene analogue sequences from mustard (Brassica juncea) bearing the Accession
Numbers AF533232, AF533233, AF533234, AF533235, AF533236, AF533237, AF533238, AF533239, AF533240, AF533241, AF533242, AF533243,
AF533244, AF533245, AF533246, AF533247, AF533248, AF53324)
A CAPS marker (OPB061000) for use in marker-assisted selection for white rust resistance gene in
mustard (Theor Appl Genet, 109:153-159).
A STMS (RM6100) marker was identified for use in marker-assisted selection for fertility restorer gene in rice.
Rice lines were developed by combining Basmati quality characteristics with bacterial blight resistance through marker-assisted
selection (Molecular Breeding, 13: 377-387).Two of these lines are under evaluation in the All India Co-ordinated Trials
A new concept was developed and published on the cross-transferability and thus the use of maize microsatellite markersin sugarcane for establishing species relationship and variety
identification (Genome, 46: 394-403).
A new concept on the use of mapped microsatellite markers for establishing distinctness, uniformity and stability (DUS) of the aromatic rice including the Basmati was developed and published
(Euphytica, 135: 135-143).
A new concept was developed on the DNA marker based BAR CODE for the elite crop varieties in general and rice and wheat in particular (Euphytica, 118: 243-251 and Current
Sci, 84: 1125-1129).
A novel process for isolation of DNA from plant tissues without the use of liquid nitrogen was developed (Plant Molecular Biol. Reporter, -50).
A new concept on the random chloroplast segregation in the somatic cell hybrids was published based molecular marker
analysis (Plant Cell Reports 17: 814-818).
The first set of RFLP markers developed and used subsequently for genome mapping and gene tagging in Indian mustard (Current Science 62: 482-484).
Dr. Trilochan Mohapatra
Principal Scientist National Research Center on Plant Biotechnology Lal Bahadur Shashtri Building Indian
Agricultural Research Institute New Delhi-110012 Telephone:91-11-25841787/25824789/25848783/25841154 TeleFax: 91-11-25843984