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Curriculum Vitae

1 Name of the award : Khosla National Award (Science)2 Subject area in which application

to be considered : Agricultural Sciences

3 Year : 2020

4 Name and designation of the scientist in full (underline surname) : Dr. Swarup Kumar Parida

Scientist IV, FNASc, FNAAS

5 Father’s Name : Dr. Kumuda Ranjan Parida

6 Date and place of birth : 26th May 1979, Balasore, Odisha

7 Marital status : Married

8 Complete postal address : Lab 109, National Institute of Plant Genome Research (NIPGR),Aruna Asaf Ali Marg, New Delhi – 110067

9 Mobile No./email : Mobile: 9968207166, 8383946979E-mail: [email protected], [email protected]

10 Educational qualifications beginning with the first-degree or equivalent

Degree Subject Division Institution Year

B.Sc. B.Sc.(Agriculture)

First Class with Hons. (80.8%) Orissa University of Agriculture and Technology (OUAT), Bhubaneswar, Odisha

2001

M.Sc. M.Sc.(Agricultural Biotechnology)

First Class with Hons. (84.2%) and Thesis works on “Development of Biochemical and SCAR Markers for Wheat Quality Improvement” at Bhabha Atomic Research Centre (BARC), Mumbai

Indira Gandhi Agricultural University (IGAU), Raipur, Chhattisgarh

2004

Ph.D. Ph.D.(Biotechnology)

Thesis works on “Development and Characterization of Microsatellite and Single Nucleotide Polymorphism (SNP) Markers in Sugarcane and their Use in Comparative Genome Analysis of Cereals”

Jamia Hamdard University, Hamdard Nagar, New Delhi-62

and

National Research Centre on Plant Biotechnology (NRCPB), New Delhi-12

2010

2

11 Employment record

Period Position Employer1st August 2018 toTill date

Staff Scientist IVPay Level 12 (Rs. 81,200)

National Institute of Plant Genome Research(NIPGR), New Delhi-67

23rd July 2014 to 31st

July 2018Staff Scientist IIIPay Level 11 (Rs. 78,500)


07th March 2011 to22nd July 2014

Staff Scientist IIPay Level 10 (Rs. 63,000)


25th January 2010 to06th March 2011

Post-doctoral FellowRs. 32,000 (Including HRA)

National Research Centre on Plant Biotechnology(NRCPB), New Delhi-12

12 Training undergone

Period Place Nature of trainingJuly 2013 to Dec 2013 (Six months)

Department of Plant Breeding andGenetics, Cornell University, Ithaca, NY, USA

Association mapping and quantitative genetics in cereals and legumes

June 2015 to Sep 2015 (Four months)

University of Hohenheim, Germany QTL mapping and construction of high- resolution genetic linkage maps and association geneticsQuantitative genetics and breeding

March 2016 to May 2016 (Three months)

CIMMYT (International Maize and Wheat Improvement Centre), Mexico

Genomic selection and constructinggenomic models for trait-environment interaction

July 2017 to Sep 2017 (Three months)

International Rice Research Institute (IRRI), Manila, Philippines

Marker-assisted selection and breeding for rice genetic improvement for yield anda/biotic stress

13 Foreign visits (period and purpose)

S.No. Period of visit Institute/ country visited Purpose of visitFrom To

1 July 2013 Dec 2013 Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA

Training for association mapping and quantitative genetics in cereals and legumes

2 Jan 2013 Feb 2013 International Plant & Animal Genome Conference, San Deigo, USA

To attend and deliver oral presentation at International Plant & Animal Genome Conference (PAG 2013)

3 June 2015 Sep 2015 University of Hohenheim, Germany

Training for QTL mapping and genetic linkage mapping and quantitative genetics and breeding



3

S.No. Period of visit Institute/ country visited Purpose of visitFrom To

5 March 2016 May 2016 CIMMYT (International Maize and Wheat Improvement Centre), Mexico

Training for genomic selection and constructing genomic models for trait- environment interaction



7 July 2017 Sep 2017 International Rice Research Institute (IRRI), Manila, Philippines

Training for marker-assisted selection and breeding for rice genetic improvement for yield and a/biotic stress



14 When, where and how the research work was conceptualized?

Dr. Swarup K. Parida, as a Senior Scientist at National Institute of Plant Genome Research (NIPGR), New Delhi, has made significant contribution in the area of Agricultural Genomics, Molecular Genetics and Breeding. His remarkable research outcomes reflect his potential to translate scientific ideas into reality as they represent top 5% of the quality output in molecular genetics and genomics-assisted crop improvement. His research contributions are original and based on novel hypothesis reflecting his out-of- the-box thinking on basic, strategic and applied sciences.

When Where Research Works How

2013-2018

NIPGR,New Delhi

Development of A High-yielding Protein-rich Variety in Chickpea

As a Scientist and Group Leader at NIPGR with financial support from DBT funded Seed Biology Project

2016-2019

NIPGR,New Delhi

Development of A Semi-Dwarf and Optimum Plant Width Chickpea Cultivar with Enhanced Planting Density and Productivity


2017-2019

NIPGR,New Delhi

Development of An Early-Flowering and High- yielding (High-Flower number) Chickpea Variety


2011-2019

NIPGR,New Delhi

Development of Early-Flowering/Maturing, Climate- Resilient, Nutritionally-Enriched Semi-dwarf and Erect Chickpea Varieties with Enhanced Yield and Productivity


2013-2019

NIPGR,New Delhi

Development and deployment of diverse integrated genomics-assisted breeding strategies for rapid genetic and molecular dissection of complex yield and abiotic stress tolerance quantitative traits in rice and chickpea


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When Where Research Works How

2011-2019

NIPGR,New Delhi

Novel Concept and Development of Informative, User-friendly and Cost-effective Genetic Marker Resources/Database for their Efficient and Rapid Use in Genomics-assisted Crop Improvement Especially in Legumes (Chickpea)

As a Scientist and Group Leader at NIPGR with financial support from DBT funded Seed Biology Project and NIPGR Core Grant

2004-2010

NRCPB,New Delhi

Novel Concept and Development of Informative, User-friendly and Cost-effective Genetic Marker Resources/Database for their Efficient and Rapid Use in Genomics-assisted Crop Improvement Especially in Cereals and Dicots (Brassica andArabidopsis)

Under the guidance of my Esteemed Ph.D. Supervisor Dr. Trilochan Mohapatra, Principal Scientist, NRCPB, New Delhi

2009-2011

NRCPB,New Delhi

Variety Identification in Basmati Rice Trade and Commerce

Under the guidance of my Esteemed Ph.D. Supervisor Dr. Trilochan Mohapatra, PrincipalScientist, NRCPB, New Delhi

2008-2011

NRCPB,New Delhi

Molecular Mapping of Genes Governing Traits of Agronomic Importance in Rice, Sugarcane and Brassica

Under the guidance of my Esteemed Ph.D. Supervisor Dr. T. Mohapatra, Scientist, NRCPB,New Delhi

15 Significant Research work carried out (Advancement in Science/technology generated, varieties developed/new concepts developed and accepted) 1. Development of A Nutritionally-enriched High-yielding Variety in Chickpea

A rapid, integrated, genomics-assisted breeding and functional genomics strategy involving GWAS, QTL/fine mapping, map-based cloning and molecular haplotyping delineated superior alleles from an ABC transporter gene, CaABCC3(6) and its marker (haplotype)-assisted introgression enhanced the seed weight, yield, and productivity without compromising any agronomic performance by modulating glutathione conjugate transport in seeds of both desi and kabuli chickpea [Basu et al. (2019) Plant Physiology 180:253-275].

An informative molecular marker tightly linked to superior natural haplotypes of an ABC transporter gene, CaABCC3(6) has been identified for large seed size/weight in chickpea. This marker has been used to transfer large seeded characteristic from an Ethiopian variety (ICC 14649) of chickpea into a commercially important Indian variety (ICCV 93954, popularly called as JG 11) that has high seed number but small seed size/weight.

The newly developed chickpea lines exhibited overall 13-20% enhancement of yield/productivity as well as 15% increase in protein content as compared to the parent line ICCV 93954 (JG 11). The newly developed lines are being evaluated in “ICAR-AICRP (All India Coordinated Research Projects) on Chickpea” Advanced Varietal Trail 1 (AVT1) during Rabi season (2018-19) at different rainfed areas of India. These improved lines developed through marker (haplotype)-assisted selection will be further evaluated for one more year under Advanced Varietal Trail 2 (AVT2) during Rabi 2019-20 prior to possible release as a variety in India [Basu et al. (2019) Plant Physiology 180:253-275].

Certificate on “ICAR-AICRP (All India Coordinated Research Projects) on Chickpea Advanced Varietal Trial 1 (AVT1)” of this improved JG11 line is attached in ANNEXURE I

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Relevant Publication: Basu U, Upadhyaya HD, Srivastava R, Daware A, Malik N, Sharma A, Bajaj D, Narnoliya L, Thakro V, Kujur A, Tripathi S, Bharadwaj C, Hegde VS, Pandey AK, Singh AK, Tyagi AK, Parida SK* (2019) ABC transporter-mediated transport of glutathione conjugates enhances seed yield and quality in chickpea. Plant Physiology 180:253-275. [*Corresponding Author]

SUMMARY

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SUMMARY OF DETAILED PHENOTYPING INFORMATION OF IMPROVED JG11 LINE OBTAINED FOR DIVERSE AGRONOMIC TRAITS AFTER THEIR LARGE-SCALE PHENOTYPING EVALUATION IN THE ICAR- AICRP (CHICKPEA) AVT1-INTROGRESSION TRIALS (2018-2019)

2. Development of A Semi-Dwarf and Optimum Plant Width Chickpea Cultivar with Enhanced Planting Density and Productivity

A rapid, integrated, genomics-assisted breeding and functional genomics strategy involving GWAS, QTL/fine mapping, map-based cloning and molecular haplotyping, transcript profiling and protein-DNA interaction assays delineated superior transcriptional signatures from a CabHLH121 transcription factor gene and its marker (haplotype)-assisted introgression enhanced yield and productivity by modulating vital plant architectural (plant width and plant height) and SAM morphometric traits without compromising any component of agronomic performance in chickpea [Narnoliya et al. (2019) Plant Journal 98:864-883].

The restructured cultivars with desirable plant height (semi-dwarf) and plant width will ensure maximal planting density (25% increase in planting density) in a specified cultivable field area, thereby enhancing the overall yield and productivity (15% increase) of chickpea. This can essentially facilitate the achievement of better remunerative outputs by farmers with rational land use, thus ensuring global food security in the present scenario of an increasing population density and shrinking per capita land area [Narnoliya et al. (2019) Plant Journal 98:864-883].

Relevant Publication: Narnoliya L, Basu U, Bajaj D, Malik N, Thakro V, Daware A, Sharma A, Tripathi S, Hegde VS, Upadhyaya HD, Singh AK, Tyagi AK, Parida SK* (2019) Transcriptional signatures modulating shoot apical meristem morphometric and plant architectural traits enhance yield and productivity in chickpea. Plant Journal 98:864-883. [*Corresponding Author]

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SUMMARY

3. Development of An Early-Flowering and High-yielding (High-Flower number) Chickpea Variety

A rapid combinatorial genomics-assisted breeding and functional genomic strategy involving GWAS, QTL/fine mapping, map-based cloning and molecular haplotyping and transcript profiling delineated functionally relevant novel alleles and superior haplotypes of a CLAVATA gene (CaCLV3) and its marker (haplotype)-assisted introgression led to development of the early flowering (15 days early days to 50% flowering) chickpea cultivars with high flower number and enhanced yield/productivity (13% increase) without compromising agronomic performance [Basu et al. (2019) Theoretical and Applied Genetics 132:2017-2038].

Relevant Publication: Basu U, Narnoliya L, Srivastava R, Sharma A, Bajaj D, Daware A, Thakro V, Malik N, Upadhyaya HD, Tripathi S, Hegde VS, Tyagi AK, Parida SK* (2019) CLAVATA signaling pathway genes modulating flowering time and flower number in chickpea. Theoretical and Applied Genetics 32:2017- 2038. [*Corresponding Author]

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SUMMARY

4. Development of Early-Flowering/Maturing, Climate-Resilient, Nutritionally-Enriched Semi-dwarf and Erect Chickpea Varieties with Enhanced Yield and Productivity

Developed and optimized diverse integrated novel genomic strategies combining association analysis and genetic/QTL (eQTL) mapping with differential expression profiling, high-resolution molecular haplotyping (linkage disequilibrium mapping) and haplotype-based gene evolution study for rapid delineation of genomic loci regulating agromorphological (yield and stress tolerance) traits especially in chickpea (ANNEXURE II).

These combinatorial strategies include: Pool-based trait association mapping, genetical genomics/expression QTL (eQTL) mapping, QTL region-specific association mapping, comprehensive QTL-based comparative genome mapping, QTL-Seq, mQTL-Seq and EcoTILLING assays (ANNEXURE II).

By exploiting these combinatorial genome-wide approaches in phenotypically well-characterized diverse natural germplasm lines and bi-parental mapping populations, 18 novel alleles and six haplotypes in 13 transcription factor genes and 20 major QTLs/eQTLs governing seed weight, pod/seed number, flowering time, branch number, plant height, seed colour, seed-protein content, yield under drought stress and photosynthetic efficiency have been delineated and mapped on 10 ultra-high density intra-/inter-specific genetic linkage maps of chickpea (ANNEXURE II).

Delineated multiple trait-associated novel natural allelic variants from numerous core/minicore germplasm lines and mapping populations by integrated genomic approach and deployed them in genomics-assisted crop improvement. Potential major genes and haplotypes regulating seed weight and pod/seed number are being introduced into multiple high-yielding Indian varieties (JG11, ICCV2 and Pusa362) for improving chickpea seed and pod yield through marker-assisted breeding.

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Delineated five seed weight and pod/seed number-associated natural gene/allelic variants and major QTLs from wild Cicer gene pools by combinatorial genomic strategy to facilitate genetic improvement of cultivated chickpea for higher seed/pod yield through marker-assisted introgression breeding.

SUMMARY

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5. Novel Concept and Development of Informative, User-friendly and Cost-effective Genetic Marker Resources/Database for their Efficient and Rapid Use in Genomics-assisted Crop Improvement Especially in Cereals and Legumes

Developed novel concepts and designed a large number (~50,000) of genic microsatellite markers namely, “UGMS” (unigene derived microsatellite) in five cereal species (rice, wheat, maize, sorghum and barley), sugarcane, Brassica and Arabidopsis thaliana, “SEGMS” (sugarcane enriched genomic microsatellite) and “GNMS” (genic non-coding microsatellite) from different regulatory (5’UTRs and promoters) and non-coding (3’UTRs and intronic) sequence components of protein coding rice genes as well as “FDMS” (functional domain-associated microsatellite), “TFGMS” (transcription factor gene-derived microsatellite) and “CNMS” (conserved non-coding microsatellite) in chickpea for genomics-assisted breeding applications and genetic enhancement studies of these crop species (ANNEXURE III & IV).

Developed and optimized an integrated reference genome and de novo-based GBS (genotyping-by sequencing) pipeline for simultaneous large-scale discovery and genotyping of genome-wide SNPs especially among accessions of crop plants with low-quality draft genomes (ANNEXURE IV) [Kujur A….Parida SK* (2015) Front. Plant Sci. 6:162].

Adopting this optimized pipeline, generated more than 10 million genome-wide SNP markers and 50,000 InDel markers by simultaneous sequencing and genotyping of a large set of cultivated (desi and kabuli) and wild accessions for high-throughput genetic analysis in chickpea with narrow genetic base (ANNEXURE IV).

These informative and robust sequence-based microsatellite and SNP markers developed from nine diverse crop plants (rice, wheat, maize, sorghum, barley, sugarcane, Brassica, Arabidopsis and chickpea) at a genome-wide scale have already been placed in public domain (NCBI Probe, NCBI GSS, NCBI-dbSNP and NCBI-SRA databases) for unrestricted use, which would extend the accessibility of such gene-

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specific functional and genomic markers to researchers facilitating genetic studies in these crop species with a wider genome coverage (ANNEXURE III & IV).

These developed markers have been extensively utilized by several research groups of the world including Indian groups (as evident from highly-cited publications in Journals of International Repute) for variety identification, understanding the natural allelic diversity, population genetic structure, domestication pattern and phylogenetic relationship, comparative genome mapping, construction of high- resolution genome maps, QTL/gene mapping, and trait association analysis in crop plants.

For instance, using the informative genic (UGMS) and genomic (SEGMS) microsatellite markers, the sugarcane molecular geneticists and breeders at UPCSR (UP Council of Sugarcane Research), Shahjahanpur and SBI (Sugarcane Breeding Institute), Coimbatore have identified six major QTLs associated with sugar-traits and red-rot resistance for marker-assisted improvement of sugarcane for sugar content and red-rot resistance in India which have been published in the journals of International repute with high citations [Singh et al. (2013) Euphytica 191:333-353, Swapna and Srivastava (2012) Springer Briefings in Plant Science 1-19, Singh et al. (2011) Euphytica 182:335-354].

A user-friendly web-resource, “Oryza ISM-ILP marker” database comprising 84634 ISM (intron-spanning marker) and 16510 InDel-fragment length polymorphism-based ILP (intron-length polymorphism) markers developed from rice genes at a genome-wide scale has been made, which is publicly accessible through web-links: http://webapp.cabgrid.res.in/ismdb/ or http://bioinformatics.iasri.res.in/ismdb/.

A user-friendly web-resource, “Chickpea ISM-ILP marker” database comprising 119169 and 110491 ISM (intron-spanning marker) and 7454 InDel-fragment length polymorphism-based ILP (intron-length polymorphism) markers developed from chickpea genes at a genome-wide scale has been made, which is publicly accessible through web-links: http://webapp.cabgrid.res.in/chickpea/ or http://bioinformatics.iasri.res.in/chickpea.

These two constructed marker database serve as a useful genomic resource for their immense utilization in high-throughput genotyping of markers among natural and mapping populations employing a user- friendly and simpler agarose gel-based assay with optimal expense of resources.

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Developed A database “CNSNP-CICARBASE” which provides unrestricted public access (http://www.cnsnpcicarbase.com) of diverse information about 431,194 CNSNPs harbouring 4213 genes annotated on chickpea genome for its genomics-assisted crop Improvement. [Sharma et al. (2019) Functional Integrative Genomics DOI:10.1007/s10142-019-00691-2]

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6. Development and optimization of a 90K Pan Genome SNP Array for the first-time for high-throughput genotyping of SNPs among natural germplasm accessions (association panel) and mapping populations to accelerate genomics-assisted breeding and crop improvement in rice.

7. Variety Identification in Basmati Rice Trade and Commerce Developed “Molecular Bar Codes” of commercially important Indian Basmati rice varieties based on

DNA fingerprints using a set of informative gene-based markers for their utility in Basmati trade and commerce. [Parida SK et al. (2010) Mol Breed 26:275-292]

Demonstrated the efficacy of five mitochondrial gene-specific markers for testing the purity of Pusa6A parental lines during seed production of Pusa Rice Hybrid 10, which have immense potential utility for marker-assisted production of pure hybrid rice seeds in India. [Parida SK et al. (2010) Mol Breed 26:275-292]

8. Molecular Mapping of Genes Governing Traits of Agronomic Importance Mapped a major locus for fertility restoration in Basmati restorer line PRR78, which is currently being

utilized in efficient marker-assisted selection for fertility restoration in hybrid breeding program for WA-CMS in rice. [Parida SK et al. (2010) Mol Breed 26:275-292]

16 What were the socio-economic, technological and scientific relevance of this work? Development of A Protein-rich High-yielding Variety in Chickpea

Development of nutritionally-enriched chickpea varieties with enhanced yield and productivity is essential to ensure global food and nutritional security.

The ABC transporter superior gene haplotype-introgressed newly developed improved chickpea lines exhibited overall 13-20% enhancement of yield/productivity as well as 15% increase in protein content as compared to the parent line ICCV 93954 (JG 11) after are being evaluated in “ICAR-AICRP (All India Coordinated Research Projects) on Chickpea” Advanced Varietal Trail 1 (AVT1) during Rabi season (2018-19) at different rainfed areas of India. These improved lines developed through marker (haplotype)-assisted selection will be further evaluated for one more year under Advanced Varietal Trail 2 (AVT2) during Rabi 2019-20 prior to possible release as a variety in India [Basu et al. (2019) Plant Physiology 180:253-275].

Development of A Chickpea Variety with Enhanced Productivity

The bHLH transcription factor gene superior haplotype introgressed restructured cultivars with desirable plant height (semi-dwarf) and plant width will ensure maximal planting density (25% increase) in a specified cultivable field area, thereby enhancing the overall yield and productivity (15% increase) of chickpea. This can essentially facilitate the achievement of better remunerative outputs by farmers with rational land use, thus ensuring global food security in the present scenario of an increasing population density and shrinking per capita land area [Narnoliya et al. (2019) Plant Journal 98:864-883].

Development of An Early-Flowering and High-yielding (High-Flower number) Chickpea Variety

A rapid combinatorial genomics-assisted breeding and functional genomic strategy involving GWAS, QTL/fine mapping, map-based cloning and molecular haplotyping and transcript profiling delineated functionally relevant novel alleles and superior haplotypes of a CLAVATA gene (CaCLV3) and its marker (haplotype)-assisted introgression led to development of the early flowering (15 days aerly days to 50% flowering) chickpea cultivars with high flower number and enhanced yield/productivity

14

(13% increase) without compromising agronomic performance [Basu et al. (2019) Theoretical and Applied Genetics 132:2017-2038].

Novel Concepts and Development of Genome-wide Informative Marker Resource and Database for Genomics-assisted Crop Improvement

The developed novel concepts on designing of numerous informative and robust sequence-based microsatellite and SNP markers and user-friendly freely-accessible Databases (web-resources) from nine diverse crop plants (rice, wheat, maize, sorghum, barley, sugarcane, Brassica, Arabidopsis and chickpea) at a genome-wide scale have already been placed in public domain (NCBI Probe, NCBI GSS, NCBI-dbSNP and NCBI-SRA databases) for unrestricted use, which would extend the accessibility of such gene-specific functional and genomic markers to researchers facilitating genetic studies in these crop species with a wider genome coverage.

These developed markers have been extensively utilized by several research groups of the world including Indian groups (as evident from highly-cited publications in Journals of International Repute) for variety identification, understanding the natural allelic diversity, population genetic structure, domestication pattern and phylogenetic relationship, comparative genome mapping, construction of high-resolution genome maps, QTL/gene mapping, and trait association analysis in crop plants.

For instance, using the informative genic (UGMS) and genomic (SEGMS) microsatellite markers, the sugarcane molecular geneticists and breeders at UPCSR (UP Council of Sugarcane Research), Shahjahanpur and SBI (Sugarcane Breeding Institute), Coimbatore have identified six major QTLs associated with sugar-traits and red-rot resistance for marker-assisted improvement of sugarcane for sugar content and red-rot resistance in India which have been published in the journals of International repute with high citations [Singh et al. (2013) Euphytica 191:333-353, Swapna and Srivastava (2012) Springer Brief. in Plant Sci. 1-19, Singh et al. (2011) Euphytica 182:335-354].

The constructed user-friendly and freely-accessible marker database serve as a useful genomic resource for their immense utilization in high-throughput genotyping of markers among natural and mapping populations employing a user-friendly and simpler agarose gel-based assay with optimal expense of resources.

Designing and optimization of a 90K Pan Genome SNP Array for the first-time for high- throughput genotyping of SNPs among natural germplasm accessions (association panel) and mapping populations to accelerate genomics-assisted breeding and crop improvement in rice.


Developed “Molecular Bar Codes” of commercially important Indian Basmati rice varieties based on DNA fingerprints using a set of informative gene-based markers for their utility in Basmati trade and commerce. [Parida SK et al. (2010) Mol Breed 26:275-292]

Demonstrated the efficacy of five mitochondrial gene-specific markers for testing the purity of Pusa6A parental lines during seed production of Pusa Rice Hybrid 10, which have immense potential utility for marker-assisted production of pure hybrid rice seeds in India. [Parida SK et al. (2010) Mol Breed 26:275-292]

15

Molecular Mapping of Genes Governing Traits of Agronomic Importance Mapped a major locus for fertility restoration in Basmati restorer line PRR78, which is currently being

utilized in efficient marker-assisted selection for fertility restoration in hybrid breeding program for WA- CMS in rice. [Parida SK et al. (2010) Mol Breed 26:275-292]

Diverse Integrated Genomics-assisted Breeding Strategies for Dissection of Complex Yield and Abiotic Stress Tolerance Quantitative Traits in Chickpea

Developed and optimized diverse integrated novel genomic strategies combining association analysis and genetic/QTL (eQTL) mapping with differential expression profiling, high-resolution molecular haplotyping (linkage disequilibrium mapping) and haplotype-based gene evolution study for rapid delineation of genomic loci regulating agromorphological (yield and stress tolerance) traits especially in chickpea and rice.

These combinatorial strategies include: Pool-based trait association mapping, genetical genomics/eQTL mapping, QTL region-specific association mapping, comprehensive QTL-based comparative genome mapping, QTL-Seq, mQTL-Seq and EcoTILLING assays (ANNEXURE II).

Rapid Delineation of Functionally Relevant Molecular Tags Regulating Yield Component & Stress Tolerance Traits

By exploiting these combinatorial genome-wide approaches in phenotypically well-characterized diverse natural germplasm lines and bi-parental mapping populations, functionally relevant QTLs and eQTLs, novel genes (transcription factors), natural alleles and haplotypes regulating seed size/100- seed weight, pod and seed number/plant, flowering time, branch number, plant height, seed colour, seed-protein content and seed-iron and zinc concentration, etc. and stress-tolerance traits have been mapped on 10 ultra-high density intra-/inter-specific genetic linkage maps of chickpea and rice (ANNEXURE II).

By exploiting these combinatorial genome-wide approaches in phenotypically well-characterized diverse natural germplasm lines and bi-parental mapping populations, 12 novel alleles and six haplotypes in 10 transcription factor genes and 16 major QTLs/eQTLs governing seed weight, pod/seed number, flowering time, branch number, plant height, seed colour and seed-protein content mapped on 10 ultra-high density intra-/inter-specific genetic linkage maps has been delineated in chickpea (ANNEXURE II).

Delineated five seed weight and pod/seed number-associated natural gene/allelic variants and major QTLs from wild Cicer gene pools by combinatorial genomic strategy to facilitate genetic improvement of cultivated chickpea for higher seed/pod yield through marker-assisted introgression breeding.

Currently, as a multi-laboratories/institutional Mega-project aimed at combining epigenomic, transcriptomic and molecular genetics for genetic enhancement of rice and chickpea pertinent to seed/pod traits and yield. The research efforts with regard to association and QTL mapping in this project identified six informative genic markers tightly linked to major QTLs/genes and 10 novel natural allelic variants regulating grain size/weight for genomics-assisted crop improvement of rice for high grain weight and yield.

These functionally relevant molecular tags in chickpea and rice would be of immense use in marker- assisted genetic enhancement of these two major cereal and legume crop species for developing high-yielding stress tolerant varieties.

Strategies to Counter Climate Change The multiple integrated genomic strategies (combining association/QTL mapping with molecular

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haplotyping & transcript profiling) developed by him will enable to select trait-associated superior novel favorable natural gene/allelic variants influencing agronomic trait variation in crop accessions adapted to diverse agro-climatic conditions & deploy them most effectively for marker-assisted genetic improvement. Collectively, these inputs will be useful for devising most efficient strategies to produce high-yielding and durable stress tolerant cultivars/climate resilient crop varieties for sustaining global food security amid acute climatic change.

Deploying Novel Natural Allelic Variants in Marker-assisted Genetic Enhancement Delineated multiple trait-associated novel natural allelic variants from numerous core/minicore

germplasm lines & mapping populations by integrated genomic approach & deployed them in genomics-assisted crop improvement. Potential major genes and haplotypes regulating seed weight and pod/seed number are being introduced into multiple high-yielding Indian varieties (JG11, ICCV2 & Pusa362) for improving chickpea seed and pod yield through marker-assisted breeding.

More recently, delineated superior natural alleles from an ABCC3-type ABC transporter gene and introgressed in to an Indian popular desi chickpea variety JG11 though marker (haplotype)-assisted selection which led to develop a nutrient (protein content)-rich improved JG11 variety with increased seed weight as well as enhanced yield and productivity.

17 List the Principal associate scientists at various stages of the research work?

When Where Research Works Principal Associate Scientists involved2013-2018

NIPGR,New Delhi

Development of A High-yielding Protein- rich Variety in Chickpea

Dr. Trilochan Mohapatra, DG, ICAR, New Delhi

Prof. A.K. Singh, Head Genetics, IARI, New Delhi

Prof. Akhilesh K. Tyagi, Delhi University, South Campus, New Delhi

Dr. C. Bharadwaj, Pulse Division, IARI, New Delhi

Dr. Shailesh Tripathi, Pulse Division, IARI, New Delhi

Dr. K.C. Bansal, NBPGR, New Delhi Dr. Mohar Singh, NBPGR, New Delhi Dr. H.D. Upadhyaya, Head Genebank,

ICRISAT, Hyderabad Dr. Rajeev Varshney, Head Genomics,

ICRISAT, Hyderabad Dr. Manoj Prasad, Scientist, NIPGR Dr. Debasis Chattopadhyay, Scientist,

NIPGR Dr. Sabhyta Bhatia, Scientist, NIPGR Dr. Mukesh Jain, Professor, JNU, New

Delhi Dr. Ramesh V. Sonti, Director, NIPGR,

New Delhi

2016-2019

NIPGR,New Delhi

Development of A Semi-Dwarf and Optimum Plant Width Chickpea Cultivar with Enhanced Planting Density and Productivity

2017-2019

NIPGR,New Delhi

Development of An Early-Flowering and High-yielding (High-Flower number) Chickpea Variety

2017-2019

NIPGR,New Delhi

Designing and optimization of a 90K Pan Genome SNP Array for the first-time for high-throughput genotyping of SNPs among natural germplasm accessions (association panel) and mapping populations to accelerate genomics- assisted breeding and crop improvement in rice.

2011-2019

NIPGR,New Delhi

Development of Early- Flowering/Maturing, Climate-Resilient, Nutritionally-Enriched Semi-dwarf and Erect Chickpea Varieties with Enhanced Yield and Productivity

2011-2019

NIPGR,New Delhi

Novel Concept and Development of Informative, User-friendly and Cost- effective Genetic Marker Resources/Database for their Efficient and Rapid Use in Genomics-assisted Crop Improvement Especially in Chickpea

17

When Where Research Works Principal Associate Scientists involved2004-2010

NRCPB,New Delhi

Novel Concept and Development of Informative, User-friendly and Cost- effective Genetic Marker Resources/Database for their Efficient and Rapid Use in Genomics-assisted Crop Improvement Especially in Cereals and Dicots (Brassica and Arabidopsis)

Dr. Trilochan Mohapatra, DG, ICAR, New Delhi

Prof. A.K. Singh, Head Genetics, IARI, New Delhi

Prof. N.K. Singh, Director, NIPB, New Delhi

Prof. R.P. Sharma, Professor Eminence, NIPB, New Delhi

Dr. T.R. Sharma, Director, NABI, Mohali, Punjab

Dr. Kuldeep Singh, Director, NBPGR, New Delhi

Dr. Kishor Gaikwad, Scientist, NRCPB, New Delhi

2009-2011

NRCPB,New Delhi


2008-2011

NRCPB,New Delhi


18 What is the potential value of the research results in increasing production, productivity, profitability and sustainability of agricultural enterprises in the relevant field (with clear evidence)? Or significant advancement in science

Research Results/ Technologies/ Strategies/ Methods developed

Increasing production, productivity, profitability and sustainability of agricultural enterprises and significant advancement in science

Evidences

Development of A High- yielding Protein-rich Variety in Chickpea[An informative molecular marker tightly linked to superior natural haplotypes of an ABC transporter gene, CaABCC3(6) has been identified for large seed size/weight in chickpea. This marker has been used to transfer large seeded characteristic from an Ethiopian variety (ICC 14649) of chickpea into a commercially important Indian variety (ICCV 93954, popularly called as JG 11) that has high seed number but small seed size/weight.]

The newly developed chickpea lines exhibited overall 13-20% enhancement of yield/productivity as well as 15% increase in protein content as compared to the parent line ICCV 93954 (JG 11). The newly developed lines are being evaluated in “ICAR-AICRP (All India Coordinated Research Projects) on Chickpea” Advanced Varietal Trail 1 (AVT1) during Rabi season (2018-19) at different rainfed areas of India. These improved lines developed through marker (haplotype)- assisted selection will be further evaluated for one more year under Advanced Varietal Trail 2 (AVT2) during Rabi 2019-20 prior to possible release as a variety in India.

“ICAR-AICRP (AllIndia Coordinated Research Projects) on Chickpea Advanced Varietal Trial 1(AVT1)” of this improved JG11 line is attached.[Basu et al. (2019) Plant Physiology 180:253-275].

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Development of A Semi-Dwarf and Optimum Plant Width Chickpea Cultivar with Enhanced Planting Density and Productivity[A rapid, integrated, genomics- assisted breeding and functional genomics strategy involving GWAS, QTL/fine mapping, map- based cloning and molecular haplotyping, transcript profiling and protein-DNA interaction assays delineated superior transcriptional signatures from a CabHLH121 transcription factor gene and its marker (haplotype)- assisted introgression enhanced yield and productivity by modulating vital plant architectural (plant width and plant height) and SAM morphometric traits without compromising any component of agronomic performance in chickpea

The restructured cultivars with desirable plant height (semi-dwarf) and plant width will ensure maximal planting density (25% increase) in a specified cultivable field area, thereby enhancing the overall yield and productivity (15% increase) of chickpea. This can essentially facilitate the achievement of better remunerative outputs by farmers with rational land use, thus ensuring global food security in the present scenario of an increasing population density and shrinking per capita land area

“ICAR-AICRP (AllIndia Coordinated Research Projects) on Chickpea Advanced Varietal Trial 1(AVT1)” of this improved line is attached.[Narnoliya et al. (2019) Plant Journal 98:864-883].

Development of An Early- Flowering and High-yielding (High-Flower number) Chickpea Variety [A rapid combinatorial genomics-assisted breeding and functional genomic strategy involving GWAS, QTL/fine mapping, map-based cloning and molecular haplotyping and transcript profiling delineated functionally relevant novel alleles and superior haplotypes of a CLAVATA gene (CaCLV3) and its marker (haplotype)-assisted introgression led to development of the early flowering chickpea cultivars with high flower number and enhanced yield/productivity without compromising agronomic performance]

Developed Early-Flowering/Maturing (15 days early days to 50% Flowering), Climate-Resilient, Nutritionally-Enriched Semi-dwarf and Erect Chickpea Varieties with Enhanced Yield and Productivity (13% increase).

ICAR-AICRP (All India Coordinated Research Projects) on Chickpea Advanced Varietal Trial 1 (AVT1)” of this improved line is attached.[Basu et al. (2019) Theoretical and Applied Genetics 132:2017-2038].

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Development and optimization Useful in drive genomics-assisted Technologyof a 90K Pan Genome SNP breeding and crop improvement in commercialized withArray for the first-time for rice. Affymetrixhigh-throughput genotyping Technologies, USA forof SNPs among natural Designing Universalgermplasm accessions Array for Large-scale(association panel) and SNP Genotypingmapping populations to Applications in Riceaccelerate genomics-assistedbreeding and cropimprovement in rice.

Novel Concept and Development of Informative, User-friendly and Cost- effective Genetic Marker Resources/Database for their Efficient and Rapid Use in Genomics-assisted Crop Improvement Especially in Cereals and Dicots (Brassica and Arabidopsis) as well as Legumes (Chickpea)

Numerous informative and robust sequence-based microsatellite and SNP markers developed from nine diverse crop plants (rice, wheat, maize, sorghum, barley, sugarcane, Brassica, Arabidopsis and chickpea) at a genome- wide scale have already been placed in public domain (NCBI Probe, NCBI GSS, NCBI-dbSNP and NCBI-SRAdatabases) for unrestricted use, which would extend the accessibility of such gene-specific functional and genomic markers to researchers facilitating genetic studies in these crop specieswith a wider genome coverage.

Details regarding marker development and their applicability in genomics-assisted crop improvement is attached.

These developed markers have been extensively utilized by several research groups of the world including Indian groups (as evident from highly-cited publications in Journals of International Repute) for variety identification, understanding the natural allelic diversity, population genetic structure, domestication pattern and phylogenetic relationship, comparative genome mapping, construction of high-resolution genome maps, QTL/gene mapping, and trait association analysis in cropplants.

For instance, using the informative genic (UGMS) and genomic (SEGMS) microsatellite markers, the sugarcane

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molecular geneticists and breeders at UPCSR (UP Council of Sugarcane Research), Shahjahanpur and SBI (Sugarcane Breeding Institute), Coimbatore have identified six major QTLs associated with sugar-traits and red-rot resistance for marker- assisted improvement of sugarcane for sugar content and red-rot resistance in India which have been published in the journals of International repute with high citations

Diverse Integrated Genomics- assisted Breeding Strategies for Dissection of Complex Yield and Abiotic Stress Tolerance Quantitative Traits in Chickpea[Developed and optimized diverse integrated novel genomic strategies combining association analysis and genetic/QTL (eQTL) mapping with differential expression profiling, high-resolution molecular haplotyping (linkage disequilibrium mapping) and haplotype-based gene evolution study for rapid delineation of genomic loci regulating agromorphological (yield and stress tolerance) traits especially in chickpea and rice]These combinatorial strategies include: Pool-based trait association mapping, genetical genomics/eQTL mapping, QTL region-specific association mapping, comprehensive QTL- based comparative genome mapping, QTL-Seq, mQTL-Seq and EcoTILLING assays.

This strategy is useful for rapid delineation of functionally relevant molecular tags (QTLs, genes and novel alleles) regulating yield and stress tolerance traits in crop plants including rice and chickpea

Details regarding marker development and their applicability in genomics-assisted crop improvement is attached.

21

Deploying novel natural allelic variants in Marker-assisted Genetic Enhancement in Chickpea

Delineated functionally significant natural allelic variants and superior haplotypes and developed a haplotype- assisted foreground and background section strategy for introgressing superior haplotypes in to multiple high- yielding Indian varieties (JG11, ICCV2 & Pusa362) for chickpea genetic improvement.

Details on haplotype- assisted breeding and genetic enhancement of chickpea is attached.


Developed “Molecular Bar Codes” of commercially important Indian Basmati rice varieties based on DNA fingerprints using a set of informative gene-based markers for their utility in Basmatitrade and commerce.

[Parida SK et al. (2010) Mol Breed 26:275-292]

Demonstrated the efficacy of five mitochondrial gene-specific markers for testing the purity of Pusa6A parental lines during seed production of Pusa Rice Hybrid 10, which have immense potential utility for marker- assisted production of pure hybrid rice seeds in India.


Mapped a major locus for fertility restoration in Basmati restorer line PRR78, which is currently being utilized in efficient marker-assisted selection for fertility restoration in hybrid breeding program for WA-CMS in rice. Delineated major genomic loci governing abiotic stress tolerance in rice as well as QTLs for red rot disease resistance and sugar content in sugarcane.

[Parida SK et al. (2010) Mol Breed 26:275-292]

19 Impact of the results obtained in quantifiable and verifiable terms

Brief Impact of the Outcomes Obtained in Quantifiable and Verifiable Terms Developed nutritionally-enriched (15% more protein-rich) improved chickpea variety with 13-

20% enhanced yield and productivity using integrated genomics-assisted breeding and through marker (haplotype)-assisted selection.

Developed a semi-dwarf and optimal canopy width erect/semi-erect chickpea variety with enhanced planting density (25% increase) and productivity (15% increase) using integrated genomics-assisted breeding and through marker (haplotype)-assisted selection.

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Developed an early-flowering (15 days early days to 50% flowering) and high-yielding (13% increase in flower number and yield) chickpea variety using integrated genomics-assisted breeding and through marker (haplotype)-assisted selection.

Developed and optimized a 90K high-density Pan Genome SNP Array for the first-time for high- throughput genotyping of SNPs to accelerate genomics-assisted breeding and crop improvement in rice. This technology has been commercialized with Affymetrix Technologies, USA for designing universal array for large-scale SNP genotyping applications in rice.

Developed 15 novel concepts on designing of informative user-friendly cost-effective genetic marker resource and six freely-accessible database to drive large-scale genotyping applications and genomics-assisted crop breeding-led improvement especially in cereals and legumes.

Developed 10 novel integrated genomics-assisted breeding strategies for quick genetic and molecular dissection of complex yield and abiotic stress tolerance traits in rice and chickpea.

The molecular Bar Codes and potential functionally relevant molecular tags identified have been commonly utilized in Indian Basmati trade and commerce for marker-assisted selection of fertility restoration and production of pure hybrid rice seeds.

Constructed 10 ultra high-density (marker distance ≤ 1 cM) genetic linkage maps and delineated 12 novel alleles and six haplotypes in 25 genes as well as 16 major QTLs/eQTLs governing traits of agronomic importance such as flowering/maturity time, plant height, branch number, pod/seed number, canopy width, seed weight, plant growth habit, photosynthetic efficiency, drought stress tolerance, seed protein content and seed iron/zinc content, etc. in chickpea using both integrated genomics-assisted breeding strategies.

Identified and mapped genes controlling fertility restorer for hybrid seed production and abiotic stress tolerance in rice as well as red rot disease resistance and sugar content in sugarcane.

Published more than 85 articles in journals of international-repute (333.7 impact-factor with 32 H-index and 3227 Citations) in the area of molecular genetics and genomics-assisted breeding for crop improvement.

Conferred with prestigious National Awards and Fellows of major National Science Academies of India. Currently he serves as Editors and reviewers in multiple national and international journals.

Supervised 10 Ph.D. students and trained students/researchers and collaborated with scientists of multiple national/international institutions and providing frontline know how and technical inputs specifically for next-generation sequencing (NGS)-driven integrated genomics-assisted breeding to accelerate genetic improvement in major food crops.

SUMMARY

Made significant contribution in the area of Agricultural Genomics, Molecular Genetics and Breeding. His remarkable research outcomes reflect his potential to translate scientific ideas into reality as they represent top 5% of the quality output in molecular genetics and genomics- assisted crop improvement. His research contributions are original and based on novel hypothesis reflecting his out-of-the-box thinking on basic, strategic and applied sciences.

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Instrumental in developing novel concepts on highly-informative novel genic and genomic microsatellite and single nucleotide polymorphism (SNP) markers designing and database development in an array of crops (rice, wheat, maize, sorghum, barley, Brassica, sugarcane and chickpea) and utilized them for understanding genome structure and evolution, molecular diversity and domestication pattern, variety identification, construction of high-resolution genome maps, gene mapping and trait association analysis.

Significantly contributed towards development of diverse integrated genomics-assisted breeding strategies as well as delineated numerous functionally relevant molecular signatures regulating vital agronomic traits at a genome-wide scale that have been extensively utilized by several researchers (as evident from publications in journals of international repute with high citations) world-wide for multiple high-throughput genetic analyses in major food crops especially in rice and chickpea.

Significantly accelerated the process of quantitative dissection of complex stress tolerance and yield/quality component traits aimed at efficient marker-assisted genetic enhancement of cereals and pulses.

Substantial efforts have also been made to meticulously integrate diverse genomics-assisted strategies of QTL and association mapping with molecular haplotyping and expression profiling, which led him to delineate numerous molecular tags (genes, QTLs, alleles and haplotypes) governing fertility restorer, hybrid production and stress tolerance traits in rice as well as diverse seed and pod yield and nutrient/quality component traits in chickpea.

Generated 10 ultra-high density intra-/inter-specific genetic linkage maps that he constructed alongside discovery of 12 novel alleles and six haplotypes in 10 transcription factors genes and 16 major QTLs/eQTLs regulating seed weight, pod/seed number, flowering time, branch number, plant height, plant architecture, seed colour, seed-protein content and seed-iron/zinc content in chickpea.

Developed and optimized a 90K Pan Genome SNP Array for the first-time for high-throughput genotyping of SNPs among natural germplasm accessions (association panel) and mapping populations to accelerate genomics-assisted breeding and crop improvement in rice. This high-density SNP array will be useful to drive genomics-assisted breeding and crop improvement in rice. This technology has been commercialized with Affymetrix Technologies, USA for designing universal array for large-scale SNP genotyping applications in rice.

The molecular Bar Codes and potential functionally relevant molecular tags identified have been commonly utilized in Indian Basmati trade and commerce for marker-assisted selection of fertility restoration and production of pure hybrid rice seeds.

The multiple integrated genomic strategies developed have enabled effective delineation and selection of novel superior trait-associated favorable natural gene/allelic variants and haplotypes from diverse natural germplasm accessions representing varied agro-climatic conditions to be utilized in marker-assisted genetic enhancement of rice and chickpea.

Deployed successfully marker-assisted breeding to introgress two most-promising high-seed weight and pod/seed number-associated superior molecular haplotypes delineated from cultivated and wild Cicer gene pools (through a genome-wide integrated strategy) into a number of Indian high-yielding chickpea varieties for improving their overall yield and productivity.

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Delineated superior natural alleles from an ABCC3-type ABC transporter gene and introgressed in to an Indian popular desi chickpea variety JG11 though marker (haplotype)-assisted selection which led to develop a nutrient (protein content)-rich improved JG11 variety with increased seed weight as well as enhanced yield and productivity.

Developed early-flowering/maturing, climate-resilient, nutritionally-enriched semi-dwarf and erect chickpea varieties with enhanced yield and productivity.

These vital research outcomes have got immense applicability to produce high-yielding climate resilient crop varieties enriched with desirable quality traits for enhancing global productivity as well as sustaining global food and nutritional security amid current acute climate change.

Published more than 85 articles in journals of international-repute (333.7 impact-factor with 32 H-index and 3227 Citations) in the area of molecular genetics and genomics-assisted breeding for crop improvement.

Conferred with prestigious National Awards and Fellows of major National Science Academies of India. Currently he serves as Editors and reviewers in multiple national and international journals.

Trained students/researchers and collaborated with scientists of multiple national/international institutions and providing frontline know how and technical inputs specifically for next-generation sequencing (NGS)-driven integrated genomics-assisted breeding to accelerate genetic improvement in major food crops.

20 Research publications: List Research papers in bibliographic format with NAAS rating (Include publication having NAAS Rating of ≥ 6.0 only)

As Corresponding Authors (40 Publications)List of Publications NAAS Rating

(2019)InternationalImpact Factors

Number ofCitations

1. Narnoliya L, Basu U, Bajaj D, Malik N, Thakro V, Daware A, Sharma A, Tripathi S, Hegde VS, Upadhyaya HD, Singh AK, Tyagi AK, Parida SK* (2019) Transcriptional signatures modulating shoot apical meristem morphometric and plant architectural traits enhance yield and productivity in chickpea.Plant Journal 98:864-883.

11.78 5.8 -

2. Basu U, Upadhyaya HD, Srivastava R, Daware A, Malik N, Sharma A, Bajaj D, Narnoliya L, Thakro V, Kujur A, Tripathi S, Bharadwaj C, Hegde VS, Pandey AK, Singh AK, Tyagi AK, Parida SK* (2019) ABC transporter-mediated transport of glutathione conjugates enhances seed yield and quality inchickpea. Plant Physiology 180:253-275.

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3. Basu U, Narnoliya L, Srivastava R, Sharma A, Bajaj D, Daware A, Thakro V, Malik N, Upadhyaya HD, Tripathi S, Hegde VS, Tyagi AK, Parida SK* (2019) CLAVATA signaling pathway genes modulating flowering time and flower number in chickpea.Theoretical and Applied Genetics 132:2017-2038.

9.93 3.9 -

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List of Publications NAAS Rating(2019)

InternationalImpact Factors

Number ofCitations

4. Basu U, Bajaj D, Sharma A, Malik N, Daware A, Narnoliya L, Thakro V, Upadhyaya HD, Kumar R, Tripathi S, Bharadwaj C, Tyagi AK, Parida SK* (2018) Genetic dissection of photosynthetic efficiency traits for enhancing seed yield in chickpea. Plant, Cell &Environment 42:158-173.

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5. Sharma A, Basu U, Malik N, Daware A, Thakro V, Narnoliya L, Bajaj D, Tripathi S, Hegde VS, Upadhyaya HD, Singh AK, Tyagi AK, Parida SK (2019) Genome-wide cis-regulatory signatures for modulation of agronomic traits as exemplified by drought yield index (DYI) in chickpea. Functional Integrative Genomics DOI:10.1007/s10142-019-00691-2.

9.89 3.5 -

6. Basu U, Srivastava R, Bajaj D, Thakro V, Daware A, Malik N, Upadhyaya HD, Parida SK* (2018) Genome- wide generation and genotyping of informative SNPs to scan molecular signatures for seed yield inchickpea. Scientific Reports 8:13240.

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7. Dwivedi V, Parida SK*, Chattopadhyay D (2017) A repeat length variation in myo-inositol monophosphate gene contributes to seed size trait inchickpea. Scientific Reports 7:4764.

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8. Srivastava R, Upadhyaya HD, Kumar R, Daware A, Basu U, Shimray PW, Tripathi S,Bharadwaj C, Tyagi AK and Parida SK* (2017) A Multiple QTL-Seq strategy delineates potential genomic loci governing flowering time in chickpea. Frontiers in PlantScience 8:1105.

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9. Daware AV, Srivastava R, Singh AK, Parida SK* and Tyagi AK (2017) Regional association analysis of metaQTLs delineates candidate grain size genes inrice. Frontiers in Plant Science 8:807.

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10. Upadhyaya HD, Bajaj D, Tripathi S, Bharadwaj C, Tyagi AK, Parida SK* (2017) Genetic dissection of plant growth habit in chickpea. Functional &Integrative Genomics 17:711-723.

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11. Parida SK*, Srivastava R, Bajaj D (2017) A genome- wide mQTL-seq scan identifies potential molecular signatures regulating plant height in chickpea. PlantMolecular Biology Reporter 35:273-286.

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12. Shimray PW, Bajaj D, Srivastava R, Daware A, Upadhyaya HD, Kumar R, Bharadwaj C, Tyagi AK and Parida SK* (2017) Identifying transcription factor genes associated with yield traits in chickpea. PlantMolecular Biology Reporter 35:562-574

7.84 2.3 -

13. Kujur A, Upadhyaya HD, Bajaj D, Gowda CL, Sharma S, Tyagi AK, Parida SK* (2016) Identification of candidate genes and natural allelic variants for QTLs governing plant height in chickpea. Scientific Reports6:27968.

10.12 5.6 37

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List of Publications NAAS Rating (2019)

International Impact Factors

Number of Citations

14. Srivastava R, Bajaj D, Malik A, Singh M, Parida SK* (2016) Transcriptome landscape of perennial wild Cicer microphyllum uncovers functionally relevant molecular tags regulating agronomic traits in chickpea. ScientificReports 6:33616.

10.12 5.6 33

15. Upadhyaya HD, Bajaj D, Das S, Kumar V, Gowda CLL, Sharma S, Tyagi AK, Parida SK* (2016) Genetic dissection of seed-iron and zinc concentrations inchickpea. Scientific Reports 6:24050.

10.12 5.6 30

16. Badoni S, Das S, Sayal SYK, Gopalakrishnan S, Singh AK, Rao AR, Agarwal P, Parida SK*, Tyagi AK (2016) Genome-wide generation and use of informative intron- spanning and intron-length polymorphism markers forhigh-throughput genetic analysis in rice. Scientific Reports 6:23765.

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17. Das S, Singh M, Srivastava R, Bajaj D, Saxena MS, Rana JC, Bansal KC, Tyagi AK, Parida SK* (2016) mQTL-seq delineates functionally relevant candidategene harbouring a major QTL regulating pod number in chickpea. DNA Research 23:53-65.

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18. Daware A, Das S, Srivastava R, Badoni S, Singh AK, Agarwal P, Parida SK*, Tyagi AK (2016) An efficient strategy combining SSR markers-and advanced QTL- seq-driven QTL mapping unravels candidate genesregulating grain weight in rice. Frontiers in Plant Science 7: 1535.

9.68 4.5 2

19. Srivastava R, Singh M, Bajaj D, Parida SK* (2016) A high-resolution InDel (Insertion-Deletion) markers- anchored consensus genetic map identifies major QTLs governing pod number and seed yield inchickpea. Frontiers in Plant Science 7:1362.

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20. Upadhyaya HD, Bajaj D, Narnoliya L, Das S, Kumar V, Gowda CLL, Sharma S, Tyagi AK and Parida SK* (2016) Genome-Wide Scans for Delineation of Candidate Genes Regulating Seed-Protein Content inChickpea. Frontier in Plant Science 7:302.

9.68 4.5 2

21. Bajaj D, Srivastava R, Tripathi S, Bharadwaj C, Upadhyaya HD, Tyagi AK, Parida SK* (2016) EcoTILLING-based association mapping efficiently delineates functionally relevant natural allelic variantsof candidate genes governing agronomic traits in chickpea. Frontiers in Plant Science 7:450.

9.68 4.5 3

22. Bajaj D, Upadhyaya HD, Das S, Kumar V, Gowda CL, Sharma S, Tyagi AK, Parida SK* (2016) Identification of candidate genes for dissecting complex branchnumber trait in chickpea. Plant Science 245:61-70.

9.71 3.9 2

23. Srivastava R, Bajaj D, Sayal YK, Meher PK, Upadhyaya HD, Kumar R, Tripathi S, Bharadwaj C, Rao AR, Parida SK* (2016) Genome-wide development and deployment of informative intron- spanning and intron-length polymorphism markers for genomics-assisted breeding applications in chickpea.Plant Science 252:374-387.

9.71 3.9 4

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Number of Citations

24. Das S, Bajaj D, Krishnan SG, Singh AK, Parida SK* (2016) Revisiting the decoded genomes to promptly reveal their genomic perspectives. Current Science112:279-294.

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25. Bajaj D, Saxena MS, Kujur A, Das S, Badoni S, Tripathi S, Upadhyaya HD, Gowda CLL, Sharma S, Singh S, Tyagi AK, Parida SK* (2015) Genome-wide conserved non-coding microsatellite (CNMS) marker-based integrative genetical genomics for quantitative dissection of seed weight in chickpea. Journal ofExperimental Botany 66:1271-1290

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26. Das S, Upadhyaya HD, Srivastava R, Bajaj D, Gowda CLL, Sharma S, Singh S, Tyagi AK, Parida SK* (2015) Genome-wide insertion-deletion (InDel) marker discovery and genotyping for genomics-assisted breeding applications in chickpea. DNA Research22:377-386.

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27. Das S, Upadhyaya HD, Bajaj D, Kujur A, Badoni S, Laxmi, Kumar V, Tripathi S, Gowda CLL, Sharma S, Singh S, Tyagi AK, Parida SK* (2015) Deploying QTL- seq for rapid delineation of a potential candidate gene underlying major trait-associated QTL in chickpea.DNA Research 22:193-203.

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28. Bajaj D, Upadhyaya H, Khan Y, Das S, Badoni S, Shree T, Kumar V, Tripathi S, Gowda CLL, Singh S, Sharma S, Tyagi AK, Chattopadhyay D, Parida SK* (2015) A combinatorial approach of comprehensive QTL-based comparative genome mapping and transcript profiling identified a seed weight-regulating candidate gene in chickpea. Scientific Reports5:9264.

10.12 5.6 20

29. Kujur A, Upadhyaya HD, Shree T, Bajaj D, Das S, Saxena M, Badoni S, Kumar V, Tripathi S, Gowda CLL, Sharma S, Singh S, Tyagi AK, Parida SK* (2015) Ultra- high density intra-specific genetic linkage maps accelerate identification of functionally relevant molecular tags governing important agronomic traits inchickpea. Scientific Reports 5:9468.

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30. Kujur A, Bajaj D, Upadhyaya HD, Das S, Ranjan R, Shree T, Saxena MS, Badoni S, Kumar V, Tripathi S, Gowda CLL, Sharma S, Singh S, Tyagi AK, Parida SK* (2015) A genome-wide SNP scan accelerates trait- regulatory genomic loci identification in chickpea.Scientific Reports 5:11166.

10.12 5.6 45

31. Bajaj D, Das S, Badoni S, Kumar V, Singh M, Bansal KC, Tyagi AK, Parida SK* (2015) Genome-wide high- throughput SNP discovery and genotyping for understanding natural (functional) allelic diversity and domestication patterns in wild chickpea. ScientificReports 5:11627.

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Number of Citations

32. Bajaj D, Das S, Upadhyaya HD, Ranjan R, Badoni S, Kumar V, Tripathi S, Gowda CLL, Sharma S, Singh S, Tyagi AK and Parida SK* (2015) A genome-wide combinatorial strategy dissects complex genetic architecture of seed coat color in chickpea. Frontiersin Plant Science 6:979.

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33. Kujur A, Bajaj D, Saxena MS, Upadhyaya HD, Das S, Ranjan R, Shree T, Saxena MS, Badoni S, Kumar V, Tripathi S, Gowda CLL, Sharma S, Singh S, Tyagi AK, Jain M, Parida SK* (2015) Employing genome-wide SNP discovery and genotyping strategy to extrapolate the natural allelic diversity and domestication patternsin chickpea. Frontiers in Plant Science 6:162.

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34. Upadhyaya HD, Bajaj D, Das S, Saxena MS, Badoni S, Kumar V, Tripathi S, Sharma S, Tyagi AK, Parida SK* (2015) A genome-scale integrated approach aids in genetic dissection of complex flowering time trait inchickpea. Plant Molecular Biology 89:403-420.

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35. Bajaj D, Das S, Parida SK* (2015) CNMS: The preferred genic markers for comparative genomic, molecular phylogenetic, functional genetic diversity and differential gene regulatory expression analyses inchickpea. Journal of Biosciences 40:579-592

7.53 2.1 8

36. Saxena MS, Bajaj D, Das S, Kujur A, Kumar V, Singh M, Bansal KC, Tyagi AK, Parida SK* (2014) An integrated genomic approach for rapid delineation of candidate genes regulating agro-morphological traits inchickpea. DNA Research 21:695-710.

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37. Saxena MS, Bajaj D, Kujur A, Das S, Badoni S, Kumar V, Singh M, Bansal KC, Tyagi AK, Parida SK* (2014) Natural allelic diversity, genetic structure and linkage disequilibrium pattern in wild chickpea. PLOS ONE9:e107484.

8.77 3.8


38. Kujur A, Bajaj D, Saxena MS, Tripathi S, Upadhyaya HD, Gowda CLL, Singh S, Tyagi AK, Jain M, Parida SK* (2014) An efficient and cost-effective approach for genic microsatellite marker-based large-scale trait association mapping: identification of candidate genes for seed weight in chickpea. Molecular Breeding32:241-265.

8.08 3.365(Popular article)

39. Kujur A, Bajaj D, Saxena MS, Tripathi S, Upadhyaya HD, Gowda CLL, Singh S, Jain M, Tyagi AK, Parida SK* (2013) Functionally relevant microsatellite markers from chickpea transcription factor genes for efficient genotyping applications and trait association mapping.DNA Research 20:355-374.

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40. Kujur A, Saxena MS, Bajaj D, Laxmi and Parida SK* (2013) Integrated genomics and molecular breeding approaches for dissecting the complex quantitative traits in crop plants. Journal of Biosciences 38:1-17.

7.53 2.1 7

Total 395.32 182.2 1077

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As First Authors (10 Publications)

List of Publications NA9.68ASRating (2019)


Number of Citations

1. Agarwal P, Parida SK, Raghuvanshi S, Kapoor S, Khurana P, Khurana JP and Tyagi AK (2016) Rice improvement through genome-based functional analysis and molecular breeding in India. Rice 9:1 (As Joint FirstAuthor)

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2. Parida SK, Kalia S, Pandit A, Nayak P, Singh RK, Gaikwad K, Srivastava PS, Singh NK, Mohapatra T (2016) Single nucleotide polymorphism in sugar pathway and disease resistance genes in sugarcane. Plant CellReports 35:1629-1653.

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3. Parida SK, Verma M, Yadav SK, Ambawat S, Das S, Garg R and Jain M (2015) Development of genome-wide informative simple sequence repeat markers for large- scale genotyping applications in chickpea and development of web resource. Frontiers in PlantScience 6:645.

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4. Parida SK, Mukerji M, Singh AK, Singh NK and Mohapatra T (2012) SNPs in stress responsive rice genes: validation and genotyping using Illumina GoldenGate assay. BMC Genomics 13:426.

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85Highly accessed (~5000times)

5. Parida SK, Pandit A, Gaikwad K, Sharma TR, Srivastava PS, Singh NK and Mohapatra T (2010). Functionally relevant microsatellites in sugarcane unigenes. BMC Plant Biology 10:251.

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6. Ngangkham Umakanta, Parida SK, Dey SK, Raj Kumar KA, Singh AK, Singh NK and Mohapatra T (2010). Genic markers for WA cytoplasm based male sterility and its fertility restoration in rice. Molecular Breeding 26:275-292 (As Joint First Author).

8.08 3.3 50

7. Parida SK, Yadava DK and Mohapatra T (2010). Microsatellites in Brassica unigenes: Relative abundance, marker design and use in comparative physical mapping and genome analysis. Genome 53:55-67.

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8. Parida SK, Dalal V, Singh NK and Mohapatra T (2009) Genic non-coding microsatellites in the rice genome: characterization, marker design and use in assessing genetic and evolutionary relationships amongdomesticated groups. BMC Genomics 10:140.

9.73 4.4


9. Parida SK, Kalia SK, Kaul S, Dalal V, Hemaprabha G, Selvi A, Pandit A, Singh A, Gaikwad K, Sharma TR, Srivastava PS, Singh NK and Mohapatra T (2009) Informative genomic microsatellite markers for efficient genotyping applications in sugarcane. Theoretical andApplied Genetics 118:327-338.

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180Most viewed and Highly accessed

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List of Publications NA9.68ASRating (2019)


Number of Citations

10. Parida SK, Raj Kumar KA, Dalal V, Singh NK and Mohapatra T (2006) Unigene derived microsatellite markers for the cereal genomes. Theoretical and Applied Genetics 112:808-817.

9.93 3.9

228Most viewed and Highlyaccessed

Total 92.93 37.2 1044

As Co-authors (> 50% contributions) (40 Publications)


InternationalImpact Factors

Number of Citations

1. Malik N, Ranjan R, Parida SK, Agarwal P, Tyagi AK (2019) Mediator subunit OsMED14_1 plays an important role in rice development. Plant JournalDOI:10.1111/tpj.14605.

11.78 5.8 -

2. Das S, Parida SK, Agarwal P, Tyagi AK (2019)Transcription factor OsNF-YB9 regulates reproductive growth and development in rice. Planta 250:1849-1865.

9.25 3.06 -

3. Dwivedi N, Maji S, Waseem M, Thakur P, Kumar V, Parida SK, Thakur JK (2019) The Mediator subunit OsMED15a is a transcriptional co-regulator of seed size/weight-modulating genes in rice. Biochim BiophysActa Gene Regul Mech. 1862:194432.

11.18 4.9

4. Pandey S, Kumari A, Shree M, Kumar V, Singh P, Bharadwaj C, Loake GJ, Parida SK, Masakapalli SK, Gupta KJ (2019) Nitric oxide accelerates germination via the mregulation of respiration in chickpea. Journal ofExperimental Botany DOI:10.1093/jxb/erz185.

11.35 6.1 -

5. Jha UC, Bohra A, Jha R, Parida SK (2019) Salinity stress response and 'omics' approaches for improving salinity stress tolerance in major grain legumes. PlantCell Reports 38:255-277.

8.99 3.0 -

6. Daware A, Parida SK, Tyagi AK (2019) Integrated Genomic Strategies for Cereal Genetic Enhancement: Combining QTL and Association Mapping. Methods Mol Biol. 2072:15-25.

-

7. Ngangkham U, Parida SK, Singh AK, Mohapatra T (2019) Differential RNA editing of mitochondrial genes in WA-Cytoplasmic based male sterile line Pusa6A, its maintainer and restorer lines of rice hybrids. RiceScience 4:26.

7.52 1.5 -

8. Kumar K, Purayannur S, Kaladhar VC, Parida SK and Verma PK (2019) mQTL-seq and classical mapping implicates the role of an AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) family gene in Ascochyta blight resistance of chickpea. Plant Cell & Environment41:2128-2140.

11.41 6.2 -

31



Number of Citations

9. Jha UC, Bohra A, Nayyar H, Rani A, Devi P, Saabale PR, Parida SK (2019) Breeding and Genomics Approaches for Improving Productivity Gains in Chickpea Under Changing Climate. In: Kole C. (eds) Genomic Designing of Climate-Smart Pulse Crops. Springer,Cham, pp-135-164.

- - -

10. Jha UC, Jha R, Bohra A, Parida SK, Kole PC, Thakro V, Singh D and Singh NP (2018) Population structure and association analysis of heat stress relevant traits inchickpea (Cicer arietinum L.). 3 Biotech 8:43.

7.5 1.4 -

11. Ranjan R, Khurana R, Malik N, Badoni S, Parida SK, Kapoor S, Tyagi AK (2017) bHLH142 regulates various metabolic pathway-related genes to affect pollen development and anther dehiscence in rice. ScientificReports 7:43397.

10.12 5.6 -

12. Malik N, Dwivedi N, Singh AK, Parida SK, Agarwal P, Thakur JK, Tyagi AK (2016) An integrated genomic strategy delineates candidate mediator genes regulating grain size and weight in rice. Scientific Reports6:23253.

10.12 5.6 26

13. Bhadouria J, Singh AP, Mehra P, Verma L, Srivastawa R, Parida SK, Giri J (2017) Identification of purple acid phosphatases in chickpea and potential roles of CaPAP7 in seed phytate accumulation. Scientific Reports7:11012.

10.12 5.6 5

14. Jha UC, Bohra A, Parida SK, Jha R (2017) Integrated “omics” approaches to sustain global productivity of major grain legumes under heat stress. Plant Breeding136:437-459

7.39 1.2 -

15. Gupta S, Nawaz K, Parween S, Roy R, Sahu K, Pole AK, Khandal H, Srivastava R, Parida SK, Chattopadhyay D (2016) Draft genome sequence of Cicer reticulatum L., the wild progenitor of chickpea provides a resource foragronomic trait improvement. DNA Research 24:1-10.

11.41 5.5 13

16. Kumar V, Singh A, Amitha Mithra SV, Krishnamurthy SL, Parida SK, Jain S, Tiwari KK, Kumar P, Rao AR, Sharma SK, Khurana JP, Singh NK, Mohapatra T (2015) Genome-wide association mapping of salinity tolerancein rice (Oryza sativa). DNA Research 22:133-145.

11.41 5.5 45

17. Parween S, Nawaz K, Roy R, Pole AK, Venkata Suresh B, Misra G, Jain M, Yadav G, Parida SK, Tyagi AK, Bhatia S, Chattopadhyay D (2015) An advanced draft genome assembly of a desi type chickpea (Cicerarietinum L.). Scientific Reports 5:12806.

10.12 5.6 24

18. Singh AP, Pandey BK, Deveshwar P, Narnoliya L, Parida SK, Giri J (2015) JAZ repressors: potential involvement in nutrients deficiency response in rice andchickpea. Frontier in Plant Science 6:975.

9.68 4.5 15

32



Number of Citations

19. Khajuria YP, Saxena MS, Gaur R, Chattopadhyay D, Jain M, Parida SK, Bhatia S (2015) Development and integration of genome-wide polymorphic microsatellite markers onto a reference linkage map for constructing a high-density genetic map of chickpea. PLOS ONE10:e0125583.

8.77 3.8 19

20. Agarwal P, Parida SK, Mahto A, Das S, Mathew IE, Malik N, Tyagi AK (2014) Expanding frontiers in plant transcriptomics in aid of functional genomics and molecular breeding. Biotechnology Journal 9:1480-1492.

9.51 3.7 24

21. Mishra AK, Muthamilarasan M, Khan Y, Parida SK, Prasad M (2014) Genome-wide investigation and expression analyses of WD40 protein family in the model plant foxtail millet (Setaria italica L.). PLOS ONE9:e86852.

8.77 3.8 30

22. Gupta S, Kumari K, Muthamilarasan M, Parida SK and Prasad M (2014) Population structure and association mapping of yield contributing agronomic traits in foxtailmillet. Plant Cell Reports 33:881-893.

8.99 3.3 23

23. Tiwari KK, Singh A, Pattnaik S, Sandhu M, Kaur S, Jain S, Tiwari S, Mehrotra S, Anumalla M, Samal R, Bhardwaj J, Dubey N, Sahu V, Kharshing GA, Zeliang PK, Sreenivasan K, Kumar P, Parida SK, Mithra SVA, Rai V, Tyagi W, Agarwal PK, Rao AK, Pattanayak A, Chandel G, Singh AK, Bisht IS, Bhat KV, Rao GJN, Khurana JP, Singh NK, Mohapatra T (2014) Identification of a diverse mini-core panel of Indian rice germplasm based on genotyping using microsatellite markers. Plant Breeding134:164-171.

7.39 1.2 14

24. Muthamilarasan M, Parida SK, Prasad M (2014) Advances in wheat genomics and its potential in ensuring food security in the scenario of climate change. Proceedings of the Indian National Science Academy80:325-331.

5.89 - 15

25. Pandey G, Misra G, Kumari K, Gupta S, Parida SK, Chattopadhyay D and Prasad M (2013) Genome-wide development and use of microsatellite markers for large- scale genotyping applications in foxtail millet [Setariaitalica (L.)]. DNA Research 20:197-207.

11.41 5.5 70

26. Muthamilarasan M, Venkata SB, Pandey G, Kumari K, Parida SK, Prasad M (2014) Development of 5123 Intron length polymorphic (ILP) markers for large-scale genotyping applications in foxtail millet. DNA Research21:41-52.

11.41 5.5 42

33


International ImpactFactors

Number of Citations

27. Puranik S, Sahu PP, Mandal SN, Parida SK and Prasad M (2014) Comprehensive genome-wide survey, genomic constitution and expression profiling of the NAC transcription factor family in foxtail millet [Setaria italica(L.)]. PLOS ONE 8:e64594.

8.77 3.8 31

28. Kumari K, Muthamilarasan M, Misra G, Gupta S, Subramanian A, Parida SK, Chattopadhyay D and Prasad M (2014) Development of eSSR-markers in Setaria italica and their applicability in studying genetic diversity, cross-transferability and comparative mappingin millet and non-millet species. PLOS ONE 8:e67742.

8.77 3.8 36

29. Thakur JK, Agarwal P, Parida SK, Bajaj D and Pasrija R (2014) Sequence and expression analyses of KIX domain proteins suggest their importance in seed development and determination of seed size in rice, and genome stability in Arabidopsis. Molecular Geneticsand Genomics 288:329-346.

8.73 2.8 20

30. Das B, Sengupta S, Parida SK, Roy B, Ghosh M, Prasad M, Ghose TK (2014) Genetic diversity and population structure of rice landraces from Eastern andNorth Eastern States of India. BMC Genetics 14:71.

8.47 2.8 41

31. Dixit N, Dokku P, Amitha Mithra SV, Parida SK, Singh AK, Singh NK, Mohapatra T (2014) Haplotype structure in grain weight gene GW2 and its association with graincharacteristics in rice. Euphytica 192:55-61.

7.55 1.7 21

32. Das A and Parida SK (2014) Advances in biotechnological applications in three important foodlegumes. Plant Biotechnology Reports 8:83-99.

7.30 1.1 15

33. Jhanwar S, Priya P, Garg R, Parida SK, Tyagi AK and Jain M (2012) Transcriptome sequencing of wild chickpea as a rich resource for marker development.Plant Biotechnology Journal 10:690-702.

12.31 6.3 85

34. Agarwal G, Jhanwar S, Priya P, Singh VK, Saxena MS, Parida SK, Garg R, Tyagi AK, Jain M (2012) Comparative analysis of kabuli chickpea transcriptome with desi and wild chickpea provides a rich resource for development of functional markers. PLOS ONE7:e52443.

8.77 3.8 80

35. Bharathi LK, Parida SK, Munshi AD, Behera TK, Raman KV and Mohapatra T (2011) Molecular diversity and phylogeny of Momordica spp. of Indian occurrence.Genetic Resources and Crop Evolution 59:937-948.

7.13 1.6 47

36. Naik PK, Alam MA, Singh H, Goyal V, Parida SK, Kalia S and Mohapatra T (2010) Assessment of genetic diversity through RAPD, ISSR and AFLP markers in Podophyllum hexandrum: a medicinal herb from the Northwestern Himalayan region. Physiology andMolecular Biology of Plants 16:1-13.

7.15 - 34

34


International ImpactFactors

Number of Citations

37. Yadava, DK, Parida SK, Dwivedi VK, Varshney A, Ghazi IA, Sujata V and Mohapatra T (2009). Cross- transferability and polymorphic potential of genomic STMS markers of Brassica species. Journal of Plant Biochemistry and Biotechnology 18:29-36.

6.77 1.4 28

38. Sonah H, Desmukh R, Parida SK and Kotasthane A (2009) Morphological and genetic variation among different isolates of Magnaporthe grisea collected from Chhattisgarh. Indian Phytopathology 62:469-477.

5.90 - 20

39. Koundal V, Parida SK, Yadava DK, Ali A, Koundal KR and Mohapatra T (2008). Evaluation of microsatellite markers for genome mapping in Indian mustard (Brassica juncea L.). Journal of Plant Biochemistry and Biotechnology 17:69-72.

6.77 1.4 23

40. Verma VK, Behera TK, Munshi AD, Parida SK and Mohapatra T (2007). Genetic diversity of ash gourd [(Benincasa hispida (Thunb.) Cogn.] inbred lines based on RAPD and ISSR markers and their hybrid performance. Scientia Horticulturae 113:231-237.

7.76 1.4 65

Total 291.09 117.8 1246

Cumulative impact factor of publications: 337.2

Published more than 85 articles in journals of international-repute (337.2 impact-factor with 32 H- index and 3345 Citations) in the area of molecular genetics and genomics-assisted breeding for crop improvement.

35

BRIEF OVERVIEW OF PUBLISHED RESEARCH PAPERSCharacteristics Corresponding

AuthorFirst Author Co-Author with

> 50% research contribution

Total

Published in Referred Journals 40 10 40 90Total (Average) NAAS ImpactFactors

395.32 (9.9) 92.93 (9.3) 291.09 (7.3) 779.34 (8.7)

Total (Average) InternationalImpact Factors

182.2 (4.6) 37.2 (3.7) 117.8 (3.3) 337.2 (4.0)

Total (Average) Citations 1077 (29.9) 1044 (104.4) 1246 (34.6) 3367 (40.0)Published Research Paperswith ≥ 10 Citations

30 10 28 68

Published Research Paperswith Maximum Citations

110 228 85 -

Short Communications 2 - 1 3Book Chapters/Proceedings 1 1 1 3Scientific Reviews 2 1 2 5

Complete list of publications are accessible at http://www.nipgr.res.in/research/dr_sparida.php and http://scholar.google.co.in/citations?user=K_CDT6IAAAAJ&hl=en.

ORCID ID: https://orcid.org/0000-0001-7843-3031

H-index: 32

36

21 Citation for twenty most important publications based on ISI Science Citation Index

[Attached First-page Reprints of 20 Most Important Publications in ANNEXURE V]



Number of Citations

Narnoliya L, Basu U, Bajaj D, Malik N, Thakro V, Daware A, Sharma A, Tripathi S, Hegde VS, Upadhyaya HD, Singh AK, Tyagi AK, Parida SK* (2019) Transcriptional signatures modulating shoot apical meristem morphometric and plant architectural traits enhance yieldand productivity in chickpea. Plant Journal 98:864-883.

11.78 5.8 -

Basu U, Upadhyaya HD, Srivastava R, Daware A, Malik N, Sharma A, Bajaj D, Narnoliya L, Thakro V, Kujur A, Tripathi S, Bharadwaj C, Hegde VS, Pandey AK, Singh AK, Tyagi AK, Parida SK* (2019) ABC transporter- mediated transport of glutathione conjugates enhances seed yield and quality in chickpea. Plant Physiology180:253-275.

11.95 5.9 -

Basu U, Narnoliya L, Srivastava R, Sharma A, Bajaj D, Daware A, Thakro V, Malik N, Upadhyaya HD, Tripathi S, Hegde VS, Tyagi AK, Parida SK* (2019) CLAVATA signaling pathway genes modulating flowering time and flower number in chickpea. Theoretical and AppliedGenetics 132:2017-2038.

9.93 3.9 -

Basu U, Bajaj D, Sharma A, Malik N, Daware A, Narnoliya L, Thakro V, Upadhyaya HD, Kumar R, Tripathi S, Bharadwaj C, Tyagi AK, Parida SK* (2018) Genetic dissection of photosynthetic efficiency traits for enhancing seed yield in chickpea. Plant, Cell & Environment42:158-173.

11.41 6.2 -

Sharma A, Basu U, Malik N, Daware A, Thakro V, Narnoliya L, Bajaj D, Tripathi S, Hegde VS, Upadhyaya HD, Singh AK, Tyagi AK, Parida SK (2019) Genome-wide cis-regulatory signatures for modulation of agronomic traits as exemplified by drought yield index (DYI) in chickpea. Functional Integrative GenomicsDOI:10.1007/s10142-019-00691-2.

9.89 3.5 -

Upadhyaya HD, Bajaj D, Tripathi S, Bharadwaj C, Tyagi AK, Parida SK* (2017) Genetic dissection of plant growth habit in chickpea. Functional & Integrative Genomics17:711-723.

9.89 2.3 -

Upadhyaya HD, Bajaj D, Das S, Kumar V, Gowda CLL, Sharma S, Tyagi AK, Parida SK* (2016) Genetic dissection of seed-iron and zinc concentrations in chickpea. ScientificReports 6:24050.

10.12 5.6 30

Das S, Singh M, Srivastava R, Bajaj D, Saxena MS, Rana JC, Bansal KC, Tyagi AK, Parida SK* (2016) mQTL-seq delineates functionally relevant candidate gene harbouring a major QTL regulating pod number in chickpea. DNAResearch 23:53-65.

11.41 5.5 57

Bajaj D, Upadhyaya HD, Das S, Kumar V, Gowda CL, Sharma S, Tyagi AK, Parida SK* (2016) Identification of candidate genes for dissecting complex branch number traitin chickpea. Plant Science 245:61-70.

9.71 3.9 2

37



Number of Citations

Bajaj D, Saxena MS, Kujur A, Das S, Badoni S, Tripathi S, Upadhyaya HD, Gowda CLL, Sharma S, Singh S, Tyagi AK, Parida SK* (2015) Genome-wide conserved non-coding microsatellite (CNMS) marker-based integrative genetical genomics for quantitative dissection of seed weight inchickpea. Journal of Experimental Botany 66:1271-1290

11.35 6.1


Das S, Upadhyaya HD, Srivastava R, Bajaj D, Gowda CLL, Sharma S, Singh S, Tyagi AK, Parida SK* (2015) Genome- wide insertion-deletion (InDel) marker discovery and genotyping for genomics-assisted breeding applications inchickpea. DNA Research 22:377-386.

11.41 5.5 38

Das S, Upadhyaya HD, Bajaj D, Kujur A, Badoni S, Laxmi, Kumar V, Tripathi S, Gowda CLL, Sharma S, Singh S, Tyagi AK, Parida SK* (2015) Deploying QTL-seq for rapid delineation of a potential candidate gene underlying major trait-associated QTL in chickpea. DNA Research 22:193-203.

11.41 5.5 49

Kujur A, Upadhyaya HD, Shree T, Bajaj D, Das S, Saxena M, Badoni S, Kumar V, Tripathi S, Gowda CLL, Sharma S, Singh S, Tyagi AK, Parida SK* (2015) Ultra-high density intra-specific genetic linkage maps accelerate identification of functionally relevant molecular tags governing importantagronomic traits in chickpea. Scientific Reports 5:9468.

10.12 5.6 61

Kujur A, Bajaj D, Upadhyaya HD, Das S, Ranjan R, Shree T, Saxena MS, Badoni S, Kumar V, Tripathi S, Gowda CLL, Sharma S, Singh S, Tyagi AK, Parida SK* (2015) A genome-wide SNP scan accelerates trait-regulatory genomic loci identification in chickpea. Scientific Reports5:11166.

10.12 5.6 45

Bajaj D, Das S, Badoni S, Kumar V, Singh M, Bansal KC, Tyagi AK, Parida SK* (2015) Genome-wide high- throughput SNP discovery and genotyping for understanding natural (functional) allelic diversity and domestication patterns in wild chickpea. Scientific Reports5:11627.

10.12 5.6 48

Bajaj D, Das S, Upadhyaya HD, Ranjan R, Badoni S, Kumar V, Tripathi S, Gowda CLL, Sharma S, Singh S, Tyagi AK and Parida SK* (2015) A genome-wide combinatorial strategy dissects complex genetic architecture of seed coatcolor in chickpea. Frontiers in Plant Science 6:979.

9.68 4.5 4

Kujur A, Bajaj D, Saxena MS, Upadhyaya HD, Das S, Ranjan R, Shree T, Saxena MS, Badoni S, Kumar V, Tripathi S, Gowda CLL, Sharma S, Singh S, Tyagi AK, Jain M, Parida SK* (2015) Employing genome-wide SNP discovery and genotyping strategy to extrapolate the natural allelic diversity and domestication patterns in chickpea.Frontiers in Plant Science 6:162.

9.68 4.5 91

38



Number of Citations

Upadhyaya HD, Bajaj D, Das S, Saxena MS, Badoni S, Kumar V, Tripathi S, Sharma S, Tyagi AK, Parida SK* (2015) A genome-scale integrated approach aids in genetic dissection of complex flowering time trait in chickpea. PlantMolecular Biology 89:403-420.

9.54 4.3 56

Saxena MS, Bajaj D, Das S, Kujur A, Kumar V, Singh M, Bansal KC, Tyagi AK, Parida SK* (2014) An integrated genomic approach for rapid delineation of candidate genes regulating agro-morphological traits in chickpea. DNAResearch 21:695-710.

11.41 5.5


Kujur A, Bajaj D, Saxena MS, Tripathi S, Upadhyaya HD, Gowda CLL, Singh S, Tyagi AK, Jain M, Parida SK* (2014) An efficient and cost-effective approach for genic microsatellite marker-based large-scale trait association mapping: identification of candidate genes for seed weightin chickpea. Molecular Breeding 32:241-265.

8.08 3.365(Popular article)

Kujur A, Bajaj D, Saxena MS, Tripathi S, Upadhyaya HD, Gowda CLL, Singh S, Jain M, Tyagi AK, Parida SK* (2013) Functionally relevant microsatellite markers from chickpea transcription factor genes for efficient genotyping applications and trait association mapping. DNA Research20:355-374.

11.41 5.5

95(Highly accessed: 1500times)

Parida SK, Kalia S, Pandit A, Nayak P, Singh RK, Gaikwad K, Srivastava PS, Singh NK, Mohapatra T (2016) Single nucleotide polymorphism in sugar pathway and disease resistance genes in sugarcane. Plant Cell Reports35:1629-1653.

8.99 3.3 2

Parida SK, Mukerji M, Singh AK, Singh NK and Mohapatra T (2012) SNPs in stress responsive rice genes: validation and genotyping using Illumina GoldenGate assay. BMC Genomics 13:426.

9.73 4.4


Parida SK, Pandit A, Gaikwad K, Sharma TR, Srivastava PS, Singh NK and Mohapatra T (2010). Functionally relevant microsatellites in sugarcane unigenes. BMC Plant Biology 10:251.

9.93 4.4


Ngangkham Umakanta, Parida SK, Dey SK, Raj Kumar KA, Singh AK, Singh NK and Mohapatra T (2010). Genic markers for WA cytoplasm based male sterility and its fertility restoration in rice. Molecular Breeding 26:275-292(As Joint First Author).

8.08 3.3 50

Parida SK, Dalal V, Singh NK and Mohapatra T (2009) Genic non-coding microsatellites in the rice genome: characterization, marker design and use in assessing genetic and evolutionary relationships among domesticatedgroups. BMC Genomics 10:140.

9.73 4.4


39



Number of Citations

Parida SK, Kalia SK, Kaul S, Dalal V, Hemaprabha G, Selvi A, Pandit A, Singh A, Gaikwad K, Sharma TR, Srivastava PS, Singh NK and Mohapatra T (2009) Informative genomic microsatellite markers for efficient genotyping applications in sugarcane. Theoretical and Applied Genetics 118:327-338.

9.93 3.9


Parida SK, Raj Kumar KA, Dalal V, Singh NK and Mohapatra T (2006) Unigene derived microsatellite markers for the cereal genomes. Theoretical and Applied Genetics 112:808-817. 9.93 3.9


22 Patent obtained, if any. Number of Indian Patents: Two “An ABC transporter gene modulating glutathione conjugates transport and utilization thereof

in enhancing seed yield and quality in chickpea” [Provisional Applications NO.: 5467IN004; LexOrbis, NewDelhi]. (Under Process).

“A bHLH transcription factor modulating Abscisic Acid signalling and utilization thereof for enhancing yield under drought stress in chickpea” [Provisional Applications NO.: 5467IN005; LexOrbis, NewDelhi]. (Under Process).

23 Whether this research work has been submitted for any other award/recognition? If so, what was the outcome?

MEMBERSHIP/ FELLOWSHIP IN ACADEMIES/ SOCIETIES/ PROFESSIONAL BODIES

INTERNATIONAL

NAME CONFERRING AGENCY YEAR NATURE PURPOSE

Selected a Member to the Genetics Society of UK

Genetics Society of UK 2014 Citation For significant contribution in plant genomicsand molecular breeding

Selected a Member to the Crop Science Society of America

Crop Science Society of America 2016 Citation For significant contribution in plant genomicsand molecular breeding

40


Editors (International Journals)

Scientific Reports (Nature Publishing Group)

BMC Genomics BMC Plant Biology PLOS ONE Frontiers in Plant Science Plant Molecular Biology Reporter Molecular Breeding Journal of Plant Biochemistry

and Biotechnology Journal of Plant Genomics Journal of Genetics and Genomic

Research Express Biology

2014 –Till date

Plant Biology/ plant genomics/ plant genetics and genomics

For significant contribution in plant genomicsand molecular breeding

Associate Topic Editor of Frontiers inPlant Science

A Special issue on Research Topic “Plant Translational Research in Genomics Era”

2016-2017

- For significant contribution in plant translationalgenomics

Associate Topic Editorof Frontiers in PLOS ONE

A Special issue on Research Topic “Future Crops”

2019-2020

- For significant contribution inplant translational genomics

Reviewers of International Journals

Nature Genetics, Nature Plant, Molecular Plant, Nature Biotechnology, PLoS Genetics, Genome Biology, Nucleic Acids Research, Bioinformatics, Planta, Plant Cell & Physiology, Plant Molecular Biology, Molecular Biology Reports, Journal of Plant Biochemistry and Biotechnology, Euphytica, Theoretical and Applied Genetics, Molecular Breeding, Genetic Resources and Crop Evolution, Molecular Genetics and Genomics, Functional & Integrative Genomics, BMC Plant Biology, BMC Genetics, BMC Genomics, Plant Molecular Biology Reporter, Plant Molecular Biology, Molecular Biotechnology, Crop Science, The Plant Genome, Plant Journal, Plant Physiology, Plant Science, Frontiers in Plant Science, Frontiers in Genetics, Frontiers in Bioscience, Journal of Heredity, Heredity, Plant Cell Reports, Journal of Genetics, Journal of Biosciences, Current Science, PLOS ONE, Scientific Reports, Genetics, DNA Research, PlantBiotechnology Journal etc.

2014onwards

- For significant contribution in plant genetics, genomics and molecular breeding

41

NATIONAL


NASI-Fellow National Academy of Sciences, India (NASI)

2018 Fellow For significant contribution in crop improvement

NAAS-Fellow National Academy of Agricultural Sciences (NAAS)

2019 Fellow For significant contribution in plant genomicsand molecular breeding

NAAS- National Academy of Agricultural 2016- Citation For significantAssociate Sciences (NAAS), New Delhi. 2020 contribution inFellow plant

improvement

Expert member to develop DNAFingerprinting protocol of rice and chickpea

Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resource (NBPGR)

2018 ICAR- NBPGR

For significant contribution in developing informative molecular markers

and molecular barcodes forefficient DNA Fingerprinting

Reviewers of R&D projects

Submitted by scientists of different research institutes and universities for possible funding with DBT, DST & ICAR

2015onward s

DBT DST- SERB

& Plant Genomics, Genetics and Molecular Breeding (Genomics- assisted breeding)

Member of DBTBrainstorming Sessions tofinalize theSpecial R&D Project Proposal Calls

Department of Biotechnology (DBT), Ministry of Science and Technology, Govt. of India, New Delhi

2016onward s

DBT “Accelerated domestication of underutilized crops”“Nutritional genetic enhancement of major food crops in the interface of agriculture”

“DBT-NIPGR PlantGenomics and Genotyping Facilities”

42


Mentor and an expert member in INSPIRE(Innovation in science Pursuit for Inspired Research) program

Department of Science and Technology (DST), Govt. of India, New Delhi

2011 DST To communicate the youth of the country theexcitements of creative pursuit of science and attract young talents and students (agebetween 10-32years) to the study of science at an early age

Life member of Indian Science Congress Association(ISCA)

Indian Science Congress Association (ISCA), Kolkata

2015 ISCA For significant contribution in plant genomicsand molecularbreeding

Life member of Indian Society for Plant Biochemistry andBiotechnology

Plant Biochemistry and Biotechnology

2015 PBB For significant contribution in plant genomicsand molecular breeding

Life member of The Indian Society of Genetics andPlant Breeding

Indian Society of Genetics and Plant Breeding

2015 ISGPB For significant contribution in plant genomicsand molecularbreeding

NASI–Reliance Industries Platinum Jubilee Awards

National Academy of Sciences, India (NASI)

2019 Cash award of Rs.3,00,000/-and aCitation

Application Oriented Innovations Covering BiologicalSciences

NASI-SCOPUSYoung Scientist Award in AgricultureScience

National Academy of Sciences India (NASI), Allahabad and ELSEVIER

2015 Cash award of Rs.75,000/-and aCitation

For significant contribution in agricultural science

NAAS Young Scientist Award in Plant Improvement

National Academy of Agricultural Sciences (NAAS)

2013-2014

Cash award of Rs.50,000/-, aGoldMedal and a Citation

For significant contribution in plant improvement

43


INSA Young Scientist Award

in Agricultural Sciences

Indian National Science Academy (INSA)

2010 Cash award of Rs.25,000/-, aBronze Medal and a Citation

For significant original contribution in developing gene- based markers in a number of plant species and demonstrating their utility in cropimprovement

NASI Young Scientist Platinum Jubilee Award in PlantSciences

National Academy of Sciences India (NASI)

2011 Cash award of Rs.25,000/-, aBronze Medal and a Citation

For significant original contribution in development and use of novel sequence based robust molecular markers for large- scale genotyping applications in important cropspecies

Odisha Young Scientist Award

Odisha Science Academy, Government of Odisha

2014-2015

Cash Award of Rs.25,000/-, aBronze Medal and a Certificate

For Significant contributions in Science & Technology

Jawaharlal Nehru Award in Plant Biotechnology- 2011

Indian Council of Agricultural Research (ICAR)

2011 Cash award of Rs.50,000/-, aGold Medal and aCitation

For outstanding doctoral thesisresearch in agricultural and allied sciences (cropbiotechnology)

Prof. B.K. Bachhawat Memorial Young ScientistLecture Award

National Academy of Sciences, India (NASI)

2018 Cash Award of Rs.10,000/- and a Citation

For significant contribution in agricultural science

ISCA Pran Vohra Award

The Indian Science Congress Association (ISCA)

2014-2015

Cash award of Rs.10,000/- anda Citation

For significant contribution in agriculturalscience


44

Indian Genetics Congress Young Scientist Researcher Awardin Plant Science

SRM University, Chennai, Tamil Nadu

2015 Citation For significant contribution in molecular genetics and plantgenomics

Qualified National Eligibility Test(NET) in LifeSciences

Council of Scientific and Industrial Research (CSIR) and University Grant Commission (UGC), Govt. ofIndia

2004 - Qualified NET in Life Sciences

Qualified Graduate Aptitude Test in Engineering (GATE) in LifeSciences

Indian Institute of Science (IISc), Indian Institute of Technology (IIT) and Ministry of Human Resource Development (HRD), Govt. of India

2003 - Qualified GATE in Life Sciences and secured 98.2percentile

Board of Research in Nuclear Sciences (BRNS) - Human Resource Development (HRD), Govt. ofIndia Fellowship

Bhabha Atomic Research Centre (BARC), Mumbai

2003 to2004

Scholarship of Rs.2,000/- per month

Pursuing the M.Sc. thesis research works

All IndiaCombined Biotechnology Entrance Examination (CEEB) M.Sc.(AgriculturalBiotechnology) Merit Scholarship

Dept. of Biotechnology (DBT), Govt. of India, New Delhi

2001 to2003

Scholarship of Rs.1,200/- per month

Qualified CEEB M.Sc.(Agricultural Biotechnology) Entrance on 2001

Orissa University of Agriculture and Technology (OUAT) MeritScholarship

Govt. of Odisha, Bhubaneswar 1997 to2001

Scholarship For securing First class with Hons.>80% marks in B.Sc. (Agriculture)examination

National RuralTalent Search(NRTS) Merit Scholarship

Board of Secondary Education, Govt. of Odisha, Bhubaneswar

1990 to1994

Scholarship Award forsecond best performance at the block level inclass VI

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24 A concise statement highlighting the most significant aspect of the research work done that you would like to see in your citation, if chosen

Dr. Swarup has made significant contribution in the area of next-generation molecular breeding and genomics-assisted breeding for crop improvement. He is instrumental in developing novel concepts on highly-informative genic and genomic microsatellite and single nucleotide polymorphism markers designing and database development in an array of crops and utilized them for understanding genome structure and evolution, molecular diversity and domestication pattern, variety identification, construction of high-resolution genome maps, gene mapping and trait association analysis. Substantial efforts have been made by him to meticulously integrate diverse integrated genomics-assisted breeding strategies which led to delineate numerous functionally relevant molecular signatures (genes, QTLs, alleles and haplotypes) governing fertility restorer, hybrid production and stress tolerance traits in rice as well as diverse seed and pod yield, plant architectural and nutrient/quality traits in chickpea. The molecular Bar Codes and potential functionally relevant molecular tags identified by him have been commonly utilized in Indian Basmati trade and commerce for marker-assisted selection of fertility restoration and production of pure hybrid rice seeds. He successfully deployed marker (haplotype)-assisted breeding to introgress two most-promising delineated superior molecular haplotypes into a number of Indian high-yielding chickpea varieties for improving their overall yield and productivity as well as nutritional quality traits.

Referees

Dr. Ramesh V. SontiFNASc, FASc, FNAAS, FNA,Director,National Institute of Plant Genome Research (NIPGR),Aruna Asaf Ali Marg, P.O. Box No. 10531,New Delhi - 110 067Email: [email protected], [email protected], [email protected]

Dr. Trilochan MohapatraFNASc, FNAAS, FNASecretary, DARE & Director General, Indian Council of Agricultural Research (ICAR), Dr. Rajendra Prasad Road, Krishi Bhawan, New Delhi - 110001Email: [email protected]; [email protected]

Prof. Akhilesh K. TyagiFNASc, FASc, FNAAS, FNA, FTWASProfessor & JC Bose National FellowDepartment of Plant Molecular BiologyUniversity of Delhi, South CampusNew Delhi - 110021Email: [email protected]

Prof. Deepak Pental

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FNASc, FASc, FNAAS, FNA, FTWASProfessor, Centre for Genetic Manipulation of Crop Plants, Department of Genetics, University of Delhi South Campus, New Delhi 110021Email: [email protected]

Prof. Nagendra Kumar SinghFNASc, FNAAS, FNAProject Director, National Professor B.P. Pal Chair, National Institute on Plant Biotechnology (NIPB), Indian Council of Agricultural Research (ICAR), IARI, Pusa CampusNew Delhi 110012Email: [email protected]

Prof. Ashok Kumar SinghFNASc, FNAAS, FNADirector, ICAR-Indian Agricultural Research Institute (IARI)IARI, Pusa CampusNew Delhi 110012 Email: [email protected]; [email protected]

Prof. Rajeev K. Varshney ML, FTWAS, FCSSA, FNA, FNASc, FNAASResearch Program Director, Genetic GainsDirector, Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru 502324, Hyderabad, Telangana, IndiaEmail: [email protected]

Dr. Tilak Raj SharmaFNASc, FASc, FNAAS, FNA, FTWASDeputy Director General (Crop Sciences)Indian Council of Agricultural Research (ICAR)Dr. Rajendra Prasad Road, Krishi Bhawan, New Delhi - 110001Email: [email protected]

Prof. Jitendra Paul KhuranaFNASc, FASc, FNAAS, FNA, FTWASProfessor & Head, Coordinator (UGC-SAP), Department of Plant Molecular Biology (DPMB), University of Delhi South Campus, New Delhi 110021Email: [email protected]

mailto:[email protected]

mailto:R.K.Varshney@cgiar

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Prof. Sudhir Kumar SoporyFNASc, FASc, FNAAS, FNA, FTWASFalaschi Emeritus Scientist, International Centre for Genetic Engineering & Biotechnology (ICGEB), Aruna Asaf Ali MargNew Delhi 110067 Email: [email protected]

Dr. Renu SwarupSecretary to the Government of IndiaDepartment of Biotechnology (DBT)Ministry of Science & TechnologyBlock - 2, CGO Complex, Lodi RoadNew Delhi - 110003 INDIAEmail: [email protected]

Prof. Partha P. MajumderFNASc, FASc, FNAAS, FNA, FTWASDistinguished Professor, National Institute of Biomedical Genomics (NIBMG), Post Netaji Subhas Sanitorium, Kalyani 741251, W.B.Email: [email protected]

Dr. Ajay ParidaFNASc, FNAASDirectorInstitute of Life Sciences (ILS)(Dept. of Biotechnology, Govt. of India)NALCO Square, ChandrasekarpurBhubaneswar - 751023, IndiaEmail: [email protected]

Place: NIPGR, New DelhiDate: April 29, 2020

Swarup K. Parida(Signature of applicant)

mailto:[email protected]

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