About the Bioinformatics Centre

The Bioinformatics Infrastructure Facility (BIF)  at Ch. Charan Singh University, Meerut located in the Department of Genetics & Plant Breeding was established in 2007 as a part of the Biotechnology Information System Network (BTISNET) program of Department of Biotechnology, Government of India. Since its inception, the BIF provides an environment for teaching  of   bioinformatics to students of Biology and Agriculture and also provides an opportunity for collaborative interdisciplinary research in the area of Bioinformatics. Further, the BIF  also functions as a bridge between in-silico and the wet-lab experiments designed to answer a variety of questions related specifically to genetics and at large to the biology of crop plants. The center mainly focuses  on crop biotechnology, computational identification of genes related to different traits (nutrient uptake, drought and heat tolerance, plant architecture and grain weight), development of molecular markers,  QTL analysis  and  association mapping. The facility is  also instrumental in imparting knowkedge of  bioinformatics through  training to students and the faculty members.

Area of Specialization: Genetics, Plant Breeding, (including Molecular Breeding) and Bioinformatics.


About the Institution

Ch.  Charan Singh University (formerly, Meerut University) was established in 1965, to cater to the needs of higher education in western Uttar Pradesh. The University celebrated its silver jubilee in 1991. Presently, it is one of the premier educational institutions of the country encompassing a vast, beautiful and pollution-free campus spread over 222 acres of land having vast playgrounds, experimental fields, botanical garden, rose garden with a life-size statue of the late Prime Minister Ch. Charan Singh, gymnasium, indoor stadium, well equipped library, hostels for both girls and boys, administrative block, spacious auditorium, guest house, community center, medical center, residential quarters for faculty members and employees, canteen, bank and post office. The teaching departments belonging to different faculties, are housed in spacious buildings and have well-equipped laboratories and  reasonable  research facilities. The university also has a separate engineering college, which is currently offering courses leading to B.Tech. degree in several different branches of engineering.

Initially, in this university,  M. Phil and Ph.D. programs were started in 1969 taking credit of becoming the first University in the country to introduce M.Phil. programme. In 1973, Post Graduate  courses were also introduced. Since then, the University has progressed at a steady pace. During the VIII five year plan,  self-financed courses were also introduced keeping in view of  the changing demands of the society and also for human resources development. Now, there are five faculties which conduct teaching/research in  22  regular  courses and 35 self financed/job oriented courses  in the university campus.

The University has always been proud of its alumni who are occupying high positions of great responsibilities and distinction in educational and research institutions in India and abroad as well as administrative positions in  industries, defense and civil services. The success of the students of the university in NET, GATE, ARS, GRE tests and other examinations such as civil and administrative services etc. speak of the high standard and quality of education provided by the university. The research activities in the various departments of the university are supported by grants in the form of research projects sanctioned by UGC, DBT, DST, ICAR, AICTE, UPSTC, CSIR and other funding agencies of the central and state governments. For further information please visit
  • Plan to develop database of genes for crop nutrient use efficiency.
  • Promoting biological and agriculture education and human resource development in Bioinformatics.
  • Dissemination of  e-Bioinformatics lectures on the web.
Achievements at a glance

Since 2007, we have published nearly  100 research papers in peer reviewed journals and international conferences and supervised M.Sc./M.Phil. dissertations.The BIF also  organized either individually or in collaboration four  workshop-cum-hands on traning and trained more than 150 presonnels. The facilities provided by BIF are routanoly used by teachers, research scholars and students of  different  departments of this university and elsewhere.

Current areas of Research
Since our specialization is in the area of Genetics and Plant Breeding, we focuss  our research efforts on the following aspects, which also involved in silico analysis. (i) Identification and wet lab validation of genes for nitrogen use efficiency (NUE) and phosphorus use efficiency (PUE) in wheat.  (ii) Analysis of wheat orthologs of rice genes for grain related traits. (iii) Analysis of wheat orthologs of dwarf4, Aux1, Pin1  responsible for dwarfness in Arabidopdsis, CCD8 gene for tiller number and Roc5 gene for leaf rolling in rice. (iv)Identification of genes controlling plant architecture in wheat. (v) Identification and gene expression analysis of stress (drought and salt) responsive genes in wheat.  (vi) Analysis of wheat orthologs of candidate genes for induced mutants in wheat. (vii) Analysis of wheat orthologs of genes for human health related components of wheat grain. (viii) Identification and exporession analysis of two component system (TCS) genes in wheat. (ix) Digital gene expression analysis using wheat ESTs and unigenes generated following leaf rust infection. (x) Identifications of stress responsive miRNAs in wheat. (xi) Analysis of gDNA sequences of jute and designing of primers for SSRs and the fragments amplified through AFLP.  (xii) Development of molecular maps in wheat and also the first molecular genetic map in jute. (xiii) Linkage and association mapping analysis for various traits of economic importance such as pre-harvest sprouting tolerance, grain weight, grain protein content as well as yield and related traits in wheat. (xiv) QTL analysis for fibre yield and fibre quality traits in jute and cotton. (xv) Diversity analysis in wheat and jute germplasms.
Database/applications developed
Propose to develop database of genes for crop nutrient use efficiency.
Inter Institutional collaboration

Center has both international & national collaborations in the field of Crop biotechnology and bioinformatics with the following institutions.

(i) Washington State University, Pullman, USA, (ii) PAU, Ludhiana, (iii) ARI,  Pune,  (iv)  GB   Pant  University  of  Agriculture  &  Technology,  Pantangar,  (v)  BHU, Varanasi, (vi) CRIJAF, Barrakapore, (vii) IARI, New Delhi, (viii) BITS, Ranchi, etc.
Infrastructural Facilities
A. Computer & Communication facility:
i) IBM THINK CENTRE: 10 Numbers; RAM 256 DDR-2 (Make IBM additional 256 MB DDR 2 Ram):   10 Numbers; IBM TFT 17” (in lieu of 17” monitor):  10 Numbers; (ii) IBM SERVER with 2 Dual Core Processor:  One Number; IBM TFT 17” In lieu of 17” monitor):  One Number; (iii) IBM SERVER Intel Xeon 3.00 Ghz Dual Core Processor EM 64 T:  One Number; RAM 1 GB (Make IBM additional 1GB DDR2 RAM, 2×512 MB):  One Number; IBM TFT 17” (in lieu of 17” monitor):  One Number; (iv) 420 CP Multifunction Xerox Machine: One Number;  (v) HP Laser Jet Printer (Model 5200 series):  One Number; (vi) Scanner HP 2400C:  One Number; (vii) Desk Jet HP 1360 Laser Jet Printer:  One Number; (viii) DELL Laptop XPS L401X, Intel (R) Core (TM) i7CPU Q740 @1.73GHz, RAM 8.0GB, 64 Bit Operating System, 600 GB Disc. (viii) High speed internet facility

B. Scientific Software Packages:
Geneious 10 user perpetual package,Windows 2003 Server 10 clients:One Number; Microsoft ISA Server 2005:  One Number; Microsoft Visual Studio Standard 2005: One Number; MS SQUL Server 2005 Standard: One Number; MS Office 2003: One Number

Faculty Members
Dr.H.S Balyan Professor & Coordinator
Dr. B.Ramesh Professor & Head
Dr. P.K Gupta Emeritus Professor & NASI Sr.Scientist
Dr. P.K Sharma Reader
Dr. S.S Gaurav Sr.Lecturer

Name of the Coordinator: Prof. H.S. Balyan

Postal Address: Department of Genetics & Plant Breeding,

CCS University, Meerut- 250004 (U.P).

Phone  Number: +91-9412515497, Fax No.: +91-121-2768195



Name of Contact Person (s): Prof. H.S. Balyan (Coordinator)

Mr. Anuj Kumar (JRF), 
Recent publications

Tyagi S, Mir RR, Kaur H, Chhuneja P, Ramesh B. Balyan HS and Gupta PK (2014). ­­­­­Marker assisted pyramiding of eight QTLs/genes for seven different traits in common wheat (Triticum aestivum L. (Revised MS submitted).

Gupta PK (2013). Competing   endogenous   RNA   (ceRNA):   A  new class of RNA working as miRNA  sponges. Curr Sci 105 (in press)
Agarwal P, Kumar S, Mir RR, Balyan HS, Gupta PK (2013). Some ENU induced mutation: a   resource for functional genomics in bread wheat. Plant Mutation Reports 3:1-8

Balyan HS, Gupta PK, Kumar S, Dhariwal R, Jaiswal V, Tyagi S, Agarwal P, Gahlaut  V, Kumari S  (2013). Genetic  improvement  of  grain  protein  content  and  other  health  related constituents of wheat grain. Pl Breed 132:446-557

Gupta PK, Balyan HS, Kumar J, Mir RR, Kumar S, Dhariwal R, Jaiswal V, Tyagi S, Agarwal P, Gahlaut V, Kumari S (2013). Molecular breeding, induced mutagenesis, and transcriptome analysis in wheat. Annual wheat newsletter. 59: 20-26

Kumar S, Goyal A, Mohan A, Balyan HS, Gupta PK (2013). An integrated physical map of simple sequence repeats in bread wheat Austr J Crop Sci 7:460­468

Topdar N,  Kundu A, Sinha MK, Sarkara D, Das M, Banerjee S, Kara CS, Satya P, Balyan HS, Mahapatra BS, Gupta PK (2013). A complete genetic linkage map and QTL analyses for bast fibre quality traits, yield and yield components in jute (Corchorus olitorius L.). Cytol & Genet 47:129–137

Kumar A, Chhuneja P, Jain S, Kaur S,  Balyan HS,  Gupta PK (2013). Mapping  main  effect QTL  and  epistatic  interactions  for  leaf  rust  and  yellow  rust  using  high  density  ITMI linkage map. Aust J Crop Sci 7:492-499

Gupta PK (2013). Professor Kameshwar Sahai Bhargava (19 October 1918- 13 September  2010), Biog. Mem. Fell. INSA, New Delhi 40:1-13

Kundu A, Topdar N, Sarkar D, Sinha MK, Ghosh A, Banerji S, Das M, Balyan HS, Mahapatra BS, Gupta PK (2013). Origins of white (Corchorus capsularis L.) and dark (C. olitorius L.) jute: a reevaluation based on nuclear and chloroplast microsatellites. J. Plant Biochem. Biotechnol. 22:372–381

Gupta PK, Rustgi S, Mir RR (2013). Array-based  high-throughput  DNA  markers  and genotyping platforms for cereal  genetics and  genomics.  In Gupta PK, and Varshney RK (Eds.). “Cereal Genomics II”. Springer Pp. 11-56

Gupta PK, Kulwal PL, Mir RR (2013). QTL  mapping: methodology  and  applications  in cereal breeding. In Gupta PK, and Varshney RK (Eds.).“Cereal GenomicsII”. Springer. Pp. 275-318

Edwards D, Gupta PK (2013). Sequencing-based  DNA markers  and  genotyping  for  cereal genomics and breeding. In Gupta PK, Varshney RK (Eds.). ‘Cereal GenomicsII”. Springer. Pp 57-76

Kianian SF, Kumar A, Bassi FM, Paux E, Al -AzzamO, de Jimenez M M, Denton AM, Gu YQ, Huttner E, Kilian A, Kumar S, Goyal A, Iqbal  MJ, Tiwari V, Dogramaci M, Balyan HS,  Dhaliwal  HS,  Gupta  PK,  Randhawa  GS,  Feuillet  C, Pawlowski  WP  (2012). DNA repair  and  crossing  over  favor  similar  chromosome  regions  as  discovered  in  radiation hybrid of Triticum aestivum. BMC Genomics 13: 339-362

Das M, Banerjee S, Dhaliwal R, Vyas S, Mir RR, Topdar N, Kundu A,  Khurana JP, Tyagi AK, Sarkar D, Sinha MK, Balyan HS, Gupta PK (2012). Development of SSR markers and construction of a linkage map in Jute. J Genet 91:21-31

Jaiswal V,  Mir RR,  Mohan A,  Balyan HS, Gupta PK (2012).  Association  mapping  for  preharvest  sprouting  tolerance  in  common  wheat  (Triticum  aestivum L.). Euphytica  188:89-102

Kumar S, Balyan HS, Gupta PK (2012). Comparative  DNA  sequence  analysis  involving wheat,  brachypodium  and  rice  genomes  using  mapped  wheat  ESTs. Triticeae  Genomics and Genetics 3: 25-37

Banerjee S, Das M, Mir RR, Kundu A, Topdar N, Sarkar D, Sinha MK, Balyan HS, Gupta PK  (2012). Assessment  of  genetic  diversity  and  population  structure  in  a  selected germplasm collection of 292 jute genotypes by microsatellite (SSR) markers. Mol Pl Breed 3: 11-25

Tyagi S, Gupta PK (2012). Meta-analysis  of  QTLs  involved  in  pre-harvest  sprouting tolerance and dormancy in bread wheat. Triticeae Genomics Genet 3: 9-24

Gupta PK, Balyan HS, Kulwal PL, Gahlaut V (2012). Phenotyping, genetic dissection, and breeding  for  drought  and  heat  tolerance  in  common  wheat:  status  and  prospects.  Plant Breed Rev 37: 85-168

Gupta PK (2012). Angiosperm taxonomy in the age of genomics and information technology. In  Maiti,  GG  &  Mukherjee,  S.K.  (eds.).  Proc.  International  Seminar  “Multidisciplinary Approaches in Angiosperm Systematics”, Univ. of Kalyani (11th–13th October, 2008), Pp 284-296

Gupta PK (2012). Molecular breeding for crop improvement: harnessing the genes. Biotech News 6: 135-137

Gupta PK (2012). Regulating  the  dual-use  and  dual-impact  life  science  research:  influenza virus versusbiotech crops. Curr Sci103: 995-1002

Mir RR, Kumar N,  Girdharwal N,  Jaiswal V,  Prasad M,  Balyan HS,  Gupta PK (2011). Genetic  dissection  of  grain  weight  in  bread  wheat  through  QTL  interval  and  association mapping. Mol Breed 29: 963-972

Das M, Banerjee S, Topdar N, Kundu A, Mir RR, Sarkar D, Sinha MK, Balyan HS ,Gupta PK (2012). QTL identification for molecular breeding of fibre yield and fibre quality traits in jute.Euphytica 187: 175-189

Rustgi S, Balyan HS, Gupta PK (2011). MSL  and  SNPL:  softwares  for  in  silico  mining  of SSRs and SNPs. International Journal of Biological Sciences. ISSN 1449-2288

Gupta  PK, Balyan HS, Singh G, Singh SS, Gahlaut V, Tyagi S (2011). Marker-assisted selection (MAS) for development of drought and heattolerant bread wheat. In: Singh SS, Hanchilal RR, Singh G, Sharma RK, Tyagi BS, Saharan MS, Sharma I (Eds.) "Wheat: Productivity Enhancement under Changing Climate". Narosa Publishing House Pvt. Ltd., New Delhi

Bandopadhyay R, Rustgi S, Chaudhuri RK, Khurana P, Khurana JP, Tyagi AK, Balyan HS, Houben A, Gupta PK  (2011). Use  of  methylation  filtration  and  C(0)t  fractionation  for analysis of genome composition and comparative genomics in bread wheat. J Genetics & Genomics (Elsevier) 38:315-325

Das M, Banerjee S, Topdar N, Kundu A, Sarkar D, Sarkar MK, Balyan HS, Gupta PK (2011). Development of large-scale AFLP markers in jute. J Plant Biochem. Biotech. 20: 270-275

Mir RR, Kumar J, Balyan HS, Gupta PK (2011). A study of genetic diversity among Indian bread wheat cultivars released during last 100 years. Genet Res and Crop Evol. 59:717-726

Kumar J, Jaiswal V, Kumar A, Kumar N, Mir RR, Kumar S, Kumar R, Tyagi S, Prabhu KV, Balyan HS, Gupta PK (2011). Introgression of a majorgene for high grain protein content in some Indian bread wheat cultivars. Field Crops Res 123: 226-233

Dhariwal R, Vyas S, Bhaganagre GR, Jha SK, Khurana JP, Tyagi AK, Prabhu KV, Balyan HS, Gupta PK (2011). Analysis of differentially expressed genes in leaf rust infected bread wheat involving seedling resistance gene Lr28. Funct Plant Biol 38:479-492

Gupta PK (2011). Engineered  zinc  finger  nucleases  for  gene  targeting  in  crop  plants.  In Hasnain, S.E. et al. (eds.) “Biotechnology for Sustainable Development: Achievements and Challenges” (Prof. A.B. Prasad Commemorative Volume). Tata McGraw Hill, New Delhi. Pp. 31-49

Sablok  G,  Gupta  PK,  Baek  JM,  Vazquez  F,  Min  XJ  (2011). Genome -wide  survey  of alternative splicing in the grass Brachypodium distachyon: a emerging model biosystem for plant functional genomics. Biotechnol. Lett. 33: 629-636

Gupta PK (2011). SNPs and sequencing-based genotyping for wheat molecular breeding. In: Singh SS, Hanchilal RR, Singh G, Sharma RK, Tyagi BS, Saharan MS, Sharma I (Eds.) “Wheat: Productivity Enhancement under Climate Change”, Proc. 3rdIGM, UAS Dharwar, 9-12 Feb, 2011. Pp. 115-125

Gupta PK, Balyan HS, Singh G, Singh SS, Gahlaut V, Tyagi S (2011). Marker-assisted selection (MAS) for development of drought and heattolerant bread wheat. In: Singh SS, Hanchilal  RR, Singh G, Sharma RK, Tyagi BS, Saharan MS, Sharma I. (Eds.) “Wheat: Productivity  Enhancement  under  Climate  Change”,  Proc.  3rdIGM,  UAS  Dharwar,  9-12 Feb, 2011. Pp. 151-161

Kulwal PL, Mir RR, Kumar S, Gupta PK (2011). QTL analysis and molecular breeding for seed dormancy and pre-harvest sprouting tolerance in bread wheat. J. Plant Biol., Vol. 37: 59–74

Gupta  PK  (2011). Molecular  mapping  and  marker-assisted  breeding  for  quality  traits  in wheat.  In:  Muralidharan  K,  Siddiq  EA  (Eds.)  “Genomics  and  Crop  Improvement: Relevance and Reservations”. Proc. Symp. ANGRAU, Hyderabad (Feb 25-27, 2010.  Pp. 363-372

Kumar J, Gupta PK (2011). Non-transgenic  molecular  approaches  for  improvement  of Cymbopogon species for aromatic and medicinal uses: current status and future prospects. In: Ahamad A, Siddiqi TO, Iqbal M (Eds) “Medicinal  Plants in Changing Environment”, Capital Publishing Company, New Delhi. Pp. 11-19

Gupta PK, Balyan HS, Kumar J, Mohan A, Kumar A, Mir RR, Kumar S, Kumar R, Jaiswal V, Tyagi S, Agarwal P, Gahlaut V, Das M, Banerjee  S (2010). Deployment of molecular markers for the improvement of some important quality traits in bread wheat. Ann Wheat Newsletter 56:60-65

Gupta PK, Balyan  HS, Varshney RK (2010). Quantitative  genetics  and plant  genomics:  an overview. Mol Breed 26:133-134

Rakshit A, Rakshit S, Singh J, Chopra SK, Balyan HS, Gupta PK, Bhat SR (2010). Association  of  AFLP  and  SSR  markers  with  agronomic  and  fiber  quality  traits  in Gossypium hirsutum L. J. Genetics 89:155-62

Rakshit A, Rakshit S, Santhy V, Gotmare VP, Mohan P, Singh VV, Singh S, Singh J, Balyan HS, Gupta PK, Bhat SR (2010). Evaluation of SSR markers for the assessment of genetic diversity  and  fingerprinting  of  Gossypium  hirsutum L  accessions.  J.  Plant  Biochem  and Biotech 19: 153-160

Azhaguvel  P,  Weng  Y,  Babu  R,  Manickavel  A,  Saraswathi  DV,  Balyan  HS  (2010). Fundamentals  of  physical  mapping.  In:  Kole  C,  Abbot AG,  editors.  Principles  and Practices  of  Plant  Genomics,  Volume  3:  Advanced  Genomics.  Boca  Raton,  FL:  CRC Press. p. 24-62

Kumar  J, Mir RR,  Kumar  N,  Kumar  A, Mohan  A,  Prabhu  KV,  Balyan  HS,   Gupta  PK (2010). Marker-assisted selection for pre-harvest sprouting tolerance and leaf rust resistance in bread wheat. Plant Breed.129: 617-621

Gupta PK, Kumar J, Mir RR, Kumar A (2010). Marker-assisted selection as a component of conventional plant breeding. Plant Breed Rev 33: 145-217

Gupta PK, Langridge P, Mir RR (2010). Marker-assisted wheat breeding: present status and future possibilities. Molecular Breeding 26: 145-161


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