Dr. Kuldeep Singh

ICAR-National Bureau of Plant Genetic Resoruces
Plant Breeding, Molecular Breeding, Molecular Genetics, Genomics and Wide Hybridization, Plant Genet
+91-11-25843697, Fax:+91-11-25842495
kuldeep.singh4(AT), director.nbpgr(AT)
Personal Webpage:
Salient Achievements:

Professional Achievements                

  1. Research

April 1992 to October 1995

During this period, I Worked as postdoctoral research fellow at International Rice Research Institute (IRRI), Philippines in the group led by Dr. GS Khush. I developed a complete series of secondary trisomics that were used for mapping 45 mutant genes onto classical linkage map and a few hundred RFLP markers to specific chromosome arms. Thus centromere positions were mapped on both the classical and the molecular linkage maps and these maps were presented in a corrected orientation. Publications emerging from this work appeared in two leading international journals, Proc. Natl. Acad. Sci., USA and Genetics. Rice Genome Research Project, Japan, later used these novel stocks for mapping centromere positions on the molecular map originating from their lab.


March 1990 to May 1999 (excluding April 1992 to October 1995)

During this period I worked as wheat breeder with objectives focused on three aspects viz. pure line varietal development, exploring possibilities of hybrid wheat development, standardizing the protocols for haploid production through wheat x maize crosses, and establishing a collection of wild species of wheat.


Participation in Varietal Development

I worked as research fellow in a USAID funded project ‘Transfer of desirable alien genes into wheat from March 1990 to June 1990. This involved wide hybridization studies using embryo rescue technique and generation of interspecific hybrids. From July 1990 onwards as a team member I was associated for development of varieties for several agro climatic Zones. Evaluation and selections performed during this period lead to identification and release of wheat varieties PBW 343 & PBW 443, recommended for irrigated conditions, and PBW 396 recommended for water stress conditions.


Development of Hybrid wheat

  • More than 1000 hand-made F1 hybrid combinations were evaluated in replicated yield trials for assessing the magnitude of standard heterosis and to identify yield components that can best be targeted for hybrid wheat development. Some heterotic combinations, yielding 15-20% more than the standard check were identified.
  • Several chemical hybridizing agents (CHAs) (developed by NCL, Pune, under the coordinated project) were tested for their efficacy in inducing male sterility. Some CHAs have been identified that induce complete male sterility without severely affecting female fertility.
  • Transfer of Triticum timopheevi based cytoplasmic male sterility (CMS) and the restores genes, in good agronomic lines, were initiated and some of these are now being used for developing hybrids.
  • Work on development of new CMS sources especially from Aegilops kotschyii was initiated and advance backcross generations are now available.
Wheat x Maize crosses for Haploid production
  • We developed a simple and inexpensive technique for identifying embryo-carrying caryopses, thus improving efficiency of the system several fold (published in Plant Breeding). We also identified a maize line that showed a significant positive effect on regeneration of haploid embryos (published in Crop Science). The third aspect of this system, which was recently standardized concerns chromosome doubling of haploid embryos prior to regeneration (published in Plant Breeding).


May 1999 to-date

Rice Molecular Breeding
  • Under an Asian Development Bank (ADB) sponsored Asian Rice Biotechnology Network (ARBN) project, we pyramided three bacterial blight resistance genes, xa5, xa13 and Xa21 in the background one of our popular varieties PR106 and Pusa44. Two PR106 pyramid lines IET 17848 and IET 17849 and three Pusa44 pyramid lines, IET19339, IET19340 and IET19341 (designations given by the Directorate of Rice Research, Hydrabad, India) were tested at national level under the aegis of All India Coordinated Rice Improvement Programme (a pre-requisite for variety release) during summer 2002 and 2005 respectively for their agronomic performance.
  • Using Marker Assisted Breeding, we released four varieties if indica rice (PR121, PR122, PR123, PR124, and PR126) and three of Bamati rice (Punjab Basmati 3 and Punjab Basmati 4, Punjab Basmati 5) during years 2012, 2014 and 2015, and 2017.
  • Three new lines designated as RYT3316 (Parmal rice) and RYT3404 and RYT3432 (Basmati rice) nominated for farmers’ Field Trials for 2016 crop season
  • Improved version of PAU201 (highest yielding indica variety but red grain), developed through MAS is under evaluation at national level under AVT-2015.
  • Identification, transfer mapping and designation of a novel bacterial blight (BB) resistance genes Xa38 transferred from O. nivara into O. sativa. This gene is dominant in nature, maps on chromosomes 4 and effective against all the known virulences in India.
  • Identification, transfer and mapping of two novel recessive BB resistance genes from African rice O. glaberrima to O. sativa. One of these genes maps on chromosome 6 and is tentatively designated as xa_g6.
  •  Mapping of xa8 that is highly effective under Punjab conditions, on chromosome 7 using microsatellite markers.
  • About 2000 accessions of wild species of rice procured from IRRI, Philippines and CRRI, Cuttack
  • A set of 300 accessions belonging to six A genome species of Oryza has been analyzed with microsatellite markers and levels of genetic diversity within each species assayed. A selected set of 5-10 diverse accessions from each of the six ‘A’ genome species O. glaberrima, O. barthii, O. nivara, O. rufipogon, O. meridionalis, and O. glumaepatula are being used for identification, mapping and transfer of novel alleles for productivity related QTL from these species using the AB-QTL strategy. A set of 3000 introgression lines having alien genome from more than 30 accessions of five different species have been generated and are being evaluated for their agronomic performance. Some lines having higher yield than the recurrent parent have been identified and these have been analyzed using for SSR markers and graphical genotypes of some of the introgression lines have been generated to for identifying the alien chromatin. This material should help Rice Breeders for broadening genetic base of their working germplasm.
  • We have mapped grain number QTL designated tentatively as qSPP2 and it explained more than 35 per cent of the phenotypic variability. We have fine mapped the QTL to 167kb region and identified putative candidate gene (PLoS ONE – under review). This QTL is now being transferred to Punjab Basmati 3 for increasing its grain number, hence productivity.
  • A large number of wild species accessions of rice have been screened for BB resistance and novel sources of resistance identified. Four new BB resistance genes, one from O. nivara (Xa38), one each from O. glaberrima and O. barthii and one from O. rufipogon have been mapped and transferred to cultivated rice O. sativa. These genes have been mapped to about 200 kb regions on different chromosomes and markers suitable for MAS identified.
  • A new resistance gene for blast transferred from O. glumaepatula is effective both at vegetative stage as well as neck blast stage throughout India. The gene is being mapped in collaboration with IIRR, Hyderabad (Manuscript under review).
  • Root-knot nematode (Meloidogyne graminicola) resistance transferred from three different accessions of O. glaberimma (Manuscript under review).
  • New sources of resistance to brown plant bopper (BPH) identified from O. nivara and has been mapped to less than 100kb region (Manuscript under review)
  • Basmati, which is specialty rice, is highly prized but low yielding and susceptible to diseases. No significant improvement could be made in improving basmati through conventional breeding procedures. Desired traits in basmati are aroma, specific amylose content, grain elongation after cooking and photoperiod sensitivity. DNA markers linked to all these traits have become available. Using MAS we have developed a dwarf prototype of basmati with two bacterial blight resistance genes xa13, and Xa21, and also selected for desirable alleles of amylose, aroma and photoperiod sensitivity. One of these lines has been released for cultivation as Punjab Basmati 3 in 2013.

Wheat molecular breeding

  • Under an Indo-Swiss collaborative project on biotechnology (ISCB) we have generated a linkage map of A genome of wheat with 180 markers (including SSRs, RFLPs and bin mapped ESTs) using a RIL population developed from a cross involving T. boeoticum and T. monococcum. ( T.%20boeoticum%20x%20monococcum). This map has now been saturated with other SSR and DArT markers and is one of th ecomprehensiive maps in A geneome of wheat
  • Genes for leaf rust, stripe rust, Karnal bunt, cereal cyst nematode and powdery mildew have been mapped in this population and closely linked markers suitable for MAS have been identified. Two new genes for stripe, two for leaf rust, one for powdery mildew and one for cereal cyst nematode have been identified from the diploid wheat and transferred to hexaploid wheat.
  • Genes conferring resistance to leaf rust, stripe rust, and Karnal bunt have been transferred in tetraploid and hexaploid background.
  • A few wild species accessions with high Iron and Zinc content have been identified and these are being used for mapping and transferring the genes contributing to high Fe and Zn contents. A number of lines with high grain Zn and Fe content have been identified and will be evaluated under multi-location testing.

Stocks Generated Though Alien Introgression

Improved Lines

Present Status

  1. PBW722 and PBW723 with leaf rust and stripe rust resistance genes LrU-YrU, Lr37-Yr17and LrU-YrU-Yr15, respectivelyin state trials

Promoted to special AVT on Marker Assisted Backcross Breeding in 2013-14

  1. PBW693 with leaf rust and stripe rust resistance genes LrU-YrU – state trials

Promoted to AVT for NEPZ in 2013-14

  1. BWL3283, BWL3294, BWL3268, BWL3275, BWL3269, BWL3267, BWL3346 with different gene combinations- station trials

In special state trials at 10 locations in 2013-14

  1. Mapping of a novel leaf rust resistance gene transferred from Aegilops caudata to cultivated wheat

Being fine mapped

  1. Identification and mapping of two powdery mildew resistance genes from Triticum boeoticum

Being transferred to bread wheat using MAS

  1. Identification and transfer of a leaf rust and a stripe rust resistance gene from Ae. tauschii acc. pau14195 to cultivated wheat

Being fine mapped


Wheat Genome Sequencing

Sequencing of wheat genome was considered as an uphill task until International Wheat Genome Sequencing Consortium (initially comprising of a few countries including India) initiated chromosome arm based sequencing approach. I took over the challenge of leading the group in India for sequencing chromosome 2A (900 Mb). Under the aegis of IWGSC, India has the responsibility of sequencing chromosome 2A (900Mb) which is 2.5X larger than whole rice genome. As consortium members the draft sequence using NextGen sequencing approach was completed and published (Science 345: 1251788-1 to 11). We have generated 133,000 chromosome arm specific BAC clones for the chromosome 2A and completed their fingerprinting following high information content fingerprinting (HICF) approach. We have generated physical map of chromosome 2A and initiated BAC-by-BAC sequencing which is expected to be completed by 2017. Using the NextGen sequencing data we have identified more than 2000 SSR markers and mapped 200 of these markers. Likewise, we have identified more than 500 genes whose full length cDNA are available and mapped 148 genes in the linkage map of 2A.


II. Teaching Experience

I am involved in teaching courses both at under graduate and post-graduate levels. The courses I taught/teach at Punjab Agricultural University are:


a) Undergraduate level


Course No.

Course title

Credit hours

1990- 1992

PB 301

Introductory Plant Breeding




Fundamentals of Plant Breeding




Introductory Biotechnology


2015 -

Biotech 421

Introduction to Genomics & Proteomics




b) Post graduate level


Course No.

Course title

Credit hours

1996 - 2000

PB 604

Advances in Cytogenetics of Crop Plants



Biotech 527

Techniques in Biotechnology



Biotech 602

Advances in Plant Biotechnology


2004 to 2007

PBGB 525

Principles of Biotechnology


2004 to 2007

PBGB 531

Molecular Biology: Basics and Applications in Plant Breeding


2004 to 2007


Advances in Plant Biotechnology


2008 onwards

Biotech 523

Molecular Biotechnology and Genomics


2010 onwards

Biotech 602

Advances in Plant Molecular Biology


2010 onwards

Biotech 604

Advances in Functional Genomics and Proteomics



Titles of theses completed/continuing under my supervision


M.S. Degree

  1. Vinesh Kumar - Identification of efficient pollinators for wide cross mediated haploid production in wheat (1998)
  2. Rahul Dhawan - Alternative chromosome doubling strategies for improving the efficiency of wheat x maize system of haploid production in wheat. (2000)
  3. Bharat Bhushan - Genetic and cytogenetic analysis of leaf blight resistance in Triticum aestivum L. em Thell. (2000)
  4. Pawan Kumar - Molecular markers for varietal identification and genetic diversity studies in cotton, Gossypium species. (2001)
  5. Kuljit Kaur - Molecular analysis of high yielding IR64/oryza rufipogon (Griff.) introgression lines (2004)
  6. Navjeet Grewal- Inheritance and molecular mapping of bacterial blight resistance gene(s) in Oryza nivara accession 81825 (2005)
  7. Hemal Bhasin - Map based cloning of bacterial blight resistance gene xa30(t) in rice (2011)
  8. Nguyen Le Van - Molecular profiling of introgression lines derived from crosses of O. sativa (L.) X O. longistaminata (A. Chev. & Roehr.) (2012)
  9. Kannu Sadhana – Mapping yield and yield component QTL in interspecific crosses of O. sativa (L.)  X O. longistaminata (A. Chev. & Roehr.) (2013)
  10. Karminderbir  Kaur - Allele mining for identification of haplotypes for grain number and grain gene in Oryza species (2014)
  11. Amandeep Kaur – Fine mapping and cloning of candidate gene for the grain number QTL qSPP2 transferred from Oryza longistaminata to O. stativa (2015)
  12. Sarbjeet Kaur – Molecular mapping and transfer of a bacterial blight resistance gene from Oryza rufipogon (2016).
  13. Sadhan Debnath - Marker assisted transfer of high grain number QTL from Oryza longistaminata to Punjab Basmati 3 (2016)


Ph. D. Degree

  1. Meenu Ghai - Fine mapping of leaf rust resistance genes in diploid wheat Triticum monococcum L. (2004)
  2. Shalesh Joshi - QTL mapping and introgression of yield-related traits from related A-genome species to cultivated rice Oryza sativa (2005)
  3. Ritu Mahajan – Molecular mapping and transfer of bacterial blight resistance gene (s) from O. glaberrima to O. sativa (2007)
  4. Simarjit Kaur – Fine mapping of stripe rust resistance genes transferred from Triticum monococcum L. into T. aestivum L (2009)
  5. Vikas Gupta – Fine mapping and cloning of a recessive bacterial resistance gene identified from Oryza glaberrima (2011)
  6. Surichi Jindal – Physical and genetic mapping of chromosome 2AL of wheat, Triticum aestivum L. (2015)
  7. Pratibha - Cloning and characterization of heat shock protein gene(s) from aegilops speltoides  and their association with heat tolerance (2015)
  8. Parampreet Kaur -  Physical mapping and gene annotation of chromosome 2A of wheat (2015)
  9. Dharminder Bhatia – Molecular Characterization of interspecific backcross inbred lines of rice (Oryza sativa L.) for mapping of yield component QTL (2015) (Monsanto Beachell-Borlaug International Scholarship awardee)
  10. Ahmad Elkot – Fine mapping and transfer of powdery mildew resistance gene from T. boeoticum to T. aestivum (2015)
  11. Amandeep K Sandhu - Genomic approaches to improve the rice bran quality: allele mining for phospholipase D locus and transfer through MAS into elite breeding lines  (2016) (Monsanto Beachell-Borlaug International Scholarship awardee)
  12. Kishore Gaikward - Genetic mapping and transfer of brown plant hopper resistance gene(s) from Oryza nivara to rice (2016)
  13. Palavi Malik - Genome wide selection for rapid introgression of productivity traits from Oryza rufipogon into O. sativa (ongoing) (Monsanto Beachell-Borlaug International Scholarship awardee) (Ongoing)
  14. Karminderbir Kaur – Development of an in vivo haploid induction system in rice through distant hybridization and manipulation of CenH3 gene (Ongoing)



  1. Member of advisory committee of 80 students pursuing MS and Ph D degree in different disciplines of Agricultural and Basic science.
  2. Nominee of the Dean Post Graduate Studies for academic years 2009-10, 2010-11



III. Membership of professional societies

  • Indian Society of genetics and Plant Breeding, New Delhi
  • Crop Improvement Society of India, Ludhiana
  • Association for the promotion of DNA fingerprinting and other DNA technologies (ADNAT), Hyderabad


IV. Opportunities for Scientific Leadership, Networking and Fund Raising

Since 1999, I had to move beyond the basic lab-bench and field-work to take up additional tasks formulating viable research proposals and generating financial support, setting up extensive lab facilities and contributing to training of students/researchers so that the projects attain a critical mass. Volume of funds raised during last 10-12 years amounts to more than 500 million INR. Manpower in the form of students and research fellows are financed out of these projects. Since 2003, I am leading Wide Hybridization, Molecular Breeding and Genomics teams at PAU, Ludhiana. Currently, I have six faculty members, more than 20 research fellows and 12 Ph D students working exclusively in my research group. Most of our externally funded projects are operated in network modes which has given us strength of interacting with different national and international groups and keeping up of our commitments. Since November 2010, I am officiating as Director School of Agricultural Biotechnology where in addition to core research we are running teaching programmes in B. Sc, M Sc and Ph D in Biotechnology.

Recent Publications Research Papers
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Last Updated : 01/03/2018