17022011

National Symposium : Frontiers in Biotechnology 17 th Feb 2011 Biotechnology Department, PU, Chandigarh Quest of DNA signature of species of animal, plant & microbes : Can we have a PIN code? Dinesh Kumar , B.Sc. Hons Zoo(BHU), M.Sc. Biotechnology(BHU), Ph.D. Biotechnology (BHU), PDF(USA) Senior Scientist(Animal Biotechnology) National Bureau of Animal Genetic Resources, Karnal-132 001, Haryana, INDIA Email: dineshkumarbhu@gmail.com, dinesh@iastate.edu

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],DNA signature- Quest 02/17/11 Dinesh-PU-Talk-17-02-2011

How DNA signature is made for each species? The number of nucleic acid or amino acid differences between two organisms is proportional to the time since they diverged from a common ancestor . TIME MOLECULAR DIFFERENCES 1 AAGG C TA 2 AAGG G TA 3 AAGG AT G Example Rate of Evolution = 1bp per 100 years 1 2 3 100years 200 years

Which marker for which purpose? ,[object Object],[object Object],[object Object],[object Object],[object Object],02/17/11 Dinesh-PU-Talk-17-02-2011

DNA barcoding of species ,[object Object],02/17/11 Dinesh-PU-Talk-17-02-2011

Origin of species bar code ,[object Object],[object Object],02/17/11 Dinesh-PU-Talk-17-02-2011

Identification of birds by species bar code ,[object Object],02/17/11 Dinesh-PU-Talk-17-02-2011

Identifying flowering plants by species DNA bar code ,[object Object],[object Object],[object Object],[object Object],02/17/11 Dinesh-PU-Talk-17-02-2011

Microbial species signature ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],02/17/11 Dinesh-PU-Talk-17-02-2011

rRNA genes - the ideal markers for microbial identification ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],02/17/11 Dinesh-PU-Talk-17-02-2011

Plant pathogen signature ,[object Object],[object Object],[object Object],[object Object],02/17/11 Dinesh-PU-Talk-17-02-2011

Can we use microsatellite in Fungi? 02/17/11 Dinesh-PU-Talk-17-02-2011

How fungal microsatellite data gives signature 02/17/11 Dinesh-PU-Talk-17-02-2011

Why we need molecular & bioinformatics tool? ,[object Object],Stem rust never sleeps- Norman E. Borlaug , 26th April, 2008, New York Times 02/17/11 Dinesh-PU-Talk-17-02-2011

Can we have DNA based signatures of Ug99? ,[object Object],[object Object],[object Object],02/17/11 Dinesh-PU-Talk-17-02-2011

A case study updates- How to identify Ug99? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],02/17/11 Dinesh-PU-Talk-17-02-2011

What are the available DNA markers to identify Ug99 SSR AFLP Mol Plant Path Latest Nov 2008 issue 02/17/11 Dinesh-PU-Talk-17-02-2011

SSR data- no DNA signature Mol Plant Path Nov 2008 issue 02/17/11 Dinesh-PU-Talk-17-02-2011

AFLP adapters used to generate signature data Mol Plant Path Nov 2008 issue 02/17/11 Dinesh-PU-Talk-17-02-2011

AFLP signatures Mol Plant Path Nov 2008 issue 02/17/11 Dinesh-PU-Talk-17-02-2011

No clear signature of Ug55 & 99 by SSR Mol Plant Path Nov 2008 issue 02/17/11 Dinesh-PU-Talk-17-02-2011

AFLP again poor signature b/w Ug99/55 Mol Plant Path Nov 2008 issue 02/17/11 Dinesh-PU-Talk-17-02-2011

DNA signature of Ug99 by combining data of SSR+AFLP Mol Plant Path Nov 2008 issue 02/17/11 Dinesh-PU-Talk-17-02-2011

Clear DNA signature by Minimum-spanning network analysis Mol Plant Path Nov 2008 issue 02/17/11 Dinesh-PU-Talk-17-02-2011

What bioinformatics can do more in Ug99 identification? ,[object Object],[object Object],[object Object],[object Object],02/17/11 Dinesh-PU-Talk-17-02-2011

Puccinia graminis database Genome of P. graminis tritici 88.54 Mb, 392 scaffolds, contigs 4557 02/17/11 Dinesh-PU-Talk-17-02-2011

Our experiences-DNA based gender signature using bioinformatics tools 02/17/11 Dinesh-PU-Talk-17-02-2011

New PCR-RFLP test developed for Lactobacillus species differentiation ,[object Object],L P P R R R P P R R R P P R R R KEU1 5'-AAY ATG ATI ACI GGI GCI GCI CAR ATG GA-3' KEU 2 5'-AYR TTI TCI CCI GGC ATI ACC AT-3'. Ksp AI L. paracasei 542,158bp; L. rhamnosa 701bp Bsh 1236I L. paracasei 547,153bp; L. rhamnosa 701bp Mun I L. paracasei 594,106bp; L. rhamnosa 701bp Our experiences-DNA based microbial species signature using bioinformatics House Keeping Genes - CLUSTAL-W -signature with spelling mistake- CLEAVER 02/17/11 Dinesh-PU-Talk-17-02-2011

DNA based signature of domestic species ,[object Object],[object Object],[object Object],[object Object],[object Object],02/17/11 Dinesh-PU-Talk-17-02-2011

DNA based signature of domestic animal breeds ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],02/17/11 Dinesh-PU-Talk-17-02-2011

STR & breed-specific signatures/profiles ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],02/17/11 Dinesh-PU-Talk-17-02-2011

Development of breed hybrid indices/ profiles ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],02/17/11 Dinesh-PU-Talk-17-02-2011

Future breed signature of domestic animals Courtesy: Curt & his group USDA 02/17/11 Dinesh-PU-Talk-17-02-2011

02/17/11 Dinesh-PU-Talk-17-02-2011

Few examples: Signature applications ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],02/17/11 Dinesh-PU-Talk-17-02-2011

DNA based signature of plant variety, example-Basmati rice ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],02/17/11 Dinesh-PU-Talk-17-02-2011

DNA based bar-coded signature of fish ,[object Object],[object Object],[object Object],[object Object],02/17/11 Dinesh-PU-Talk-17-02-2011

Few examples of individual DNA signature and family signature ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],02/17/11 Dinesh-PU-Talk-17-02-2011

http://www.dnabarcodes.org 02/17/11 Dinesh-PU-Talk-17-02-2011

What is CBOL? ,[object Object],02/17/11 Dinesh-PU-Talk-17-02-2011

http://www.fishbol.org/ 02/17/11 Dinesh-PU-Talk-17-02-2011

Barcode of Life Data systems 02/17/11 Dinesh-PU-Talk-17-02-2011

Mito Fish Database http://mitofish.ori.u-tokyo.ac.jp/ 02/17/11 Dinesh-PU-Talk-17-02-2011

http://www.fishbase.org/search.php 02/17/11 Dinesh-PU-Talk-17-02-2011

02/17/11 Dinesh-PU-Talk-17-02-2011 If no RE site then? Which RE is species specific?

Real time PCR-Taqman probe designing 02/17/11 Dinesh-PU-Talk-17-02-2011

Conclusion ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],02/17/11 Dinesh-PU-Talk-17-02-2011

Dinesh-PU-Talk-17-02-2011 Acknowledgements Dr Jagdeep Kaur , Dr Jagtar Singh & team, Biotechnology Department , Punjab University, Chandigarh My students- Prashant, Prem, Nishant, Dhiraj (NBAGR) My UG/PG students- Pooja(NISER) & Uday(GU) Dr James Reecy & his group, Iowa State University, USA Dr DK Arora, NBAIM(ICAR) Dr Rameshwar Singh & Dr SK Tomar, NDRI 02/17/11

17022011

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