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Moderated conference on Genomics in Food and Agriculture

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Biotech-Mod3 <[log in to unmask]>
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Biotech-Mod3 <[log in to unmask]>
Date:
Tue, 5 Mar 2013 16:25:26 +0100
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I am Vadivel Arunachalam, Principal Scientist and Head Horticulture section and I work at the Indian Council of Agricultural Research (ICAR) at Goa centre. I worked on computational genomics and mining of genome sequences, expressed sequence tag (EST) libraries for new molecular markers (SSR, SNP, priming sites of RAPD/iSCAR). I authored a book on genomics of cultivated palms published by Elsevier. The book is a review of genomics research on palms (the plants belong to Arecaceae family). We also developed on molecular markers associated with resistance to root (wilt) disease, eriophyid mite pest in coconut. Root (wilt) is a serious disease in coconut palms of Southern India. These identified (SSR, RAPD, SNP region) markers we identified have potential in 70% accuracy of identifying the given DNA sample as resistant or susceptible. 

We also developed two softwares for genomics applications: 
1. Marker express 1.0 for a) locating priming sites of RAPD/ISSR primers on genome/EST sequences and b) to design in silico SCAR (iSCAR) primers. It was validated using oil palm expressed sequences and comparing with published polymorphic RAPDs (Premkrishnan, BV and V. Arunachalam. 2012. In silico RAPD priming sites in expressed sequences and iSCAR markers for oil palm. Comparative and Functional Genomics, http://www.ncbi.nlm.nih.gov/pubmed/22474414). 
2. DG MAP was developed to map the primers and genes on a given genome sequence. We validated it on F locus of cucumber and found additional markers linked to F locus.

We (the authors of the software - BV Premkrishnan and myself) can help researchers to analyse the genomes using these softwares and provide the results. We also analyse few fruit and vegetable genomes and in the process of putting a database of iSCAR markers. We provide the software services only to academic (non-profit) researchers free of cost. They can explain the research problem or give details of the organism of their choice, input files of sequences to be searched and primers to be mined. Premkrishnan and I will analyse and send the output to the researchers.

Implication of these softwares in interpreting the marker-trait-gene relationship in whole genome sequencing efforts in organisms of agricultural importance is tremendous. Most of genome sequencing project aim at annotation of genes and mine for SSR, SNP regions. Quantitative trait loci (QTL) mapping experiments reveal marker-trait-gene associations in genomic regions on specific chromosomes. But the software-aided interpretation of these regions for fine mapping has important implication for population genetics/genetic improvement. Resequencing of fine mapped regions in potential populations/individuals of organisms of interest has potential in fine tuning the breeding programs. 
 
Dr. V. Arunachalam
Principal Scientist and Head (Horticulture)
ICAR Research Complex for Goa 
(Indian Council of Agricultural Research)
Ela Old Goa Goa 403402
India 
Phone 0832-2284678 ext 115
Fax 0832-2285649 M 09823991917, 09495237971
http://www.icargoa.res.in/Arunachalam.html
e-mail: arun.ceo.innovations (at) gmail.com , vadivelarunachalam (at) yahoo.com

[ISSR, RAPD, SCAR, SNP and SSR molecular markers were mentioned above. These acronyms stand for inter simple sequence repeat (ISSR), random amplified polymorphic DNA (RAPD), sequence characterized amplified region (SCAR), simple sequence repeat (SSR, or microsatellite) and single nucleotide polymorphism (SNP). For more information on the different kinds of molecular markers, see Conference 10 of the FAO Biotechnology Forum, dedicated to "Molecular marker assisted selection as a potential tool for genetic improvement of crops, forest trees, livestock and fish in developing countries" (http://www.fao.org/biotech/biotech-forum/conference-10/en/) or the FAO book on "Marker-assisted selection: Current status, and future perspectives in crops, livestock, forestry and fish" (http://www.fao.org/docrep/010/a1120e/a1120e00.htm) ...Moderator].

[To contribute to this conference, send your message to [log in to unmask] For further information on this FAO Biotechnology Forum, see http://www.fao.org/biotech/biotech-forum/ ]

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