Annual Report 2011-2012 - Nabi.res.in

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NATIONAL AGRI-FOOD BIOTECHNOLOGY INSTITUTE5. COMPUTATIONAL BIOLOGY APPROACHES FORMARKER AND GENE DISCOVERY FOR NUTRITION ANDPROCESSING TRAITS IN GENOMES OF FOOD CROPS5.1 Development of advanced algorithms, Research Objectives:databases, tools and pipeline for data miningland comparative analysis of food cropgenomes, transcriptome and small RNA basedregulation.lCoordinator:Rakesh TuliInvestigators:Shrikant Subhash MantriJoy K. RoyProject Scientists:Shailesh SharmaVandana MishralllTranscriptome sequencing, assembly andannotation for contrasting wheat varieties.Digital expression profiling and microarraydatamining for identification of SingleFeature Polymorphism (SFP) in Indiancultivars and annotation of hypotheticalproteins.SNP database development in wheat.Comparative genomics and related datamining.Small RNA analysis pipeline development.Research Fellows:l Microarray datamining for SFP.Gourab Dasl Repository of germplasm.Anuradha SinghLong Term Objectives:Introduction:lBread wheat, Triticum aestivum, is anFramework map development for wheatgenome (assembly and annotation).allohexaploid species. Its genome is composed ofl Identification of genes involved in highthe three distinct ancestral genomes A, B and D.accumulation of micronutrients.The polyploid nature of the wheat genometogether with its large size and high percentage of l Genome wide association analysis forrepeat elements makes it extremely complex and co-rrelating quality and processing relatedcomputationally intensive to analyze ever traits with the identified SNP's.increasing transcriptome and genome data. With5.1.1 SNP database development in hexaploidthe advent of next-generation sequencingwheattechnology it is now possible to generate wholegenome/transcriptome sequences for a number of Research in Progress:wheat genome. We are interested to harness the Datamining of non-synonymous mutations orpublic domain data of wheat for different projects Single Amino acid Polymorphisms (SAPs) fromon crop improvement in terms of nutritional and ESTs and homoeologous SNPs from chromosomeprocessing quality. Additionally, NABI has 1 of Triticum aestivum, resulted into theinitiated experiments to generate transcriptome identification putative 35395 and 1817 SNPssequences for Indian wheat varities showing respectively.contrasting characters. Bioinformatics Labortarywhich has the high performance computing nsSNP mining in ESTs from dbEST:infrastructure is a gateway for NABI scientists to Non-synonymous deleterious mutations are fairlyuse computational methods and databases tocommon in crop genomes. Statistical analysis ofdeepen and integrate their research.homologous sequence from multiple genomes can35
NATIONAL AGRI-FOOD BIOTECHNOLOGY INSTITUTEamino acid across species suggests that the non-synonymous change (indicated by the red 'G')observed in maize is likely to be deleterious.Synonymous changes are shown in black.identify amino acid changes that are likely to bedisadvantageous. Figure 1 shows a hypotheticalalignment of coding sequence from multiple grassspecies. The conserved nature of the histidineFigure 1: Hypothetical alignment of coding sequence from multiple grass species.Non-synonymous change indicated in red, synonymous change indicated in black.Highly putative nsSNPs in hexaploid wheat ESTs were found through the following steps (Table 1-7):1. dbEST records were parsed using custom perl script and multifasta containing all EST sequenceswas generated.Table 1: dbEST summary (updated February 1, 2012).No. of Triticumaestivum ESTsNo. ofcultivarsNo. of tissuesNo. of developmentalstages1073845 101 108 1322. These EST sequences were clustered using BLAST algorithm.Table 2: EST clustering results. Current release March 19, 2012contains 36692 unigenes.No. of Triticumaestivum probe setsNo. of unigenescoveredNo. of probe setshaving no clusterinfoNo. of probe setshaving cluster depth> 5 sequences61115 24697 123 463723. SNPs were determined using autosnpV2 script.Table 3: Overall SNPs summary.No. ofProbesetsSNPsSynonymous SNPsSynonymousSNPs inCDSSynonymousSNPs in flankingCoding regionproteinsubstitutionsSNPs indomains20699 161188 94654 67478 27176 35395 248636
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