Genes and Genetic Resources Molecular Analysis Laboratory

Haryana, India

Genes and Genetic Resources Molecular Analysis Laboratory

Haryana, India
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Sarika,Indian Agricultural Research Institute | Arora V.,Indian Agricultural Research Institute | Iquebal M.A.,Indian Agricultural Research Institute | Rai A.,Indian Agricultural Research Institute | And 2 more authors.
BMC Genomics | Year: 2013

Background: Though India has sequenced water buffalo genome but its draft assembly is based on cattle genome BTau 4.0, thus de novo chromosome wise assembly is a major pending issue for global community. The existing radiation hybrid of buffalo and these reported STR can be used further in final gap plugging and " finishing" expected in de novo genome assembly. QTL and gene mapping needs mining of putative STR from buffalo genome at equal interval on each and every chromosome. Such markers have potential role in improvement of desirable characteristics, such as high milk yields, resistance to diseases, high growth rate. The STR mining from whole genome and development of user friendly database is yet to be done to reap the benefit of whole genome sequence.Description: By in silico microsatellite mining of whole genome, we have developed first STR database of water buffalo, BuffSatDb (Buffalo MicroSatellite Database ( which is a web based relational database of 910529 microsatellite markers, developed using PHP and MySQL database. Microsatellite markers have been generated using MIcroSAtellite tool. It is simple and systematic web based search for customised retrieval of chromosome wise and genome-wide microsatellites. Search has been enabled based on chromosomes, motif type (mono-hexa), repeat motif and repeat kind (simple and composite). The search may be customised by limiting location of STR on chromosome as well as number of markers in that range. This is a novel approach and not been implemented in any of the existing marker database. This database has been further appended with Primer3 for primer designing of the selected markers enabling researcher to select markers of choice at desired interval over the chromosome. The unique add-on of degenerate bases further helps in resolving presence of degenerate bases in current buffalo assembly.Conclusion: Being first buffalo STR database in the world , this would not only pave the way in resolving current assembly problem but shall be of immense use for global community in QTL/gene mapping critically required to increase knowledge in the endeavour to increase buffalo productivity, especially for third world country where rural economy is significantly dependent on buffalo productivity. © 2013 Sarika et al.; licensee BioMed Central Ltd.

Bajetha G.,Indian Agricultural Research Institute | Bhati J.,Indian Agricultural Research Institute | Sarika,Indian Agricultural Research Institute | Iquebal M.A.,Indian Agricultural Research Institute | And 4 more authors.
Animal Biotechnology | Year: 2013

An elucidated genome of domestic livestock river buffalo will contribute enormously to economy and better understanding of genome evolution as well. An attempt is made to obtain genomic information on buffalo, based on total Expressed Sequence Tags (ESTs) of Bubalus bubalis available in public domain. These ESTs were annotated and classified into 15 different functional categories based on their homology to the known proteins. Interestingly, 41.79% of the contigs were found to be buffalo specific novel ESTs with respect to other species used in analysis which needs further studies. Also, 224 pSNPs (putative Single Nucleotide Polymorphism) were detected. This study will provide a home base for further genomic studies of buffalo and comparative studies enabling a starting point for the genome annotation of the organism. Supplementary materials are available for this article online. Copyright © Taylor and Francis Group, LLC.

Vohra V.,National Bureau of Animal Genetic Resources | Chakravarty A.K.,National Bureau of Animal Genetic Resources | Singh A.,National Bureau of Animal Genetic Resources | Gupta I.D.,National Bureau of Animal Genetic Resources | And 4 more authors.
Indian Journal of Animal Sciences | Year: 2011

Leptin protein is synthesized by adipose tissue and is involved in regulation of milk yield. We investigated the association of genetic polymorphism in the bovine leptin gene with 305 days milk yield for the first 3 lactations. The study was conducted on 209 lactating Karan Fries cattle with known pedigree belonging to 3 genetic groups at an organized herd. All the cattle were genotyped by PCR-RFLP assay, and 3 genotypes, viz. TT, TC and CC were identified in the exon-2 region of leptin gene. Representative PCR products of the genotyped animals were sequenced across the polymorphism. Karan Fries cattle with TT genotype showed significantly higher 305 days milk yield as compared to cattle with CC genotype.

Nanda D.K.,Genes and Genetic Resources Molecular Analysis Laboratory | Tomar S.K.,National Dairy Research Institute | Singh R.,National Dairy Research Institute | Mal G.,National Research Center on Camel | And 5 more authors.
International Journal of Dairy Technology | Year: 2011

Thirty-two Lactobacilli strains were isolated from four samples of camel cheese collected from Bikaner, India. These isolates were identified based on phenotypic and genotypic characteristics. Sequencing of 16S rDNA was performed for species identification and diversity analysis. Lactobacillus delbrueckii and Lb. fermentum were found to be dominant species followed by Lb. plantarum and Lb. casei. On evaluation of technological properties of these isolates, 20 isolates were observed to be good acid producers, eight were found positive for citrate utilisation and 11 showed presence of Prtp gene. Isolates obtained can be potential for development of defined strain starter for camel cheese. © 2011 Society of Dairy Technology.

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