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. 2017 Nov 2;7(1):14968.
doi: 10.1038/s41598-017-14998-2.

MiSNPDb: a web-based genomic resources of tropical ecology fruit mango (Mangifera indica L.) for phylogeography and varietal differentiation

M A Iquebal  1 , Sarika Jaiswal  1 , Ajay Kumar Mahato  2 , Pawan K Jayaswal  2 , U B Angadi  1 , Neeraj Kumar  1 , Nimisha Sharma  3 , Anand K Singh  3 , Manish Srivastav  3 , Jai Prakash  3 , S K Singh  3 , Kasim Khan  4 , Rupesh K Mishra  4 , Shailendra Rajan  4 , Anju Bajpai  4 , B S Sandhya  5 , Puttaraju Nischita  5 , K V Ravishankar  5 , M R Dinesh  5 , Anil Rai  1 , Dinesh Kumar  6 , Tilak R Sharma  2 , Nagendra K Singh  2
Affiliations

MiSNPDb: a web-based genomic resources of tropical ecology fruit mango (Mangifera indica L.) for phylogeography and varietal differentiation

M A Iquebal et al. Sci Rep. .

Abstract

Mango is one of the most important fruits of tropical ecological region of the world, well known for its nutritive value, aroma and taste. Its world production is >45MT worth >200 billion US dollars. Genomic resources are required for improvement in productivity and management of mango germplasm. There is no web-based genomic resources available for mango. Hence rapid and cost-effective high throughput putative marker discovery is required to develop such resources. RAD-based marker discovery can cater this urgent need till whole genome sequence of mango becomes available. Using a panel of 84 mango varieties, a total of 28.6 Gb data was generated by ddRAD-Seq approach on Illumina HiSeq 2000 platform. A total of 1.25 million SNPs were discovered. Phylogenetic tree using 749 common SNPs across these varieties revealed three major lineages which was compared with geographical locations. A web genomic resources MiSNPDb, available at http://webtom.cabgrid.res.in/mangosnps/ is based on 3-tier architecture, developed using PHP, MySQL and Javascript. This web genomic resources can be of immense use in the development of high density linkage map, QTL discovery, varietal differentiation, traceability, genome finishing and SNP chip development for future GWAS in genomic selection program. We report here world's first web-based genomic resources for genetic improvement and germplasm management of mango.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Figure 1
Figure 1
Radial phylogenetic tree showing four major lineages and one minor lineage using the SNP data generated from dd-RAD sequencing information of 84 mango varieties.
Figure 2
Figure 2
Workflow of the MiSNPDb genomic resource.
See this image and copyright information in PMC

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