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.
Highlights
Mango (Mangifera indica L.) a member of order Sapindales, family Anacardiaceae, is one of the popular fruit crops of tropical and sub-tropical ecological regions of the world
Overall Single nucleotide polymorphisms (SNPs) density over entire genome was estimated to be 357 bp. All these data have been populated in MiSNPDb to develop genomic resources
749 SNPs were found common to all 84 varieties, which were subsequently used for diversity analysis and phylogeography studies
Summary
Mango (Mangifera indica L.) a member of order Sapindales, family Anacardiaceae, is one of the popular fruit crops of tropical and sub-tropical ecological regions of the world. RAD-Seq can be applied to study the population genetics of a species with no or very less sequence data and has several advantages over other methods for SNP discovery. Such approach reduces the complexity of the genome by sub-sampling only at the sites identified by restriction enzymes[21]. Till whole genome sequencing of Mango genome is completed such RAD-based bulk SNP discovery approach is most cost-effective and readily feasible alternative. Such SNP can directly be used for phylogeography and varietal differentiation. The RAD-seq technique can be used for rapid marker discovery and genotyping in crops for highly heterozygous and outbreeding species like mango where de novo genome assembly is challenging[26]
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