Development of SNP Markers from the Mango Transcriptome for Mapping and Estimation of Genetic Diversity

We have initiated development of tools for genomic studies in Mangifera indica (mango).  With origin centered in southeast asia, mangos are grown throughout the world as a nutritious fruit exhibiting remarkable intraspecific phenotypic diversity.  With the goal of building a high density genetic map, we have undertaken variant discovery using transcriptome sequencing  of a broad range of mango cultivars. To generate a reference transcriptome, six libraries from RNA from leaves, flowers, and four tissues of the developing fruit (exocarp, mesocarp, seed coat, seed) of the Florida cultivar TOMMY ATKINS were sequenced on the Illumina HiSeq platform.  Reads were assembled by tissue type and as a whole using multiple approaches.  Assemblies were classified according to their protein coding potential and overall quality was assessed by alignment to those of other plants. Single nucleotide polymorphisms (SNPs) relative to the reference were determined from alignment of RNA reads generated similarly from 24 mango cultivars of diverse origins:  AMIN ABRAHIMPUR (India), AROEMANIS  (Indonesia), BURMA (Burma), CAC (Hawaii), DUNCAN (Florida), EDWARD, (Florida), EVERBEARING (Florida), GARY (Florida), HODSON (Florida), ITAMARACA (Brazil), JAKARATA (Florida), LONG (Jamaica), M. CASTURI 'PURPLE' (Borneo), MALINDI  (Kenya), MULGOBA (India), NEELUM (India), PEACH (unknown), PRIETO (Cuba), SANDERSHA (India), TETE NENE (Puerto Rico), THAI EVERBEARING (Thailand), TOLEDO (Cuba), TOMMY ATKINS (Florida) and TURPENTINE (West Indies).  SNPs are currently being converted into Fluidigm assays for genotyping of mapping populations and germplasm collections.  SNPs (144) discovered by sequencing of candidate genes in the cultivar KENSINGTON PRIDE have already been converted and used for genotyping.