Identification of Genic SSR and SNP By Leaf Transcriptome Sequencing of Mango (Mangifera indica L.) Varieties Neelam and Dushehari

Mango (Mangifera indica L.) is a member of the family Anacardiaceae and is an allotetraploid (2n= 40) fruit tree. India is the largest producer of mango in the world, with an annual production of 15.25 million tons from an area of 2.29 million hectares (FAOSTAT, 2012), contributing about 55% of the total world production. Here we used SOLiD RNA-seq technology for sequencing of leaf transcriptome from mango varieties “Neelam” and “Dushehari”. We generated 60,359,815 and 58,121,961 reads that were assembled into 27,528 and 20,771 TSA contigs, having average length 506 bp and 439 bp in Neelam and Dushehari respectively. A total of 20,750 (75.37%) Neelam and 17,193 (82.77%) Dushehari contigs were annotated using similarity search against NCBI nr protein database with E-value above 10^-6, of which 10,253 and 12,310 contigs were assigned to one of more Gene Ontology terms receptively. Similarity, search against the plant transcription factor database and COG database of NCBI categorized a total of 5,447 and 4,494 contigs to 58 transcription factor and 2,021 and 1,751 contigs to 24 COG categories for varieties Neelam and Dushehari respectively. Total 3,319 SSR loci were identified in 3,208 unigene contigs, representing 9.26% of the total 34,654 unigene contigs. From this 100 SSR primers were synthesized, and validated for wet lab amplification. In addition, total 38,287, 35,943 SNPs and 654, 424 INDELs were identified in Neelam and Dushehari respectively. Our analysis will help in development of molecular markers which is important to speed up mango variety improvement.