Allele Mining from Gene Specific Microsatellites among Diverse Aphid Species Collections

There are ~5000 different species of Aphids that can directly damage crops by sucking or indirectly by being vectors to transmit various diseases. SSRs are proven tools to understand molecular diversity and eco-geography relationships among the aphid species. Current SSR search revealed that one in every five aphid genes contains a repeat motif and this is one of the genomes that harbour maximum number of microsatellites. We report 9,290 SSRs (2724 from ORF, 6266 from 5’UTR and 3’UTR) mined from Aphididae (41517 ESTs from Pea aphid and 3050 from Aphis gossypii). Di nucleotide repeats (DNR) with atleast 7 unit length (eg. (AT)7)were 13% (1534), tri- nucleotide (TNR) with unit length of 5 were 3570 (30%), tetra-nucleotide repeats and penta-nucleotide repeats with the length of at least 3 units were 42% and 14% respectively. AT, ATA, AAT, AATA and ATTT were 80% and rest 20% were the repeat classes contained either Gs or Cs. All the sequences with SSRs were annotated using the BLAST search. One hundred and six primer pairs of both DNRs and TNRs representing ORFs and UTRs were synthesized to amplify 15 different species belonging to (subfamily, Aphidinae) of which 10 species of tribe Aphidini and 5 of tribe Macrosiphini. These 15 species were collected from a diverse range of hosts that are crops of various families. Two hundred and forty eight polymorphic alleles were totally amplified by 71 of 91 amplified primer set. Twenty five of TNRs and 16 of DNRs amplified across all the species. PIC values of primer sets ranged from 0.24 to 0.88 amplifying 2 to 13 alleles. Genetic distances were noted up to 68% among the species. A UPGMA tree and PCA built using the transportable alleles across all the species resolved known taxonomic relationships with some minor exceptions. Observed and expected heterozygosities for various primer sets will be discussed.