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In silico mining of microsatellites and analysis of genetic diversity among inter- and intra-generic aphids of the subfamily Aphidinae

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Title In silico mining of microsatellites and analysis of genetic diversity among inter- and intra-generic aphids of the subfamily Aphidinae
Not Available
 
Creator Sridhar Vaddi
Venkatesan Thiruvengadam
Sunil Joshi
Sushil Kumar Jalali
Lakshmana Reddy Dhoranalapalli Chinnappareddy
Padma Nimmakayala
Yan Tomason
Gopinath Vajja
Umesh K. Reddy
 
Subject cross-amplification
phenogram
polymorphism
tribe
Aphis gossypii
Acyrthosiphon pisum
Hemiptera
Aphididae
 
Description Not Available
Nearly 5 000 aphid species damage crops, either by sucking plant sap or as disease-transmitting vectors. Microsatellites are used for understanding molecular diversity and eco-geographical relationships among aphid species. Expressed sequence tag (EST)-microsatellite motifs were identified through an in silico approach using inbuilt simple sequence repeat mining tools in aphid EST dataset. Microsatellite mining revealed one in every five aphid genes as containing a repeat motif, and out of 9 290 EST microsatellites mined from Aphis gossypii Glover and Acyrthosiphon pisum (Harris) (both Hemiptera: Aphididae), 80% were of A and/or T (AT, ATA, AAT, AATA, and ATTT) motifs, and the rest contained G and/or C motifs. All microsatellite sequences were annotated using BLAST. Primers for EST microsatellites were designed using the Primer 3.0 tool. 106 primer pairs of both dinucleotide repeats (DNRs) and trinucleotide repeats (TNRs), representing open reading frames (ORFs) and untranslated regions (UTRs), were synthesized to amplify 15 aphid species belonging to the subfamily Aphidinae, collected from diverse hosts. Four hundred forty-five polymorphic alleles were amplified. Fifty TNR and 23 DNR microsatellites amplified across the species studied. Polymorphism information content values of microsatellites ranged from 0.23 to 0.91, amplifying 2–16 alleles.Genetic similarity indices were estimated using the ‘NTSYS-pc’ software package. Unweighted pair group with arithmetic mean and principal component analysis resolved taxonomic relationships of the aphid species studied. The new aphid microsatellites developed will provide valuable information to researchers to study Indian aphid species diversity and genetic relationships.
Not Available
 
Date 2019-03-21T07:11:09Z
2019-03-21T07:11:09Z
2016
 
Type Research Paper
 
Identifier Not Available
1570-7458
http://krishi.icar.gov.in/jspui/handle/123456789/17596
 
Language English
 
Relation Not Available;
 
Publisher The Netherlands Entomological society