Page Banner

United States Department of Agriculture

Agricultural Research Service

Research Project: BIOLOGY, ETIOLOGY, GENETICS, AND CONTROL OF VIRUS DISEASES OF CORN AND SOYBEAN

Location: Corn, Soybean and Wheat Quality Research Unit

Title: Development of genic-SSR markers from soybean aphid sequences generated by high-throughput sequencing of cDNA library

Authors
item Jun, Tae-Hwan -
item Mian, Rouf
item Freewalt, Keith
item Mittapalli, Omprakash -
item Michel, Andrew -

Submitted to: Journal of Applied Entomology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: November 16, 2011
Publication Date: December 28, 2011
Repository URL: http://handle.nal.usda.gov/10113/54474
Citation: Jun, T., Mian, R.M., Freewalt, K.R., Mittapalli, O., Michel, A.P. 2011. Development of genic-SSR markers from soybean aphid sequences generated by high-throughput sequencing of cDNA library. Journal of Applied Entomology. 136:614-625.

Interpretive Summary: The soybean aphid has been a pest of soybean in Asian soybean growing countries for centuries. However, following its invasion of USA in 2000, it is now the most important insect pest of soybean in North America. Three biotypes of the aphid (variations in the aphid that can defeat the aphid resistance gene of soybean plants) have been confirmed. Knowledge of aphid population genetics is needed for deployment of host-plant resistance and other control measures against the aphid. Simple sequence repeats (SSR) markers are very useful for genetic studies of the aphid, but there are very few SSR markers currently available for soybean aphid research. In this study, we designed primers for 342 genic-SSR markers from a dataset of more than 30 million transcript reads generated by sequencing of a cDNA library of the soybean aphid. The genic-SSR markers are located in the exons or in the expressed regions of the gene sequences. Two hundred forty six markers generated Polymerase Chain Reaction amplification products of expected size and 26 were polymorphic among 4 pooled aphid DNA samples. The genetic diversity among 96 soybean aphids, 24 each from four soybean aphid populations, was assessed with 21 polymorphic SSR markers. These markers discriminated lab colonies from field collections, field collections from different states and among individuals in a field collection. The 246 genic-SSR markers developed in this study will be a large addition to the limited number of SSR makers, mostly genomic-SSR, currently available for the soybean aphid. These markers should be useful for entomologists, population geneticists, and soybean breeders among others involved in soybean aphid research.

Technical Abstract: The soybean aphid (Aphis glycines Matsumura) is the most important insect pest of soybean [Glycine max (L.) Merr.] in North America and three biotypes of the aphid have been confirmed. Knowledge of aphid population genetics is needed for deployment of host-plant resistance and other control measures against the aphid. Simple sequence repeats (SSR) markers are very useful for genetic studies of the aphid, but there are very few SSR markers currently available for soybean aphid research. In this study, we designed primers for 342 genic-SSR markers from a dataset of more than 30 million transcript reads generated by 454 GS FLX sequencing of a cDNA library of the soybean aphid. Two hundred forty six markers generated PCR products of expected size and 26 were polymorphic among 4 pooled aphid DNA samples. Sequencing of the PCR products generated by two polymorphic SSR markers revealed that the polymorphisms were strictly due to variations in the SSR repeats among the aphids tested. The genetic diversity among 96 soybean aphids, 24 each from four soybean aphid populations, was assessed with 21 polymorphic SSR markers. These markers discriminated lab colonies from field collections, field collections from different states and among individuals in a field collection. The 246 genic-SSR markers developed and validated in this study will be a large addition to the limited number of SSR markers, mostly genomic-SSR, currently available for the soybean aphid. These markers should be useful for entomologists, population geneticists, and soybean breeders among others involved in soybean aphid research.

Last Modified: 9/22/2014
Footer Content Back to Top of Page